From holland at ebi.ac.uk  Wed Jan  2 06:52:12 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 02 Jan 2008 11:52:12 +0000
Subject: [Biojava-dev] BioJava 3 design discussion coming to an end
Message-ID: <477B7AEC.9000401@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
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Hi all.

At the end of January I will be taking the contents of our BioJava 3
discussion wiki page and compiling them into a more formal design proposal.

If you have made any comments elsewhere (e.g. by email) which you would
like to be considered in the final design proposal, then please add them
to the wiki page (or its associated Talk page) before the end of the month.

(I won't be trawling through email archives looking for comments so you
really must copy your comments across to the wiki if you want them to be
included!).

The wiki address is:

   http://www.biojava.org/wiki/BioJava3_Proposal

cheers,
Richard

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From ap3 at sanger.ac.uk  Sun Jan  6 07:41:37 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Sun, 6 Jan 2008 12:41:37 +0000 (GMT)
Subject: [Biojava-dev] bioperl like blastparser
Message-ID: <Pine.LNX.4.64.0801061227560.11140@deskpro349.dynamic.sanger.ac.uk>

Hi Michael,

I just had a look at your patch for the query length.
Several of the unit tests are now failing at
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase.java:143)

The problem is that most blast related unit tests extend the SSBindCase, 
which expects a fixed number of attributes. With the new patch some of the 
blast-flavors have the additional queryLength attribute.

Could you have a look at the behaviour of the parser for some of the files 
where the tests now fail? If you think the new behaviour of the 
parser is correct, we can simply update the tests to accept the different 
number of attributes.

Thanks,
Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From markjschreiber at gmail.com  Mon Jan  7 03:05:33 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 16:05:33 +0800
Subject: [Biojava-dev] Biojava - svn migration
In-Reply-To: <Pine.GSO.4.44.0712272329560.18511-100000@shell3.shore.net>
References: <93b45ca50712271748x3019ce27m2d45008c8ce13ece@mail.gmail.com>
	<Pine.GSO.4.44.0712272329560.18511-100000@shell3.shore.net>
Message-ID: <93b45ca50801070005n10338f8q572b1295bc9ccdff@mail.gmail.com>

Hi -

This URL also works on Windows Vista. I made a secure tunnel using
plink which is part of the PuTTY package.

Thanks,

- Mark

On Dec 28, 2007 12:34 PM, Michael Heuer <heuermh at acm.org> wrote:
> Hello Mark, Andreas
>
> I was able to check out on linux with commandline subversion and
> in eclipse with the following URL:
>
> svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk
>
>   michael
>
>
>
> On Fri, 28 Dec 2007, Mark Schreiber wrote:
>
> > Hi all -
> >
> > I am trying to do a SVN check out with Netbeans but the connection
> > just seems to hang without doing anything (same happens with command
> > line?). I am using the path specified in the biojava wiki but the
> > conversation below suggests that the actual path may be different.
> > What then is the 'home' path?
> >
> > Also, does the SSH+SVN command need to be prepended by an SSH command
> > (or plink -ssh on windows)?
> >
> > - Mark
> >
> > On Dec 28, 2007 5:37 AM, Hilmar Lapp <hlapp at duke.edu> wrote:
> > > I see. Makes sense. -hilmar
> > >
> > >
> > > On Dec 27, 2007, at 4:30 PM, Jason Stajich wrote:
> > >
> > > > My  idea was that just like
> > > > /home/reposiitory/biojava
> > > >   we'd put the SVN in
> > > > /home/svn-repository/biojava
> > > >
> > > > So each of the biojava SVN sub-projects ought would be
> > > >  /home/svn-repository/biojava/biojava-live
> > > >  /home/svn-repository/biojava/biojava-ensj
> > > >
> > > > /home/svn is really the homedir for the svn user and som utility
> > > > stuff like the svn login passwords so I think it is better not to
> > > > put the repos in there.
> > > >
> > > > -jason
> > > > On Dec 27, 2007, at 1:31 PM, Hilmar Lapp wrote:
> > > >
> > > >>
> > > >> On Dec 27, 2007, at 12:32 PM, Chris Fields wrote:
> > > >>
> > > >>>
> > > >>> I agree, but there is already a /home/svn directory which appears
> > > >>> related to blipkit.  We would need to move the blipkit stuff into
> > > >>> it's own subdir and go from there.
> > > >>>
> > > >>
> > > >>
> > > >> I.e., it was set up such that blipkit would be the only project
> > > >> with in it? I'd assume that was by mistake. Also, the last update
> > > >> that I have is that blipkit hasn't been active for a while, though
> > > >> I'm not sure.
> > > >>
> > > >> ChrisM - do you recall the decisions leading to the blipkit svn
> > > >> setup? Could it be moved to a subdirectory as ChrisF suggests?
> > > >>
> > > >>      -hilmar
> > > >> --
> > > >> ===========================================================
> > > >> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> > > >> ===========================================================
> > > >>
> > > >>
> > > >>
> > > >
> > >
> > > --
> > > ===========================================================
> > > : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> > > ===========================================================
> > >
> > >
> > >
> > >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
>

From ayates at ebi.ac.uk  Mon Jan  7 04:34:33 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:34:33 +0000
Subject: [Biojava-dev] Error while reading byte data for creating a
	Trace.
In-Reply-To: <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
Message-ID: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>

Hi,

As far as I am aware there isn't a problem with the current ABI parser  
however if you could send a code snippit of reading in the byte array  
& the stack trace of the index out of bounds exception that would be  
most helpful

Andy

On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:

> Hi all,
> I am having a byte array which is having the data from an .ab1  
> file.The
> biojava library provides a class called as ABITrace which takes as  
> input
> either a byte[] array , a file or a url.If i use the later  
> parameters (the
> file or the url )the program works but if I pass the byte array to the
> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> problem with the ABITrace class or how can I bypass this particular  
> error.
> I am printing the length of the byte array and it comes to  
> 144930...Can
> that cause a problem in my code?
>
> Thanks in advance.
> Abhinav
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From markjschreiber at gmail.com  Mon Jan  7 04:43:14 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 17:43:14 +0800
Subject: [Biojava-dev] JUnit
Message-ID: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>

Hi all -

What do people think about adding the JUnit jar to the test directory
of the biojava-live repository and make the appropriate changes to the
ant classpath?  This would make it easier for people to test the
package directly from the ant build rather than having to specifically
place junit on the system classpath.  It would probably make it more
likely that people run and contribute tests as well.

If we add JUnit 4.1 then it will allow the creation of Unit tests by
just annotating class methods.

If there are no objections I will add it in the next few days.

- Mark

From ayates at ebi.ac.uk  Mon Jan  7 04:46:56 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:46:56 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
Message-ID: <42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>

Yeah I'm happy for that to happen. Just on a side note is Junit 4  
compatible with Junit 3's tests? Otherwise will we have to maintain  
two sets of unit test directories depending on the age of the test?

Andy

On 7 Jan 2008, at 09:43, Mark Schreiber wrote:

> Hi all -
>
> What do people think about adding the JUnit jar to the test directory
> of the biojava-live repository and make the appropriate changes to the
> ant classpath?  This would make it easier for people to test the
> package directly from the ant build rather than having to specifically
> place junit on the system classpath.  It would probably make it more
> likely that people run and contribute tests as well.
>
> If we add JUnit 4.1 then it will allow the creation of Unit tests by
> just annotating class methods.
>
> If there are no objections I will add it in the next few days.
>
> - Mark
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From markjschreiber at gmail.com  Mon Jan  7 04:48:31 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 17:48:31 +0800
Subject: [Biojava-dev] JUnit
In-Reply-To: <42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
	<42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
Message-ID: <93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>

>From my preliminary tests it seems to be compatable.

It seems that version 4.4 is out now.  Allows all kinds of strange
assertions, assumptions and theorys.

- Mark

On Jan 7, 2008 5:46 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Yeah I'm happy for that to happen. Just on a side note is Junit 4
> compatible with Junit 3's tests? Otherwise will we have to maintain
> two sets of unit test directories depending on the age of the test?
>
> Andy
>
>
> On 7 Jan 2008, at 09:43, Mark Schreiber wrote:
>
> > Hi all -
> >
> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> > package directly from the ant build rather than having to specifically
> > place junit on the system classpath.  It would probably make it more
> > likely that people run and contribute tests as well.
> >
> > If we add JUnit 4.1 then it will allow the creation of Unit tests by
> > just annotating class methods.
> >
> > If there are no objections I will add it in the next few days.
> >
> > - Mark
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>

From ayates at ebi.ac.uk  Mon Jan  7 04:50:02 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:50:02 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
	<42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
	<93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>
Message-ID: <D9934B7C-0867-4EFD-9EF2-642528CAD1FC@ebi.ac.uk>

Sounds good to me :)

Andy

On 7 Jan 2008, at 09:48, Mark Schreiber wrote:

>> From my preliminary tests it seems to be compatable.
>
> It seems that version 4.4 is out now.  Allows all kinds of strange
> assertions, assumptions and theorys.
>
> - Mark
>
> On Jan 7, 2008 5:46 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
>> Yeah I'm happy for that to happen. Just on a side note is Junit 4
>> compatible with Junit 3's tests? Otherwise will we have to maintain
>> two sets of unit test directories depending on the age of the test?
>>
>> Andy
>>
>>
>> On 7 Jan 2008, at 09:43, Mark Schreiber wrote:
>>
>>> Hi all -
>>>
>>> What do people think about adding the JUnit jar to the test  
>>> directory
>>> of the biojava-live repository and make the appropriate changes to  
>>> the
>>> ant classpath?  This would make it easier for people to test the
>>> package directly from the ant build rather than having to  
>>> specifically
>>> place junit on the system classpath.  It would probably make it more
>>> likely that people run and contribute tests as well.
>>>
>>> If we add JUnit 4.1 then it will allow the creation of Unit tests by
>>> just annotating class methods.
>>>
>>> If there are no objections I will add it in the next few days.
>>>
>>> - Mark
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>


From ap3 at sanger.ac.uk  Mon Jan  7 05:08:42 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 7 Jan 2008 10:08:42 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
Message-ID: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>

> What do people think about adding the JUnit jar to the test directory
> of the biojava-live repository and make the appropriate changes to the
> ant classpath?  This would make it easier for people to test the
>

I would suggest to move all the jar files where we have dependencies  
on into a common subdirectory.
e.g something called "libs" or "jars"

Andreas



-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From michaelgang at gmail.com  Mon Jan  7 05:16:22 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Mon, 7 Jan 2008 12:16:22 +0200
Subject: [Biojava-dev] Fwd:  bioperl like blastparser
In-Reply-To: <6994d82b0801070050t5d9b513fhc53ff758554116ff@mail.gmail.com>
References: <Pine.LNX.4.64.0801061227560.11140@deskpro349.dynamic.sanger.ac.uk>
	<6994d82b0801070050t5d9b513fhc53ff758554116ff@mail.gmail.com>
Message-ID: <6994d82b0801070216q1df26e72ic131592048100f3f@mail.gmail.com>

Hi Andreas,

You are correct.
The junit.jar library was missing in my ant_home.
Eclipse wrote that it was running the tests, but did not run any.
Now I corrected it and see that tests are failing.
I ran the program BlastEcho.java manually on the blast test files and
on the ncbi blast.
Judging after manually curation it worked good but at wu_blast id did
not parse the query length.
The reason is that in wu_blast the query length line has just 8 spaces
at the beginning instead of 9.
So I corrected the line which identifies the querylength at
org.biojava.bio.program.sax.BlastSaxParser
line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {

Now it works also on wu_blast.
It would be now a good idea to update the blast tests regarding the
number of arguments and see if the fail still.

Thanks in advance,
Michael



On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi Michael,
>
> I just had a look at your patch for the query length.
> Several of the unit tests are now failing at
> org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase.java:143)
>
> The problem is that most blast related unit tests extend the SSBindCase,
> which expects a fixed number of attributes. With the new patch some of the
> blast-flavors have the additional queryLength attribute.
>
> Could you have a look at the behaviour of the parser for some of the files
> where the tests now fail? If you think the new behaviour of the
> parser is correct, we can simply update the tests to accept the different
> number of attributes.
>
> Thanks,
> Andreas
>
>
> --------------------------------------------------
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                     Hinxton, Cambridge CB10 1SA, UK
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>

From holland at ebi.ac.uk  Mon Jan  7 07:01:55 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
Subject: [Biojava-dev] Error while reading byte data for creating a
 Trace.
In-Reply-To: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
	<04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
Message-ID: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>

This problem was resolved back in November. For some reason during the
last couple of weeks the BioJava mailing list has been sending out
occasional duplicate copies of emails sent several months ago! This was
one of them.

cheers,
Richard

On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> Hi,
>
> As far as I am aware there isn't a problem with the current ABI parser
> however if you could send a code snippit of reading in the byte array
> & the stack trace of the index out of bounds exception that would be
> most helpful
>
> Andy
>
> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>
>> Hi all,
>> I am having a byte array which is having the data from an .ab1
>> file.The
>> biojava library provides a class called as ABITrace which takes as
>> input
>> either a byte[] array , a file or a url.If i use the later
>> parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular
>> error.
>> I am printing the length of the byte array and it comes to
>> 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK


From ayates at ebi.ac.uk  Mon Jan  7 07:18:50 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 12:18:50 +0000
Subject: [Biojava-dev] Error while reading byte data for creating a
	Trace.
In-Reply-To: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
	<04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
	<50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>
Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB@ebi.ac.uk>

Oh for ... :). Thought I'd seen this one before

Andy

On 7 Jan 2008, at 12:01, Richard Holland wrote:

> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This  
> was
> one of them.
>
> cheers,
> Richard
>
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI  
>> parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to  
>>> the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is  
>>> there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> -- 
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK


From ap3 at sanger.ac.uk  Mon Jan  7 16:54:21 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 7 Jan 2008 21:54:21 +0000 (GMT)
Subject: [Biojava-dev] bioperl like blastparser
Message-ID: <Pine.LNX.4.64.0801072149400.15544@deskpro349.dynamic.sanger.ac.uk>

Hi Michael,

thanks for your patch, I commited it to the new svn repository
and updated the unit tests to now either take 4 or 5 args.

Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From heuermh at acm.org  Mon Jan  7 19:36:04 2008
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 7 Jan 2008 19:36:04 -0500 (EST)
Subject: [Biojava-dev] JUnit
In-Reply-To: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>
Message-ID: <Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>

Andreas Prlic wrote:

> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> >
>
> I would suggest to move all the jar files where we have dependencies
> on into a common subdirectory.
> e.g something called "libs" or "jars"

Using maven would resolve all of these issues.

Or alternatively, a maven build can create an ant build.xml that downloads
its dependencies from the maven central repository

http://maven.apache.org/plugins/maven-ant-plugin/

or there is Ivy for ant, which can be configured to use the maven central
repository

http://ant.apache.org/ivy/

The 'lib' directory doesn't really have a place any more.

   michael


From markjschreiber at gmail.com  Mon Jan  7 22:17:35 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 8 Jan 2008 11:17:35 +0800
Subject: [Biojava-dev] JUnit
In-Reply-To: <Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>
References: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>
	<Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>
Message-ID: <93b45ca50801071917t1cef45epf8772b4370ef3f97@mail.gmail.com>

Hi -

I have added the junit jar and modified the build.xml

I will leave the decision about a lib directory etc for some more debate.

- Mark

On Jan 8, 2008 8:36 AM, Michael Heuer <heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
> > > What do people think about adding the JUnit jar to the test directory
> > > of the biojava-live repository and make the appropriate changes to the
> > > ant classpath?  This would make it easier for people to test the
> > >
> >
> > I would suggest to move all the jar files where we have dependencies
> > on into a common subdirectory.
> > e.g something called "libs" or "jars"
>
> Using maven would resolve all of these issues.
>
> Or alternatively, a maven build can create an ant build.xml that downloads
> its dependencies from the maven central repository
>
> http://maven.apache.org/plugins/maven-ant-plugin/
>
> or there is Ivy for ant, which can be configured to use the maven central
> repository
>
> http://ant.apache.org/ivy/
>
> The 'lib' directory doesn't really have a place any more.
>
>   michael
>
>

From heuermh at acm.org  Mon Jan  7 23:55:42 2008
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 7 Jan 2008 23:55:42 -0500 (EST)
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801071917t1cef45epf8772b4370ef3f97@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0801072342240.4891-100000@shell3.shore.net>

Mark Schreiber wrote:

> I will leave the decision about a lib directory etc for some more debate.

Now that we have a subversion repository in place, I would be happy to
create a maven-based build out on branch for consideration at some point.

Ideally this would happen after refactoring/cleanup/purge so I have less
work to do.  ;)

   michael


From michaelgang at gmail.com  Tue Jan  8 03:23:56 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Tue, 8 Jan 2008 10:23:56 +0200
Subject: [Biojava-dev] read fasta file
Message-ID: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>

Dear All,

I want to read a fasta file of dna (the accessions are internal to our
company and may not be like the convention), make manipulations on it
and write it to another file.
When i take the example from the book "Biojava in Anger" it works
fine, but I get warnings that the SeqIOTools type is deprecated.
When using the RichSequence.IOTools package I have problems that when
writing the fasta it changes the fasta header (it adds the lcl:
prefix).
I want that the fasta header will be in the output file like in the input file.
Will the SeqIOTools type supported further ?
If not, is there another way to solve the problem ?

Thanks in advance,
Michael

From holland at ebi.ac.uk  Tue Jan  8 03:51:32 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Tue, 08 Jan 2008 08:51:32 +0000
Subject: [Biojava-dev] read fasta file
In-Reply-To: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
References: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
Message-ID: <47833994.7090608@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

SeqIOTools is deprecated - this means that it _may_ get dropped in a
future release and so you can't rely on it being present in any future
release.

RichSequence.IOTools follows the FASTA format exactly, which requires a
namespace prefix in the header, and it will change the existing header
if it does not already meet the FASTA standard. There is currently no
way to stop it from doing that, although you might want to raise a bug
report so that it goes on our list of things to change. You can do that
here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava

cheers,
Richard

Michael Gang wrote:
> Dear All,
> 
> I want to read a fasta file of dna (the accessions are internal to our
> company and may not be like the convention), make manipulations on it
> and write it to another file.
> When i take the example from the book "Biojava in Anger" it works
> fine, but I get warnings that the SeqIOTools type is deprecated.
> When using the RichSequence.IOTools package I have problems that when
> writing the fasta it changes the fasta header (it adds the lcl:
> prefix).
> I want that the fasta header will be in the output file like in the input file.
> Will the SeqIOTools type supported further ?
> If not, is there another way to solve the problem ?
> 
> Thanks in advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From bugzilla-daemon at portal.open-bio.org  Tue Jan  8 10:00:58 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 8 Jan 2008 10:00:58 -0500
Subject: [Biojava-dev] [Bug 2432] New: non conventional fasta header &&
	RichSequence.IOTools
Message-ID: <bug-2432-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2432

           Summary: non conventional fasta header && RichSequence.IOTools
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: michaelgang at gmail.com


When reading a fasta file with non conventional header (for example company
intern accessions) and writing it with RichSequence.IOTools the fasta header
get changed.
With deprecated SeqIOTools it works


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

From minhduc.cao at gmail.com  Tue Jan  8 19:57:43 2008
From: minhduc.cao at gmail.com (Minh Duc, Cao)
Date: Wed, 9 Jan 2008 11:57:43 +1100
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
Message-ID: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>

Hi,

I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
alone application, it works perfectly. However, when the code is called from
an applet, the following exception is thrown

Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
    at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
    at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
SimpleFeatureHolder.java:54)
    at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
RichFeature.java:167)
    at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
:61)
    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
SimpleRichSequenceBuilder.java:100)
    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
SimpleRichSequenceBuilder.java:81)
    at
org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
(SimpleRichSequenceBuilderFactory.java:68)
    at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
RichStreamReader.java:109)
    at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
RichStreamReader.java:92)
    at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
ReadFormatFileFunction.java:134)
    at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
Caused by: java.security.AccessControlException: access denied (
java.lang.RuntimePermission createClassLoader)
    at java.security.AccessControlContext.checkPermission(Unknown Source)
    at java.security.AccessController.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.<init>(Unknown Source)
    at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
GeneratedClassLoader.java:29)
    at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
    at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
:51)
    at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
:58)
    at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
FeatureFilter.java:1270)
    ... 11 more

It is noted that the applet is signed and can read files from client
harddisk if other method is used.

Do anyone have an idea how can I go about to fix this problem?

Thank you very much

Minh

From markjschreiber at gmail.com  Wed Jan  9 03:30:45 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 9 Jan 2008 16:30:45 +0800
Subject: [Biojava-dev] read fasta file
In-Reply-To: <47833994.7090608@ebi.ac.uk>
References: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
	<47833994.7090608@ebi.ac.uk>
Message-ID: <93b45ca50801090030t6ffd9907ieb1082fd20c5b713@mail.gmail.com>

Along these lines I have plans to add a way to format the Fasta header
in the RichSequence.IOTools so that the content of it can be
customised. Currently it follows the NCBI model and tries to add
everything it can.

I would be interested in proposals for a template mechanism.

- Mark

On Jan 8, 2008 4:51 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> SeqIOTools is deprecated - this means that it _may_ get dropped in a
> future release and so you can't rely on it being present in any future
> release.
>
> RichSequence.IOTools follows the FASTA format exactly, which requires a
> namespace prefix in the header, and it will change the existing header
> if it does not already meet the FASTA standard. There is currently no
> way to stop it from doing that, although you might want to raise a bug
> report so that it goes on our list of things to change. You can do that
> here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava
>
> cheers,
> Richard
>
>
> Michael Gang wrote:
> > Dear All,
> >
> > I want to read a fasta file of dna (the accessions are internal to our
> > company and may not be like the convention), make manipulations on it
> > and write it to another file.
> > When i take the example from the book "Biojava in Anger" it works
> > fine, but I get warnings that the SeqIOTools type is deprecated.
> > When using the RichSequence.IOTools package I have problems that when
> > writing the fasta it changes the fasta header (it adds the lcl:
> > prefix).
> > I want that the fasta header will be in the output file like in the input file.
> > Will the SeqIOTools type supported further ?
> > If not, is there another way to solve the problem ?
> >
> > Thanks in advance,
> > Michael
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHgzmT4C5LeMEKA/QRAoF8AJ9SLAMGvm7SpByOyfL1/7tUZ9NbZgCgjeTq
> FjmCDFlMygy68q1zkbpwX2o=
> =bTSb
> -----END PGP SIGNATURE-----
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From holland at ebi.ac.uk  Wed Jan  9 03:38:12 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 09 Jan 2008 08:38:12 +0000
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
Message-ID: <478487F4.3090209@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

This is the root of your problem:

Caused by: java.security.AccessControlException: access denied (
java.lang.RuntimePermission createClassLoader)
     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
 GeneratedClassLoader.java:29)
     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)

The applet runtime environment is not allowing BioJava to create a
custom class loader. It's not to do with disk access at all unfortunately.

I don't know of a solution myself as I've not done much work with applets.

Does anyone else on this list have any suggestions?

cheers,
Richard


Minh Duc, Cao wrote:
> Hi,
> 
> I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> alone application, it works perfectly. However, when the code is called from
> an applet, the following exception is thrown
> 
> Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
>     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
>     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> SimpleFeatureHolder.java:54)
>     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> RichFeature.java:167)
>     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> :61)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:100)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:81)
>     at
> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> (SimpleRichSequenceBuilderFactory.java:68)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> RichStreamReader.java:109)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> RichStreamReader.java:92)
>     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> ReadFormatFileFunction.java:134)
>     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at java.security.AccessControlContext.checkPermission(Unknown Source)
>     at java.security.AccessController.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
>     at java.lang.ClassLoader.<init>(Unknown Source)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :51)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :58)
>     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> FeatureFilter.java:1270)
>     ... 11 more
> 
> It is noted that the applet is signed and can read files from client
> harddisk if other method is used.
> 
> Do anyone have an idea how can I go about to fix this problem?
> 
> Thank you very much
> 
> Minh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Wed Jan  9 03:50:11 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 9 Jan 2008 16:50:11 +0800
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <478487F4.3090209@ebi.ac.uk>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
	<478487F4.3090209@ebi.ac.uk>
Message-ID: <93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>

Consulting a good book on the java security model may reveal a way
that you can modify the policy to allow this.

However, I think you should give serious consideration to why you
would want to use an applet in any context. The technology has major
limitations and has been long since superceeded by either severlet or
other technologies for server side stuff or webstart for client side
apps distributed from a server.

- Mark

On Jan 9, 2008 4:38 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello.
>
> This is the root of your problem:
>
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
>  GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>
> The applet runtime environment is not allowing BioJava to create a
> custom class loader. It's not to do with disk access at all unfortunately.
>
> I don't know of a solution myself as I've not done much work with applets.
>
> Does anyone else on this list have any suggestions?
>
> cheers,
> Richard
>
>
>
> Minh Duc, Cao wrote:
> > Hi,
> >
> > I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> > alone application, it works perfectly. However, when the code is called from
> > an applet, the following exception is thrown
> >
> > Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
> >     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
> >     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> > SimpleFeatureHolder.java:54)
> >     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> > RichFeature.java:167)
> >     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> > :61)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:100)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:81)
> >     at
> > org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> > (SimpleRichSequenceBuilderFactory.java:68)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> > RichStreamReader.java:92)
> >     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> > ReadFormatFileFunction.java:134)
> >     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> > Caused by: java.security.AccessControlException: access denied (
> > java.lang.RuntimePermission createClassLoader)
> >     at java.security.AccessControlContext.checkPermission(Unknown Source)
> >     at java.security.AccessController.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
> >     at java.lang.ClassLoader.<init>(Unknown Source)
> >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> > GeneratedClassLoader.java:29)
> >     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :51)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :58)
> >     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> > FeatureFilter.java:1270)
> >     ... 11 more
> >
> > It is noted that the applet is signed and can read files from client
> > harddisk if other method is used.
> >
> > Do anyone have an idea how can I go about to fix this problem?
> >
> > Thank you very much
> >
> > Minh
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
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> =WayD
> -----END PGP SIGNATURE-----
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From jcope at cableone.net  Wed Jan  9 10:59:16 2008
From: jcope at cableone.net (Jeff Cope)
Date: Wed, 9 Jan 2008 08:59:16 -0700
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
Message-ID: <000801c852d8$966eb370$6402a8c0@roadrunner>

Hi,
	
	My name is Jeff Cope, and I'm currently working on a bioinformatics
project for a professor at BSU.  What we have so far is mostly in java, but
with the data calculations taking place using functionality found in the
BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
protein sequences, and thought that we could help you out on the BioJava
project by seeing if that functionality could be added into your library
instead...

	So I guess my question is, now that I'm signed up on the developers
mail list, what would I need to do to get started (assuming you want my
help), and what kind of programming ground rules do you have...

	I feel pretty comfortable in Java code, and if you would like to see
an example of my source code, and some of the work I've done so far, you can
find it here:
	Current project:
	http://trac.boisestate.edu/protcalc/
	Source Code:
	http://trac.boisestate.edu/protcalc/src/
	API docs:
	http://trac.boisestate.edu/protcalc/docs/
	

Thanks,
	Jeff Cope

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
biojava-dev-request at lists.open-bio.org
Sent: Tuesday, January 08, 2008 1:52 AM
To: biojava-dev at lists.open-bio.org
Subject: biojava-dev Digest, Vol 59, Issue 2

Send biojava-dev mailing list submissions to
	biojava-dev at lists.open-bio.org

To subscribe or unsubscribe via the World Wide Web, visit
	http://lists.open-bio.org/mailman/listinfo/biojava-dev
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
	biojava-dev-owner at lists.open-bio.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of biojava-dev digest..."


Today's Topics:

   1. Fwd:  bioperl like blastparser (Michael Gang)
   2. Re: Error while reading byte data for creating a Trace.
      (Richard Holland)
   3. Re: Error while reading byte data for creating a	Trace.
      (Andy Yates)
   4. Re: bioperl like blastparser (Andreas Prlic)
   5. Re: JUnit (Michael Heuer)
   6. Re: JUnit (Mark Schreiber)
   7. Re: JUnit (Michael Heuer)
   8. read fasta file (Michael Gang)
   9. Re: read fasta file (Richard Holland)


----------------------------------------------------------------------

Message: 1
Date: Mon, 7 Jan 2008 12:16:22 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] Fwd:  bioperl like blastparser
To: biojava-dev at biojava.org
Message-ID:
	<6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Andreas,

You are correct.
The junit.jar library was missing in my ant_home.
Eclipse wrote that it was running the tests, but did not run any.
Now I corrected it and see that tests are failing.
I ran the program BlastEcho.java manually on the blast test files and
on the ncbi blast.
Judging after manually curation it worked good but at wu_blast id did
not parse the query length.
The reason is that in wu_blast the query length line has just 8 spaces
at the beginning instead of 9.
So I corrected the line which identifies the querylength at
org.biojava.bio.program.sax.BlastSaxParser
line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {

Now it works also on wu_blast.
It would be now a good idea to update the blast tests regarding the
number of arguments and see if the fail still.

Thanks in advance,
Michael



On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi Michael,
>
> I just had a look at your patch for the query length.
> Several of the unit tests are now failing at
>
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
.java:143)
>
> The problem is that most blast related unit tests extend the SSBindCase,
> which expects a fixed number of attributes. With the new patch some of the
> blast-flavors have the additional queryLength attribute.
>
> Could you have a look at the behaviour of the parser for some of the files
> where the tests now fail? If you think the new behaviour of the
> parser is correct, we can simply update the tests to accept the different
> number of attributes.
>
> Thanks,
> Andreas
>
>
> --------------------------------------------------
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                     Hinxton, Cambridge CB10 1SA, UK
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>


------------------------------

Message: 2
Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
From: "Richard Holland" <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
	a Trace.
To: "Andy Yates" <ayates at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
	abhi232 at cc.gatech.edu
Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
Content-Type: text/plain;charset=iso-8859-1

This problem was resolved back in November. For some reason during the
last couple of weeks the BioJava mailing list has been sending out
occasional duplicate copies of emails sent several months ago! This was
one of them.

cheers,
Richard

On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> Hi,
>
> As far as I am aware there isn't a problem with the current ABI parser
> however if you could send a code snippit of reading in the byte array
> & the stack trace of the index out of bounds exception that would be
> most helpful
>
> Andy
>
> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>
>> Hi all,
>> I am having a byte array which is having the data from an .ab1
>> file.The
>> biojava library provides a class called as ABITrace which takes as
>> input
>> either a byte[] array , a file or a url.If i use the later
>> parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular
>> error.
>> I am printing the length of the byte array and it comes to
>> 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK



------------------------------

Message: 3
Date: Mon, 7 Jan 2008 12:18:50 +0000
From: Andy Yates <ayates at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
	a	Trace.
To: "Richard Holland" <holland at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
	abhi232 at cc.gatech.edu
Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB at ebi.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Oh for ... :). Thought I'd seen this one before

Andy

On 7 Jan 2008, at 12:01, Richard Holland wrote:

> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This  
> was
> one of them.
>
> cheers,
> Richard
>
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI  
>> parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to  
>>> the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is  
>>> there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> -- 
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK



------------------------------

Message: 4
Date: Mon, 7 Jan 2008 21:54:21 +0000 (GMT)
From: Andreas Prlic <ap3 at sanger.ac.uk>
Subject: Re: [Biojava-dev] bioperl like blastparser
To: michaelgang at gmail.com
Cc: biojava-dev at biojava.org
Message-ID:
	<Pine.LNX.4.64.0801072149400.15544 at deskpro349.dynamic.sanger.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Michael,

thanks for your patch, I commited it to the new svn repository
and updated the unit tests to now either take 4 or 5 args.

Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


------------------------------

Message: 5
Date: Mon, 7 Jan 2008 19:36:04 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Andreas Prlic <ap3 at sanger.ac.uk>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801071929590.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Andreas Prlic wrote:

> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> >
>
> I would suggest to move all the jar files where we have dependencies
> on into a common subdirectory.
> e.g something called "libs" or "jars"

Using maven would resolve all of these issues.

Or alternatively, a maven build can create an ant build.xml that downloads
its dependencies from the maven central repository

http://maven.apache.org/plugins/maven-ant-plugin/

or there is Ivy for ant, which can be configured to use the maven central
repository

http://ant.apache.org/ivy/

The 'lib' directory doesn't really have a place any more.

   michael



------------------------------

Message: 6
Date: Tue, 8 Jan 2008 11:17:35 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-dev] JUnit
To: "Michael Heuer" <heuermh at acm.org>
Cc: biojava-dev at biojava.org
Message-ID:
	<93b45ca50801071917t1cef45epf8772b4370ef3f97 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi -

I have added the junit jar and modified the build.xml

I will leave the decision about a lib directory etc for some more debate.

- Mark

On Jan 8, 2008 8:36 AM, Michael Heuer <heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
> > > What do people think about adding the JUnit jar to the test directory
> > > of the biojava-live repository and make the appropriate changes to the
> > > ant classpath?  This would make it easier for people to test the
> > >
> >
> > I would suggest to move all the jar files where we have dependencies
> > on into a common subdirectory.
> > e.g something called "libs" or "jars"
>
> Using maven would resolve all of these issues.
>
> Or alternatively, a maven build can create an ant build.xml that downloads
> its dependencies from the maven central repository
>
> http://maven.apache.org/plugins/maven-ant-plugin/
>
> or there is Ivy for ant, which can be configured to use the maven central
> repository
>
> http://ant.apache.org/ivy/
>
> The 'lib' directory doesn't really have a place any more.
>
>   michael
>
>


------------------------------

Message: 7
Date: Mon, 7 Jan 2008 23:55:42 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801072342240.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Mark Schreiber wrote:

> I will leave the decision about a lib directory etc for some more debate.

Now that we have a subversion repository in place, I would be happy to
create a maven-based build out on branch for consideration at some point.

Ideally this would happen after refactoring/cleanup/purge so I have less
work to do.  ;)

   michael



------------------------------

Message: 8
Date: Tue, 8 Jan 2008 10:23:56 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] read fasta file
To: biojava-dev at biojava.org
Message-ID:
	<6994d82b0801080023y3cdcc005g57b08c6566c37445 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear All,

I want to read a fasta file of dna (the accessions are internal to our
company and may not be like the convention), make manipulations on it
and write it to another file.
When i take the example from the book "Biojava in Anger" it works
fine, but I get warnings that the SeqIOTools type is deprecated.
When using the RichSequence.IOTools package I have problems that when
writing the fasta it changes the fasta header (it adds the lcl:
prefix).
I want that the fasta header will be in the output file like in the input
file.
Will the SeqIOTools type supported further ?
If not, is there another way to solve the problem ?

Thanks in advance,
Michael


------------------------------

Message: 9
Date: Tue, 08 Jan 2008 08:51:32 +0000
From: Richard Holland <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] read fasta file
To: Michael Gang <michaelgang at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <47833994.7090608 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

SeqIOTools is deprecated - this means that it _may_ get dropped in a
future release and so you can't rely on it being present in any future
release.

RichSequence.IOTools follows the FASTA format exactly, which requires a
namespace prefix in the header, and it will change the existing header
if it does not already meet the FASTA standard. There is currently no
way to stop it from doing that, although you might want to raise a bug
report so that it goes on our list of things to change. You can do that
here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava

cheers,
Richard

Michael Gang wrote:
> Dear All,
> 
> I want to read a fasta file of dna (the accessions are internal to our
> company and may not be like the convention), make manipulations on it
> and write it to another file.
> When i take the example from the book "Biojava in Anger" it works
> fine, but I get warnings that the SeqIOTools type is deprecated.
> When using the RichSequence.IOTools package I have problems that when
> writing the fasta it changes the fasta header (it adds the lcl:
> prefix).
> I want that the fasta header will be in the output file like in the input
file.
> Will the SeqIOTools type supported further ?
> If not, is there another way to solve the problem ?
> 
> Thanks in advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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------------------------------

_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev


End of biojava-dev Digest, Vol 59, Issue 2
******************************************


From holland at ebi.ac.uk  Wed Jan  9 12:09:13 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 09 Jan 2008 17:09:13 +0000
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <000801c852d8$966eb370$6402a8c0@roadrunner>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
Message-ID: <4784FFB9.1050402@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Jeff.

Thanks for volunteering! Sounds like you've got a useful set of tools
which we would definitely appreciate as new BioJava features.

We're currently planning a Big Reorganisation for a new BioJava 3 from
the ground-up. Details will be published some time in February I expect,
if not then early March. See this Wiki for things that are currently
being considered (most will make it into the plan, some may not, but I
won't know until I've written it up and identified the conflicting areas):

  http://www.biojava.org/wiki/BioJava3_Proposal

(also see the associated Discussion page for further comments)

If I were you, I'd hang on until the final plan is published. It will
contain everything you need to know on how to write modules for the new
BioJava 3.

However, if you're in a rush to get it into the current BioJava 2
release, then take a look round the JavaDocs to see what is present and
what is not. You'll soon get a good idea of how things are organised and
what features are absent. We also have a bugzilla page with some
unresolved bugs - always a good starting point to learn how a system
works and where the opportunities for development are!
 http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED

cheers,
Richard

Jeff Cope wrote:
> Hi,
> 	
> 	My name is Jeff Cope, and I'm currently working on a bioinformatics
> project for a professor at BSU.  What we have so far is mostly in java, but
> with the data calculations taking place using functionality found in the
> BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
> Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> protein sequences, and thought that we could help you out on the BioJava
> project by seeing if that functionality could be added into your library
> instead...
> 
> 	So I guess my question is, now that I'm signed up on the developers
> mail list, what would I need to do to get started (assuming you want my
> help), and what kind of programming ground rules do you have...
> 
> 	I feel pretty comfortable in Java code, and if you would like to see
> an example of my source code, and some of the work I've done so far, you can
> find it here:
> 	Current project:
> 	http://trac.boisestate.edu/protcalc/
> 	Source Code:
> 	http://trac.boisestate.edu/protcalc/src/
> 	API docs:
> 	http://trac.boisestate.edu/protcalc/docs/
> 	
> 
> Thanks,
> 	Jeff Cope
> 
> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org
> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> biojava-dev-request at lists.open-bio.org
> Sent: Tuesday, January 08, 2008 1:52 AM
> To: biojava-dev at lists.open-bio.org
> Subject: biojava-dev Digest, Vol 59, Issue 2
> 
> Send biojava-dev mailing list submissions to
> 	biojava-dev at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-dev
> or, via email, send a message with subject or body 'help' to
> 	biojava-dev-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-dev-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of biojava-dev digest..."
> 
> 
> Today's Topics:
> 
>    1. Fwd:  bioperl like blastparser (Michael Gang)
>    2. Re: Error while reading byte data for creating a Trace.
>       (Richard Holland)
>    3. Re: Error while reading byte data for creating a	Trace.
>       (Andy Yates)
>    4. Re: bioperl like blastparser (Andreas Prlic)
>    5. Re: JUnit (Michael Heuer)
>    6. Re: JUnit (Mark Schreiber)
>    7. Re: JUnit (Michael Heuer)
>    8. read fasta file (Michael Gang)
>    9. Re: read fasta file (Richard Holland)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 7 Jan 2008 12:16:22 +0200
> From: "Michael Gang" <michaelgang at gmail.com>
> Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> To: biojava-dev at biojava.org
> Message-ID:
> 	<6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Andreas,
> 
> You are correct.
> The junit.jar library was missing in my ant_home.
> Eclipse wrote that it was running the tests, but did not run any.
> Now I corrected it and see that tests are failing.
> I ran the program BlastEcho.java manually on the blast test files and
> on the ncbi blast.
> Judging after manually curation it worked good but at wu_blast id did
> not parse the query length.
> The reason is that in wu_blast the query length line has just 8 spaces
> at the beginning instead of 9.
> So I corrected the line which identifies the querylength at
> org.biojava.bio.program.sax.BlastSaxParser
> line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> 
> Now it works also on wu_blast.
> It would be now a good idea to update the blast tests regarding the
> number of arguments and see if the fail still.
> 
> Thanks in advance,
> Michael
> 
> 
> 
> On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
>> Hi Michael,
>>
>> I just had a look at your patch for the query length.
>> Several of the unit tests are now failing at
>>
> org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> .java:143)
>> The problem is that most blast related unit tests extend the SSBindCase,
>> which expects a fixed number of attributes. With the new patch some of the
>> blast-flavors have the additional queryLength attribute.
>>
>> Could you have a look at the behaviour of the parser for some of the files
>> where the tests now fail? If you think the new behaviour of the
>> parser is correct, we can simply update the tests to accept the different
>> number of attributes.
>>
>> Thanks,
>> Andreas
>>
>>
>> --------------------------------------------------
>>
>> Andreas Prlic      Wellcome Trust Sanger Institute
>>                     Hinxton, Cambridge CB10 1SA, UK
>>
>>
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
>>  office is 215 Euston Road, London, NW1 2BE.
>>
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> From: "Richard Holland" <holland at ebi.ac.uk>
> Subject: Re: [Biojava-dev] Error while reading byte data for creating
> 	a Trace.
> To: "Andy Yates" <ayates at ebi.ac.uk>
> Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> 	abhi232 at cc.gatech.edu
> Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> Content-Type: text/plain;charset=iso-8859-1
> 
> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This was
> one of them.
> 
> cheers,
> Richard
> 
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> 
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From minhduc.cao at gmail.com  Wed Jan  9 14:47:28 2008
From: minhduc.cao at gmail.com (Minh Duc, Cao)
Date: Thu, 10 Jan 2008 06:47:28 +1100
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
	<478487F4.3090209@ebi.ac.uk>
	<93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>
Message-ID: <f8101ff00801091147p76463ff0m62a432b031b71bd3@mail.gmail.com>

Hi,
I figured out the problem. Once the biojava jar file is signed, the applet
can read files without any problems.  Many thanks to you both.

Also thank Mark for your suggestions, I will certainly try WebStart out.

Cheers
Minh


On Jan 9, 2008 7:50 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Consulting a good book on the java security model may reveal a way
> that you can modify the policy to allow this.
>
> However, I think you should give serious consideration to why you
> would want to use an applet in any context. The technology has major
> limitations and has been long since superceeded by either severlet or
> other technologies for server side stuff or webstart for client side
> apps distributed from a server.
>
> - Mark
>
> On Jan 9, 2008 4:38 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > Hello.
> >
> > This is the root of your problem:
> >
> > Caused by: java.security.AccessControlException: access denied (
> > java.lang.RuntimePermission createClassLoader)
> >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> >  GeneratedClassLoader.java:29)
> >     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java
> :68)
> >
> > The applet runtime environment is not allowing BioJava to create a
> > custom class loader. It's not to do with disk access at all
> unfortunately.
> >
> > I don't know of a solution myself as I've not done much work with
> applets.
> >
> > Does anyone else on this list have any suggestions?
> >
> > cheers,
> > Richard
> >
> >
> >
> > Minh Duc, Cao wrote:
> > > Hi,
> > >
> > > I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a
> stand
> > > alone application, it works perfectly. However, when the code is
> called from
> > > an applet, the following exception is thrown
> > >
> > > Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
> > >     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java
> :1813)
> > >     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> > > SimpleFeatureHolder.java:54)
> > >     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> > > RichFeature.java:167)
> > >     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(
> RichSeqIOAdapter.java
> > > :61)
> > >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > > SimpleRichSequenceBuilder.java:100)
> > >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > > SimpleRichSequenceBuilder.java:81)
> > >     at
> > >
> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> > > (SimpleRichSequenceBuilderFactory.java:68)
> > >     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > > RichStreamReader.java:109)
> > >     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> > > RichStreamReader.java:92)
> > >     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> > > ReadFormatFileFunction.java:134)
> > >     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> > > Caused by: java.security.AccessControlException: access denied (
> > > java.lang.RuntimePermission createClassLoader)
> > >     at java.security.AccessControlContext.checkPermission(Unknown
> Source)
> > >     at java.security.AccessController.checkPermission(Unknown Source)
> > >     at java.lang.SecurityManager.checkPermission(Unknown Source)
> > >     at java.lang.SecurityManager.checkCreateClassLoader(Unknown
> Source)
> > >     at java.lang.ClassLoader.<init>(Unknown Source)
> > >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> > > GeneratedClassLoader.java:29)
> > >     at org.biojava.utils.walker.WalkerFactory.<init>(
> WalkerFactory.java:68)
> > >     at org.biojava.utils.walker.WalkerFactory.getInstance(
> WalkerFactory.java
> > > :51)
> > >     at org.biojava.utils.walker.WalkerFactory.getInstance(
> WalkerFactory.java
> > > :58)
> > >     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> > > FeatureFilter.java:1270)
> > >     ... 11 more
> > >
> > > It is noted that the applet is signed and can read files from client
> > > harddisk if other method is used.
> > >
> > > Do anyone have an idea how can I go about to fix this problem?
> > >
> > > Thank you very much
> > >
> > > Minh
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >
> >
> > - --
> > Richard Holland (BioMart)
> > EMBL EBI, Wellcome Trust Genome Campus,
> > Hinxton, Cambridgeshire CB10 1SD, UK
> > Tel. +44 (0)1223 494416
> >
> > http://www.biomart.org/
> > http://www.biojava.org/
> > -----BEGIN PGP SIGNATURE-----
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> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >
> > iD8DBQFHhIfz4C5LeMEKA/QRAhZqAJ9k36tFYC7wdBt6eScgCn5MK9uVZwCeIVHU
> > R0e4dCpmpjJnHOrfjfw0wYc=
> > =WayD
> > -----END PGP SIGNATURE-----
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>

From markjschreiber at gmail.com  Thu Jan 10 02:04:00 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 10 Jan 2008 15:04:00 +0800
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <4784FFB9.1050402@ebi.ac.uk>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
	<4784FFB9.1050402@ebi.ac.uk>
Message-ID: <93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>

Hi Jeff -

I think the type of functionality you describe would be best placed in
the proteomic package where there is already some stuff for
calculating MW and PI.

Probably the reorganisation for BJ3 won't mean much change for your
code as these types of algorithms can usually be readily ported to any
new system.

- Mark

On Jan 10, 2008 1:09 AM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jeff.
>
> Thanks for volunteering! Sounds like you've got a useful set of tools
> which we would definitely appreciate as new BioJava features.
>
> We're currently planning a Big Reorganisation for a new BioJava 3 from
> the ground-up. Details will be published some time in February I expect,
> if not then early March. See this Wiki for things that are currently
> being considered (most will make it into the plan, some may not, but I
> won't know until I've written it up and identified the conflicting areas):
>
>  http://www.biojava.org/wiki/BioJava3_Proposal
>
> (also see the associated Discussion page for further comments)
>
> If I were you, I'd hang on until the final plan is published. It will
> contain everything you need to know on how to write modules for the new
> BioJava 3.
>
> However, if you're in a rush to get it into the current BioJava 2
> release, then take a look round the JavaDocs to see what is present and
> what is not. You'll soon get a good idea of how things are organised and
> what features are absent. We also have a bugzilla page with some
> unresolved bugs - always a good starting point to learn how a system
> works and where the opportunities for development are!
>  http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED
>
> cheers,
> Richard
>
>
> Jeff Cope wrote:
> > Hi,
> >
> >       My name is Jeff Cope, and I'm currently working on a bioinformatics
> > project for a professor at BSU.  What we have so far is mostly in java, but
> > with the data calculations taking place using functionality found in the
> > BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
> > Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> > protein sequences, and thought that we could help you out on the BioJava
> > project by seeing if that functionality could be added into your library
> > instead...
> >
> >       So I guess my question is, now that I'm signed up on the developers
> > mail list, what would I need to do to get started (assuming you want my
> > help), and what kind of programming ground rules do you have...
> >
> >       I feel pretty comfortable in Java code, and if you would like to see
> > an example of my source code, and some of the work I've done so far, you can
> > find it here:
> >       Current project:
> >       http://trac.boisestate.edu/protcalc/
> >       Source Code:
> >       http://trac.boisestate.edu/protcalc/src/
> >       API docs:
> >       http://trac.boisestate.edu/protcalc/docs/
> >
> >
> > Thanks,
> >       Jeff Cope
> >
> > -----Original Message-----
> > From: biojava-dev-bounces at lists.open-bio.org
> > [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> > biojava-dev-request at lists.open-bio.org
> > Sent: Tuesday, January 08, 2008 1:52 AM
> > To: biojava-dev at lists.open-bio.org
> > Subject: biojava-dev Digest, Vol 59, Issue 2
> >
> > Send biojava-dev mailing list submissions to
> >       biojava-dev at lists.open-bio.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > or, via email, send a message with subject or body 'help' to
> >       biojava-dev-request at lists.open-bio.org
> >
> > You can reach the person managing the list at
> >       biojava-dev-owner at lists.open-bio.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of biojava-dev digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Fwd:  bioperl like blastparser (Michael Gang)
> >    2. Re: Error while reading byte data for creating a Trace.
> >       (Richard Holland)
> >    3. Re: Error while reading byte data for creating a        Trace.
> >       (Andy Yates)
> >    4. Re: bioperl like blastparser (Andreas Prlic)
> >    5. Re: JUnit (Michael Heuer)
> >    6. Re: JUnit (Mark Schreiber)
> >    7. Re: JUnit (Michael Heuer)
> >    8. read fasta file (Michael Gang)
> >    9. Re: read fasta file (Richard Holland)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Jan 2008 12:16:22 +0200
> > From: "Michael Gang" <michaelgang at gmail.com>
> > Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> > To: biojava-dev at biojava.org
> > Message-ID:
> >       <6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Andreas,
> >
> > You are correct.
> > The junit.jar library was missing in my ant_home.
> > Eclipse wrote that it was running the tests, but did not run any.
> > Now I corrected it and see that tests are failing.
> > I ran the program BlastEcho.java manually on the blast test files and
> > on the ncbi blast.
> > Judging after manually curation it worked good but at wu_blast id did
> > not parse the query length.
> > The reason is that in wu_blast the query length line has just 8 spaces
> > at the beginning instead of 9.
> > So I corrected the line which identifies the querylength at
> > org.biojava.bio.program.sax.BlastSaxParser
> > line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> >
> > Now it works also on wu_blast.
> > It would be now a good idea to update the blast tests regarding the
> > number of arguments and see if the fail still.
> >
> > Thanks in advance,
> > Michael
> >
> >
> >
> > On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> >> Hi Michael,
> >>
> >> I just had a look at your patch for the query length.
> >> Several of the unit tests are now failing at
> >>
> > org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> > .java:143)
> >> The problem is that most blast related unit tests extend the SSBindCase,
> >> which expects a fixed number of attributes. With the new patch some of the
> >> blast-flavors have the additional queryLength attribute.
> >>
> >> Could you have a look at the behaviour of the parser for some of the files
> >> where the tests now fail? If you think the new behaviour of the
> >> parser is correct, we can simply update the tests to accept the different
> >> number of attributes.
> >>
> >> Thanks,
> >> Andreas
> >>
> >>
> >> --------------------------------------------------
> >>
> >> Andreas Prlic      Wellcome Trust Sanger Institute
> >>                     Hinxton, Cambridge CB10 1SA, UK
> >>
> >>
> >>
> >>
> >> --
> >>  The Wellcome Trust Sanger Institute is operated by Genome Research
> >>  Limited, a charity registered in England with number 1021457 and a
> >>  company registered in England with number 2742969, whose registered
> >>  office is 215 Euston Road, London, NW1 2BE.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> > From: "Richard Holland" <holland at ebi.ac.uk>
> > Subject: Re: [Biojava-dev] Error while reading byte data for creating
> >       a Trace.
> > To: "Andy Yates" <ayates at ebi.ac.uk>
> > Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> >       abhi232 at cc.gatech.edu
> > Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > This problem was resolved back in November. For some reason during the
> > last couple of weeks the BioJava mailing list has been sending out
> > occasional duplicate copies of emails sent several months ago! This was
> > one of them.
> >
> > cheers,
> > Richard
> >
> > On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> >> Hi,
> >>
> >> As far as I am aware there isn't a problem with the current ABI parser
> >> however if you could send a code snippit of reading in the byte array
> >> & the stack trace of the index out of bounds exception that would be
> >> most helpful
> >>
> >> Andy
> >>
> >> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
> >>
> >>> Hi all,
> >>> I am having a byte array which is having the data from an .ab1
> >>> file.The
> >>> biojava library provides a class called as ABITrace which takes as
> >>> input
> >>> either a byte[] array , a file or a url.If i use the later
> >>> parameters (the
> >>> file or the url )the program works but if I pass the byte array to the
> >>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> >>> problem with the ABITrace class or how can I bypass this particular
> >>> error.
> >>> I am printing the length of the byte array and it comes to
> >>> 144930...Can
> >>> that cause a problem in my code?
> >>>
> >>> Thanks in advance.
> >>> Abhinav
> >>> _______________________________________________
> >>> biojava-dev mailing list
> >>> biojava-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHhP+44C5LeMEKA/QRAroBAJ9oU/by7joNIkdpkOoEtPFzcP+6ZwCfcVYV
> YpEnZK4o2READMXOsaE9oMo=
> =QZDP
>
> -----END PGP SIGNATURE-----
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From michaelgang at gmail.com  Thu Jan 10 07:44:49 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Thu, 10 Jan 2008 14:44:49 +0200
Subject: [Biojava-dev] problem with blast parser
Message-ID: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>

Hi All,
I've observed the following pronlem with the blast parser.
When parsing a blast with more than one query, it skips a part of the queries.
When I wanted to understand what the problem is I got to the following
conclusion.(There are good chances that I am wrong)
When the BlastSaxParser in the function hitsSectionReached calls the
line: oHits.parse(oContents,poLine,"Database:");.
It just get's back when it get to the line :Database= but this is in
the middle of the next query (the query began with the line "BLASTX
2.2.16 [Mar-25-2007]".
I also tested it with the blastecho program
Did someone observed the same problem.
 Can someone help me in this issue ?

Thanks in Advance,
Michael

From holland at ebi.ac.uk  Thu Jan 10 07:50:21 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 10 Jan 2008 12:50:21 +0000
Subject: [Biojava-dev] problem with blast parser
In-Reply-To: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>
References: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>
Message-ID: <4786148D.5010003@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

This is related to your previous email about it not being able to read
all data (e.g. query length).

I believe Andreas Prlic (copied on this) is looking into this, and some
other people might be as well. One of them will get back to you.

cheers,
Richard

Michael Gang wrote:
> Hi All,
> I've observed the following pronlem with the blast parser.
> When parsing a blast with more than one query, it skips a part of the queries.
> When I wanted to understand what the problem is I got to the following
> conclusion.(There are good chances that I am wrong)
> When the BlastSaxParser in the function hitsSectionReached calls the
> line: oHits.parse(oContents,poLine,"Database:");.
> It just get's back when it get to the line :Database= but this is in
> the middle of the next query (the query began with the line "BLASTX
> 2.2.16 [Mar-25-2007]".
> I also tested it with the blastecho program
> Did someone observed the same problem.
>  Can someone help me in this issue ?
> 
> Thanks in Advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From ap3 at sanger.ac.uk  Sun Jan 13 08:44:42 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Sun, 13 Jan 2008 13:44:42 +0000
Subject: [Biojava-dev] anonymous svn
Message-ID: <E531DA0A-BBA9-4652-AC9E-0FACFCFBE692@sanger.ac.uk>

Hi,

seems the anonymous svn access is making progress, but I need to do  
some admin work on the svn repository in the next hours:

The decision from open-bio was to move the svn repository data store  
from berkely db to fsfs, which will make the replication
of the developer repository onto the server that will provide the  
anonymous access much more smoothly.

so checkout and commits will not work for 1 or 2 hours now, but  
should be fine again afterwards.


>> http://svnbook.red-bean.com/en/1.4/svn- 
>> book.html#svn.reposadmin.basics.backends
>>
>> http://subversion.tigris.org/faq.html#bdb-fsfs-convert

Andreas



-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From bugzilla-daemon at portal.open-bio.org  Sun Jan 13 22:31:53 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 13 Jan 2008 22:31:53 -0500
Subject: [Biojava-dev] [Bug 2434] New: bio.seq.io.UniProtFormat error?
Message-ID: <bug-2434-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2434

           Summary: bio.seq.io.UniProtFormat error?
           Product: BioJava
           Version: 1.5
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: lisujun at gmail.com


Exception in thread "main" org.biojava.bio.BioException: Could not read
sequence
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextSequence(RichStreamReader.java:92)
        at DeleteHighAbundance.getDescription(DeleteHighAbundance.java:41)
        at DeleteHighAbundance.main(DeleteHighAbundance.java:47)
Caused by: org.biojava.bio.seq.io.ParseException: 

A Exception Has Occurred During Parsing. 
Please submit the details that follow to biojava-l at biojava.org or post a bug
report to http://bugzilla.open-bio.org/ 

Format_object=org.biojavax.bio.seq.io.UniProtFormat
Accession=null
Id=
Comments=Bad ID line
Parse_block=ID   IPI00000001.1         IPI;      PRT;   577 AA.
Stack trace follows ....


        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:286)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 3 more

========

when i used the RichSequence.IOTools.readUniprot to read the IPI DAT(Uniprot
format), this error happened.


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From ap3 at sanger.ac.uk  Mon Jan 14 12:26:30 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 14 Jan 2008 17:26:30 +0000
Subject: [Biojava-dev] biojava svn migration complete
Message-ID: <1B7EE4F0-142D-47BC-8143-677627AAC1AC@sanger.ac.uk>

Hi!

The BioJava SVN migration has been completed.
Thanks a lot to everyone who has made contributions to this!!

The new anonymous checkout of BioJava is now possible via
svn co svn://code.open-bio.org/biojava/biojava-live/trunk biojava-live

Developers can obtain a checkout from
svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/ 
biojava-live/trunk/  ./biojava-live

and it is possible to browse the repository online at
http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/ 
trunk

Also the automated builds have been updated
http://www.spice-3d.org/cruise/

see http://biojava.org/wiki/CVS_to_SVN_Migration
for more details.

Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




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 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jcope at cableone.net  Tue Jan 15 11:27:38 2008
From: jcope at cableone.net (Jeff Cope)
Date: Tue, 15 Jan 2008 09:27:38 -0700
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
	<4784FFB9.1050402@ebi.ac.uk>
	<93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>
Message-ID: <000001c85793$8b8c83f0$6402a8c0@roadrunner>

Hi Richard and Mark,

	Thanks for the quick response, and help in pointing out where the
new classes should go.  Here are the classes I wanted to propose and where I
thought they should be.  Due time constraints, this would probably be
something that I could put into BioJava 2, and would be willing to translate
to BioJava 3 when time came around.

	As Mark had suggested it appears that the org.biojava.bio.proteomics
package would be the ideal area for the added classes, so I would be
interpreting functionality for most of the classes from the BioPython
library.

	AromaticityCalc.java - Returns the sum of the percentage of the AA
sequence that is made up of the AA's Tyrosine, Tryptophan, and
Phenylalanine. 

	GRAVYCalc.java (Grand Average of Hydropathy) - Returns the average
sum of hydropathy of the AA sequence

	InstabilityIndexCalc.java - Returns an estimated stability for a
protein sequence (<= 40 is considered stable)

	AACompositionCalc.java - Breaks down protein sequences, and returns
the percent that individual AA's make up the sequence.

	The functionality for Aromaticity, GRAVY, and Instability Index
would all come from the biopython library
(biopython-1.43/Bio/SeqUtils/ProtParam.py), and AAComposition is something
that we worked together that was useful for our application.

	Most of the classes are pretty simple for the most part, I think the
most difficult part would be figuring out how the strings of characters are
translated to protein sequences in BioJava.

	Anyway, Let me know if this sounds like it would be useful...

Thanks,
	Jeff


-----Original Message-----
From: Mark Schreiber [mailto:markjschreiber at gmail.com] 
Sent: Thursday, January 10, 2008 12:04 AM
To: Richard Holland
Cc: Jeff Cope; biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] BioJava Development

Hi Jeff -

I think the type of functionality you describe would be best placed in
the proteomic package where there is already some stuff for
calculating MW and PI.

Probably the reorganisation for BJ3 won't mean much change for your
code as these types of algorithms can usually be readily ported to any
new system.

- Mark

On Jan 10, 2008 1:09 AM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jeff.
>
> Thanks for volunteering! Sounds like you've got a useful set of tools
> which we would definitely appreciate as new BioJava features.
>
> We're currently planning a Big Reorganisation for a new BioJava 3 from
> the ground-up. Details will be published some time in February I expect,
> if not then early March. See this Wiki for things that are currently
> being considered (most will make it into the plan, some may not, but I
> won't know until I've written it up and identified the conflicting areas):
>
>  http://www.biojava.org/wiki/BioJava3_Proposal
>
> (also see the associated Discussion page for further comments)
>
> If I were you, I'd hang on until the final plan is published. It will
> contain everything you need to know on how to write modules for the new
> BioJava 3.
>
> However, if you're in a rush to get it into the current BioJava 2
> release, then take a look round the JavaDocs to see what is present and
> what is not. You'll soon get a good idea of how things are organised and
> what features are absent. We also have a bugzilla page with some
> unresolved bugs - always a good starting point to learn how a system
> works and where the opportunities for development are!
>
http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_
status=ASSIGNED&bug_status=REOPENED
>
> cheers,
> Richard
>
>
> Jeff Cope wrote:
> > Hi,
> >
> >       My name is Jeff Cope, and I'm currently working on a
bioinformatics
> > project for a professor at BSU.  What we have so far is mostly in java,
but
> > with the data calculations taking place using functionality found in the
> > BioPython library (Molecular Weight, Instability Index, Isoelectric
Point,
> > Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> > protein sequences, and thought that we could help you out on the BioJava
> > project by seeing if that functionality could be added into your library
> > instead...
> >
> >       So I guess my question is, now that I'm signed up on the
developers
> > mail list, what would I need to do to get started (assuming you want my
> > help), and what kind of programming ground rules do you have...
> >
> >       I feel pretty comfortable in Java code, and if you would like to
see
> > an example of my source code, and some of the work I've done so far, you
can
> > find it here:
> >       Current project:
> >       http://trac.boisestate.edu/protcalc/
> >       Source Code:
> >       http://trac.boisestate.edu/protcalc/src/
> >       API docs:
> >       http://trac.boisestate.edu/protcalc/docs/
> >
> >
> > Thanks,
> >       Jeff Cope
> >
> > -----Original Message-----
> > From: biojava-dev-bounces at lists.open-bio.org
> > [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> > biojava-dev-request at lists.open-bio.org
> > Sent: Tuesday, January 08, 2008 1:52 AM
> > To: biojava-dev at lists.open-bio.org
> > Subject: biojava-dev Digest, Vol 59, Issue 2
> >
> > Send biojava-dev mailing list submissions to
> >       biojava-dev at lists.open-bio.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > or, via email, send a message with subject or body 'help' to
> >       biojava-dev-request at lists.open-bio.org
> >
> > You can reach the person managing the list at
> >       biojava-dev-owner at lists.open-bio.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of biojava-dev digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Fwd:  bioperl like blastparser (Michael Gang)
> >    2. Re: Error while reading byte data for creating a Trace.
> >       (Richard Holland)
> >    3. Re: Error while reading byte data for creating a        Trace.
> >       (Andy Yates)
> >    4. Re: bioperl like blastparser (Andreas Prlic)
> >    5. Re: JUnit (Michael Heuer)
> >    6. Re: JUnit (Mark Schreiber)
> >    7. Re: JUnit (Michael Heuer)
> >    8. read fasta file (Michael Gang)
> >    9. Re: read fasta file (Richard Holland)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Jan 2008 12:16:22 +0200
> > From: "Michael Gang" <michaelgang at gmail.com>
> > Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> > To: biojava-dev at biojava.org
> > Message-ID:
> >       <6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Andreas,
> >
> > You are correct.
> > The junit.jar library was missing in my ant_home.
> > Eclipse wrote that it was running the tests, but did not run any.
> > Now I corrected it and see that tests are failing.
> > I ran the program BlastEcho.java manually on the blast test files and
> > on the ncbi blast.
> > Judging after manually curation it worked good but at wu_blast id did
> > not parse the query length.
> > The reason is that in wu_blast the query length line has just 8 spaces
> > at the beginning instead of 9.
> > So I corrected the line which identifies the querylength at
> > org.biojava.bio.program.sax.BlastSaxParser
> > line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> >
> > Now it works also on wu_blast.
> > It would be now a good idea to update the blast tests regarding the
> > number of arguments and see if the fail still.
> >
> > Thanks in advance,
> > Michael
> >
> >
> >
> > On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> >> Hi Michael,
> >>
> >> I just had a look at your patch for the query length.
> >> Several of the unit tests are now failing at
> >>
> >
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> > .java:143)
> >> The problem is that most blast related unit tests extend the
SSBindCase,
> >> which expects a fixed number of attributes. With the new patch some of
the
> >> blast-flavors have the additional queryLength attribute.
> >>
> >> Could you have a look at the behaviour of the parser for some of the
files
> >> where the tests now fail? If you think the new behaviour of the
> >> parser is correct, we can simply update the tests to accept the
different
> >> number of attributes.
> >>
> >> Thanks,
> >> Andreas
> >>
> >>
> >> --------------------------------------------------
> >>
> >> Andreas Prlic      Wellcome Trust Sanger Institute
> >>                     Hinxton, Cambridge CB10 1SA, UK
> >>
> >>
> >>
> >>
> >> --
> >>  The Wellcome Trust Sanger Institute is operated by Genome Research
> >>  Limited, a charity registered in England with number 1021457 and a
> >>  company registered in England with number 2742969, whose registered
> >>  office is 215 Euston Road, London, NW1 2BE.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> > From: "Richard Holland" <holland at ebi.ac.uk>
> > Subject: Re: [Biojava-dev] Error while reading byte data for creating
> >       a Trace.
> > To: "Andy Yates" <ayates at ebi.ac.uk>
> > Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> >       abhi232 at cc.gatech.edu
> > Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > This problem was resolved back in November. For some reason during the
> > last couple of weeks the BioJava mailing list has been sending out
> > occasional duplicate copies of emails sent several months ago! This was
> > one of them.
> >
> > cheers,
> > Richard
> >
> > On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> >> Hi,
> >>
> >> As far as I am aware there isn't a problem with the current ABI parser
> >> however if you could send a code snippit of reading in the byte array
> >> & the stack trace of the index out of bounds exception that would be
> >> most helpful
> >>
> >> Andy
> >>
> >> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
> >>
> >>> Hi all,
> >>> I am having a byte array which is having the data from an .ab1
> >>> file.The
> >>> biojava library provides a class called as ABITrace which takes as
> >>> input
> >>> either a byte[] array , a file or a url.If i use the later
> >>> parameters (the
> >>> file or the url )the program works but if I pass the byte array to the
> >>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> >>> problem with the ABITrace class or how can I bypass this particular
> >>> error.
> >>> I am printing the length of the byte array and it comes to
> >>> 144930...Can
> >>> that cause a problem in my code?
> >>>
> >>> Thanks in advance.
> >>> Abhinav
> >>> _______________________________________________
> >>> biojava-dev mailing list
> >>> biojava-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
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> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHhP+44C5LeMEKA/QRAroBAJ9oU/by7joNIkdpkOoEtPFzcP+6ZwCfcVYV
> YpEnZK4o2READMXOsaE9oMo=
> =QZDP
>
> -----END PGP SIGNATURE-----
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From bugzilla-daemon at portal.open-bio.org  Wed Jan 16 10:16:30 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 16 Jan 2008 10:16:30 -0500
Subject: [Biojava-dev] [Bug 2435] New: Mistake in createRecord( ) of
	GFF3Parser
Message-ID: <bug-2435-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435

           Summary: Mistake in createRecord( ) of GFF3Parser
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P3
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: pudimat at gmail.com
                CC: pudimat at gmail.com


When setting the fields in a new GFF3Record, the source field is set twice,
however the second time it is set to the GFF type value. Thus, a record has its
type in the source field, and the type field has value "any".

See line: 256 in GFF3Parser


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 16 12:07:36 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 16 Jan 2008 12:07:36 -0500
Subject: [Biojava-dev] [Bug 2435] Mistake in createRecord( ) of GFF3Parser
In-Reply-To: <bug-2435-485@http.bugzilla.open-bio.org/>
Message-ID: <200801161707.m0GH7a8C005347@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435





------- Comment #1 from pudimat at gmail.com  2008-01-16 12:07 EST -------
Another error in line 344 (method parseAttribute() ):
when splitting the key-value-pair of an attribute, the separating '=' is the
first
symbol of the attribute value.

Reason:  attValList = attVal.substring(spaceIndex).trim();
must be changed to 
attValList = attVal.substring(spaceIndex+1).trim();


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From bugzilla-daemon at portal.open-bio.org  Thu Jan 17 07:36:06 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 17 Jan 2008 07:36:06 -0500
Subject: [Biojava-dev] [Bug 2435] Mistake in createRecord( ) of GFF3Parser
In-Reply-To: <bug-2435-485@http.bugzilla.open-bio.org/>
Message-ID: <200801171236.m0HCa6eE030734@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from holland at ebi.ac.uk  2008-01-17 07:36 EST -------
I have fixed this in the new subversion repository.


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 02:17:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 02:17:42 -0500
Subject: [Biojava-dev] [Bug 2360] saving of ProfileHmm cause
	NullPointerException
In-Reply-To: <bug-2360-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200717.m0K7Hg0H009027@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2360


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from mark.schreiber at novartis.com  2008-01-20 02:17 EST -------
Bug was caused by serialization of an untrained distribution with no weights.
Now fixed with Unit test


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 02:26:00 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 02:26:00 -0500
Subject: [Biojava-dev] [Bug 2371] ChromatogramFactory.create fails on Windows
In-Reply-To: <bug-2371-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200726.m0K7Q013009324@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2371


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |WORKSFORME




------- Comment #1 from mark.schreiber at novartis.com  2008-01-20 02:25 EST -------
This works using biojava 1.6 RC-1 on Windows Vista. I can't replicate the error
using your chromatogram. 


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 03:28:33 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 03:28:33 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200828.m0K8SXrV011671@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #10 from mark.schreiber at novartis.com  2008-01-20 03:28 EST -------
As suggested I have added back the synchronized blockas as they are certainly
needed even though this doesn't fully solve the problem.  Interestingly on
windows vista on a dual core CPU a race condition develops and never seems to
resolve (not even a stack trace)!  Notably this was on a short sequence not one
likely to be a PackedSymbolList as mentioned below.

I wonder if there is a problem with the SimpleThreadPool. Maybe a switch to a
normal Java thread pool might be better?


(In reply to comment #9)
> Here are the comments at the top of org.biojava.bio.symbol.PackedSymbolList,
> and I quote:
> "WARNING: these variables constitute an opportunity
> for things to go wrong when doing multithreaded access
> via symbolAt().  Keep SymbolAt() synchronized so they
> don't get changed during a lookup! Naaasssty."


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 21 04:47:37 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 21 Jan 2008 04:47:37 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801210947.m0L9lbY5028968@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #11 from andyyatz at gmail.com  2008-01-21 04:47 EST -------
If we're looking at Java5+ features here then maybe something like:

http://java.sun.com/j2se/1.5.0/docs/api/java/util/concurrent/locks/ReadWriteLock.html

This is a far superior solution to synchronized blocks as they offer a
difference between reading something & altering it. The blocks can last for as
little or as long as required with us only needing to make sure that we perform
the code in a try {} finally {} block to ensure we do not continually lock out
a resource.

(In reply to comment #10)
> As suggested I have added back the synchronized blockas as they are certainly
> needed even though this doesn't fully solve the problem.  Interestingly on
> windows vista on a dual core CPU a race condition develops and never seems to
> resolve (not even a stack trace)!  Notably this was on a short sequence not one
> likely to be a PackedSymbolList as mentioned below.
> 
> I wonder if there is a problem with the SimpleThreadPool. Maybe a switch to a
> normal Java thread pool might be better?
> 
> 


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 21 14:15:24 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 21 Jan 2008 14:15:24 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801211915.m0LJFOcP031316@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #12 from gwaldon at geneinfinity.org  2008-01-21 14:15 EST -------
I have seen a similar problem (at least producing similar log) and it was
solved by adding pool.stopThreads() at the end of your code:

SequenceIterator iter = SeqIOTools.readFastaDNA(br);
SimpleThreadPool pool = new SimpleThreadPool();
RestrictionMapper mapper = new RestrictionMapper(pool);

 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("MseI"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("HpaII"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("AluI"));
 Sequence seq;
 while(iter.hasNext()){
     seq = iter.nextSequence();
     mapper.annotate(seq);
 }
pool.stopThreads();

Hope it helps. 
- George


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From ap3 at sanger.ac.uk  Tue Jan 22 03:25:49 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Tue, 22 Jan 2008 08:25:49 +0000
Subject: [Biojava-dev] biojava looking for maintainers
Message-ID: <20765D52-2C0E-40C6-A769-7D13CF1DB489@sanger.ac.uk>

Hi,

BioJava is a widely used Java library that provides standard APIs,  
parsers, and solutions for common bioinformatics problems.
It is used in a number of applications and referenced in many  
scientific publications.
See here for an overview of these: http://biojava.org/wiki/ 
BioJava:BioJavaInside

In order to continue our first class efforts to serve the community  
and to further the quality of our source code we are looking
for motivated individuals who want to claim responsibility for some  
of the core libraries and take over maintenance of these.

Please see here for a list of modules for which we are currently  
looking for maintainers:
http://biojava.org/wiki/Maintainers_wanted

If you want to become a BioJava maintainer, please post to the  
biojava-dev mailing list.

As always - happy biojavaing,
Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From felipe.albrecht at gmail.com  Wed Jan 23 01:58:04 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Wed, 23 Jan 2008 04:58:04 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
Message-ID: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>

Hello all,

I have a simple question about pairwise alignment classes (SmithWaterman and
NeedlemanWunsch):
Why it is necessary two Sequence for alignment and not two SymbolList?

Example, I have a SymbolList collection to align between then,
by this way I need to create some "dummies"  Sequence for to do the
alignment.

Reading the source, I saw that the unique field that is exclusive to
Sequence is the name, for the alignment output,
but if I need only the alignment result, it is useless.

It is not possible to override the pairwiseAlignment to accept SymbolList or
may be a new method that the parameters are 2 SymbolList and returns the
alignment score?

Thank you

Felipe Albrecht

From markjschreiber at gmail.com  Wed Jan 23 03:50:05 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 23 Jan 2008 16:50:05 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
Message-ID: <93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>

Hi Felipe -

I agree this is a barrier to ease of use. Even if Sequences are
required internally for some obscure reason there is no reason why
dummy Sequences cannot be made inside the aligner.  These sequences
could be given names like 'query' and 'subject' or even 'seq1' and
'seq2'.

I will take a look at adding some methods.

Best regards,

- Mark

On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello all,
>
> I have a simple question about pairwise alignment classes (SmithWaterman and
> NeedlemanWunsch):
> Why it is necessary two Sequence for alignment and not two SymbolList?
>
> Example, I have a SymbolList collection to align between then,
> by this way I need to create some "dummies"  Sequence for to do the
> alignment.
>
> Reading the source, I saw that the unique field that is exclusive to
> Sequence is the name, for the alignment output,
> but if I need only the alignment result, it is useless.
>
> It is not possible to override the pairwiseAlignment to accept SymbolList or
> may be a new method that the parameters are 2 SymbolList and returns the
> alignment score?
>
> Thank you
>
> Felipe Albrecht
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From dankoc at gmail.com  Wed Jan 23 16:56:19 2008
From: dankoc at gmail.com (Charles Danko)
Date: Wed, 23 Jan 2008 16:56:19 -0500
Subject: [Biojava-dev] Direct access to public genome databases
Message-ID: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>

Hello,

Direct access to public genome databases (i.e. a class to import
sequence, annotations, etc. and create the applicable biojava object)
would be a very useful addition to BioJava.  The Ensj project doesn't
look like it has been updated since official support was dropped.  Are
there any plans to work these features into BioJava?  Have I missed
features that already exist?

Depending on the amount of time required, I may be willing to
contribute to such an endeavor -- particularly for the purpose of
importing sequence.  I have quite a bit of experience working with
java, but not much in a collaborative environment.

Best,
Charles

From heuermh at acm.org  Wed Jan 23 20:06:53 2008
From: heuermh at acm.org (Michael Heuer)
Date: Wed, 23 Jan 2008 20:06:53 -0500 (EST)
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>

Charles Danko wrote:

> Hello,
>
> Direct access to public genome databases (i.e. a class to import
> sequence, annotations, etc. and create the applicable biojava object)
> would be a very useful addition to BioJava.  The Ensj project doesn't
> look like it has been updated since official support was dropped.  Are
> there any plans to work these features into BioJava?  Have I missed
> features that already exist?
>
> Depending on the amount of time required, I may be willing to
> contribute to such an endeavor -- particularly for the purpose of
> importing sequence.  I have quite a bit of experience working with
> java, but not much in a collaborative environment.

What sort of client API would you have in mind?


I'm not a Taverna expert, but it seems to me that access to third-party
data resources is already well covered with the web services available
there.

> http://taverna.sourceforge.net/
> http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices

Or simply call the web services directly.

   michael


From markjschreiber at gmail.com  Wed Jan 23 23:00:27 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 23 Jan 2008 23:00:27 -0500
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
References: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>
	<Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
Message-ID: <93b45ca50801232000p1cfd83c0o47f7b714abfd2d01@mail.gmail.com>

Hi -

>From personal experience you can access data from NCBI and KEGG using
their webservice API's and (depending on the result) use the biojava
parsers to return biojava objects.

The question is, should this activity be wrapped into biojava (ie
should the webservice stuff be inside biojava)?

Pros:  Happens behind the scenes, users don't need to know about WS,
possible uniform interface to several sources
Cons: Lots more dependencies on WS jars (take a look at JAX-WS for
example) and WS client jars

I'm interested in hearing more pros and cons from other people. This
is timely given the upcoming webservices meet up in Tokyo.

Best regards,

- Mark


On Jan 23, 2008 8:06 PM, Michael Heuer <heuermh at acm.org> wrote:
> Charles Danko wrote:
>
> > Hello,
> >
> > Direct access to public genome databases (i.e. a class to import
> > sequence, annotations, etc. and create the applicable biojava object)
> > would be a very useful addition to BioJava.  The Ensj project doesn't
> > look like it has been updated since official support was dropped.  Are
> > there any plans to work these features into BioJava?  Have I missed
> > features that already exist?
> >
> > Depending on the amount of time required, I may be willing to
> > contribute to such an endeavor -- particularly for the purpose of
> > importing sequence.  I have quite a bit of experience working with
> > java, but not much in a collaborative environment.
>
> What sort of client API would you have in mind?
>
>
> I'm not a Taverna expert, but it seems to me that access to third-party
> data resources is already well covered with the web services available
> there.
>
> > http://taverna.sourceforge.net/
> > http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
>
> Or simply call the web services directly.
>
>    michael
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From markjschreiber at gmail.com  Thu Jan 24 02:50:32 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 24 Jan 2008 15:50:32 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
Message-ID: <93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>

Hi Felipe -

Thanks for the input on this. As a general rule the GC should never be
called from code. Generally this degrades performance of the JVM.
Unless there is a very good reason I will remove this. Probably you
are right a method parameter may work better.

- Mark

On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello,
>
> I think that it can be solved by a simple way:
> Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList as
> parameters and do no creating a alignment, just the calculating it and
> returning the value.
>
> Another thing that is a bit stange for me, is the utilization of garbage
> collector direcly, that is: The field "scoreMatrix" is a class field, why at
> the end of pairwiseAlignment it is set to null and the garbage collector
> run? It is not better (and simpler) to use scoreMatrix as method variable?
>
> I'm annexing the class code with my changes that is doing well the (4^8) *
> (4^8) SymbolList pairwise alignments that I am needing :-)
>
> Thank you,
>
> Felipe Albrecht
>
>
>
>
>
>  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > I agree this is a barrier to ease of use. Even if Sequences are
> > required internally for some obscure reason there is no reason why
> > dummy Sequences cannot be made inside the aligner.  These sequences
> > could be given names like 'query' and 'subject' or even 'seq1' and
> > 'seq2'.
> >
> > I will take a look at adding some methods.
> >
> > Best regards,
> >
> > - Mark
> >
> >
> >
> >
> > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hello all,
> > >
> > > I have a simple question about pairwise alignment classes (SmithWaterman
> and
> > > NeedlemanWunsch):
> > > Why it is necessary two Sequence for alignment and not two SymbolList?
> > >
> > > Example, I have a SymbolList collection to align between then,
> > > by this way I need to create some "dummies"  Sequence for to do the
> > > alignment.
> > >
> > > Reading the source, I saw that the unique field that is exclusive to
> > > Sequence is the name, for the alignment output,
> > > but if I need only the alignment result, it is useless.
> > >
> > > It is not possible to override the pairwiseAlignment to accept
> SymbolList or
> > > may be a new method that the parameters are 2 SymbolList and returns the
> > > alignment score?
> > >
> > > Thank you
> > >
> > > Felipe Albrecht
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >
> >
>
>

From ap3 at sanger.ac.uk  Thu Jan 24 03:40:39 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Thu, 24 Jan 2008 08:40:39 +0000 (GMT)
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
Message-ID: <Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>

Hi,

>> Direct access to public genome databases (i.e. a class to import
>> sequence, annotations, etc. and create the applicable biojava object)
>> would be a very useful addition to BioJava.  The Ensj project doesn't
>> look like it has been updated since official support was dropped.  Are
>> there any plans to work these features into BioJava?  Have I missed
>> features that already exist?
>>
>> Depending on the amount of time required, I may be willing to
>> contribute to such an endeavor -- particularly for the purpose of
>> importing sequence.  I have quite a bit of experience working with
>> java, but not much in a collaborative environment.
>

Ensembl provides access to more and more of its data via DAS,
the Distributed Annotation System. DAS is a RESTful protocol to
access data from distributed sites over the internet.

http://www.ensembl.org/info/using/external_data/das/ensembl_das.html

it is quite heavily used and to see a list of available DAS services
see
http://www.dasregistry.org

Andreas


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From bugzilla-daemon at portal.open-bio.org  Thu Jan 24 07:22:41 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 24 Jan 2008 07:22:41 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801241222.m0OCMfZ2026239@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #13 from mark.schreiber at novartis.com  2008-01-24 07:22 EST -------
Using the stopThread() method prevents the race condition. The other option is
to make the threads deamon threads which terminate when all other threads are
finished.

I have tested this on a dual core machine with windows vista on a 1 million
base pair sequence and there is no problem. Unless someone can determine this
bug remains on other operating systems I will close the bug. Please use the
current version of biojava from SVN for testing.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

From felipe.albrecht at gmail.com  Thu Jan 24 08:05:39 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 11:05:39 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
Message-ID: <f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>

If you prefer, I can send a diff and should I do the same thing in
SequenceAlignment and NeedlemanWunsch classes?

Thank  you,

Felipe Albrecht

On Jan 24, 2008 5:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> Thanks for the input on this. As a general rule the GC should never be
> called from code. Generally this degrades performance of the JVM.
> Unless there is a very good reason I will remove this. Probably you
> are right a method parameter may work better.
>
> - Mark
>
> On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello,
> >
> > I think that it can be solved by a simple way:
> > Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList
> as
> > parameters and do no creating a alignment, just the calculating it and
> > returning the value.
> >
> > Another thing that is a bit stange for me, is the utilization of garbage
> > collector direcly, that is: The field "scoreMatrix" is a class field,
> why at
> > the end of pairwiseAlignment it is set to null and the garbage collector
> > run? It is not better (and simpler) to use scoreMatrix as method
> variable?
> >
> > I'm annexing the class code with my changes that is doing well the (4^8)
> *
> > (4^8) SymbolList pairwise alignments that I am needing :-)
> >
> > Thank you,
> >
> > Felipe Albrecht
> >
> >
> >
> >
> >
> >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > I agree this is a barrier to ease of use. Even if Sequences are
> > > required internally for some obscure reason there is no reason why
> > > dummy Sequences cannot be made inside the aligner.  These sequences
> > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > 'seq2'.
> > >
> > > I will take a look at adding some methods.
> > >
> > > Best regards,
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hello all,
> > > >
> > > > I have a simple question about pairwise alignment classes
> (SmithWaterman
> > and
> > > > NeedlemanWunsch):
> > > > Why it is necessary two Sequence for alignment and not two
> SymbolList?
> > > >
> > > > Example, I have a SymbolList collection to align between then,
> > > > by this way I need to create some "dummies"  Sequence for to do the
> > > > alignment.
> > > >
> > > > Reading the source, I saw that the unique field that is exclusive to
> > > > Sequence is the name, for the alignment output,
> > > > but if I need only the alignment result, it is useless.
> > > >
> > > > It is not possible to override the pairwiseAlignment to accept
> > SymbolList or
> > > > may be a new method that the parameters are 2 SymbolList and returns
> the
> > > > alignment score?
> > > >
> > > > Thank you
> > > >
> > > > Felipe Albrecht
> > > > _______________________________________________
> > > > biojava-dev mailing list
> > > > biojava-dev at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > >
> > >
> >
> >
>

From markjschreiber at gmail.com  Thu Jan 24 08:35:43 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 24 Jan 2008 21:35:43 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
Message-ID: <93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>

Hi -

I have just commited changes that let you use SymbolLists in all parts
of the NW and SW SequenceAlignment objects.

As you suggested I made the matrix a method local variable. I also
removed calls to the garbage collector.

This can be checked out from SVN.

- Mark

On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> If you prefer, I can send a diff and should I do the same thing in
> SequenceAlignment and NeedlemanWunsch classes?
>
> Thank  you,
>
> Felipe Albrecht
>
>
>
> On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > Thanks for the input on this. As a general rule the GC should never be
> > called from code. Generally this degrades performance of the JVM.
> > Unless there is a very good reason I will remove this. Probably you
> > are right a method parameter may work better.
> >
> > - Mark
> >
> > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hello,
> >
> >
> >
> > >
> > > I think that it can be solved by a simple way:
> > > Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList
> as
> > > parameters and do no creating a alignment, just the calculating it and
> > > returning the value.
> > >
> > > Another thing that is a bit stange for me, is the utilization of garbage
> > > collector direcly, that is: The field "scoreMatrix" is a class field,
> why at
> > > the end of pairwiseAlignment it is set to null and the garbage collector
> > > run? It is not better (and simpler) to use scoreMatrix as method
> variable?
> > >
> > > I'm annexing the class code with my changes that is doing well the (4^8)
> *
> > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > >
> > > Thank you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > >
> > >
> > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com >
> wrote:
> > > > Hi Felipe -
> > > >
> > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > required internally for some obscure reason there is no reason why
> > > > dummy Sequences cannot be made inside the aligner.  These sequences
> > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > 'seq2'.
> > > >
> > > > I will take a look at adding some methods.
> > > >
> > > > Best regards,
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > wrote:
> > > > > Hello all,
> > > > >
> > > > > I have a simple question about pairwise alignment classes
> (SmithWaterman
> > > and
> > > > > NeedlemanWunsch):
> > > > > Why it is necessary two Sequence for alignment and not two
> SymbolList?
> > > > >
> > > > > Example, I have a SymbolList collection to align between then,
> > > > > by this way I need to create some "dummies"  Sequence for to do the
> > > > > alignment.
> > > > >
> > > > > Reading the source, I saw that the unique field that is exclusive to
> > > > > Sequence is the name, for the alignment output,
> > > > > but if I need only the alignment result, it is useless.
> > > > >
> > > > > It is not possible to override the pairwiseAlignment to accept
> > > SymbolList or
> > > > > may be a new method that the parameters are 2 SymbolList and returns
> the
> > > > > alignment score?
> > > > >
> > > > > Thank you
> > > > >
> > > > > Felipe Albrecht
> > > > > _______________________________________________
> > > > > biojava-dev mailing list
> > > > > biojava-dev at lists.open-bio.org
> > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > >
> > > >
> > >
> > >
> >
>
>

From felipe.albrecht at gmail.com  Thu Jan 24 14:40:48 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 17:40:48 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
Message-ID: <f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>

Hello,

I saw the commit and I think that this solution is not the better.
I think it because you are creating internally two Sequence and probably the
programmer will not use others alignment information,  he will use only the
score.

Because it, I think that if you have 2 SymbolList, just do the alignment and
return the score, as I did.Otherwise, If the programmer want the "visual
alignment", he should create externally the SimpleSequences, it is, not the
method must do it.

IMHO, one [serious] problem in biojava is the memory consumption, it have
not "lightweight" classes or methods that do the things quickly. Because it,
may be is a good choice to have a method that simply gives the alignment
score, and not do the others things, like backtracking. Another think, the
cost of the "instanceof" is high.

Thank you,

Felipe Albrecht


On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi -
>
> I have just commited changes that let you use SymbolLists in all parts
> of the NW and SW SequenceAlignment objects.
>
> As you suggested I made the matrix a method local variable. I also
> removed calls to the garbage collector.
>
> This can be checked out from SVN.
>
> - Mark
>
> On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > If you prefer, I can send a diff and should I do the same thing in
> > SequenceAlignment and NeedlemanWunsch classes?
> >
> > Thank  you,
> >
> > Felipe Albrecht
> >
> >
> >
> > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > Thanks for the input on this. As a general rule the GC should never be
> > > called from code. Generally this degrades performance of the JVM.
> > > Unless there is a very good reason I will remove this. Probably you
> > > are right a method parameter may work better.
> > >
> > > - Mark
> > >
> > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hello,
> > >
> > >
> > >
> > > >
> > > > I think that it can be solved by a simple way:
> > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> SymboList
> > as
> > > > parameters and do no creating a alignment, just the calculating it
> and
> > > > returning the value.
> > > >
> > > > Another thing that is a bit stange for me, is the utilization of
> garbage
> > > > collector direcly, that is: The field "scoreMatrix" is a class
> field,
> > why at
> > > > the end of pairwiseAlignment it is set to null and the garbage
> collector
> > > > run? It is not better (and simpler) to use scoreMatrix as method
> > variable?
> > > >
> > > > I'm annexing the class code with my changes that is doing well the
> (4^8)
> > *
> > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > >
> > > > Thank you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com >
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > > required internally for some obscure reason there is no reason why
> > > > > dummy Sequences cannot be made inside the aligner.  These
> sequences
> > > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > > 'seq2'.
> > > > >
> > > > > I will take a look at adding some methods.
> > > > >
> > > > > Best regards,
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > Hello all,
> > > > > >
> > > > > > I have a simple question about pairwise alignment classes
> > (SmithWaterman
> > > > and
> > > > > > NeedlemanWunsch):
> > > > > > Why it is necessary two Sequence for alignment and not two
> > SymbolList?
> > > > > >
> > > > > > Example, I have a SymbolList collection to align between then,
> > > > > > by this way I need to create some "dummies"  Sequence for to do
> the
> > > > > > alignment.
> > > > > >
> > > > > > Reading the source, I saw that the unique field that is
> exclusive to
> > > > > > Sequence is the name, for the alignment output,
> > > > > > but if I need only the alignment result, it is useless.
> > > > > >
> > > > > > It is not possible to override the pairwiseAlignment to accept
> > > > SymbolList or
> > > > > > may be a new method that the parameters are 2 SymbolList and
> returns
> > the
> > > > > > alignment score?
> > > > > >
> > > > > > Thank you
> > > > > >
> > > > > > Felipe Albrecht
> > > > > > _______________________________________________
> > > > > > biojava-dev mailing list
> > > > > > biojava-dev at lists.open-bio.org
> > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>

From dankoc at gmail.com  Thu Jan 24 15:17:38 2008
From: dankoc at gmail.com (Charles Danko)
Date: Thu, 24 Jan 2008 15:17:38 -0500
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
Message-ID: <8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>

DAS looks just wonderful, and I am very glad to be made aware of it ?
it seems like a much better solution than my initial, highly naive
reaction (accessing public SQL connections).

As I understand it, the easiest way to access DAS services in Java is
via an API such as JAX-WS?   Jumping into the Javadocs, and looking
over a JAX-WS tutorial that I found here:
http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
is a lot to this.

In this sense, a BioJava class that that takes care of much of the
connecting, data transfer, and parsing would be a welcome convenience
for users not already familiar with this API (like me :).  Even for
those who are well-versed in all of this, such a class would allow DB
access with a lot less code.  Given the frequency that most of us
accesses these public databases, this seems like a worthy goal to me!!

Since its so easy to understand the basics of constructing a DAS
request URL, even something as simple as a class that takes a
pre-formed URL (in the constructor) and acts as an iterator over
whatever information is in the result, would be very useful.

Best,
Charles

On Jan 24, 2008 3:40 AM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi,
>
> >> Direct access to public genome databases (i.e. a class to import
> >> sequence, annotations, etc. and create the applicable biojava object)
> >> would be a very useful addition to BioJava.  The Ensj project doesn't
> >> look like it has been updated since official support was dropped.  Are
> >> there any plans to work these features into BioJava?  Have I missed
> >> features that already exist?
> >>
> >> Depending on the amount of time required, I may be willing to
> >> contribute to such an endeavor -- particularly for the purpose of
> >> importing sequence.  I have quite a bit of experience working with
> >> java, but not much in a collaborative environment.
> >
>
> Ensembl provides access to more and more of its data via DAS,
> the Distributed Annotation System. DAS is a RESTful protocol to
> access data from distributed sites over the internet.
>
> http://www.ensembl.org/info/using/external_data/das/ensembl_das.html
>
> it is quite heavily used and to see a list of available DAS services
> see
> http://www.dasregistry.org
>
> Andreas
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>


From markjschreiber at gmail.com  Thu Jan 24 20:26:41 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 09:26:41 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
Message-ID: <93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>

Hi Felipe -

I agree your method is more efficient but I think it violates the
SequenceAlignment interface which would cause compatibility problems.
I also wonder what should happen if a user calls the getAlignment()
method if you have only calculated a score.

instanceof is potentially expensive but it is nothing compared to
actually performing the SmithWaterman.

Biojava is somewhat memory heavy but this is largely because it is
object oriented. Certainly something in C would be lighter and faster
but the whole point in using Java is the relative benefits of object
oriented design.  While ultra optimized algorithms where once a major
feature of bioinformatics this is becoming less necessary as standard
desktops are now equivalent to the super computers of 5 years ago.

I actually find the SW and NW to be reasonably fast. This is because
all the heavy lifting is done in loops that the JVM presumably
compiles and executes natively.

- Mark


On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello,
>
> I saw the commit and I think that this solution is not the better.
> I think it because you are creating internally two Sequence and probably the
> programmer will not use others alignment information,  he will use only the
> score.
>
> Because it, I think that if you have 2 SymbolList, just do the alignment and
> return the score, as I did.Otherwise, If the programmer want the "visual
> alignment", he should create externally the SimpleSequences, it is, not the
> method must do it.
>
> IMHO, one [serious] problem in biojava is the memory consumption, it have
> not "lightweight" classes or methods that do the things quickly. Because it,
> may be is a good choice to have a method that simply gives the alignment
> score, and not do the others things, like backtracking. Another think, the
> cost of the "instanceof" is high.
>
> Thank you,
>
> Felipe Albrecht
>
>
>
>
> On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi -
> >
> > I have just commited changes that let you use SymbolLists in all parts
> > of the NW and SW SequenceAlignment objects.
> >
> > As you suggested I made the matrix a method local variable. I also
> > removed calls to the garbage collector.
> >
> > This can be checked out from SVN.
> >
> > - Mark
> >
> >
> >
> >
> > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> wrote:
> > > If you prefer, I can send a diff and should I do the same thing in
> > > SequenceAlignment and NeedlemanWunsch classes?
> > >
> > > Thank  you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> wrote:
> > > > Hi Felipe -
> > > >
> > > > Thanks for the input on this. As a general rule the GC should never be
> > > > called from code. Generally this degrades performance of the JVM.
> > > > Unless there is a very good reason I will remove this. Probably you
> > > > are right a method parameter may work better.
> > > >
> > > > - Mark
> > > >
> > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > wrote:
> > > > > Hello,
> > > >
> > > >
> > > >
> > > > >
> > > > > I think that it can be solved by a simple way:
> > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> SymboList
> > > as
> > > > > parameters and do no creating a alignment, just the calculating it
> and
> > > > > returning the value.
> > > > >
> > > > > Another thing that is a bit stange for me, is the utilization of
> garbage
> > > > > collector direcly, that is: The field "scoreMatrix" is a class
> field,
> > > why at
> > > > > the end of pairwiseAlignment it is set to null and the garbage
> collector
> > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > variable?
> > > > >
> > > > > I'm annexing the class code with my changes that is doing well the
> (4^8)
> > > *
> > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > >
> > > > > Thank you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber < markjschreiber at gmail.com
> >
> > > wrote:
> > > > > > Hi Felipe -
> > > > > >
> > > > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > > > required internally for some obscure reason there is no reason why
> > > > > > dummy Sequences cannot be made inside the aligner.  These
> sequences
> > > > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > > > 'seq2'.
> > > > > >
> > > > > > I will take a look at adding some methods.
> > > > > >
> > > > > > Best regards,
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> <felipe.albrecht at gmail.com >
> > > > > wrote:
> > > > > > > Hello all,
> > > > > > >
> > > > > > > I have a simple question about pairwise alignment classes
> > > (SmithWaterman
> > > > > and
> > > > > > > NeedlemanWunsch):
> > > > > > > Why it is necessary two Sequence for alignment and not two
> > > SymbolList?
> > > > > > >
> > > > > > > Example, I have a SymbolList collection to align between then,
> > > > > > > by this way I need to create some "dummies"  Sequence for to do
> the
> > > > > > > alignment.
> > > > > > >
> > > > > > > Reading the source, I saw that the unique field that is
> exclusive to
> > > > > > > Sequence is the name, for the alignment output,
> > > > > > > but if I need only the alignment result, it is useless.
> > > > > > >
> > > > > > > It is not possible to override the pairwiseAlignment to accept
> > > > > SymbolList or
> > > > > > > may be a new method that the parameters are 2 SymbolList and
> returns
> > > the
> > > > > > > alignment score?
> > > > > > >
> > > > > > > Thank you
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > > _______________________________________________
> > > > > > > biojava-dev mailing list
> > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>

From felipe.albrecht at gmail.com  Thu Jan 24 21:06:53 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 00:06:53 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
Message-ID: <f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>

Hi,

is not possible to add into the SequenceAlignment interface something like:
"double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
symbolList2)"?
Okay, the name is horrible, but you know what it means.

> While ultra optimized algorithms where once a major
> feature of bioinformatics this is becoming less necessary as standard
> desktops are now equivalent to the super computers of 5 years ago.

Okay, but do not forget that the bioinformatics data size is growing faster
than the computer processing and main memory capacity.

What im trying to say is that the actual methods are fast [and light] enough
for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in my
case, 65k * 65k.
Really, I dont see problems of having optimized functions for specifics
operations, as unix phylosofies: "do small programs for specifics things,
for big things join then" (Something like it :-) ).

Thank you,

Felipe Albrecht


On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> I agree your method is more efficient but I think it violates the
> SequenceAlignment interface which would cause compatibility problems.
> I also wonder what should happen if a user calls the getAlignment()
> method if you have only calculated a score.
>
> instanceof is potentially expensive but it is nothing compared to
> actually performing the SmithWaterman.
>
> Biojava is somewhat memory heavy but this is largely because it is
> object oriented. Certainly something in C would be lighter and faster
> but the whole point in using Java is the relative benefits of object
> oriented design.  While ultra optimized algorithms where once a major
> feature of bioinformatics this is becoming less necessary as standard
> desktops are now equivalent to the super computers of 5 years ago.
>
> I actually find the SW and NW to be reasonably fast. This is because
> all the heavy lifting is done in loops that the JVM presumably
> compiles and executes natively.
>
> - Mark
>
>
> On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello,
> >
> > I saw the commit and I think that this solution is not the better.
> > I think it because you are creating internally two Sequence and probably
> the
> > programmer will not use others alignment information,  he will use only
> the
> > score.
> >
> > Because it, I think that if you have 2 SymbolList, just do the alignment
> and
> > return the score, as I did.Otherwise, If the programmer want the "visual
> > alignment", he should create externally the SimpleSequences, it is, not
> the
> > method must do it.
> >
> > IMHO, one [serious] problem in biojava is the memory consumption, it
> have
> > not "lightweight" classes or methods that do the things quickly. Because
> it,
> > may be is a good choice to have a method that simply gives the alignment
> > score, and not do the others things, like backtracking. Another think,
> the
> > cost of the "instanceof" is high.
> >
> > Thank you,
> >
> > Felipe Albrecht
> >
> >
> >
> >
> > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi -
> > >
> > > I have just commited changes that let you use SymbolLists in all parts
> > > of the NW and SW SequenceAlignment objects.
> > >
> > > As you suggested I made the matrix a method local variable. I also
> > > removed calls to the garbage collector.
> > >
> > > This can be checked out from SVN.
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > wrote:
> > > > If you prefer, I can send a diff and should I do the same thing in
> > > > SequenceAlignment and NeedlemanWunsch classes?
> > > >
> > > > Thank  you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > Thanks for the input on this. As a general rule the GC should
> never be
> > > > > called from code. Generally this degrades performance of the JVM.
> > > > > Unless there is a very good reason I will remove this. Probably
> you
> > > > > are right a method parameter may work better.
> > > > >
> > > > > - Mark
> > > > >
> > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > Hello,
> > > > >
> > > > >
> > > > >
> > > > > >
> > > > > > I think that it can be solved by a simple way:
> > > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> > SymboList
> > > > as
> > > > > > parameters and do no creating a alignment, just the calculating
> it
> > and
> > > > > > returning the value.
> > > > > >
> > > > > > Another thing that is a bit stange for me, is the utilization of
> > garbage
> > > > > > collector direcly, that is: The field "scoreMatrix" is a class
> > field,
> > > > why at
> > > > > > the end of pairwiseAlignment it is set to null and the garbage
> > collector
> > > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > > variable?
> > > > > >
> > > > > > I'm annexing the class code with my changes that is doing well
> the
> > (4^8)
> > > > *
> > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > >
> > > > > > Thank you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > >
> > > > wrote:
> > > > > > > Hi Felipe -
> > > > > > >
> > > > > > > I agree this is a barrier to ease of use. Even if Sequences
> are
> > > > > > > required internally for some obscure reason there is no reason
> why
> > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > sequences
> > > > > > > could be given names like 'query' and 'subject' or even 'seq1'
> and
> > > > > > > 'seq2'.
> > > > > > >
> > > > > > > I will take a look at adding some methods.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > <felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > Hello all,
> > > > > > > >
> > > > > > > > I have a simple question about pairwise alignment classes
> > > > (SmithWaterman
> > > > > > and
> > > > > > > > NeedlemanWunsch):
> > > > > > > > Why it is necessary two Sequence for alignment and not two
> > > > SymbolList?
> > > > > > > >
> > > > > > > > Example, I have a SymbolList collection to align between
> then,
> > > > > > > > by this way I need to create some "dummies"  Sequence for to
> do
> > the
> > > > > > > > alignment.
> > > > > > > >
> > > > > > > > Reading the source, I saw that the unique field that is
> > exclusive to
> > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > >
> > > > > > > > It is not possible to override the pairwiseAlignment to
> accept
> > > > > > SymbolList or
> > > > > > > > may be a new method that the parameters are 2 SymbolList and
> > returns
> > > > the
> > > > > > > > alignment score?
> > > > > > > >
> > > > > > > > Thank you
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > > _______________________________________________
> > > > > > > > biojava-dev mailing list
> > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>

From markjschreiber at gmail.com  Thu Jan 24 22:43:30 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 11:43:30 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
Message-ID: <93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>

On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hi,
>
> is not possible to add into the SequenceAlignment interface something like:
> "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> symbolList2)"?
> Okay, the name is horrible, but you know what it means.
>

You could but you would break backwards compatibility with anyone who
implemented this interface previously.  We have sometimes done this in
biojava but we would need to make sure it will break no ones code.
Another option would be to extend the interface with another that adds
this method (not very tidy I know).

>
> > While ultra optimized algorithms where once a major
> > feature of bioinformatics this is becoming less necessary as standard
> > desktops are now equivalent to the super computers of 5 years ago.
>
> Okay, but do not forget that the bioinformatics data size is growing faster
> than the computer processing and main memory capacity.
>
> What im trying to say is that the actual methods are fast [and light] enough
> for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in my
> case, 65k * 65k.

One could also argue that Smith Waterman is not ideal for large
sequences. I think it is o(NM) or something.

> Really, I dont see problems of having optimized functions for specifics
> operations, as unix phylosofies: "do small programs for specifics things,
> for big things join then" (Something like it :-) ).
>

Yes, this would be an argument for workflow or service oriented
architecture built from multiple inter operable biojava sub-projects.
This is obviously not what biojava is. Indeed biojava is not even an
application you just use it to build applications. Maybe for your use
case you could use biojava to handle the I/O and then do the more
efficient SW using your own code. BioJava is a collection of objects
that are (somewhat) related and interoperable. It doesn't mean you
have to use biojava throughout your application.

- Mark

> On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > I agree your method is more efficient but I think it violates the
> > SequenceAlignment interface which would cause compatibility problems.
> > I also wonder what should happen if a user calls the getAlignment()
> > method if you have only calculated a score.
> >
> > instanceof is potentially expensive but it is nothing compared to
> > actually performing the SmithWaterman.
> >
> > Biojava is somewhat memory heavy but this is largely because it is
> > object oriented. Certainly something in C would be lighter and faster
> > but the whole point in using Java is the relative benefits of object
> > oriented design.  While ultra optimized algorithms where once a major
> > feature of bioinformatics this is becoming less necessary as standard
> > desktops are now equivalent to the super computers of 5 years ago.
> >
> > I actually find the SW and NW to be reasonably fast. This is because
> > all the heavy lifting is done in loops that the JVM presumably
> > compiles and executes natively.
> >
> > - Mark
> >
> >
> >
> >
> >
> > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> wrote:
> > > Hello,
> > >
> > > I saw the commit and I think that this solution is not the better.
> > > I think it because you are creating internally two Sequence and probably
> the
> > > programmer will not use others alignment information,  he will use only
> the
> > > score.
> > >
> > > Because it, I think that if you have 2 SymbolList, just do the alignment
> and
> > > return the score, as I did.Otherwise, If the programmer want the "visual
> > > alignment", he should create externally the SimpleSequences, it is, not
> the
> > > method must do it.
> > >
> > > IMHO, one [serious] problem in biojava is the memory consumption, it
> have
> > > not "lightweight" classes or methods that do the things quickly. Because
> it,
> > > may be is a good choice to have a method that simply gives the alignment
> > > score, and not do the others things, like backtracking. Another think,
> the
> > > cost of the "instanceof" is high.
> > >
> > > Thank you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > >
> > > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > > Hi -
> > > >
> > > > I have just commited changes that let you use SymbolLists in all parts
> > > > of the NW and SW SequenceAlignment objects.
> > > >
> > > > As you suggested I made the matrix a method local variable. I also
> > > > removed calls to the garbage collector.
> > > >
> > > > This can be checked out from SVN.
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > > wrote:
> > > > > If you prefer, I can send a diff and should I do the same thing in
> > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > >
> > > > > Thank  you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com >
> > > wrote:
> > > > > > Hi Felipe -
> > > > > >
> > > > > > Thanks for the input on this. As a general rule the GC should
> never be
> > > > > > called from code. Generally this degrades performance of the JVM.
> > > > > > Unless there is a very good reason I will remove this. Probably
> you
> > > > > > are right a method parameter may work better.
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> <felipe.albrecht at gmail.com>
> > > > > wrote:
> > > > > > > Hello,
> > > > > >
> > > > > >
> > > > > >
> > > > > > >
> > > > > > > I think that it can be solved by a simple way:
> > > > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> > > SymboList
> > > > > as
> > > > > > > parameters and do no creating a alignment, just the calculating
> it
> > > and
> > > > > > > returning the value.
> > > > > > >
> > > > > > > Another thing that is a bit stange for me, is the utilization of
> > > garbage
> > > > > > > collector direcly, that is: The field "scoreMatrix" is a class
> > > field,
> > > > > why at
> > > > > > > the end of pairwiseAlignment it is set to null and the garbage
> > > collector
> > > > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > > > variable?
> > > > > > >
> > > > > > > I'm annexing the class code with my changes that is doing well
> the
> > > (4^8)
> > > > > *
> > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > >
> > > > > > > Thank you,
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > > >
> > > > > wrote:
> > > > > > > > Hi Felipe -
> > > > > > > >
> > > > > > > > I agree this is a barrier to ease of use. Even if Sequences
> are
> > > > > > > > required internally for some obscure reason there is no reason
> why
> > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > sequences
> > > > > > > > could be given names like 'query' and 'subject' or even 'seq1'
> and
> > > > > > > > 'seq2'.
> > > > > > > >
> > > > > > > > I will take a look at adding some methods.
> > > > > > > >
> > > > > > > > Best regards,
> > > > > > > >
> > > > > > > > - Mark
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > <felipe.albrecht at gmail.com >
> > > > > > > wrote:
> > > > > > > > > Hello all,
> > > > > > > > >
> > > > > > > > > I have a simple question about pairwise alignment classes
> > > > > (SmithWaterman
> > > > > > > and
> > > > > > > > > NeedlemanWunsch):
> > > > > > > > > Why it is necessary two Sequence for alignment and not two
> > > > > SymbolList?
> > > > > > > > >
> > > > > > > > > Example, I have a SymbolList collection to align between
> then,
> > > > > > > > > by this way I need to create some "dummies"  Sequence for to
> do
> > > the
> > > > > > > > > alignment.
> > > > > > > > >
> > > > > > > > > Reading the source, I saw that the unique field that is
> > > exclusive to
> > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > >
> > > > > > > > > It is not possible to override the pairwiseAlignment to
> accept
> > > > > > > SymbolList or
> > > > > > > > > may be a new method that the parameters are 2 SymbolList and
> > > returns
> > > > > the
> > > > > > > > > alignment score?
> > > > > > > > >
> > > > > > > > > Thank you
> > > > > > > > >
> > > > > > > > > Felipe Albrecht
> > > > > > > > > _______________________________________________
> > > > > > > > > biojava-dev mailing list
> > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>

From felipe.albrecht at gmail.com  Thu Jan 24 23:25:23 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 02:25:23 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
Message-ID: <f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>

Hello again :-)

On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hi,
> >
> > is not possible to add into the SequenceAlignment interface something
> like:
> > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > symbolList2)"?
> > Okay, the name is horrible, but you know what it means.
> >
>
> You could but you would break backwards compatibility with anyone who
> implemented this interface previously.  We have sometimes done this in
> biojava but we would need to make sure it will break no ones code.
> Another option would be to extend the interface with another that adds
> this method (not very tidy I know).


If I'm correct, the SequenceAlignment is an abstract class, so, we can
define there with an empty implementation, and SmithWaterman and others
classes implements it. Anyone that implemented SequenceAlignment will not
see anything different.



>
> >
> > > While ultra optimized algorithms where once a major
> > > feature of bioinformatics this is becoming less necessary as standard
> > > desktops are now equivalent to the super computers of 5 years ago.
> >
> > Okay, but do not forget that the bioinformatics data size is growing
> faster
> > than the computer processing and main memory capacity.
> >
> > What im trying to say is that the actual methods are fast [and light]
> enough
> > for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in
> my
> > case, 65k * 65k.
>
> One could also argue that Smith Waterman is not ideal for large
> sequences. I think it is o(NM) or something.


I'm not comparing  two sequences with 65k * 65k  bases, but doing the
alignment of 65k little sequences between then.

>
>
> > Really, I dont see problems of having optimized functions for specifics
> > operations, as unix phylosofies: "do small programs for specifics
> things,
> > for big things join then" (Something like it :-) ).
> >
>
> Yes, this would be an argument for workflow or service oriented
> architecture built from multiple inter operable biojava sub-projects.
> This is obviously not what biojava is. Indeed biojava is not even an
> application you just use it to build applications. Maybe for your use
> case you could use biojava to handle the I/O and then do the more
> efficient SW using your own code. BioJava is a collection of objects
> that are (somewhat) related and interoperable. It doesn't mean you
> have to use biojava throughout your application.


Okay, now I understood, biojava is not a library for bioinformatics
applications, but for interconnect bioinformatics applications. So, biojava
in the actual way is not appropriate for the application that I am
developing. I will develop some "optimized" classes and functions for my use
and when it will be ready I will announce in this mailing list and ask if
want to merge in biojava. If biojava team needs somebody to improve some
biojava functions, specially sequences and sequences IO, can ask me.

Thank you

Felipe Albrecht




>
>
> - Mark
>
> > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > I agree your method is more efficient but I think it violates the
> > > SequenceAlignment interface which would cause compatibility problems.
> > > I also wonder what should happen if a user calls the getAlignment()
> > > method if you have only calculated a score.
> > >
> > > instanceof is potentially expensive but it is nothing compared to
> > > actually performing the SmithWaterman.
> > >
> > > Biojava is somewhat memory heavy but this is largely because it is
> > > object oriented. Certainly something in C would be lighter and faster
> > > but the whole point in using Java is the relative benefits of object
> > > oriented design.  While ultra optimized algorithms where once a major
> > > feature of bioinformatics this is becoming less necessary as standard
> > > desktops are now equivalent to the super computers of 5 years ago.
> > >
> > > I actually find the SW and NW to be reasonably fast. This is because
> > > all the heavy lifting is done in loops that the JVM presumably
> > > compiles and executes natively.
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > >
> > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > wrote:
> > > > Hello,
> > > >
> > > > I saw the commit and I think that this solution is not the better.
> > > > I think it because you are creating internally two Sequence and
> probably
> > the
> > > > programmer will not use others alignment information,  he will use
> only
> > the
> > > > score.
> > > >
> > > > Because it, I think that if you have 2 SymbolList, just do the
> alignment
> > and
> > > > return the score, as I did.Otherwise, If the programmer want the
> "visual
> > > > alignment", he should create externally the SimpleSequences, it is,
> not
> > the
> > > > method must do it.
> > > >
> > > > IMHO, one [serious] problem in biojava is the memory consumption, it
>
> > have
> > > > not "lightweight" classes or methods that do the things quickly.
> Because
> > it,
> > > > may be is a good choice to have a method that simply gives the
> alignment
> > > > score, and not do the others things, like backtracking. Another
> think,
> > the
> > > > cost of the "instanceof" is high.
> > > >
> > > > Thank you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com >
> > wrote:
> > > > > Hi -
> > > > >
> > > > > I have just commited changes that let you use SymbolLists in all
> parts
> > > > > of the NW and SW SequenceAlignment objects.
> > > > >
> > > > > As you suggested I made the matrix a method local variable. I also
> > > > > removed calls to the garbage collector.
> > > > >
> > > > > This can be checked out from SVN.
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > If you prefer, I can send a diff and should I do the same thing
> in
> > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > >
> > > > > > Thank  you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> markjschreiber at gmail.com >
> > > > wrote:
> > > > > > > Hi Felipe -
> > > > > > >
> > > > > > > Thanks for the input on this. As a general rule the GC should
> > never be
> > > > > > > called from code. Generally this degrades performance of the
> JVM.
> > > > > > > Unless there is a very good reason I will remove this.
> Probably
> > you
> > > > > > > are right a method parameter may work better.
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > <felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > Hello,
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > >
> > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> utilizing
> > > > SymboList
> > > > > > as
> > > > > > > > parameters and do no creating a alignment, just the
> calculating
> > it
> > > > and
> > > > > > > > returning the value.
> > > > > > > >
> > > > > > > > Another thing that is a bit stange for me, is the
> utilization of
> > > > garbage
> > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> class
> > > > field,
> > > > > > why at
> > > > > > > > the end of pairwiseAlignment it is set to null and the
> garbage
> > > > collector
> > > > > > > > run? It is not better (and simpler) to use scoreMatrix as
> method
> > > > > > variable?
> > > > > > > >
> > > > > > > > I'm annexing the class code with my changes that is doing
> well
> > the
> > > > (4^8)
> > > > > > *
> > > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > > >
> > > > > > > > Thank you,
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > markjschreiber at gmail.com
> > > > >
> > > > > > wrote:
> > > > > > > > > Hi Felipe -
> > > > > > > > >
> > > > > > > > > I agree this is a barrier to ease of use. Even if
> Sequences
> > are
> > > > > > > > > required internally for some obscure reason there is no
> reason
> > why
> > > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > > sequences
> > > > > > > > > could be given names like 'query' and 'subject' or even
> 'seq1'
> > and
> > > > > > > > > 'seq2'.
> > > > > > > > >
> > > > > > > > > I will take a look at adding some methods.
> > > > > > > > >
> > > > > > > > > Best regards,
> > > > > > > > >
> > > > > > > > > - Mark
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > < felipe.albrecht at gmail.com >
> > > > > > > > wrote:
> > > > > > > > > > Hello all,
> > > > > > > > > >
> > > > > > > > > > I have a simple question about pairwise alignment
> classes
> > > > > > (SmithWaterman
> > > > > > > > and
> > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > Why it is necessary two Sequence for alignment and not
> two
> > > > > > SymbolList?
> > > > > > > > > >
> > > > > > > > > > Example, I have a SymbolList collection to align between
> > then,
> > > > > > > > > > by this way I need to create some "dummies"  Sequence
> for to
> > do
> > > > the
> > > > > > > > > > alignment.
> > > > > > > > > >
> > > > > > > > > > Reading the source, I saw that the unique field that is
> > > > exclusive to
> > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > > >
> > > > > > > > > > It is not possible to override the pairwiseAlignment to
> > accept
> > > > > > > > SymbolList or
> > > > > > > > > > may be a new method that the parameters are 2 SymbolList
> and
> > > > returns
> > > > > > the
> > > > > > > > > > alignment score?
> > > > > > > > > >
> > > > > > > > > > Thank you
> > > > > > > > > >
> > > > > > > > > > Felipe Albrecht
> > > > > > > > > > _______________________________________________
> > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>

From markjschreiber at gmail.com  Fri Jan 25 00:40:20 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 13:40:20 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
	<f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
Message-ID: <93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>

On Jan 25, 2008 12:25 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello again :-)
>
>
> On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> >
> > On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hi,
> > >
> > > is not possible to add into the SequenceAlignment interface something
> like:
> > > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > > symbolList2)"?
> > > Okay, the name is horrible, but you know what it means.
> > >

> If I'm correct, the SequenceAlignment is an abstract class, so, we can
> define there with an empty implementation, and SmithWaterman and others
> classes implements it. Anyone that implemented SequenceAlignment will not
> see anything different.

OK in that case adding the method would be OK, even desirable.
Probably this would be the best way to merge in your code.

> Okay, now I understood, biojava is not a library for bioinformatics
> applications, but for interconnect bioinformatics applications. So, biojava

Actually it is a library for bioinformatics that you use to build
bioinformatics applications.  It is possibly not as loosely coupled as
you might like for your purpose. It is definitely not as loosely
coupled as the Unix collection of executables or an SOA system.  Due
to heavy use of interfaces and abstract classes there is some
possibility for custom code.  For example you can recode the
SmithWaterman object to be optimal for your needs and then create an
application where you use your class in place of the normal biojava
SmithWaterman.

> in the actual way is not appropriate for the application that I am
> developing. I will develop some "optimized" classes and functions for my use
> and when it will be ready I will announce in this mailing list and ask if
> want to merge in biojava. If biojava team needs somebody to improve some
> biojava functions, specially sequences and sequences IO, can ask me.

Code improvements and optimizations are always welcome especially if
current interfaces can be preserved (that way the end user gets the
improvement without having to change their code).  I always advise
potential optimizers to use a profiler because it is sometimes hard to
predict how the JVM will behave, for example JIT compiling may mean
parts of code that are theoretically CPU intensive may not be the CPU
bottleneck when the JVM compiles them.

- Mark

>
> Thank you
>
> Felipe Albrecht
>
>
>
>
>
> >
> >
> >
> >
> >
> > - Mark
> >
> > > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > > Hi Felipe -
> > > >
> > > > I agree your method is more efficient but I think it violates the
> > > > SequenceAlignment interface which would cause compatibility problems.
> > > > I also wonder what should happen if a user calls the getAlignment()
> > > > method if you have only calculated a score.
> > > >
> > > > instanceof is potentially expensive but it is nothing compared to
> > > > actually performing the SmithWaterman.
> > > >
> > > > Biojava is somewhat memory heavy but this is largely because it is
> > > > object oriented. Certainly something in C would be lighter and faster
> > > > but the whole point in using Java is the relative benefits of object
> > > > oriented design.  While ultra optimized algorithms where once a major
> > > > feature of bioinformatics this is becoming less necessary as standard
> > > > desktops are now equivalent to the super computers of 5 years ago.
> > > >
> > > > I actually find the SW and NW to be reasonably fast. This is because
> > > > all the heavy lifting is done in loops that the JVM presumably
> > > > compiles and executes natively.
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > > wrote:
> > > > > Hello,
> > > > >
> > > > > I saw the commit and I think that this solution is not the better.
> > > > > I think it because you are creating internally two Sequence and
> probably
> > > the
> > > > > programmer will not use others alignment information,  he will use
> only
> > > the
> > > > > score.
> > > > >
> > > > > Because it, I think that if you have 2 SymbolList, just do the
> alignment
> > > and
> > > > > return the score, as I did.Otherwise, If the programmer want the
> "visual
> > > > > alignment", he should create externally the SimpleSequences, it is,
> not
> > > the
> > > > > method must do it.
> > > > >
> > > > > IMHO, one [serious] problem in biojava is the memory consumption, it
> > > have
> > > > > not "lightweight" classes or methods that do the things quickly.
> Because
> > > it,
> > > > > may be is a good choice to have a method that simply gives the
> alignment
> > > > > score, and not do the others things, like backtracking. Another
> think,
> > > the
> > > > > cost of the "instanceof" is high.
> > > > >
> > > > > Thank you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 11:35 AM, Mark Schreiber < markjschreiber at gmail.com
> >
> > > wrote:
> > > > > > Hi -
> > > > > >
> > > > > > I have just commited changes that let you use SymbolLists in all
> parts
> > > > > > of the NW and SW SequenceAlignment objects.
> > > > > >
> > > > > > As you suggested I made the matrix a method local variable. I also
> > > > > > removed calls to the garbage collector.
> > > > > >
> > > > > > This can be checked out from SVN.
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com >
> > > > > wrote:
> > > > > > > If you prefer, I can send a diff and should I do the same thing
> in
> > > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > > >
> > > > > > > Thank  you,
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> markjschreiber at gmail.com >
> > > > > wrote:
> > > > > > > > Hi Felipe -
> > > > > > > >
> > > > > > > > Thanks for the input on this. As a general rule the GC should
> > > never be
> > > > > > > > called from code. Generally this degrades performance of the
> JVM.
> > > > > > > > Unless there is a very good reason I will remove this.
> Probably
> > > you
> > > > > > > > are right a method parameter may work better.
> > > > > > > >
> > > > > > > > - Mark
> > > > > > > >
> > > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > > <felipe.albrecht at gmail.com >
> > > > > > > wrote:
> > > > > > > > > Hello,
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > >
> > > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> utilizing
> > > > > SymboList
> > > > > > > as
> > > > > > > > > parameters and do no creating a alignment, just the
> calculating
> > > it
> > > > > and
> > > > > > > > > returning the value.
> > > > > > > > >
> > > > > > > > > Another thing that is a bit stange for me, is the
> utilization of
> > > > > garbage
> > > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> class
> > > > > field,
> > > > > > > why at
> > > > > > > > > the end of pairwiseAlignment it is set to null and the
> garbage
> > > > > collector
> > > > > > > > > run? It is not better (and simpler) to use scoreMatrix as
> method
> > > > > > > variable?
> > > > > > > > >
> > > > > > > > > I'm annexing the class code with my changes that is doing
> well
> > > the
> > > > > (4^8)
> > > > > > > *
> > > > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > > > >
> > > > > > > > > Thank you,
> > > > > > > > >
> > > > > > > > > Felipe Albrecht
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > > markjschreiber at gmail.com
> > > > > >
> > > > > > > wrote:
> > > > > > > > > > Hi Felipe -
> > > > > > > > > >
> > > > > > > > > > I agree this is a barrier to ease of use. Even if
> Sequences
> > > are
> > > > > > > > > > required internally for some obscure reason there is no
> reason
> > > why
> > > > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > > > sequences
> > > > > > > > > > could be given names like 'query' and 'subject' or even
> 'seq1'
> > > and
> > > > > > > > > > 'seq2'.
> > > > > > > > > >
> > > > > > > > > > I will take a look at adding some methods.
> > > > > > > > > >
> > > > > > > > > > Best regards,
> > > > > > > > > >
> > > > > > > > > > - Mark
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > > < felipe.albrecht at gmail.com >
> > > > > > > > > wrote:
> > > > > > > > > > > Hello all,
> > > > > > > > > > >
> > > > > > > > > > > I have a simple question about pairwise alignment
> classes
> > > > > > > (SmithWaterman
> > > > > > > > > and
> > > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > > Why it is necessary two Sequence for alignment and not
> two
> > > > > > > SymbolList?
> > > > > > > > > > >
> > > > > > > > > > > Example, I have a SymbolList collection to align between
> > > then,
> > > > > > > > > > > by this way I need to create some "dummies"  Sequence
> for to
> > > do
> > > > > the
> > > > > > > > > > > alignment.
> > > > > > > > > > >
> > > > > > > > > > > Reading the source, I saw that the unique field that is
> > > > > exclusive to
> > > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > > > >
> > > > > > > > > > > It is not possible to override the pairwiseAlignment to
> > > accept
> > > > > > > > > SymbolList or
> > > > > > > > > > > may be a new method that the parameters are 2 SymbolList
> and
> > > > > returns
> > > > > > > the
> > > > > > > > > > > alignment score?
> > > > > > > > > > >
> > > > > > > > > > > Thank you
> > > > > > > > > > >
> > > > > > > > > > > Felipe Albrecht
> > > > > > > > > > > _______________________________________________
> > > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>

From felipe.albrecht at gmail.com  Fri Jan 25 01:39:45 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 04:39:45 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
	<f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
	<93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>
Message-ID: <f6b04db30801242239l5b11f0f3o5e9e1c253264a79a@mail.gmail.com>

Okay, I agree with what you said.

I was looking the SequenceAlignment source and I realize a strange thing.
At formatOutput method, the editDistance is multiplied by -1,
if you use a NeedlemanWunsch pairwiseAlignment method, the editDistance
is returned without any multiplication.
That is, the score/editDistance of formatOutput is different from there that
is given by NeedlemanWunsch pairwiseAlignment.

What is the correct?

Thank you again

Felipe Albrecht

On Jan 25, 2008 3:40 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> On Jan 25, 2008 12:25 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello again :-)
> >
> >
> > On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > >
> > > On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hi,
> > > >
> > > > is not possible to add into the SequenceAlignment interface
> something
> > like:
> > > > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > > > symbolList2)"?
> > > > Okay, the name is horrible, but you know what it means.
> > > >
>
> > If I'm correct, the SequenceAlignment is an abstract class, so, we can
> > define there with an empty implementation, and SmithWaterman and others
> > classes implements it. Anyone that implemented SequenceAlignment will
> not
> > see anything different.
>
> OK in that case adding the method would be OK, even desirable.
> Probably this would be the best way to merge in your code.
>
> > Okay, now I understood, biojava is not a library for bioinformatics
> > applications, but for interconnect bioinformatics applications. So,
> biojava
>
> Actually it is a library for bioinformatics that you use to build
> bioinformatics applications.  It is possibly not as loosely coupled as
> you might like for your purpose. It is definitely not as loosely
> coupled as the Unix collection of executables or an SOA system.  Due
> to heavy use of interfaces and abstract classes there is some
> possibility for custom code.  For example you can recode the
> SmithWaterman object to be optimal for your needs and then create an
> application where you use your class in place of the normal biojava
> SmithWaterman.
>
> > in the actual way is not appropriate for the application that I am
> > developing. I will develop some "optimized" classes and functions for my
> use
> > and when it will be ready I will announce in this mailing list and ask
> if
> > want to merge in biojava. If biojava team needs somebody to improve some
> > biojava functions, specially sequences and sequences IO, can ask me.
>
> Code improvements and optimizations are always welcome especially if
> current interfaces can be preserved (that way the end user gets the
> improvement without having to change their code).  I always advise
> potential optimizers to use a profiler because it is sometimes hard to
> predict how the JVM will behave, for example JIT compiling may mean
> parts of code that are theoretically CPU intensive may not be the CPU
> bottleneck when the JVM compiles them.
>
> - Mark
>
> >
> > Thank you
> >
> > Felipe Albrecht
> >
> >
> >
> >
> >
> > >
> > >
> > >
> > >
> > >
> > > - Mark
> > >
> > > > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > I agree your method is more efficient but I think it violates the
> > > > > SequenceAlignment interface which would cause compatibility
> problems.
> > > > > I also wonder what should happen if a user calls the
> getAlignment()
> > > > > method if you have only calculated a score.
> > > > >
> > > > > instanceof is potentially expensive but it is nothing compared to
> > > > > actually performing the SmithWaterman.
> > > > >
> > > > > Biojava is somewhat memory heavy but this is largely because it is
> > > > > object oriented. Certainly something in C would be lighter and
> faster
> > > > > but the whole point in using Java is the relative benefits of
> object
> > > > > oriented design.  While ultra optimized algorithms where once a
> major
> > > > > feature of bioinformatics this is becoming less necessary as
> standard
> > > > > desktops are now equivalent to the super computers of 5 years ago.
> > > > >
> > > > > I actually find the SW and NW to be reasonably fast. This is
> because
> > > > > all the heavy lifting is done in loops that the JVM presumably
> > > > > compiles and executes natively.
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <
> felipe.albrecht at gmail.com >
> > > > wrote:
> > > > > > Hello,
> > > > > >
> > > > > > I saw the commit and I think that this solution is not the
> better.
> > > > > > I think it because you are creating internally two Sequence and
> > probably
> > > > the
> > > > > > programmer will not use others alignment information,  he will
> use
> > only
> > > > the
> > > > > > score.
> > > > > >
> > > > > > Because it, I think that if you have 2 SymbolList, just do the
> > alignment
> > > > and
> > > > > > return the score, as I did.Otherwise, If the programmer want the
> > "visual
> > > > > > alignment", he should create externally the SimpleSequences, it
> is,
> > not
> > > > the
> > > > > > method must do it.
> > > > > >
> > > > > > IMHO, one [serious] problem in biojava is the memory
> consumption, it
> > > > have
> > > > > > not "lightweight" classes or methods that do the things quickly.
> > Because
> > > > it,
> > > > > > may be is a good choice to have a method that simply gives the
> > alignment
> > > > > > score, and not do the others things, like backtracking. Another
> > think,
> > > > the
> > > > > > cost of the "instanceof" is high.
> > > > > >
> > > > > > Thank you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 11:35 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > >
> > > > wrote:
> > > > > > > Hi -
> > > > > > >
> > > > > > > I have just commited changes that let you use SymbolLists in
> all
> > parts
> > > > > > > of the NW and SW SequenceAlignment objects.
> > > > > > >
> > > > > > > As you suggested I made the matrix a method local variable. I
> also
> > > > > > > removed calls to the garbage collector.
> > > > > > >
> > > > > > > This can be checked out from SVN.
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <
> > felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > If you prefer, I can send a diff and should I do the same
> thing
> > in
> > > > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > > > >
> > > > > > > > Thank  you,
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> > markjschreiber at gmail.com >
> > > > > > wrote:
> > > > > > > > > Hi Felipe -
> > > > > > > > >
> > > > > > > > > Thanks for the input on this. As a general rule the GC
> should
> > > > never be
> > > > > > > > > called from code. Generally this degrades performance of
> the
> > JVM.
> > > > > > > > > Unless there is a very good reason I will remove this.
> > Probably
> > > > you
> > > > > > > > > are right a method parameter may work better.
> > > > > > > > >
> > > > > > > > > - Mark
> > > > > > > > >
> > > > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > > > <felipe.albrecht at gmail.com >
> > > > > > > > wrote:
> > > > > > > > > > Hello,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> > utilizing
> > > > > > SymboList
> > > > > > > > as
> > > > > > > > > > parameters and do no creating a alignment, just the
> > calculating
> > > > it
> > > > > > and
> > > > > > > > > > returning the value.
> > > > > > > > > >
> > > > > > > > > > Another thing that is a bit stange for me, is the
> > utilization of
> > > > > > garbage
> > > > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> > class
> > > > > > field,
> > > > > > > > why at
> > > > > > > > > > the end of pairwiseAlignment it is set to null and the
> > garbage
> > > > > > collector
> > > > > > > > > > run? It is not better (and simpler) to use scoreMatrix
> as
> > method
> > > > > > > > variable?
> > > > > > > > > >
> > > > > > > > > > I'm annexing the class code with my changes that is
> doing
> > well
> > > > the
> > > > > > (4^8)
> > > > > > > > *
> > > > > > > > > > (4^8) SymbolList pairwise alignments that I am needing
> :-)
> > > > > > > > > >
> > > > > > > > > > Thank you,
> > > > > > > > > >
> > > > > > > > > > Felipe Albrecht
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > > > markjschreiber at gmail.com
> > > > > > >
> > > > > > > > wrote:
> > > > > > > > > > > Hi Felipe -
> > > > > > > > > > >
> > > > > > > > > > > I agree this is a barrier to ease of use. Even if
> > Sequences
> > > > are
> > > > > > > > > > > required internally for some obscure reason there is
> no
> > reason
> > > > why
> > > > > > > > > > > dummy Sequences cannot be made inside the aligner.
>  These
> > > > > > sequences
> > > > > > > > > > > could be given names like 'query' and 'subject' or
> even
> > 'seq1'
> > > > and
> > > > > > > > > > > 'seq2'.
> > > > > > > > > > >
> > > > > > > > > > > I will take a look at adding some methods.
> > > > > > > > > > >
> > > > > > > > > > > Best regards,
> > > > > > > > > > >
> > > > > > > > > > > - Mark
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > > > < felipe.albrecht at gmail.com >
> > > > > > > > > > wrote:
> > > > > > > > > > > > Hello all,
> > > > > > > > > > > >
> > > > > > > > > > > > I have a simple question about pairwise alignment
> > classes
> > > > > > > > (SmithWaterman
> > > > > > > > > > and
> > > > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > > > Why it is necessary two Sequence for alignment and
> not
> > two
> > > > > > > > SymbolList?
> > > > > > > > > > > >
> > > > > > > > > > > > Example, I have a SymbolList collection to align
> between
> > > > then,
> > > > > > > > > > > > by this way I need to create some "dummies"
>  Sequence
> > for to
> > > > do
> > > > > > the
> > > > > > > > > > > > alignment.
> > > > > > > > > > > >
> > > > > > > > > > > > Reading the source, I saw that the unique field that
> is
> > > > > > exclusive to
> > > > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > > > but if I need only the alignment result, it is
> useless.
> > > > > > > > > > > >
> > > > > > > > > > > > It is not possible to override the pairwiseAlignment
> to
> > > > accept
> > > > > > > > > > SymbolList or
> > > > > > > > > > > > may be a new method that the parameters are 2
> SymbolList
> > and
> > > > > > returns
> > > > > > > > the
> > > > > > > > > > > > alignment score?
> > > > > > > > > > > >
> > > > > > > > > > > > Thank you
> > > > > > > > > > > >
> > > > > > > > > > > > Felipe Albrecht
> > > > > > > > > > > > _______________________________________________
> > > > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > > >
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>

From ap3 at sanger.ac.uk  Fri Jan 25 04:49:22 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Fri, 25 Jan 2008 09:49:22 +0000
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
	<8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
Message-ID: <80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>


> DAS looks just wonderful, and I am very glad to be made aware of it ?
> it seems like a much better solution than my initial, highly naive
> reaction (accessing public SQL connections).

don;t think that this is naive. There is also ensembldb.ensembl.org
which is a public mysql server if you prefer sql....

>
> As I understand it, the easiest way to access DAS services in Java is
> via an API such as JAX-WS?   Jumping into the Javadocs, and looking
> over a JAX-WS tutorial that I found here:
> http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
> is a lot to this.

I have not tried JAX-WS yet, so I can not comment on that, but if you  
want a library
that makes it easier to talk to DAS servers, you can use my
DAS client library at: http://www.spice-3d.org/dasobert/

Andreas


> ---------------------------------------------------------------------- 
> -


Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ayates at ebi.ac.uk  Fri Jan 25 04:58:37 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 25 Jan 2008 09:58:37 +0000
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>	<8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
	<80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>
Message-ID: <4799B2CD.3010603@ebi.ac.uk>



Andreas Prlic wrote:
> 
>> DAS looks just wonderful, and I am very glad to be made aware of it ?
>> it seems like a much better solution than my initial, highly naive
>> reaction (accessing public SQL connections).
> 
> don;t think that this is naive. There is also ensembldb.ensembl.org
> which is a public mysql server if you prefer sql....

I have to agree. There's a lot to be said about using a database 
directly (in fact my group does just that). But it is potentially a more 
fragile solution than using a public api.

>>
>> As I understand it, the easiest way to access DAS services in Java is
>> via an API such as JAX-WS?   Jumping into the Javadocs, and looking
>> over a JAX-WS tutorial that I found here:
>> http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
>> is a lot to this.
> 
> I have not tried JAX-WS yet, so I can not comment on that, but if you 
> want a library
> that makes it easier to talk to DAS servers, you can use my
> DAS client library at: http://www.spice-3d.org/dasobert/

I would stay away from JAX-WS. It's a web services framework which is 
more for SOAP access than anything else. Even when using it for SOAP 
remoting I've found it less than intuitive (maybe later version have 
gotten better about this especially with the Java6 compiler api 
hopefully removing any need for explicit annotation processing). Chances 
are it would be easier to use JAX-WS when the REST service support comes 
in but until then I would say stay away from it.

Andreas' library is a far superior solution :)

Andy

From bugzilla-daemon at portal.open-bio.org  Fri Jan 25 07:28:08 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 25 Jan 2008 07:28:08 -0500
Subject: [Biojava-dev] [Bug 2432] non conventional fasta header &&
	RichSequence.IOTools
In-Reply-To: <bug-2432-485@http.bugzilla.open-bio.org/>
Message-ID: <200801251228.m0PCS8A5003219@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2432


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from mark.schreiber at novartis.com  2008-01-25 07:28 EST -------
I have added a class called FastaHeader. This class lets you specify which
fields you want to see in the fasta header output. There are overloaded
writeFasta methods in RichSequence.IOTools that let you use this class easily.

For example the following test program reads in a fasta file from Genbank with
a full header and outputs it with only the accession number and description
after the '>'

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

package io;

import java.io.BufferedReader;
import java.io.FileReader;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.biojavax.bio.seq.io.FastaHeader;
import static org.biojavax.bio.seq.RichSequence.IOTools;

/**
 *
 * @author Mark
 */
public class WriteFasta {
    public static void main(String[] args) throws Exception{ 
        BufferedReader br = new BufferedReader(
                new FileReader("files/dna.fasta"));
        RichSequenceIterator iter = IOTools.readFastaDNA(br, null);
        //IOTools.writeFasta(System.out, iter, null);

        FastaHeader header = new FastaHeader();
        header.setShowDescription(true);
        header.setShowIdentifier(false);
        header.setShowNamespace(false);
        header.setShowName(false);
        header.setShowVersion(false);

        IOTools.writeFasta(System.out, iter, null, header);
    }
}


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

From miwalsh125 at gmail.com  Tue Jan 29 10:22:07 2008
From: miwalsh125 at gmail.com (michael walsh)
Date: Tue, 29 Jan 2008 10:22:07 -0500
Subject: [Biojava-dev] Genbank Feature extraction question.
Message-ID: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>

BioJava,

I am writing a program that extracts features from a Genbank file using
BioJava The program needs to extract the feature locations from the file.
This is easy enough to do but the location information returned by the
program does not specify whether or not the location is on the complementary
strand of DNA.

This is some of my code:
FeatureHolder fltrHold = seq.filter(codeFltr);//codeFltr is a filter that
retrieves coding features only.
        //iterate over the Features in fh
        for (Iterator i = fltrHold.features(); i.hasNext(); ){
            Feature f = (Feature)i.next();
            System.out.println(f.getLocation().toString());

An example of the output of the print command is:
join:[32775..32948,31801..32052]

However, the entry in the Genbank file reads:
complement(join(31801..32052,32775..32948))

Is there any way to get my program to output the fact that a features
location is on the complementary strand of DNA?

Any help that anyone can give me would be greatly appreciated.

Sincerely,

M Walsh

From holland at ebi.ac.uk  Wed Jan 30 03:53:29 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 30 Jan 2008 08:53:29 +0000
Subject: [Biojava-dev] Genbank Feature extraction question.
In-Reply-To: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>
References: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>
Message-ID: <47A03B09.1030905@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

If you are using the BioJavaX parsers as opposed to the older deprecated
ones, then yes, the information is there.

Your parser will be returning instances of RichSequence (there will be a
nextRichSequence or getRichSequence method depending on the way in which
you are using the parser and/or iterator).

Features on a RichSequence are all instances of RichFeature.

Locations for RichFeatures are all instances of RichLocation.

If you cast appropriately (or locate and find the getRich* equivalents
of the get* methods you already using on the non-Rich interfaces) then
you will find that RichLocation does have a getStrand method which will
give you the information you need.

cheers,
Richard

michael walsh wrote:
> BioJava,
> 
> I am writing a program that extracts features from a Genbank file using
> BioJava The program needs to extract the feature locations from the file.
> This is easy enough to do but the location information returned by the
> program does not specify whether or not the location is on the complementary
> strand of DNA.
> 
> This is some of my code:
> FeatureHolder fltrHold = seq.filter(codeFltr);//codeFltr is a filter that
> retrieves coding features only.
>         //iterate over the Features in fh
>         for (Iterator i = fltrHold.features(); i.hasNext(); ){
>             Feature f = (Feature)i.next();
>             System.out.println(f.getLocation().toString());
> 
> An example of the output of the print command is:
> join:[32775..32948,31801..32052]
> 
> However, the entry in the Genbank file reads:
> complement(join(31801..32052,32775..32948))
> 
> Is there any way to get my program to output the fact that a features
> location is on the complementary strand of DNA?
> 
> Any help that anyone can give me would be greatly appreciated.
> 
> Sincerely,
> 
> M Walsh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From felipe.albrecht at gmail.com  Thu Jan 24 00:47:37 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 05:47:37 -0000
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
Message-ID: <f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>

Hello,

I think that it can be solved by a simple way:
Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList as
parameters and do no creating a alignment, just the calculating it and
returning the value.

Another thing that is a bit stange for me, is the utilization of garbage
collector direcly, that is: The field "scoreMatrix" is a class field, why at
the end of pairwiseAlignment it is set to null and the garbage collector
run? It is not better (and simpler) to use scoreMatrix as method variable?

I'm annexing the class code with my changes that is doing well the (4^8) *
(4^8) SymbolList pairwise alignments that I am needing :-)

Thank you,

Felipe Albrecht



On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> I agree this is a barrier to ease of use. Even if Sequences are
> required internally for some obscure reason there is no reason why
> dummy Sequences cannot be made inside the aligner.  These sequences
> could be given names like 'query' and 'subject' or even 'seq1' and
> 'seq2'.
>
> I will take a look at adding some methods.
>
> Best regards,
>
> - Mark
>
> On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello all,
> >
> > I have a simple question about pairwise alignment classes (SmithWaterman
> and
> > NeedlemanWunsch):
> > Why it is necessary two Sequence for alignment and not two SymbolList?
> >
> > Example, I have a SymbolList collection to align between then,
> > by this way I need to create some "dummies"  Sequence for to do the
> > alignment.
> >
> > Reading the source, I saw that the unique field that is exclusive to
> > Sequence is the name, for the alignment output,
> > but if I need only the alignment result, it is useless.
> >
> > It is not possible to override the pairwiseAlignment to accept
> SymbolList or
> > may be a new method that the parameters are 2 SymbolList and returns the
> > alignment score?
> >
> > Thank you
> >
> > Felipe Albrecht
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
-------------- next part --------------
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From holland at ebi.ac.uk  Wed Jan  2 11:52:12 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 02 Jan 2008 11:52:12 +0000
Subject: [Biojava-dev] BioJava 3 design discussion coming to an end
Message-ID: <477B7AEC.9000401@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi all.

At the end of January I will be taking the contents of our BioJava 3
discussion wiki page and compiling them into a more formal design proposal.

If you have made any comments elsewhere (e.g. by email) which you would
like to be considered in the final design proposal, then please add them
to the wiki page (or its associated Talk page) before the end of the month.

(I won't be trawling through email archives looking for comments so you
really must copy your comments across to the wiki if you want them to be
included!).

The wiki address is:

   http://www.biojava.org/wiki/BioJava3_Proposal

cheers,
Richard

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From ap3 at sanger.ac.uk  Sun Jan  6 12:41:37 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Sun, 6 Jan 2008 12:41:37 +0000 (GMT)
Subject: [Biojava-dev] bioperl like blastparser
Message-ID: <Pine.LNX.4.64.0801061227560.11140@deskpro349.dynamic.sanger.ac.uk>

Hi Michael,

I just had a look at your patch for the query length.
Several of the unit tests are now failing at
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase.java:143)

The problem is that most blast related unit tests extend the SSBindCase, 
which expects a fixed number of attributes. With the new patch some of the 
blast-flavors have the additional queryLength attribute.

Could you have a look at the behaviour of the parser for some of the files 
where the tests now fail? If you think the new behaviour of the 
parser is correct, we can simply update the tests to accept the different 
number of attributes.

Thanks,
Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From markjschreiber at gmail.com  Mon Jan  7 08:05:33 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 16:05:33 +0800
Subject: [Biojava-dev] Biojava - svn migration
In-Reply-To: <Pine.GSO.4.44.0712272329560.18511-100000@shell3.shore.net>
References: <93b45ca50712271748x3019ce27m2d45008c8ce13ece@mail.gmail.com>
	<Pine.GSO.4.44.0712272329560.18511-100000@shell3.shore.net>
Message-ID: <93b45ca50801070005n10338f8q572b1295bc9ccdff@mail.gmail.com>

Hi -

This URL also works on Windows Vista. I made a secure tunnel using
plink which is part of the PuTTY package.

Thanks,

- Mark

On Dec 28, 2007 12:34 PM, Michael Heuer <heuermh at acm.org> wrote:
> Hello Mark, Andreas
>
> I was able to check out on linux with commandline subversion and
> in eclipse with the following URL:
>
> svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk
>
>   michael
>
>
>
> On Fri, 28 Dec 2007, Mark Schreiber wrote:
>
> > Hi all -
> >
> > I am trying to do a SVN check out with Netbeans but the connection
> > just seems to hang without doing anything (same happens with command
> > line?). I am using the path specified in the biojava wiki but the
> > conversation below suggests that the actual path may be different.
> > What then is the 'home' path?
> >
> > Also, does the SSH+SVN command need to be prepended by an SSH command
> > (or plink -ssh on windows)?
> >
> > - Mark
> >
> > On Dec 28, 2007 5:37 AM, Hilmar Lapp <hlapp at duke.edu> wrote:
> > > I see. Makes sense. -hilmar
> > >
> > >
> > > On Dec 27, 2007, at 4:30 PM, Jason Stajich wrote:
> > >
> > > > My  idea was that just like
> > > > /home/reposiitory/biojava
> > > >   we'd put the SVN in
> > > > /home/svn-repository/biojava
> > > >
> > > > So each of the biojava SVN sub-projects ought would be
> > > >  /home/svn-repository/biojava/biojava-live
> > > >  /home/svn-repository/biojava/biojava-ensj
> > > >
> > > > /home/svn is really the homedir for the svn user and som utility
> > > > stuff like the svn login passwords so I think it is better not to
> > > > put the repos in there.
> > > >
> > > > -jason
> > > > On Dec 27, 2007, at 1:31 PM, Hilmar Lapp wrote:
> > > >
> > > >>
> > > >> On Dec 27, 2007, at 12:32 PM, Chris Fields wrote:
> > > >>
> > > >>>
> > > >>> I agree, but there is already a /home/svn directory which appears
> > > >>> related to blipkit.  We would need to move the blipkit stuff into
> > > >>> it's own subdir and go from there.
> > > >>>
> > > >>
> > > >>
> > > >> I.e., it was set up such that blipkit would be the only project
> > > >> with in it? I'd assume that was by mistake. Also, the last update
> > > >> that I have is that blipkit hasn't been active for a while, though
> > > >> I'm not sure.
> > > >>
> > > >> ChrisM - do you recall the decisions leading to the blipkit svn
> > > >> setup? Could it be moved to a subdirectory as ChrisF suggests?
> > > >>
> > > >>      -hilmar
> > > >> --
> > > >> ===========================================================
> > > >> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> > > >> ===========================================================
> > > >>
> > > >>
> > > >>
> > > >
> > >
> > > --
> > > ===========================================================
> > > : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> > > ===========================================================
> > >
> > >
> > >
> > >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
>


From ayates at ebi.ac.uk  Mon Jan  7 09:34:33 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:34:33 +0000
Subject: [Biojava-dev] Error while reading byte data for creating a
	Trace.
In-Reply-To: <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
Message-ID: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>

Hi,

As far as I am aware there isn't a problem with the current ABI parser  
however if you could send a code snippit of reading in the byte array  
& the stack trace of the index out of bounds exception that would be  
most helpful

Andy

On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:

> Hi all,
> I am having a byte array which is having the data from an .ab1  
> file.The
> biojava library provides a class called as ABITrace which takes as  
> input
> either a byte[] array , a file or a url.If i use the later  
> parameters (the
> file or the url )the program works but if I pass the byte array to the
> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> problem with the ABITrace class or how can I bypass this particular  
> error.
> I am printing the length of the byte array and it comes to  
> 144930...Can
> that cause a problem in my code?
>
> Thanks in advance.
> Abhinav
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From markjschreiber at gmail.com  Mon Jan  7 09:43:14 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 17:43:14 +0800
Subject: [Biojava-dev] JUnit
Message-ID: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>

Hi all -

What do people think about adding the JUnit jar to the test directory
of the biojava-live repository and make the appropriate changes to the
ant classpath?  This would make it easier for people to test the
package directly from the ant build rather than having to specifically
place junit on the system classpath.  It would probably make it more
likely that people run and contribute tests as well.

If we add JUnit 4.1 then it will allow the creation of Unit tests by
just annotating class methods.

If there are no objections I will add it in the next few days.

- Mark


From ayates at ebi.ac.uk  Mon Jan  7 09:46:56 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:46:56 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
Message-ID: <42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>

Yeah I'm happy for that to happen. Just on a side note is Junit 4  
compatible with Junit 3's tests? Otherwise will we have to maintain  
two sets of unit test directories depending on the age of the test?

Andy

On 7 Jan 2008, at 09:43, Mark Schreiber wrote:

> Hi all -
>
> What do people think about adding the JUnit jar to the test directory
> of the biojava-live repository and make the appropriate changes to the
> ant classpath?  This would make it easier for people to test the
> package directly from the ant build rather than having to specifically
> place junit on the system classpath.  It would probably make it more
> likely that people run and contribute tests as well.
>
> If we add JUnit 4.1 then it will allow the creation of Unit tests by
> just annotating class methods.
>
> If there are no objections I will add it in the next few days.
>
> - Mark
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From markjschreiber at gmail.com  Mon Jan  7 09:48:31 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 7 Jan 2008 17:48:31 +0800
Subject: [Biojava-dev] JUnit
In-Reply-To: <42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
	<42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
Message-ID: <93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>

>From my preliminary tests it seems to be compatable.

It seems that version 4.4 is out now.  Allows all kinds of strange
assertions, assumptions and theorys.

- Mark

On Jan 7, 2008 5:46 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Yeah I'm happy for that to happen. Just on a side note is Junit 4
> compatible with Junit 3's tests? Otherwise will we have to maintain
> two sets of unit test directories depending on the age of the test?
>
> Andy
>
>
> On 7 Jan 2008, at 09:43, Mark Schreiber wrote:
>
> > Hi all -
> >
> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> > package directly from the ant build rather than having to specifically
> > place junit on the system classpath.  It would probably make it more
> > likely that people run and contribute tests as well.
> >
> > If we add JUnit 4.1 then it will allow the creation of Unit tests by
> > just annotating class methods.
> >
> > If there are no objections I will add it in the next few days.
> >
> > - Mark
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


From ayates at ebi.ac.uk  Mon Jan  7 09:50:02 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 09:50:02 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
	<42D03EDC-6AEE-4FF3-A3BC-12B304AE91EE@ebi.ac.uk>
	<93b45ca50801070148kc1fb1bel88b9c365fca4d27a@mail.gmail.com>
Message-ID: <D9934B7C-0867-4EFD-9EF2-642528CAD1FC@ebi.ac.uk>

Sounds good to me :)

Andy

On 7 Jan 2008, at 09:48, Mark Schreiber wrote:

>> From my preliminary tests it seems to be compatable.
>
> It seems that version 4.4 is out now.  Allows all kinds of strange
> assertions, assumptions and theorys.
>
> - Mark
>
> On Jan 7, 2008 5:46 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
>> Yeah I'm happy for that to happen. Just on a side note is Junit 4
>> compatible with Junit 3's tests? Otherwise will we have to maintain
>> two sets of unit test directories depending on the age of the test?
>>
>> Andy
>>
>>
>> On 7 Jan 2008, at 09:43, Mark Schreiber wrote:
>>
>>> Hi all -
>>>
>>> What do people think about adding the JUnit jar to the test  
>>> directory
>>> of the biojava-live repository and make the appropriate changes to  
>>> the
>>> ant classpath?  This would make it easier for people to test the
>>> package directly from the ant build rather than having to  
>>> specifically
>>> place junit on the system classpath.  It would probably make it more
>>> likely that people run and contribute tests as well.
>>>
>>> If we add JUnit 4.1 then it will allow the creation of Unit tests by
>>> just annotating class methods.
>>>
>>> If there are no objections I will add it in the next few days.
>>>
>>> - Mark
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>



From ap3 at sanger.ac.uk  Mon Jan  7 10:08:42 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 7 Jan 2008 10:08:42 +0000
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
References: <93b45ca50801070143jccb9deeldf23a5da80de46e9@mail.gmail.com>
Message-ID: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>

> What do people think about adding the JUnit jar to the test directory
> of the biojava-live repository and make the appropriate changes to the
> ant classpath?  This would make it easier for people to test the
>

I would suggest to move all the jar files where we have dependencies  
on into a common subdirectory.
e.g something called "libs" or "jars"

Andreas



-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From michaelgang at gmail.com  Mon Jan  7 10:16:22 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Mon, 7 Jan 2008 12:16:22 +0200
Subject: [Biojava-dev] Fwd:  bioperl like blastparser
In-Reply-To: <6994d82b0801070050t5d9b513fhc53ff758554116ff@mail.gmail.com>
References: <Pine.LNX.4.64.0801061227560.11140@deskpro349.dynamic.sanger.ac.uk>
	<6994d82b0801070050t5d9b513fhc53ff758554116ff@mail.gmail.com>
Message-ID: <6994d82b0801070216q1df26e72ic131592048100f3f@mail.gmail.com>

Hi Andreas,

You are correct.
The junit.jar library was missing in my ant_home.
Eclipse wrote that it was running the tests, but did not run any.
Now I corrected it and see that tests are failing.
I ran the program BlastEcho.java manually on the blast test files and
on the ncbi blast.
Judging after manually curation it worked good but at wu_blast id did
not parse the query length.
The reason is that in wu_blast the query length line has just 8 spaces
at the beginning instead of 9.
So I corrected the line which identifies the querylength at
org.biojava.bio.program.sax.BlastSaxParser
line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {

Now it works also on wu_blast.
It would be now a good idea to update the blast tests regarding the
number of arguments and see if the fail still.

Thanks in advance,
Michael



On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi Michael,
>
> I just had a look at your patch for the query length.
> Several of the unit tests are now failing at
> org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase.java:143)
>
> The problem is that most blast related unit tests extend the SSBindCase,
> which expects a fixed number of attributes. With the new patch some of the
> blast-flavors have the additional queryLength attribute.
>
> Could you have a look at the behaviour of the parser for some of the files
> where the tests now fail? If you think the new behaviour of the
> parser is correct, we can simply update the tests to accept the different
> number of attributes.
>
> Thanks,
> Andreas
>
>
> --------------------------------------------------
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                     Hinxton, Cambridge CB10 1SA, UK
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>


From holland at ebi.ac.uk  Mon Jan  7 12:01:55 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
Subject: [Biojava-dev] Error while reading byte data for creating a
 Trace.
In-Reply-To: <04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
	<04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
Message-ID: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>

This problem was resolved back in November. For some reason during the
last couple of weeks the BioJava mailing list has been sending out
occasional duplicate copies of emails sent several months ago! This was
one of them.

cheers,
Richard

On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> Hi,
>
> As far as I am aware there isn't a problem with the current ABI parser
> however if you could send a code snippit of reading in the byte array
> & the stack trace of the index out of bounds exception that would be
> most helpful
>
> Andy
>
> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>
>> Hi all,
>> I am having a byte array which is having the data from an .ab1
>> file.The
>> biojava library provides a class called as ABITrace which takes as
>> input
>> either a byte[] array , a file or a url.If i use the later
>> parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular
>> error.
>> I am printing the length of the byte array and it comes to
>> 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK



From ayates at ebi.ac.uk  Mon Jan  7 12:18:50 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 7 Jan 2008 12:18:50 +0000
Subject: [Biojava-dev] Error while reading byte data for creating a
	Trace.
In-Reply-To: <50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>
References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk>
	<2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu>
	<04BE1C71-B7CF-4428-86C7-300E4283DAE8@ebi.ac.uk>
	<50442.80.42.95.78.1199707315.squirrel@webmail.ebi.ac.uk>
Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB@ebi.ac.uk>

Oh for ... :). Thought I'd seen this one before

Andy

On 7 Jan 2008, at 12:01, Richard Holland wrote:

> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This  
> was
> one of them.
>
> cheers,
> Richard
>
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI  
>> parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to  
>>> the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is  
>>> there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> -- 
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK



From ap3 at sanger.ac.uk  Mon Jan  7 21:54:21 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 7 Jan 2008 21:54:21 +0000 (GMT)
Subject: [Biojava-dev] bioperl like blastparser
Message-ID: <Pine.LNX.4.64.0801072149400.15544@deskpro349.dynamic.sanger.ac.uk>

Hi Michael,

thanks for your patch, I commited it to the new svn repository
and updated the unit tests to now either take 4 or 5 args.

Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From heuermh at acm.org  Tue Jan  8 00:36:04 2008
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 7 Jan 2008 19:36:04 -0500 (EST)
Subject: [Biojava-dev] JUnit
In-Reply-To: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>
Message-ID: <Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>

Andreas Prlic wrote:

> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> >
>
> I would suggest to move all the jar files where we have dependencies
> on into a common subdirectory.
> e.g something called "libs" or "jars"

Using maven would resolve all of these issues.

Or alternatively, a maven build can create an ant build.xml that downloads
its dependencies from the maven central repository

http://maven.apache.org/plugins/maven-ant-plugin/

or there is Ivy for ant, which can be configured to use the maven central
repository

http://ant.apache.org/ivy/

The 'lib' directory doesn't really have a place any more.

   michael



From markjschreiber at gmail.com  Tue Jan  8 03:17:35 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 8 Jan 2008 11:17:35 +0800
Subject: [Biojava-dev] JUnit
In-Reply-To: <Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>
References: <034C9BC2-8AA5-4220-BB34-C3D86E991200@sanger.ac.uk>
	<Pine.GSO.4.44.0801071929590.4891-100000@shell3.shore.net>
Message-ID: <93b45ca50801071917t1cef45epf8772b4370ef3f97@mail.gmail.com>

Hi -

I have added the junit jar and modified the build.xml

I will leave the decision about a lib directory etc for some more debate.

- Mark

On Jan 8, 2008 8:36 AM, Michael Heuer <heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
> > > What do people think about adding the JUnit jar to the test directory
> > > of the biojava-live repository and make the appropriate changes to the
> > > ant classpath?  This would make it easier for people to test the
> > >
> >
> > I would suggest to move all the jar files where we have dependencies
> > on into a common subdirectory.
> > e.g something called "libs" or "jars"
>
> Using maven would resolve all of these issues.
>
> Or alternatively, a maven build can create an ant build.xml that downloads
> its dependencies from the maven central repository
>
> http://maven.apache.org/plugins/maven-ant-plugin/
>
> or there is Ivy for ant, which can be configured to use the maven central
> repository
>
> http://ant.apache.org/ivy/
>
> The 'lib' directory doesn't really have a place any more.
>
>   michael
>
>


From heuermh at acm.org  Tue Jan  8 04:55:42 2008
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 7 Jan 2008 23:55:42 -0500 (EST)
Subject: [Biojava-dev] JUnit
In-Reply-To: <93b45ca50801071917t1cef45epf8772b4370ef3f97@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0801072342240.4891-100000@shell3.shore.net>

Mark Schreiber wrote:

> I will leave the decision about a lib directory etc for some more debate.

Now that we have a subversion repository in place, I would be happy to
create a maven-based build out on branch for consideration at some point.

Ideally this would happen after refactoring/cleanup/purge so I have less
work to do.  ;)

   michael



From michaelgang at gmail.com  Tue Jan  8 08:23:56 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Tue, 8 Jan 2008 10:23:56 +0200
Subject: [Biojava-dev] read fasta file
Message-ID: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>

Dear All,

I want to read a fasta file of dna (the accessions are internal to our
company and may not be like the convention), make manipulations on it
and write it to another file.
When i take the example from the book "Biojava in Anger" it works
fine, but I get warnings that the SeqIOTools type is deprecated.
When using the RichSequence.IOTools package I have problems that when
writing the fasta it changes the fasta header (it adds the lcl:
prefix).
I want that the fasta header will be in the output file like in the input file.
Will the SeqIOTools type supported further ?
If not, is there another way to solve the problem ?

Thanks in advance,
Michael


From holland at ebi.ac.uk  Tue Jan  8 08:51:32 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Tue, 08 Jan 2008 08:51:32 +0000
Subject: [Biojava-dev] read fasta file
In-Reply-To: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
References: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
Message-ID: <47833994.7090608@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

SeqIOTools is deprecated - this means that it _may_ get dropped in a
future release and so you can't rely on it being present in any future
release.

RichSequence.IOTools follows the FASTA format exactly, which requires a
namespace prefix in the header, and it will change the existing header
if it does not already meet the FASTA standard. There is currently no
way to stop it from doing that, although you might want to raise a bug
report so that it goes on our list of things to change. You can do that
here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava

cheers,
Richard

Michael Gang wrote:
> Dear All,
> 
> I want to read a fasta file of dna (the accessions are internal to our
> company and may not be like the convention), make manipulations on it
> and write it to another file.
> When i take the example from the book "Biojava in Anger" it works
> fine, but I get warnings that the SeqIOTools type is deprecated.
> When using the RichSequence.IOTools package I have problems that when
> writing the fasta it changes the fasta header (it adds the lcl:
> prefix).
> I want that the fasta header will be in the output file like in the input file.
> Will the SeqIOTools type supported further ?
> If not, is there another way to solve the problem ?
> 
> Thanks in advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From bugzilla-daemon at portal.open-bio.org  Tue Jan  8 15:00:58 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 8 Jan 2008 10:00:58 -0500
Subject: [Biojava-dev] [Bug 2432] New: non conventional fasta header &&
	RichSequence.IOTools
Message-ID: <bug-2432-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2432

           Summary: non conventional fasta header && RichSequence.IOTools
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: michaelgang at gmail.com


When reading a fasta file with non conventional header (for example company
intern accessions) and writing it with RichSequence.IOTools the fasta header
get changed.
With deprecated SeqIOTools it works


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
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From minhduc.cao at gmail.com  Wed Jan  9 00:57:43 2008
From: minhduc.cao at gmail.com (Minh Duc, Cao)
Date: Wed, 9 Jan 2008 11:57:43 +1100
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
Message-ID: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>

Hi,

I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
alone application, it works perfectly. However, when the code is called from
an applet, the following exception is thrown

Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
    at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
    at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
SimpleFeatureHolder.java:54)
    at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
RichFeature.java:167)
    at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
:61)
    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
SimpleRichSequenceBuilder.java:100)
    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
SimpleRichSequenceBuilder.java:81)
    at
org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
(SimpleRichSequenceBuilderFactory.java:68)
    at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
RichStreamReader.java:109)
    at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
RichStreamReader.java:92)
    at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
ReadFormatFileFunction.java:134)
    at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
Caused by: java.security.AccessControlException: access denied (
java.lang.RuntimePermission createClassLoader)
    at java.security.AccessControlContext.checkPermission(Unknown Source)
    at java.security.AccessController.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.<init>(Unknown Source)
    at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
GeneratedClassLoader.java:29)
    at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
    at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
:51)
    at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
:58)
    at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
FeatureFilter.java:1270)
    ... 11 more

It is noted that the applet is signed and can read files from client
harddisk if other method is used.

Do anyone have an idea how can I go about to fix this problem?

Thank you very much

Minh


From markjschreiber at gmail.com  Wed Jan  9 08:30:45 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 9 Jan 2008 16:30:45 +0800
Subject: [Biojava-dev] read fasta file
In-Reply-To: <47833994.7090608@ebi.ac.uk>
References: <6994d82b0801080023y3cdcc005g57b08c6566c37445@mail.gmail.com>
	<47833994.7090608@ebi.ac.uk>
Message-ID: <93b45ca50801090030t6ffd9907ieb1082fd20c5b713@mail.gmail.com>

Along these lines I have plans to add a way to format the Fasta header
in the RichSequence.IOTools so that the content of it can be
customised. Currently it follows the NCBI model and tries to add
everything it can.

I would be interested in proposals for a template mechanism.

- Mark

On Jan 8, 2008 4:51 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> SeqIOTools is deprecated - this means that it _may_ get dropped in a
> future release and so you can't rely on it being present in any future
> release.
>
> RichSequence.IOTools follows the FASTA format exactly, which requires a
> namespace prefix in the header, and it will change the existing header
> if it does not already meet the FASTA standard. There is currently no
> way to stop it from doing that, although you might want to raise a bug
> report so that it goes on our list of things to change. You can do that
> here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava
>
> cheers,
> Richard
>
>
> Michael Gang wrote:
> > Dear All,
> >
> > I want to read a fasta file of dna (the accessions are internal to our
> > company and may not be like the convention), make manipulations on it
> > and write it to another file.
> > When i take the example from the book "Biojava in Anger" it works
> > fine, but I get warnings that the SeqIOTools type is deprecated.
> > When using the RichSequence.IOTools package I have problems that when
> > writing the fasta it changes the fasta header (it adds the lcl:
> > prefix).
> > I want that the fasta header will be in the output file like in the input file.
> > Will the SeqIOTools type supported further ?
> > If not, is there another way to solve the problem ?
> >
> > Thanks in advance,
> > Michael
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
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>
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> FjmCDFlMygy68q1zkbpwX2o=
> =bTSb
> -----END PGP SIGNATURE-----
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From holland at ebi.ac.uk  Wed Jan  9 08:38:12 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 09 Jan 2008 08:38:12 +0000
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
Message-ID: <478487F4.3090209@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

This is the root of your problem:

Caused by: java.security.AccessControlException: access denied (
java.lang.RuntimePermission createClassLoader)
     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
 GeneratedClassLoader.java:29)
     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)

The applet runtime environment is not allowing BioJava to create a
custom class loader. It's not to do with disk access at all unfortunately.

I don't know of a solution myself as I've not done much work with applets.

Does anyone else on this list have any suggestions?

cheers,
Richard


Minh Duc, Cao wrote:
> Hi,
> 
> I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> alone application, it works perfectly. However, when the code is called from
> an applet, the following exception is thrown
> 
> Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
>     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
>     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> SimpleFeatureHolder.java:54)
>     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> RichFeature.java:167)
>     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> :61)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:100)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:81)
>     at
> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> (SimpleRichSequenceBuilderFactory.java:68)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> RichStreamReader.java:109)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> RichStreamReader.java:92)
>     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> ReadFormatFileFunction.java:134)
>     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at java.security.AccessControlContext.checkPermission(Unknown Source)
>     at java.security.AccessController.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
>     at java.lang.ClassLoader.<init>(Unknown Source)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :51)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :58)
>     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> FeatureFilter.java:1270)
>     ... 11 more
> 
> It is noted that the applet is signed and can read files from client
> harddisk if other method is used.
> 
> Do anyone have an idea how can I go about to fix this problem?
> 
> Thank you very much
> 
> Minh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Wed Jan  9 08:50:11 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 9 Jan 2008 16:50:11 +0800
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <478487F4.3090209@ebi.ac.uk>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
	<478487F4.3090209@ebi.ac.uk>
Message-ID: <93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>

Consulting a good book on the java security model may reveal a way
that you can modify the policy to allow this.

However, I think you should give serious consideration to why you
would want to use an applet in any context. The technology has major
limitations and has been long since superceeded by either severlet or
other technologies for server side stuff or webstart for client side
apps distributed from a server.

- Mark

On Jan 9, 2008 4:38 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello.
>
> This is the root of your problem:
>
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
>  GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>
> The applet runtime environment is not allowing BioJava to create a
> custom class loader. It's not to do with disk access at all unfortunately.
>
> I don't know of a solution myself as I've not done much work with applets.
>
> Does anyone else on this list have any suggestions?
>
> cheers,
> Richard
>
>
>
> Minh Duc, Cao wrote:
> > Hi,
> >
> > I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> > alone application, it works perfectly. However, when the code is called from
> > an applet, the following exception is thrown
> >
> > Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
> >     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
> >     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> > SimpleFeatureHolder.java:54)
> >     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> > RichFeature.java:167)
> >     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> > :61)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:100)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:81)
> >     at
> > org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> > (SimpleRichSequenceBuilderFactory.java:68)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> > RichStreamReader.java:92)
> >     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> > ReadFormatFileFunction.java:134)
> >     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> > Caused by: java.security.AccessControlException: access denied (
> > java.lang.RuntimePermission createClassLoader)
> >     at java.security.AccessControlContext.checkPermission(Unknown Source)
> >     at java.security.AccessController.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
> >     at java.lang.ClassLoader.<init>(Unknown Source)
> >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> > GeneratedClassLoader.java:29)
> >     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :51)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :58)
> >     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> > FeatureFilter.java:1270)
> >     ... 11 more
> >
> > It is noted that the applet is signed and can read files from client
> > harddisk if other method is used.
> >
> > Do anyone have an idea how can I go about to fix this problem?
> >
> > Thank you very much
> >
> > Minh
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
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> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
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> R0e4dCpmpjJnHOrfjfw0wYc=
> =WayD
> -----END PGP SIGNATURE-----
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From jcope at cableone.net  Wed Jan  9 15:59:16 2008
From: jcope at cableone.net (Jeff Cope)
Date: Wed, 9 Jan 2008 08:59:16 -0700
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
Message-ID: <000801c852d8$966eb370$6402a8c0@roadrunner>

Hi,
	
	My name is Jeff Cope, and I'm currently working on a bioinformatics
project for a professor at BSU.  What we have so far is mostly in java, but
with the data calculations taking place using functionality found in the
BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
protein sequences, and thought that we could help you out on the BioJava
project by seeing if that functionality could be added into your library
instead...

	So I guess my question is, now that I'm signed up on the developers
mail list, what would I need to do to get started (assuming you want my
help), and what kind of programming ground rules do you have...

	I feel pretty comfortable in Java code, and if you would like to see
an example of my source code, and some of the work I've done so far, you can
find it here:
	Current project:
	http://trac.boisestate.edu/protcalc/
	Source Code:
	http://trac.boisestate.edu/protcalc/src/
	API docs:
	http://trac.boisestate.edu/protcalc/docs/
	

Thanks,
	Jeff Cope

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
biojava-dev-request at lists.open-bio.org
Sent: Tuesday, January 08, 2008 1:52 AM
To: biojava-dev at lists.open-bio.org
Subject: biojava-dev Digest, Vol 59, Issue 2

Send biojava-dev mailing list submissions to
	biojava-dev at lists.open-bio.org

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of biojava-dev digest..."


Today's Topics:

   1. Fwd:  bioperl like blastparser (Michael Gang)
   2. Re: Error while reading byte data for creating a Trace.
      (Richard Holland)
   3. Re: Error while reading byte data for creating a	Trace.
      (Andy Yates)
   4. Re: bioperl like blastparser (Andreas Prlic)
   5. Re: JUnit (Michael Heuer)
   6. Re: JUnit (Mark Schreiber)
   7. Re: JUnit (Michael Heuer)
   8. read fasta file (Michael Gang)
   9. Re: read fasta file (Richard Holland)


----------------------------------------------------------------------

Message: 1
Date: Mon, 7 Jan 2008 12:16:22 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] Fwd:  bioperl like blastparser
To: biojava-dev at biojava.org
Message-ID:
	<6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Andreas,

You are correct.
The junit.jar library was missing in my ant_home.
Eclipse wrote that it was running the tests, but did not run any.
Now I corrected it and see that tests are failing.
I ran the program BlastEcho.java manually on the blast test files and
on the ncbi blast.
Judging after manually curation it worked good but at wu_blast id did
not parse the query length.
The reason is that in wu_blast the query length line has just 8 spaces
at the beginning instead of 9.
So I corrected the line which identifies the querylength at
org.biojava.bio.program.sax.BlastSaxParser
line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {

Now it works also on wu_blast.
It would be now a good idea to update the blast tests regarding the
number of arguments and see if the fail still.

Thanks in advance,
Michael



On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi Michael,
>
> I just had a look at your patch for the query length.
> Several of the unit tests are now failing at
>
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
.java:143)
>
> The problem is that most blast related unit tests extend the SSBindCase,
> which expects a fixed number of attributes. With the new patch some of the
> blast-flavors have the additional queryLength attribute.
>
> Could you have a look at the behaviour of the parser for some of the files
> where the tests now fail? If you think the new behaviour of the
> parser is correct, we can simply update the tests to accept the different
> number of attributes.
>
> Thanks,
> Andreas
>
>
> --------------------------------------------------
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                     Hinxton, Cambridge CB10 1SA, UK
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>


------------------------------

Message: 2
Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
From: "Richard Holland" <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
	a Trace.
To: "Andy Yates" <ayates at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
	abhi232 at cc.gatech.edu
Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
Content-Type: text/plain;charset=iso-8859-1

This problem was resolved back in November. For some reason during the
last couple of weeks the BioJava mailing list has been sending out
occasional duplicate copies of emails sent several months ago! This was
one of them.

cheers,
Richard

On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> Hi,
>
> As far as I am aware there isn't a problem with the current ABI parser
> however if you could send a code snippit of reading in the byte array
> & the stack trace of the index out of bounds exception that would be
> most helpful
>
> Andy
>
> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>
>> Hi all,
>> I am having a byte array which is having the data from an .ab1
>> file.The
>> biojava library provides a class called as ABITrace which takes as
>> input
>> either a byte[] array , a file or a url.If i use the later
>> parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular
>> error.
>> I am printing the length of the byte array and it comes to
>> 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK



------------------------------

Message: 3
Date: Mon, 7 Jan 2008 12:18:50 +0000
From: Andy Yates <ayates at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
	a	Trace.
To: "Richard Holland" <holland at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
	abhi232 at cc.gatech.edu
Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB at ebi.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Oh for ... :). Thought I'd seen this one before

Andy

On 7 Jan 2008, at 12:01, Richard Holland wrote:

> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This  
> was
> one of them.
>
> cheers,
> Richard
>
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI  
>> parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to  
>>> the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is  
>>> there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> -- 
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK



------------------------------

Message: 4
Date: Mon, 7 Jan 2008 21:54:21 +0000 (GMT)
From: Andreas Prlic <ap3 at sanger.ac.uk>
Subject: Re: [Biojava-dev] bioperl like blastparser
To: michaelgang at gmail.com
Cc: biojava-dev at biojava.org
Message-ID:
	<Pine.LNX.4.64.0801072149400.15544 at deskpro349.dynamic.sanger.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Michael,

thanks for your patch, I commited it to the new svn repository
and updated the unit tests to now either take 4 or 5 args.

Andreas


--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


------------------------------

Message: 5
Date: Mon, 7 Jan 2008 19:36:04 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Andreas Prlic <ap3 at sanger.ac.uk>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801071929590.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Andreas Prlic wrote:

> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath?  This would make it easier for people to test the
> >
>
> I would suggest to move all the jar files where we have dependencies
> on into a common subdirectory.
> e.g something called "libs" or "jars"

Using maven would resolve all of these issues.

Or alternatively, a maven build can create an ant build.xml that downloads
its dependencies from the maven central repository

http://maven.apache.org/plugins/maven-ant-plugin/

or there is Ivy for ant, which can be configured to use the maven central
repository

http://ant.apache.org/ivy/

The 'lib' directory doesn't really have a place any more.

   michael



------------------------------

Message: 6
Date: Tue, 8 Jan 2008 11:17:35 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-dev] JUnit
To: "Michael Heuer" <heuermh at acm.org>
Cc: biojava-dev at biojava.org
Message-ID:
	<93b45ca50801071917t1cef45epf8772b4370ef3f97 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi -

I have added the junit jar and modified the build.xml

I will leave the decision about a lib directory etc for some more debate.

- Mark

On Jan 8, 2008 8:36 AM, Michael Heuer <heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
> > > What do people think about adding the JUnit jar to the test directory
> > > of the biojava-live repository and make the appropriate changes to the
> > > ant classpath?  This would make it easier for people to test the
> > >
> >
> > I would suggest to move all the jar files where we have dependencies
> > on into a common subdirectory.
> > e.g something called "libs" or "jars"
>
> Using maven would resolve all of these issues.
>
> Or alternatively, a maven build can create an ant build.xml that downloads
> its dependencies from the maven central repository
>
> http://maven.apache.org/plugins/maven-ant-plugin/
>
> or there is Ivy for ant, which can be configured to use the maven central
> repository
>
> http://ant.apache.org/ivy/
>
> The 'lib' directory doesn't really have a place any more.
>
>   michael
>
>


------------------------------

Message: 7
Date: Mon, 7 Jan 2008 23:55:42 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801072342240.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Mark Schreiber wrote:

> I will leave the decision about a lib directory etc for some more debate.

Now that we have a subversion repository in place, I would be happy to
create a maven-based build out on branch for consideration at some point.

Ideally this would happen after refactoring/cleanup/purge so I have less
work to do.  ;)

   michael



------------------------------

Message: 8
Date: Tue, 8 Jan 2008 10:23:56 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] read fasta file
To: biojava-dev at biojava.org
Message-ID:
	<6994d82b0801080023y3cdcc005g57b08c6566c37445 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear All,

I want to read a fasta file of dna (the accessions are internal to our
company and may not be like the convention), make manipulations on it
and write it to another file.
When i take the example from the book "Biojava in Anger" it works
fine, but I get warnings that the SeqIOTools type is deprecated.
When using the RichSequence.IOTools package I have problems that when
writing the fasta it changes the fasta header (it adds the lcl:
prefix).
I want that the fasta header will be in the output file like in the input
file.
Will the SeqIOTools type supported further ?
If not, is there another way to solve the problem ?

Thanks in advance,
Michael


------------------------------

Message: 9
Date: Tue, 08 Jan 2008 08:51:32 +0000
From: Richard Holland <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] read fasta file
To: Michael Gang <michaelgang at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <47833994.7090608 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

SeqIOTools is deprecated - this means that it _may_ get dropped in a
future release and so you can't rely on it being present in any future
release.

RichSequence.IOTools follows the FASTA format exactly, which requires a
namespace prefix in the header, and it will change the existing header
if it does not already meet the FASTA standard. There is currently no
way to stop it from doing that, although you might want to raise a bug
report so that it goes on our list of things to change. You can do that
here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava

cheers,
Richard

Michael Gang wrote:
> Dear All,
> 
> I want to read a fasta file of dna (the accessions are internal to our
> company and may not be like the convention), make manipulations on it
> and write it to another file.
> When i take the example from the book "Biojava in Anger" it works
> fine, but I get warnings that the SeqIOTools type is deprecated.
> When using the RichSequence.IOTools package I have problems that when
> writing the fasta it changes the fasta header (it adds the lcl:
> prefix).
> I want that the fasta header will be in the output file like in the input
file.
> Will the SeqIOTools type supported further ?
> If not, is there another way to solve the problem ?
> 
> Thanks in advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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------------------------------

_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev


End of biojava-dev Digest, Vol 59, Issue 2
******************************************



From holland at ebi.ac.uk  Wed Jan  9 17:09:13 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 09 Jan 2008 17:09:13 +0000
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <000801c852d8$966eb370$6402a8c0@roadrunner>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
Message-ID: <4784FFB9.1050402@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Jeff.

Thanks for volunteering! Sounds like you've got a useful set of tools
which we would definitely appreciate as new BioJava features.

We're currently planning a Big Reorganisation for a new BioJava 3 from
the ground-up. Details will be published some time in February I expect,
if not then early March. See this Wiki for things that are currently
being considered (most will make it into the plan, some may not, but I
won't know until I've written it up and identified the conflicting areas):

  http://www.biojava.org/wiki/BioJava3_Proposal

(also see the associated Discussion page for further comments)

If I were you, I'd hang on until the final plan is published. It will
contain everything you need to know on how to write modules for the new
BioJava 3.

However, if you're in a rush to get it into the current BioJava 2
release, then take a look round the JavaDocs to see what is present and
what is not. You'll soon get a good idea of how things are organised and
what features are absent. We also have a bugzilla page with some
unresolved bugs - always a good starting point to learn how a system
works and where the opportunities for development are!
 http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED

cheers,
Richard

Jeff Cope wrote:
> Hi,
> 	
> 	My name is Jeff Cope, and I'm currently working on a bioinformatics
> project for a professor at BSU.  What we have so far is mostly in java, but
> with the data calculations taking place using functionality found in the
> BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
> Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> protein sequences, and thought that we could help you out on the BioJava
> project by seeing if that functionality could be added into your library
> instead...
> 
> 	So I guess my question is, now that I'm signed up on the developers
> mail list, what would I need to do to get started (assuming you want my
> help), and what kind of programming ground rules do you have...
> 
> 	I feel pretty comfortable in Java code, and if you would like to see
> an example of my source code, and some of the work I've done so far, you can
> find it here:
> 	Current project:
> 	http://trac.boisestate.edu/protcalc/
> 	Source Code:
> 	http://trac.boisestate.edu/protcalc/src/
> 	API docs:
> 	http://trac.boisestate.edu/protcalc/docs/
> 	
> 
> Thanks,
> 	Jeff Cope
> 
> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org
> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> biojava-dev-request at lists.open-bio.org
> Sent: Tuesday, January 08, 2008 1:52 AM
> To: biojava-dev at lists.open-bio.org
> Subject: biojava-dev Digest, Vol 59, Issue 2
> 
> Send biojava-dev mailing list submissions to
> 	biojava-dev at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-dev
> or, via email, send a message with subject or body 'help' to
> 	biojava-dev-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-dev-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of biojava-dev digest..."
> 
> 
> Today's Topics:
> 
>    1. Fwd:  bioperl like blastparser (Michael Gang)
>    2. Re: Error while reading byte data for creating a Trace.
>       (Richard Holland)
>    3. Re: Error while reading byte data for creating a	Trace.
>       (Andy Yates)
>    4. Re: bioperl like blastparser (Andreas Prlic)
>    5. Re: JUnit (Michael Heuer)
>    6. Re: JUnit (Mark Schreiber)
>    7. Re: JUnit (Michael Heuer)
>    8. read fasta file (Michael Gang)
>    9. Re: read fasta file (Richard Holland)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 7 Jan 2008 12:16:22 +0200
> From: "Michael Gang" <michaelgang at gmail.com>
> Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> To: biojava-dev at biojava.org
> Message-ID:
> 	<6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Andreas,
> 
> You are correct.
> The junit.jar library was missing in my ant_home.
> Eclipse wrote that it was running the tests, but did not run any.
> Now I corrected it and see that tests are failing.
> I ran the program BlastEcho.java manually on the blast test files and
> on the ncbi blast.
> Judging after manually curation it worked good but at wu_blast id did
> not parse the query length.
> The reason is that in wu_blast the query length line has just 8 spaces
> at the beginning instead of 9.
> So I corrected the line which identifies the querylength at
> org.biojava.bio.program.sax.BlastSaxParser
> line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> 
> Now it works also on wu_blast.
> It would be now a good idea to update the blast tests regarding the
> number of arguments and see if the fail still.
> 
> Thanks in advance,
> Michael
> 
> 
> 
> On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
>> Hi Michael,
>>
>> I just had a look at your patch for the query length.
>> Several of the unit tests are now failing at
>>
> org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> .java:143)
>> The problem is that most blast related unit tests extend the SSBindCase,
>> which expects a fixed number of attributes. With the new patch some of the
>> blast-flavors have the additional queryLength attribute.
>>
>> Could you have a look at the behaviour of the parser for some of the files
>> where the tests now fail? If you think the new behaviour of the
>> parser is correct, we can simply update the tests to accept the different
>> number of attributes.
>>
>> Thanks,
>> Andreas
>>
>>
>> --------------------------------------------------
>>
>> Andreas Prlic      Wellcome Trust Sanger Institute
>>                     Hinxton, Cambridge CB10 1SA, UK
>>
>>
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
>>  office is 215 Euston Road, London, NW1 2BE.
>>
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> From: "Richard Holland" <holland at ebi.ac.uk>
> Subject: Re: [Biojava-dev] Error while reading byte data for creating
> 	a Trace.
> To: "Andy Yates" <ayates at ebi.ac.uk>
> Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> 	abhi232 at cc.gatech.edu
> Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> Content-Type: text/plain;charset=iso-8859-1
> 
> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This was
> one of them.
> 
> cheers,
> Richard
> 
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> 
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From minhduc.cao at gmail.com  Wed Jan  9 19:47:28 2008
From: minhduc.cao at gmail.com (Minh Duc, Cao)
Date: Thu, 10 Jan 2008 06:47:28 +1100
Subject: [Biojava-dev] Problem with read RichFormat file from an applet
In-Reply-To: <93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>
References: <f8101ff00801081657l5387438u806f841961f85406@mail.gmail.com>
	<478487F4.3090209@ebi.ac.uk>
	<93b45ca50801090050j40455c2bid1af46c277a62582@mail.gmail.com>
Message-ID: <f8101ff00801091147p76463ff0m62a432b031b71bd3@mail.gmail.com>

Hi,
I figured out the problem. Once the biojava jar file is signed, the applet
can read files without any problems.  Many thanks to you both.

Also thank Mark for your suggestions, I will certainly try WebStart out.

Cheers
Minh


On Jan 9, 2008 7:50 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Consulting a good book on the java security model may reveal a way
> that you can modify the policy to allow this.
>
> However, I think you should give serious consideration to why you
> would want to use an applet in any context. The technology has major
> limitations and has been long since superceeded by either severlet or
> other technologies for server side stuff or webstart for client side
> apps distributed from a server.
>
> - Mark
>
> On Jan 9, 2008 4:38 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > Hello.
> >
> > This is the root of your problem:
> >
> > Caused by: java.security.AccessControlException: access denied (
> > java.lang.RuntimePermission createClassLoader)
> >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> >  GeneratedClassLoader.java:29)
> >     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java
> :68)
> >
> > The applet runtime environment is not allowing BioJava to create a
> > custom class loader. It's not to do with disk access at all
> unfortunately.
> >
> > I don't know of a solution myself as I've not done much work with
> applets.
> >
> > Does anyone else on this list have any suggestions?
> >
> > cheers,
> > Richard
> >
> >
> >
> > Minh Duc, Cao wrote:
> > > Hi,
> > >
> > > I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a
> stand
> > > alone application, it works perfectly. However, when the code is
> called from
> > > an applet, the following exception is thrown
> > >
> > > Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
> > >     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java
> :1813)
> > >     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> > > SimpleFeatureHolder.java:54)
> > >     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> > > RichFeature.java:167)
> > >     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(
> RichSeqIOAdapter.java
> > > :61)
> > >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > > SimpleRichSequenceBuilder.java:100)
> > >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > > SimpleRichSequenceBuilder.java:81)
> > >     at
> > >
> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> > > (SimpleRichSequenceBuilderFactory.java:68)
> > >     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > > RichStreamReader.java:109)
> > >     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> > > RichStreamReader.java:92)
> > >     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> > > ReadFormatFileFunction.java:134)
> > >     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> > > Caused by: java.security.AccessControlException: access denied (
> > > java.lang.RuntimePermission createClassLoader)
> > >     at java.security.AccessControlContext.checkPermission(Unknown
> Source)
> > >     at java.security.AccessController.checkPermission(Unknown Source)
> > >     at java.lang.SecurityManager.checkPermission(Unknown Source)
> > >     at java.lang.SecurityManager.checkCreateClassLoader(Unknown
> Source)
> > >     at java.lang.ClassLoader.<init>(Unknown Source)
> > >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> > > GeneratedClassLoader.java:29)
> > >     at org.biojava.utils.walker.WalkerFactory.<init>(
> WalkerFactory.java:68)
> > >     at org.biojava.utils.walker.WalkerFactory.getInstance(
> WalkerFactory.java
> > > :51)
> > >     at org.biojava.utils.walker.WalkerFactory.getInstance(
> WalkerFactory.java
> > > :58)
> > >     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> > > FeatureFilter.java:1270)
> > >     ... 11 more
> > >
> > > It is noted that the applet is signed and can read files from client
> > > harddisk if other method is used.
> > >
> > > Do anyone have an idea how can I go about to fix this problem?
> > >
> > > Thank you very much
> > >
> > > Minh
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >
> >
> > - --
> > Richard Holland (BioMart)
> > EMBL EBI, Wellcome Trust Genome Campus,
> > Hinxton, Cambridgeshire CB10 1SD, UK
> > Tel. +44 (0)1223 494416
> >
> > http://www.biomart.org/
> > http://www.biojava.org/
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >
> > iD8DBQFHhIfz4C5LeMEKA/QRAhZqAJ9k36tFYC7wdBt6eScgCn5MK9uVZwCeIVHU
> > R0e4dCpmpjJnHOrfjfw0wYc=
> > =WayD
> > -----END PGP SIGNATURE-----
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>


From markjschreiber at gmail.com  Thu Jan 10 07:04:00 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 10 Jan 2008 15:04:00 +0800
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <4784FFB9.1050402@ebi.ac.uk>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
	<4784FFB9.1050402@ebi.ac.uk>
Message-ID: <93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>

Hi Jeff -

I think the type of functionality you describe would be best placed in
the proteomic package where there is already some stuff for
calculating MW and PI.

Probably the reorganisation for BJ3 won't mean much change for your
code as these types of algorithms can usually be readily ported to any
new system.

- Mark

On Jan 10, 2008 1:09 AM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jeff.
>
> Thanks for volunteering! Sounds like you've got a useful set of tools
> which we would definitely appreciate as new BioJava features.
>
> We're currently planning a Big Reorganisation for a new BioJava 3 from
> the ground-up. Details will be published some time in February I expect,
> if not then early March. See this Wiki for things that are currently
> being considered (most will make it into the plan, some may not, but I
> won't know until I've written it up and identified the conflicting areas):
>
>  http://www.biojava.org/wiki/BioJava3_Proposal
>
> (also see the associated Discussion page for further comments)
>
> If I were you, I'd hang on until the final plan is published. It will
> contain everything you need to know on how to write modules for the new
> BioJava 3.
>
> However, if you're in a rush to get it into the current BioJava 2
> release, then take a look round the JavaDocs to see what is present and
> what is not. You'll soon get a good idea of how things are organised and
> what features are absent. We also have a bugzilla page with some
> unresolved bugs - always a good starting point to learn how a system
> works and where the opportunities for development are!
>  http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED
>
> cheers,
> Richard
>
>
> Jeff Cope wrote:
> > Hi,
> >
> >       My name is Jeff Cope, and I'm currently working on a bioinformatics
> > project for a professor at BSU.  What we have so far is mostly in java, but
> > with the data calculations taking place using functionality found in the
> > BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
> > Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> > protein sequences, and thought that we could help you out on the BioJava
> > project by seeing if that functionality could be added into your library
> > instead...
> >
> >       So I guess my question is, now that I'm signed up on the developers
> > mail list, what would I need to do to get started (assuming you want my
> > help), and what kind of programming ground rules do you have...
> >
> >       I feel pretty comfortable in Java code, and if you would like to see
> > an example of my source code, and some of the work I've done so far, you can
> > find it here:
> >       Current project:
> >       http://trac.boisestate.edu/protcalc/
> >       Source Code:
> >       http://trac.boisestate.edu/protcalc/src/
> >       API docs:
> >       http://trac.boisestate.edu/protcalc/docs/
> >
> >
> > Thanks,
> >       Jeff Cope
> >
> > -----Original Message-----
> > From: biojava-dev-bounces at lists.open-bio.org
> > [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> > biojava-dev-request at lists.open-bio.org
> > Sent: Tuesday, January 08, 2008 1:52 AM
> > To: biojava-dev at lists.open-bio.org
> > Subject: biojava-dev Digest, Vol 59, Issue 2
> >
> > Send biojava-dev mailing list submissions to
> >       biojava-dev at lists.open-bio.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > or, via email, send a message with subject or body 'help' to
> >       biojava-dev-request at lists.open-bio.org
> >
> > You can reach the person managing the list at
> >       biojava-dev-owner at lists.open-bio.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of biojava-dev digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Fwd:  bioperl like blastparser (Michael Gang)
> >    2. Re: Error while reading byte data for creating a Trace.
> >       (Richard Holland)
> >    3. Re: Error while reading byte data for creating a        Trace.
> >       (Andy Yates)
> >    4. Re: bioperl like blastparser (Andreas Prlic)
> >    5. Re: JUnit (Michael Heuer)
> >    6. Re: JUnit (Mark Schreiber)
> >    7. Re: JUnit (Michael Heuer)
> >    8. read fasta file (Michael Gang)
> >    9. Re: read fasta file (Richard Holland)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Jan 2008 12:16:22 +0200
> > From: "Michael Gang" <michaelgang at gmail.com>
> > Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> > To: biojava-dev at biojava.org
> > Message-ID:
> >       <6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Andreas,
> >
> > You are correct.
> > The junit.jar library was missing in my ant_home.
> > Eclipse wrote that it was running the tests, but did not run any.
> > Now I corrected it and see that tests are failing.
> > I ran the program BlastEcho.java manually on the blast test files and
> > on the ncbi blast.
> > Judging after manually curation it worked good but at wu_blast id did
> > not parse the query length.
> > The reason is that in wu_blast the query length line has just 8 spaces
> > at the beginning instead of 9.
> > So I corrected the line which identifies the querylength at
> > org.biojava.bio.program.sax.BlastSaxParser
> > line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> >
> > Now it works also on wu_blast.
> > It would be now a good idea to update the blast tests regarding the
> > number of arguments and see if the fail still.
> >
> > Thanks in advance,
> > Michael
> >
> >
> >
> > On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> >> Hi Michael,
> >>
> >> I just had a look at your patch for the query length.
> >> Several of the unit tests are now failing at
> >>
> > org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> > .java:143)
> >> The problem is that most blast related unit tests extend the SSBindCase,
> >> which expects a fixed number of attributes. With the new patch some of the
> >> blast-flavors have the additional queryLength attribute.
> >>
> >> Could you have a look at the behaviour of the parser for some of the files
> >> where the tests now fail? If you think the new behaviour of the
> >> parser is correct, we can simply update the tests to accept the different
> >> number of attributes.
> >>
> >> Thanks,
> >> Andreas
> >>
> >>
> >> --------------------------------------------------
> >>
> >> Andreas Prlic      Wellcome Trust Sanger Institute
> >>                     Hinxton, Cambridge CB10 1SA, UK
> >>
> >>
> >>
> >>
> >> --
> >>  The Wellcome Trust Sanger Institute is operated by Genome Research
> >>  Limited, a charity registered in England with number 1021457 and a
> >>  company registered in England with number 2742969, whose registered
> >>  office is 215 Euston Road, London, NW1 2BE.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> > From: "Richard Holland" <holland at ebi.ac.uk>
> > Subject: Re: [Biojava-dev] Error while reading byte data for creating
> >       a Trace.
> > To: "Andy Yates" <ayates at ebi.ac.uk>
> > Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> >       abhi232 at cc.gatech.edu
> > Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > This problem was resolved back in November. For some reason during the
> > last couple of weeks the BioJava mailing list has been sending out
> > occasional duplicate copies of emails sent several months ago! This was
> > one of them.
> >
> > cheers,
> > Richard
> >
> > On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> >> Hi,
> >>
> >> As far as I am aware there isn't a problem with the current ABI parser
> >> however if you could send a code snippit of reading in the byte array
> >> & the stack trace of the index out of bounds exception that would be
> >> most helpful
> >>
> >> Andy
> >>
> >> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
> >>
> >>> Hi all,
> >>> I am having a byte array which is having the data from an .ab1
> >>> file.The
> >>> biojava library provides a class called as ABITrace which takes as
> >>> input
> >>> either a byte[] array , a file or a url.If i use the later
> >>> parameters (the
> >>> file or the url )the program works but if I pass the byte array to the
> >>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> >>> problem with the ABITrace class or how can I bypass this particular
> >>> error.
> >>> I am printing the length of the byte array and it comes to
> >>> 144930...Can
> >>> that cause a problem in my code?
> >>>
> >>> Thanks in advance.
> >>> Abhinav
> >>> _______________________________________________
> >>> biojava-dev mailing list
> >>> biojava-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHhP+44C5LeMEKA/QRAroBAJ9oU/by7joNIkdpkOoEtPFzcP+6ZwCfcVYV
> YpEnZK4o2READMXOsaE9oMo=
> =QZDP
>
> -----END PGP SIGNATURE-----
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From michaelgang at gmail.com  Thu Jan 10 12:44:49 2008
From: michaelgang at gmail.com (Michael Gang)
Date: Thu, 10 Jan 2008 14:44:49 +0200
Subject: [Biojava-dev] problem with blast parser
Message-ID: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>

Hi All,
I've observed the following pronlem with the blast parser.
When parsing a blast with more than one query, it skips a part of the queries.
When I wanted to understand what the problem is I got to the following
conclusion.(There are good chances that I am wrong)
When the BlastSaxParser in the function hitsSectionReached calls the
line: oHits.parse(oContents,poLine,"Database:");.
It just get's back when it get to the line :Database= but this is in
the middle of the next query (the query began with the line "BLASTX
2.2.16 [Mar-25-2007]".
I also tested it with the blastecho program
Did someone observed the same problem.
 Can someone help me in this issue ?

Thanks in Advance,
Michael


From holland at ebi.ac.uk  Thu Jan 10 12:50:21 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 10 Jan 2008 12:50:21 +0000
Subject: [Biojava-dev] problem with blast parser
In-Reply-To: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>
References: <6994d82b0801100444u653d412ara835691fe316ae2a@mail.gmail.com>
Message-ID: <4786148D.5010003@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

This is related to your previous email about it not being able to read
all data (e.g. query length).

I believe Andreas Prlic (copied on this) is looking into this, and some
other people might be as well. One of them will get back to you.

cheers,
Richard

Michael Gang wrote:
> Hi All,
> I've observed the following pronlem with the blast parser.
> When parsing a blast with more than one query, it skips a part of the queries.
> When I wanted to understand what the problem is I got to the following
> conclusion.(There are good chances that I am wrong)
> When the BlastSaxParser in the function hitsSectionReached calls the
> line: oHits.parse(oContents,poLine,"Database:");.
> It just get's back when it get to the line :Database= but this is in
> the middle of the next query (the query began with the line "BLASTX
> 2.2.16 [Mar-25-2007]".
> I also tested it with the blastecho program
> Did someone observed the same problem.
>  Can someone help me in this issue ?
> 
> Thanks in Advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From ap3 at sanger.ac.uk  Sun Jan 13 13:44:42 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Sun, 13 Jan 2008 13:44:42 +0000
Subject: [Biojava-dev] anonymous svn
Message-ID: <E531DA0A-BBA9-4652-AC9E-0FACFCFBE692@sanger.ac.uk>

Hi,

seems the anonymous svn access is making progress, but I need to do  
some admin work on the svn repository in the next hours:

The decision from open-bio was to move the svn repository data store  
from berkely db to fsfs, which will make the replication
of the developer repository onto the server that will provide the  
anonymous access much more smoothly.

so checkout and commits will not work for 1 or 2 hours now, but  
should be fine again afterwards.


>> http://svnbook.red-bean.com/en/1.4/svn- 
>> book.html#svn.reposadmin.basics.backends
>>
>> http://subversion.tigris.org/faq.html#bdb-fsfs-convert

Andreas



-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From bugzilla-daemon at portal.open-bio.org  Mon Jan 14 03:31:53 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 13 Jan 2008 22:31:53 -0500
Subject: [Biojava-dev] [Bug 2434] New: bio.seq.io.UniProtFormat error?
Message-ID: <bug-2434-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2434

           Summary: bio.seq.io.UniProtFormat error?
           Product: BioJava
           Version: 1.5
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: lisujun at gmail.com


Exception in thread "main" org.biojava.bio.BioException: Could not read
sequence
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextSequence(RichStreamReader.java:92)
        at DeleteHighAbundance.getDescription(DeleteHighAbundance.java:41)
        at DeleteHighAbundance.main(DeleteHighAbundance.java:47)
Caused by: org.biojava.bio.seq.io.ParseException: 

A Exception Has Occurred During Parsing. 
Please submit the details that follow to biojava-l at biojava.org or post a bug
report to http://bugzilla.open-bio.org/ 

Format_object=org.biojavax.bio.seq.io.UniProtFormat
Accession=null
Id=
Comments=Bad ID line
Parse_block=ID   IPI00000001.1         IPI;      PRT;   577 AA.
Stack trace follows ....


        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:286)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 3 more

========

when i used the RichSequence.IOTools.readUniprot to read the IPI DAT(Uniprot
format), this error happened.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.


From ap3 at sanger.ac.uk  Mon Jan 14 17:26:30 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Mon, 14 Jan 2008 17:26:30 +0000
Subject: [Biojava-dev] biojava svn migration complete
Message-ID: <1B7EE4F0-142D-47BC-8143-677627AAC1AC@sanger.ac.uk>

Hi!

The BioJava SVN migration has been completed.
Thanks a lot to everyone who has made contributions to this!!

The new anonymous checkout of BioJava is now possible via
svn co svn://code.open-bio.org/biojava/biojava-live/trunk biojava-live

Developers can obtain a checkout from
svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/ 
biojava-live/trunk/  ./biojava-live

and it is possible to browse the repository online at
http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/ 
trunk

Also the automated builds have been updated
http://www.spice-3d.org/cruise/

see http://biojava.org/wiki/CVS_to_SVN_Migration
for more details.

Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jcope at cableone.net  Tue Jan 15 16:27:38 2008
From: jcope at cableone.net (Jeff Cope)
Date: Tue, 15 Jan 2008 09:27:38 -0700
Subject: [Biojava-dev] BioJava Development
In-Reply-To: <93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>
References: <mailman.1638.1199782307.2774.biojava-dev@lists.open-bio.org>
	<000801c852d8$966eb370$6402a8c0@roadrunner>
	<4784FFB9.1050402@ebi.ac.uk>
	<93b45ca50801092304p6c97d4adve40f1f83959b2c32@mail.gmail.com>
Message-ID: <000001c85793$8b8c83f0$6402a8c0@roadrunner>

Hi Richard and Mark,

	Thanks for the quick response, and help in pointing out where the
new classes should go.  Here are the classes I wanted to propose and where I
thought they should be.  Due time constraints, this would probably be
something that I could put into BioJava 2, and would be willing to translate
to BioJava 3 when time came around.

	As Mark had suggested it appears that the org.biojava.bio.proteomics
package would be the ideal area for the added classes, so I would be
interpreting functionality for most of the classes from the BioPython
library.

	AromaticityCalc.java - Returns the sum of the percentage of the AA
sequence that is made up of the AA's Tyrosine, Tryptophan, and
Phenylalanine. 

	GRAVYCalc.java (Grand Average of Hydropathy) - Returns the average
sum of hydropathy of the AA sequence

	InstabilityIndexCalc.java - Returns an estimated stability for a
protein sequence (<= 40 is considered stable)

	AACompositionCalc.java - Breaks down protein sequences, and returns
the percent that individual AA's make up the sequence.

	The functionality for Aromaticity, GRAVY, and Instability Index
would all come from the biopython library
(biopython-1.43/Bio/SeqUtils/ProtParam.py), and AAComposition is something
that we worked together that was useful for our application.

	Most of the classes are pretty simple for the most part, I think the
most difficult part would be figuring out how the strings of characters are
translated to protein sequences in BioJava.

	Anyway, Let me know if this sounds like it would be useful...

Thanks,
	Jeff


-----Original Message-----
From: Mark Schreiber [mailto:markjschreiber at gmail.com] 
Sent: Thursday, January 10, 2008 12:04 AM
To: Richard Holland
Cc: Jeff Cope; biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] BioJava Development

Hi Jeff -

I think the type of functionality you describe would be best placed in
the proteomic package where there is already some stuff for
calculating MW and PI.

Probably the reorganisation for BJ3 won't mean much change for your
code as these types of algorithms can usually be readily ported to any
new system.

- Mark

On Jan 10, 2008 1:09 AM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jeff.
>
> Thanks for volunteering! Sounds like you've got a useful set of tools
> which we would definitely appreciate as new BioJava features.
>
> We're currently planning a Big Reorganisation for a new BioJava 3 from
> the ground-up. Details will be published some time in February I expect,
> if not then early March. See this Wiki for things that are currently
> being considered (most will make it into the plan, some may not, but I
> won't know until I've written it up and identified the conflicting areas):
>
>  http://www.biojava.org/wiki/BioJava3_Proposal
>
> (also see the associated Discussion page for further comments)
>
> If I were you, I'd hang on until the final plan is published. It will
> contain everything you need to know on how to write modules for the new
> BioJava 3.
>
> However, if you're in a rush to get it into the current BioJava 2
> release, then take a look round the JavaDocs to see what is present and
> what is not. You'll soon get a good idea of how things are organised and
> what features are absent. We also have a bugzilla page with some
> unresolved bugs - always a good starting point to learn how a system
> works and where the opportunities for development are!
>
http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_
status=ASSIGNED&bug_status=REOPENED
>
> cheers,
> Richard
>
>
> Jeff Cope wrote:
> > Hi,
> >
> >       My name is Jeff Cope, and I'm currently working on a
bioinformatics
> > project for a professor at BSU.  What we have so far is mostly in java,
but
> > with the data calculations taking place using functionality found in the
> > BioPython library (Molecular Weight, Instability Index, Isoelectric
Point,
> > Aromaticity, GRAVY, etc...).  Anywho, currently we are only looking at
> > protein sequences, and thought that we could help you out on the BioJava
> > project by seeing if that functionality could be added into your library
> > instead...
> >
> >       So I guess my question is, now that I'm signed up on the
developers
> > mail list, what would I need to do to get started (assuming you want my
> > help), and what kind of programming ground rules do you have...
> >
> >       I feel pretty comfortable in Java code, and if you would like to
see
> > an example of my source code, and some of the work I've done so far, you
can
> > find it here:
> >       Current project:
> >       http://trac.boisestate.edu/protcalc/
> >       Source Code:
> >       http://trac.boisestate.edu/protcalc/src/
> >       API docs:
> >       http://trac.boisestate.edu/protcalc/docs/
> >
> >
> > Thanks,
> >       Jeff Cope
> >
> > -----Original Message-----
> > From: biojava-dev-bounces at lists.open-bio.org
> > [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> > biojava-dev-request at lists.open-bio.org
> > Sent: Tuesday, January 08, 2008 1:52 AM
> > To: biojava-dev at lists.open-bio.org
> > Subject: biojava-dev Digest, Vol 59, Issue 2
> >
> > Send biojava-dev mailing list submissions to
> >       biojava-dev at lists.open-bio.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > or, via email, send a message with subject or body 'help' to
> >       biojava-dev-request at lists.open-bio.org
> >
> > You can reach the person managing the list at
> >       biojava-dev-owner at lists.open-bio.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of biojava-dev digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Fwd:  bioperl like blastparser (Michael Gang)
> >    2. Re: Error while reading byte data for creating a Trace.
> >       (Richard Holland)
> >    3. Re: Error while reading byte data for creating a        Trace.
> >       (Andy Yates)
> >    4. Re: bioperl like blastparser (Andreas Prlic)
> >    5. Re: JUnit (Michael Heuer)
> >    6. Re: JUnit (Mark Schreiber)
> >    7. Re: JUnit (Michael Heuer)
> >    8. read fasta file (Michael Gang)
> >    9. Re: read fasta file (Richard Holland)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Jan 2008 12:16:22 +0200
> > From: "Michael Gang" <michaelgang at gmail.com>
> > Subject: [Biojava-dev] Fwd:  bioperl like blastparser
> > To: biojava-dev at biojava.org
> > Message-ID:
> >       <6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Andreas,
> >
> > You are correct.
> > The junit.jar library was missing in my ant_home.
> > Eclipse wrote that it was running the tests, but did not run any.
> > Now I corrected it and see that tests are failing.
> > I ran the program BlastEcho.java manually on the blast test files and
> > on the ncbi blast.
> > Judging after manually curation it worked good but at wu_blast id did
> > not parse the query length.
> > The reason is that in wu_blast the query length line has just 8 spaces
> > at the beginning instead of 9.
> > So I corrected the line which identifies the querylength at
> > org.biojava.bio.program.sax.BlastSaxParser
> > line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
> >
> > Now it works also on wu_blast.
> > It would be now a good idea to update the blast tests regarding the
> > number of arguments and see if the fail still.
> >
> > Thanks in advance,
> > Michael
> >
> >
> >
> > On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> >> Hi Michael,
> >>
> >> I just had a look at your patch for the query length.
> >> Several of the unit tests are now failing at
> >>
> >
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
> > .java:143)
> >> The problem is that most blast related unit tests extend the
SSBindCase,
> >> which expects a fixed number of attributes. With the new patch some of
the
> >> blast-flavors have the additional queryLength attribute.
> >>
> >> Could you have a look at the behaviour of the parser for some of the
files
> >> where the tests now fail? If you think the new behaviour of the
> >> parser is correct, we can simply update the tests to accept the
different
> >> number of attributes.
> >>
> >> Thanks,
> >> Andreas
> >>
> >>
> >> --------------------------------------------------
> >>
> >> Andreas Prlic      Wellcome Trust Sanger Institute
> >>                     Hinxton, Cambridge CB10 1SA, UK
> >>
> >>
> >>
> >>
> >> --
> >>  The Wellcome Trust Sanger Institute is operated by Genome Research
> >>  Limited, a charity registered in England with number 1021457 and a
> >>  company registered in England with number 2742969, whose registered
> >>  office is 215 Euston Road, London, NW1 2BE.
> >>
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
> > From: "Richard Holland" <holland at ebi.ac.uk>
> > Subject: Re: [Biojava-dev] Error while reading byte data for creating
> >       a Trace.
> > To: "Andy Yates" <ayates at ebi.ac.uk>
> > Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
> >       abhi232 at cc.gatech.edu
> > Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > This problem was resolved back in November. For some reason during the
> > last couple of weeks the BioJava mailing list has been sending out
> > occasional duplicate copies of emails sent several months ago! This was
> > one of them.
> >
> > cheers,
> > Richard
> >
> > On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> >> Hi,
> >>
> >> As far as I am aware there isn't a problem with the current ABI parser
> >> however if you could send a code snippit of reading in the byte array
> >> & the stack trace of the index out of bounds exception that would be
> >> most helpful
> >>
> >> Andy
> >>
> >> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
> >>
> >>> Hi all,
> >>> I am having a byte array which is having the data from an .ab1
> >>> file.The
> >>> biojava library provides a class called as ABITrace which takes as
> >>> input
> >>> either a byte[] array , a file or a url.If i use the later
> >>> parameters (the
> >>> file or the url )the program works but if I pass the byte array to the
> >>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
> >>> problem with the ABITrace class or how can I bypass this particular
> >>> error.
> >>> I am printing the length of the byte array and it comes to
> >>> 144930...Can
> >>> that cause a problem in my code?
> >>>
> >>> Thanks in advance.
> >>> Abhinav
> >>> _______________________________________________
> >>> biojava-dev mailing list
> >>> biojava-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHhP+44C5LeMEKA/QRAroBAJ9oU/by7joNIkdpkOoEtPFzcP+6ZwCfcVYV
> YpEnZK4o2READMXOsaE9oMo=
> =QZDP
>
> -----END PGP SIGNATURE-----
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From bugzilla-daemon at portal.open-bio.org  Wed Jan 16 15:16:30 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 16 Jan 2008 10:16:30 -0500
Subject: [Biojava-dev] [Bug 2435] New: Mistake in createRecord( ) of
	GFF3Parser
Message-ID: <bug-2435-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435

           Summary: Mistake in createRecord( ) of GFF3Parser
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P3
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: pudimat at gmail.com
                CC: pudimat at gmail.com


When setting the fields in a new GFF3Record, the source field is set twice,
however the second time it is set to the GFF type value. Thus, a record has its
type in the source field, and the type field has value "any".

See line: 256 in GFF3Parser


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 16 17:07:36 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 16 Jan 2008 12:07:36 -0500
Subject: [Biojava-dev] [Bug 2435] Mistake in createRecord( ) of GFF3Parser
In-Reply-To: <bug-2435-485@http.bugzilla.open-bio.org/>
Message-ID: <200801161707.m0GH7a8C005347@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435





------- Comment #1 from pudimat at gmail.com  2008-01-16 12:07 EST -------
Another error in line 344 (method parseAttribute() ):
when splitting the key-value-pair of an attribute, the separating '=' is the
first
symbol of the attribute value.

Reason:  attValList = attVal.substring(spaceIndex).trim();
must be changed to 
attValList = attVal.substring(spaceIndex+1).trim();


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From bugzilla-daemon at portal.open-bio.org  Thu Jan 17 12:36:06 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 17 Jan 2008 07:36:06 -0500
Subject: [Biojava-dev] [Bug 2435] Mistake in createRecord( ) of GFF3Parser
In-Reply-To: <bug-2435-485@http.bugzilla.open-bio.org/>
Message-ID: <200801171236.m0HCa6eE030734@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2435


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from holland at ebi.ac.uk  2008-01-17 07:36 EST -------
I have fixed this in the new subversion repository.


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 07:17:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 02:17:42 -0500
Subject: [Biojava-dev] [Bug 2360] saving of ProfileHmm cause
	NullPointerException
In-Reply-To: <bug-2360-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200717.m0K7Hg0H009027@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2360


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from mark.schreiber at novartis.com  2008-01-20 02:17 EST -------
Bug was caused by serialization of an untrained distribution with no weights.
Now fixed with Unit test


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 07:26:00 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 02:26:00 -0500
Subject: [Biojava-dev] [Bug 2371] ChromatogramFactory.create fails on Windows
In-Reply-To: <bug-2371-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200726.m0K7Q013009324@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2371


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |WORKSFORME




------- Comment #1 from mark.schreiber at novartis.com  2008-01-20 02:25 EST -------
This works using biojava 1.6 RC-1 on Windows Vista. I can't replicate the error
using your chromatogram. 


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From bugzilla-daemon at portal.open-bio.org  Sun Jan 20 08:28:33 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 20 Jan 2008 03:28:33 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801200828.m0K8SXrV011671@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #10 from mark.schreiber at novartis.com  2008-01-20 03:28 EST -------
As suggested I have added back the synchronized blockas as they are certainly
needed even though this doesn't fully solve the problem.  Interestingly on
windows vista on a dual core CPU a race condition develops and never seems to
resolve (not even a stack trace)!  Notably this was on a short sequence not one
likely to be a PackedSymbolList as mentioned below.

I wonder if there is a problem with the SimpleThreadPool. Maybe a switch to a
normal Java thread pool might be better?


(In reply to comment #9)
> Here are the comments at the top of org.biojava.bio.symbol.PackedSymbolList,
> and I quote:
> "WARNING: these variables constitute an opportunity
> for things to go wrong when doing multithreaded access
> via symbolAt().  Keep SymbolAt() synchronized so they
> don't get changed during a lookup! Naaasssty."


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 21 09:47:37 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 21 Jan 2008 04:47:37 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801210947.m0L9lbY5028968@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #11 from andyyatz at gmail.com  2008-01-21 04:47 EST -------
If we're looking at Java5+ features here then maybe something like:

http://java.sun.com/j2se/1.5.0/docs/api/java/util/concurrent/locks/ReadWriteLock.html

This is a far superior solution to synchronized blocks as they offer a
difference between reading something & altering it. The blocks can last for as
little or as long as required with us only needing to make sure that we perform
the code in a try {} finally {} block to ensure we do not continually lock out
a resource.

(In reply to comment #10)
> As suggested I have added back the synchronized blockas as they are certainly
> needed even though this doesn't fully solve the problem.  Interestingly on
> windows vista on a dual core CPU a race condition develops and never seems to
> resolve (not even a stack trace)!  Notably this was on a short sequence not one
> likely to be a PackedSymbolList as mentioned below.
> 
> I wonder if there is a problem with the SimpleThreadPool. Maybe a switch to a
> normal Java thread pool might be better?
> 
> 


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From bugzilla-daemon at portal.open-bio.org  Mon Jan 21 19:15:24 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 21 Jan 2008 14:15:24 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801211915.m0LJFOcP031316@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #12 from gwaldon at geneinfinity.org  2008-01-21 14:15 EST -------
I have seen a similar problem (at least producing similar log) and it was
solved by adding pool.stopThreads() at the end of your code:

SequenceIterator iter = SeqIOTools.readFastaDNA(br);
SimpleThreadPool pool = new SimpleThreadPool();
RestrictionMapper mapper = new RestrictionMapper(pool);

 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("MseI"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("HpaII"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("AluI"));
 Sequence seq;
 while(iter.hasNext()){
     seq = iter.nextSequence();
     mapper.annotate(seq);
 }
pool.stopThreads();

Hope it helps. 
- George


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From ap3 at sanger.ac.uk  Tue Jan 22 08:25:49 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Tue, 22 Jan 2008 08:25:49 +0000
Subject: [Biojava-dev] biojava looking for maintainers
Message-ID: <20765D52-2C0E-40C6-A769-7D13CF1DB489@sanger.ac.uk>

Hi,

BioJava is a widely used Java library that provides standard APIs,  
parsers, and solutions for common bioinformatics problems.
It is used in a number of applications and referenced in many  
scientific publications.
See here for an overview of these: http://biojava.org/wiki/ 
BioJava:BioJavaInside

In order to continue our first class efforts to serve the community  
and to further the quality of our source code we are looking
for motivated individuals who want to claim responsibility for some  
of the core libraries and take over maintenance of these.

Please see here for a list of modules for which we are currently  
looking for maintainers:
http://biojava.org/wiki/Maintainers_wanted

If you want to become a BioJava maintainer, please post to the  
biojava-dev mailing list.

As always - happy biojavaing,
Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From felipe.albrecht at gmail.com  Wed Jan 23 06:58:04 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Wed, 23 Jan 2008 04:58:04 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
Message-ID: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>

Hello all,

I have a simple question about pairwise alignment classes (SmithWaterman and
NeedlemanWunsch):
Why it is necessary two Sequence for alignment and not two SymbolList?

Example, I have a SymbolList collection to align between then,
by this way I need to create some "dummies"  Sequence for to do the
alignment.

Reading the source, I saw that the unique field that is exclusive to
Sequence is the name, for the alignment output,
but if I need only the alignment result, it is useless.

It is not possible to override the pairwiseAlignment to accept SymbolList or
may be a new method that the parameters are 2 SymbolList and returns the
alignment score?

Thank you

Felipe Albrecht


From markjschreiber at gmail.com  Wed Jan 23 08:50:05 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 23 Jan 2008 16:50:05 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
Message-ID: <93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>

Hi Felipe -

I agree this is a barrier to ease of use. Even if Sequences are
required internally for some obscure reason there is no reason why
dummy Sequences cannot be made inside the aligner.  These sequences
could be given names like 'query' and 'subject' or even 'seq1' and
'seq2'.

I will take a look at adding some methods.

Best regards,

- Mark

On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello all,
>
> I have a simple question about pairwise alignment classes (SmithWaterman and
> NeedlemanWunsch):
> Why it is necessary two Sequence for alignment and not two SymbolList?
>
> Example, I have a SymbolList collection to align between then,
> by this way I need to create some "dummies"  Sequence for to do the
> alignment.
>
> Reading the source, I saw that the unique field that is exclusive to
> Sequence is the name, for the alignment output,
> but if I need only the alignment result, it is useless.
>
> It is not possible to override the pairwiseAlignment to accept SymbolList or
> may be a new method that the parameters are 2 SymbolList and returns the
> alignment score?
>
> Thank you
>
> Felipe Albrecht
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From dankoc at gmail.com  Wed Jan 23 21:56:19 2008
From: dankoc at gmail.com (Charles Danko)
Date: Wed, 23 Jan 2008 16:56:19 -0500
Subject: [Biojava-dev] Direct access to public genome databases
Message-ID: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>

Hello,

Direct access to public genome databases (i.e. a class to import
sequence, annotations, etc. and create the applicable biojava object)
would be a very useful addition to BioJava.  The Ensj project doesn't
look like it has been updated since official support was dropped.  Are
there any plans to work these features into BioJava?  Have I missed
features that already exist?

Depending on the amount of time required, I may be willing to
contribute to such an endeavor -- particularly for the purpose of
importing sequence.  I have quite a bit of experience working with
java, but not much in a collaborative environment.

Best,
Charles


From heuermh at acm.org  Thu Jan 24 01:06:53 2008
From: heuermh at acm.org (Michael Heuer)
Date: Wed, 23 Jan 2008 20:06:53 -0500 (EST)
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>

Charles Danko wrote:

> Hello,
>
> Direct access to public genome databases (i.e. a class to import
> sequence, annotations, etc. and create the applicable biojava object)
> would be a very useful addition to BioJava.  The Ensj project doesn't
> look like it has been updated since official support was dropped.  Are
> there any plans to work these features into BioJava?  Have I missed
> features that already exist?
>
> Depending on the amount of time required, I may be willing to
> contribute to such an endeavor -- particularly for the purpose of
> importing sequence.  I have quite a bit of experience working with
> java, but not much in a collaborative environment.

What sort of client API would you have in mind?


I'm not a Taverna expert, but it seems to me that access to third-party
data resources is already well covered with the web services available
there.

> http://taverna.sourceforge.net/
> http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices

Or simply call the web services directly.

   michael



From markjschreiber at gmail.com  Thu Jan 24 04:00:27 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 23 Jan 2008 23:00:27 -0500
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
References: <8adccabf0801231356o16c51b55s43b3637459277f66@mail.gmail.com>
	<Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
Message-ID: <93b45ca50801232000p1cfd83c0o47f7b714abfd2d01@mail.gmail.com>

Hi -

>From personal experience you can access data from NCBI and KEGG using
their webservice API's and (depending on the result) use the biojava
parsers to return biojava objects.

The question is, should this activity be wrapped into biojava (ie
should the webservice stuff be inside biojava)?

Pros:  Happens behind the scenes, users don't need to know about WS,
possible uniform interface to several sources
Cons: Lots more dependencies on WS jars (take a look at JAX-WS for
example) and WS client jars

I'm interested in hearing more pros and cons from other people. This
is timely given the upcoming webservices meet up in Tokyo.

Best regards,

- Mark


On Jan 23, 2008 8:06 PM, Michael Heuer <heuermh at acm.org> wrote:
> Charles Danko wrote:
>
> > Hello,
> >
> > Direct access to public genome databases (i.e. a class to import
> > sequence, annotations, etc. and create the applicable biojava object)
> > would be a very useful addition to BioJava.  The Ensj project doesn't
> > look like it has been updated since official support was dropped.  Are
> > there any plans to work these features into BioJava?  Have I missed
> > features that already exist?
> >
> > Depending on the amount of time required, I may be willing to
> > contribute to such an endeavor -- particularly for the purpose of
> > importing sequence.  I have quite a bit of experience working with
> > java, but not much in a collaborative environment.
>
> What sort of client API would you have in mind?
>
>
> I'm not a Taverna expert, but it seems to me that access to third-party
> data resources is already well covered with the web services available
> there.
>
> > http://taverna.sourceforge.net/
> > http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
>
> Or simply call the web services directly.
>
>    michael
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From markjschreiber at gmail.com  Thu Jan 24 07:50:32 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 24 Jan 2008 15:50:32 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
Message-ID: <93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>

Hi Felipe -

Thanks for the input on this. As a general rule the GC should never be
called from code. Generally this degrades performance of the JVM.
Unless there is a very good reason I will remove this. Probably you
are right a method parameter may work better.

- Mark

On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello,
>
> I think that it can be solved by a simple way:
> Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList as
> parameters and do no creating a alignment, just the calculating it and
> returning the value.
>
> Another thing that is a bit stange for me, is the utilization of garbage
> collector direcly, that is: The field "scoreMatrix" is a class field, why at
> the end of pairwiseAlignment it is set to null and the garbage collector
> run? It is not better (and simpler) to use scoreMatrix as method variable?
>
> I'm annexing the class code with my changes that is doing well the (4^8) *
> (4^8) SymbolList pairwise alignments that I am needing :-)
>
> Thank you,
>
> Felipe Albrecht
>
>
>
>
>
>  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > I agree this is a barrier to ease of use. Even if Sequences are
> > required internally for some obscure reason there is no reason why
> > dummy Sequences cannot be made inside the aligner.  These sequences
> > could be given names like 'query' and 'subject' or even 'seq1' and
> > 'seq2'.
> >
> > I will take a look at adding some methods.
> >
> > Best regards,
> >
> > - Mark
> >
> >
> >
> >
> > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hello all,
> > >
> > > I have a simple question about pairwise alignment classes (SmithWaterman
> and
> > > NeedlemanWunsch):
> > > Why it is necessary two Sequence for alignment and not two SymbolList?
> > >
> > > Example, I have a SymbolList collection to align between then,
> > > by this way I need to create some "dummies"  Sequence for to do the
> > > alignment.
> > >
> > > Reading the source, I saw that the unique field that is exclusive to
> > > Sequence is the name, for the alignment output,
> > > but if I need only the alignment result, it is useless.
> > >
> > > It is not possible to override the pairwiseAlignment to accept
> SymbolList or
> > > may be a new method that the parameters are 2 SymbolList and returns the
> > > alignment score?
> > >
> > > Thank you
> > >
> > > Felipe Albrecht
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >
> >
>
>


From ap3 at sanger.ac.uk  Thu Jan 24 08:40:39 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Thu, 24 Jan 2008 08:40:39 +0000 (GMT)
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
Message-ID: <Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>

Hi,

>> Direct access to public genome databases (i.e. a class to import
>> sequence, annotations, etc. and create the applicable biojava object)
>> would be a very useful addition to BioJava.  The Ensj project doesn't
>> look like it has been updated since official support was dropped.  Are
>> there any plans to work these features into BioJava?  Have I missed
>> features that already exist?
>>
>> Depending on the amount of time required, I may be willing to
>> contribute to such an endeavor -- particularly for the purpose of
>> importing sequence.  I have quite a bit of experience working with
>> java, but not much in a collaborative environment.
>

Ensembl provides access to more and more of its data via DAS,
the Distributed Annotation System. DAS is a RESTful protocol to
access data from distributed sites over the internet.

http://www.ensembl.org/info/using/external_data/das/ensembl_das.html

it is quite heavily used and to see a list of available DAS services
see
http://www.dasregistry.org

Andreas


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From bugzilla-daemon at portal.open-bio.org  Thu Jan 24 12:22:41 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 24 Jan 2008 07:22:41 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200801241222.m0OCMfZ2026239@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #13 from mark.schreiber at novartis.com  2008-01-24 07:22 EST -------
Using the stopThread() method prevents the race condition. The other option is
to make the threads deamon threads which terminate when all other threads are
finished.

I have tested this on a dual core machine with windows vista on a 1 million
base pair sequence and there is no problem. Unless someone can determine this
bug remains on other operating systems I will close the bug. Please use the
current version of biojava from SVN for testing.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.


From felipe.albrecht at gmail.com  Thu Jan 24 13:05:39 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 11:05:39 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
Message-ID: <f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>

If you prefer, I can send a diff and should I do the same thing in
SequenceAlignment and NeedlemanWunsch classes?

Thank  you,

Felipe Albrecht

On Jan 24, 2008 5:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> Thanks for the input on this. As a general rule the GC should never be
> called from code. Generally this degrades performance of the JVM.
> Unless there is a very good reason I will remove this. Probably you
> are right a method parameter may work better.
>
> - Mark
>
> On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello,
> >
> > I think that it can be solved by a simple way:
> > Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList
> as
> > parameters and do no creating a alignment, just the calculating it and
> > returning the value.
> >
> > Another thing that is a bit stange for me, is the utilization of garbage
> > collector direcly, that is: The field "scoreMatrix" is a class field,
> why at
> > the end of pairwiseAlignment it is set to null and the garbage collector
> > run? It is not better (and simpler) to use scoreMatrix as method
> variable?
> >
> > I'm annexing the class code with my changes that is doing well the (4^8)
> *
> > (4^8) SymbolList pairwise alignments that I am needing :-)
> >
> > Thank you,
> >
> > Felipe Albrecht
> >
> >
> >
> >
> >
> >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > I agree this is a barrier to ease of use. Even if Sequences are
> > > required internally for some obscure reason there is no reason why
> > > dummy Sequences cannot be made inside the aligner.  These sequences
> > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > 'seq2'.
> > >
> > > I will take a look at adding some methods.
> > >
> > > Best regards,
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hello all,
> > > >
> > > > I have a simple question about pairwise alignment classes
> (SmithWaterman
> > and
> > > > NeedlemanWunsch):
> > > > Why it is necessary two Sequence for alignment and not two
> SymbolList?
> > > >
> > > > Example, I have a SymbolList collection to align between then,
> > > > by this way I need to create some "dummies"  Sequence for to do the
> > > > alignment.
> > > >
> > > > Reading the source, I saw that the unique field that is exclusive to
> > > > Sequence is the name, for the alignment output,
> > > > but if I need only the alignment result, it is useless.
> > > >
> > > > It is not possible to override the pairwiseAlignment to accept
> > SymbolList or
> > > > may be a new method that the parameters are 2 SymbolList and returns
> the
> > > > alignment score?
> > > >
> > > > Thank you
> > > >
> > > > Felipe Albrecht
> > > > _______________________________________________
> > > > biojava-dev mailing list
> > > > biojava-dev at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > >
> > >
> >
> >
>


From markjschreiber at gmail.com  Thu Jan 24 13:35:43 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 24 Jan 2008 21:35:43 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
Message-ID: <93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>

Hi -

I have just commited changes that let you use SymbolLists in all parts
of the NW and SW SequenceAlignment objects.

As you suggested I made the matrix a method local variable. I also
removed calls to the garbage collector.

This can be checked out from SVN.

- Mark

On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> If you prefer, I can send a diff and should I do the same thing in
> SequenceAlignment and NeedlemanWunsch classes?
>
> Thank  you,
>
> Felipe Albrecht
>
>
>
> On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > Thanks for the input on this. As a general rule the GC should never be
> > called from code. Generally this degrades performance of the JVM.
> > Unless there is a very good reason I will remove this. Probably you
> > are right a method parameter may work better.
> >
> > - Mark
> >
> > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hello,
> >
> >
> >
> > >
> > > I think that it can be solved by a simple way:
> > > Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList
> as
> > > parameters and do no creating a alignment, just the calculating it and
> > > returning the value.
> > >
> > > Another thing that is a bit stange for me, is the utilization of garbage
> > > collector direcly, that is: The field "scoreMatrix" is a class field,
> why at
> > > the end of pairwiseAlignment it is set to null and the garbage collector
> > > run? It is not better (and simpler) to use scoreMatrix as method
> variable?
> > >
> > > I'm annexing the class code with my changes that is doing well the (4^8)
> *
> > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > >
> > > Thank you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > >
> > >
> > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com >
> wrote:
> > > > Hi Felipe -
> > > >
> > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > required internally for some obscure reason there is no reason why
> > > > dummy Sequences cannot be made inside the aligner.  These sequences
> > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > 'seq2'.
> > > >
> > > > I will take a look at adding some methods.
> > > >
> > > > Best regards,
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > wrote:
> > > > > Hello all,
> > > > >
> > > > > I have a simple question about pairwise alignment classes
> (SmithWaterman
> > > and
> > > > > NeedlemanWunsch):
> > > > > Why it is necessary two Sequence for alignment and not two
> SymbolList?
> > > > >
> > > > > Example, I have a SymbolList collection to align between then,
> > > > > by this way I need to create some "dummies"  Sequence for to do the
> > > > > alignment.
> > > > >
> > > > > Reading the source, I saw that the unique field that is exclusive to
> > > > > Sequence is the name, for the alignment output,
> > > > > but if I need only the alignment result, it is useless.
> > > > >
> > > > > It is not possible to override the pairwiseAlignment to accept
> > > SymbolList or
> > > > > may be a new method that the parameters are 2 SymbolList and returns
> the
> > > > > alignment score?
> > > > >
> > > > > Thank you
> > > > >
> > > > > Felipe Albrecht
> > > > > _______________________________________________
> > > > > biojava-dev mailing list
> > > > > biojava-dev at lists.open-bio.org
> > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > >
> > > >
> > >
> > >
> >
>
>


From felipe.albrecht at gmail.com  Thu Jan 24 19:40:48 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 17:40:48 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
Message-ID: <f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>

Hello,

I saw the commit and I think that this solution is not the better.
I think it because you are creating internally two Sequence and probably the
programmer will not use others alignment information,  he will use only the
score.

Because it, I think that if you have 2 SymbolList, just do the alignment and
return the score, as I did.Otherwise, If the programmer want the "visual
alignment", he should create externally the SimpleSequences, it is, not the
method must do it.

IMHO, one [serious] problem in biojava is the memory consumption, it have
not "lightweight" classes or methods that do the things quickly. Because it,
may be is a good choice to have a method that simply gives the alignment
score, and not do the others things, like backtracking. Another think, the
cost of the "instanceof" is high.

Thank you,

Felipe Albrecht


On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi -
>
> I have just commited changes that let you use SymbolLists in all parts
> of the NW and SW SequenceAlignment objects.
>
> As you suggested I made the matrix a method local variable. I also
> removed calls to the garbage collector.
>
> This can be checked out from SVN.
>
> - Mark
>
> On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > If you prefer, I can send a diff and should I do the same thing in
> > SequenceAlignment and NeedlemanWunsch classes?
> >
> > Thank  you,
> >
> > Felipe Albrecht
> >
> >
> >
> > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > Thanks for the input on this. As a general rule the GC should never be
> > > called from code. Generally this degrades performance of the JVM.
> > > Unless there is a very good reason I will remove this. Probably you
> > > are right a method parameter may work better.
> > >
> > > - Mark
> > >
> > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hello,
> > >
> > >
> > >
> > > >
> > > > I think that it can be solved by a simple way:
> > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> SymboList
> > as
> > > > parameters and do no creating a alignment, just the calculating it
> and
> > > > returning the value.
> > > >
> > > > Another thing that is a bit stange for me, is the utilization of
> garbage
> > > > collector direcly, that is: The field "scoreMatrix" is a class
> field,
> > why at
> > > > the end of pairwiseAlignment it is set to null and the garbage
> collector
> > > > run? It is not better (and simpler) to use scoreMatrix as method
> > variable?
> > > >
> > > > I'm annexing the class code with my changes that is doing well the
> (4^8)
> > *
> > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > >
> > > > Thank you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com >
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > > required internally for some obscure reason there is no reason why
> > > > > dummy Sequences cannot be made inside the aligner.  These
> sequences
> > > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > > 'seq2'.
> > > > >
> > > > > I will take a look at adding some methods.
> > > > >
> > > > > Best regards,
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > Hello all,
> > > > > >
> > > > > > I have a simple question about pairwise alignment classes
> > (SmithWaterman
> > > > and
> > > > > > NeedlemanWunsch):
> > > > > > Why it is necessary two Sequence for alignment and not two
> > SymbolList?
> > > > > >
> > > > > > Example, I have a SymbolList collection to align between then,
> > > > > > by this way I need to create some "dummies"  Sequence for to do
> the
> > > > > > alignment.
> > > > > >
> > > > > > Reading the source, I saw that the unique field that is
> exclusive to
> > > > > > Sequence is the name, for the alignment output,
> > > > > > but if I need only the alignment result, it is useless.
> > > > > >
> > > > > > It is not possible to override the pairwiseAlignment to accept
> > > > SymbolList or
> > > > > > may be a new method that the parameters are 2 SymbolList and
> returns
> > the
> > > > > > alignment score?
> > > > > >
> > > > > > Thank you
> > > > > >
> > > > > > Felipe Albrecht
> > > > > > _______________________________________________
> > > > > > biojava-dev mailing list
> > > > > > biojava-dev at lists.open-bio.org
> > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>


From dankoc at gmail.com  Thu Jan 24 20:17:38 2008
From: dankoc at gmail.com (Charles Danko)
Date: Thu, 24 Jan 2008 15:17:38 -0500
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
Message-ID: <8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>

DAS looks just wonderful, and I am very glad to be made aware of it ?
it seems like a much better solution than my initial, highly naive
reaction (accessing public SQL connections).

As I understand it, the easiest way to access DAS services in Java is
via an API such as JAX-WS?   Jumping into the Javadocs, and looking
over a JAX-WS tutorial that I found here:
http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
is a lot to this.

In this sense, a BioJava class that that takes care of much of the
connecting, data transfer, and parsing would be a welcome convenience
for users not already familiar with this API (like me :).  Even for
those who are well-versed in all of this, such a class would allow DB
access with a lot less code.  Given the frequency that most of us
accesses these public databases, this seems like a worthy goal to me!!

Since its so easy to understand the basics of constructing a DAS
request URL, even something as simple as a class that takes a
pre-formed URL (in the constructor) and acts as an iterator over
whatever information is in the result, would be very useful.

Best,
Charles

On Jan 24, 2008 3:40 AM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi,
>
> >> Direct access to public genome databases (i.e. a class to import
> >> sequence, annotations, etc. and create the applicable biojava object)
> >> would be a very useful addition to BioJava.  The Ensj project doesn't
> >> look like it has been updated since official support was dropped.  Are
> >> there any plans to work these features into BioJava?  Have I missed
> >> features that already exist?
> >>
> >> Depending on the amount of time required, I may be willing to
> >> contribute to such an endeavor -- particularly for the purpose of
> >> importing sequence.  I have quite a bit of experience working with
> >> java, but not much in a collaborative environment.
> >
>
> Ensembl provides access to more and more of its data via DAS,
> the Distributed Annotation System. DAS is a RESTful protocol to
> access data from distributed sites over the internet.
>
> http://www.ensembl.org/info/using/external_data/das/ensembl_das.html
>
> it is quite heavily used and to see a list of available DAS services
> see
> http://www.dasregistry.org
>
> Andreas
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>



From markjschreiber at gmail.com  Fri Jan 25 01:26:41 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 09:26:41 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
Message-ID: <93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>

Hi Felipe -

I agree your method is more efficient but I think it violates the
SequenceAlignment interface which would cause compatibility problems.
I also wonder what should happen if a user calls the getAlignment()
method if you have only calculated a score.

instanceof is potentially expensive but it is nothing compared to
actually performing the SmithWaterman.

Biojava is somewhat memory heavy but this is largely because it is
object oriented. Certainly something in C would be lighter and faster
but the whole point in using Java is the relative benefits of object
oriented design.  While ultra optimized algorithms where once a major
feature of bioinformatics this is becoming less necessary as standard
desktops are now equivalent to the super computers of 5 years ago.

I actually find the SW and NW to be reasonably fast. This is because
all the heavy lifting is done in loops that the JVM presumably
compiles and executes natively.

- Mark


On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello,
>
> I saw the commit and I think that this solution is not the better.
> I think it because you are creating internally two Sequence and probably the
> programmer will not use others alignment information,  he will use only the
> score.
>
> Because it, I think that if you have 2 SymbolList, just do the alignment and
> return the score, as I did.Otherwise, If the programmer want the "visual
> alignment", he should create externally the SimpleSequences, it is, not the
> method must do it.
>
> IMHO, one [serious] problem in biojava is the memory consumption, it have
> not "lightweight" classes or methods that do the things quickly. Because it,
> may be is a good choice to have a method that simply gives the alignment
> score, and not do the others things, like backtracking. Another think, the
> cost of the "instanceof" is high.
>
> Thank you,
>
> Felipe Albrecht
>
>
>
>
> On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi -
> >
> > I have just commited changes that let you use SymbolLists in all parts
> > of the NW and SW SequenceAlignment objects.
> >
> > As you suggested I made the matrix a method local variable. I also
> > removed calls to the garbage collector.
> >
> > This can be checked out from SVN.
> >
> > - Mark
> >
> >
> >
> >
> > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> wrote:
> > > If you prefer, I can send a diff and should I do the same thing in
> > > SequenceAlignment and NeedlemanWunsch classes?
> > >
> > > Thank  you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> wrote:
> > > > Hi Felipe -
> > > >
> > > > Thanks for the input on this. As a general rule the GC should never be
> > > > called from code. Generally this degrades performance of the JVM.
> > > > Unless there is a very good reason I will remove this. Probably you
> > > > are right a method parameter may work better.
> > > >
> > > > - Mark
> > > >
> > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > wrote:
> > > > > Hello,
> > > >
> > > >
> > > >
> > > > >
> > > > > I think that it can be solved by a simple way:
> > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> SymboList
> > > as
> > > > > parameters and do no creating a alignment, just the calculating it
> and
> > > > > returning the value.
> > > > >
> > > > > Another thing that is a bit stange for me, is the utilization of
> garbage
> > > > > collector direcly, that is: The field "scoreMatrix" is a class
> field,
> > > why at
> > > > > the end of pairwiseAlignment it is set to null and the garbage
> collector
> > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > variable?
> > > > >
> > > > > I'm annexing the class code with my changes that is doing well the
> (4^8)
> > > *
> > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > >
> > > > > Thank you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber < markjschreiber at gmail.com
> >
> > > wrote:
> > > > > > Hi Felipe -
> > > > > >
> > > > > > I agree this is a barrier to ease of use. Even if Sequences are
> > > > > > required internally for some obscure reason there is no reason why
> > > > > > dummy Sequences cannot be made inside the aligner.  These
> sequences
> > > > > > could be given names like 'query' and 'subject' or even 'seq1' and
> > > > > > 'seq2'.
> > > > > >
> > > > > > I will take a look at adding some methods.
> > > > > >
> > > > > > Best regards,
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> <felipe.albrecht at gmail.com >
> > > > > wrote:
> > > > > > > Hello all,
> > > > > > >
> > > > > > > I have a simple question about pairwise alignment classes
> > > (SmithWaterman
> > > > > and
> > > > > > > NeedlemanWunsch):
> > > > > > > Why it is necessary two Sequence for alignment and not two
> > > SymbolList?
> > > > > > >
> > > > > > > Example, I have a SymbolList collection to align between then,
> > > > > > > by this way I need to create some "dummies"  Sequence for to do
> the
> > > > > > > alignment.
> > > > > > >
> > > > > > > Reading the source, I saw that the unique field that is
> exclusive to
> > > > > > > Sequence is the name, for the alignment output,
> > > > > > > but if I need only the alignment result, it is useless.
> > > > > > >
> > > > > > > It is not possible to override the pairwiseAlignment to accept
> > > > > SymbolList or
> > > > > > > may be a new method that the parameters are 2 SymbolList and
> returns
> > > the
> > > > > > > alignment score?
> > > > > > >
> > > > > > > Thank you
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > > _______________________________________________
> > > > > > > biojava-dev mailing list
> > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>


From felipe.albrecht at gmail.com  Fri Jan 25 02:06:53 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 00:06:53 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
Message-ID: <f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>

Hi,

is not possible to add into the SequenceAlignment interface something like:
"double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
symbolList2)"?
Okay, the name is horrible, but you know what it means.

> While ultra optimized algorithms where once a major
> feature of bioinformatics this is becoming less necessary as standard
> desktops are now equivalent to the super computers of 5 years ago.

Okay, but do not forget that the bioinformatics data size is growing faster
than the computer processing and main memory capacity.

What im trying to say is that the actual methods are fast [and light] enough
for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in my
case, 65k * 65k.
Really, I dont see problems of having optimized functions for specifics
operations, as unix phylosofies: "do small programs for specifics things,
for big things join then" (Something like it :-) ).

Thank you,

Felipe Albrecht


On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> I agree your method is more efficient but I think it violates the
> SequenceAlignment interface which would cause compatibility problems.
> I also wonder what should happen if a user calls the getAlignment()
> method if you have only calculated a score.
>
> instanceof is potentially expensive but it is nothing compared to
> actually performing the SmithWaterman.
>
> Biojava is somewhat memory heavy but this is largely because it is
> object oriented. Certainly something in C would be lighter and faster
> but the whole point in using Java is the relative benefits of object
> oriented design.  While ultra optimized algorithms where once a major
> feature of bioinformatics this is becoming less necessary as standard
> desktops are now equivalent to the super computers of 5 years ago.
>
> I actually find the SW and NW to be reasonably fast. This is because
> all the heavy lifting is done in loops that the JVM presumably
> compiles and executes natively.
>
> - Mark
>
>
> On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello,
> >
> > I saw the commit and I think that this solution is not the better.
> > I think it because you are creating internally two Sequence and probably
> the
> > programmer will not use others alignment information,  he will use only
> the
> > score.
> >
> > Because it, I think that if you have 2 SymbolList, just do the alignment
> and
> > return the score, as I did.Otherwise, If the programmer want the "visual
> > alignment", he should create externally the SimpleSequences, it is, not
> the
> > method must do it.
> >
> > IMHO, one [serious] problem in biojava is the memory consumption, it
> have
> > not "lightweight" classes or methods that do the things quickly. Because
> it,
> > may be is a good choice to have a method that simply gives the alignment
> > score, and not do the others things, like backtracking. Another think,
> the
> > cost of the "instanceof" is high.
> >
> > Thank you,
> >
> > Felipe Albrecht
> >
> >
> >
> >
> > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi -
> > >
> > > I have just commited changes that let you use SymbolLists in all parts
> > > of the NW and SW SequenceAlignment objects.
> > >
> > > As you suggested I made the matrix a method local variable. I also
> > > removed calls to the garbage collector.
> > >
> > > This can be checked out from SVN.
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > wrote:
> > > > If you prefer, I can send a diff and should I do the same thing in
> > > > SequenceAlignment and NeedlemanWunsch classes?
> > > >
> > > > Thank  you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com>
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > Thanks for the input on this. As a general rule the GC should
> never be
> > > > > called from code. Generally this degrades performance of the JVM.
> > > > > Unless there is a very good reason I will remove this. Probably
> you
> > > > > are right a method parameter may work better.
> > > > >
> > > > > - Mark
> > > > >
> > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > Hello,
> > > > >
> > > > >
> > > > >
> > > > > >
> > > > > > I think that it can be solved by a simple way:
> > > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> > SymboList
> > > > as
> > > > > > parameters and do no creating a alignment, just the calculating
> it
> > and
> > > > > > returning the value.
> > > > > >
> > > > > > Another thing that is a bit stange for me, is the utilization of
> > garbage
> > > > > > collector direcly, that is: The field "scoreMatrix" is a class
> > field,
> > > > why at
> > > > > > the end of pairwiseAlignment it is set to null and the garbage
> > collector
> > > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > > variable?
> > > > > >
> > > > > > I'm annexing the class code with my changes that is doing well
> the
> > (4^8)
> > > > *
> > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > >
> > > > > > Thank you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > >
> > > > wrote:
> > > > > > > Hi Felipe -
> > > > > > >
> > > > > > > I agree this is a barrier to ease of use. Even if Sequences
> are
> > > > > > > required internally for some obscure reason there is no reason
> why
> > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > sequences
> > > > > > > could be given names like 'query' and 'subject' or even 'seq1'
> and
> > > > > > > 'seq2'.
> > > > > > >
> > > > > > > I will take a look at adding some methods.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > <felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > Hello all,
> > > > > > > >
> > > > > > > > I have a simple question about pairwise alignment classes
> > > > (SmithWaterman
> > > > > > and
> > > > > > > > NeedlemanWunsch):
> > > > > > > > Why it is necessary two Sequence for alignment and not two
> > > > SymbolList?
> > > > > > > >
> > > > > > > > Example, I have a SymbolList collection to align between
> then,
> > > > > > > > by this way I need to create some "dummies"  Sequence for to
> do
> > the
> > > > > > > > alignment.
> > > > > > > >
> > > > > > > > Reading the source, I saw that the unique field that is
> > exclusive to
> > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > >
> > > > > > > > It is not possible to override the pairwiseAlignment to
> accept
> > > > > > SymbolList or
> > > > > > > > may be a new method that the parameters are 2 SymbolList and
> > returns
> > > > the
> > > > > > > > alignment score?
> > > > > > > >
> > > > > > > > Thank you
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > > _______________________________________________
> > > > > > > > biojava-dev mailing list
> > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>


From markjschreiber at gmail.com  Fri Jan 25 03:43:30 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 11:43:30 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
Message-ID: <93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>

On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hi,
>
> is not possible to add into the SequenceAlignment interface something like:
> "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> symbolList2)"?
> Okay, the name is horrible, but you know what it means.
>

You could but you would break backwards compatibility with anyone who
implemented this interface previously.  We have sometimes done this in
biojava but we would need to make sure it will break no ones code.
Another option would be to extend the interface with another that adds
this method (not very tidy I know).

>
> > While ultra optimized algorithms where once a major
> > feature of bioinformatics this is becoming less necessary as standard
> > desktops are now equivalent to the super computers of 5 years ago.
>
> Okay, but do not forget that the bioinformatics data size is growing faster
> than the computer processing and main memory capacity.
>
> What im trying to say is that the actual methods are fast [and light] enough
> for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in my
> case, 65k * 65k.

One could also argue that Smith Waterman is not ideal for large
sequences. I think it is o(NM) or something.

> Really, I dont see problems of having optimized functions for specifics
> operations, as unix phylosofies: "do small programs for specifics things,
> for big things join then" (Something like it :-) ).
>

Yes, this would be an argument for workflow or service oriented
architecture built from multiple inter operable biojava sub-projects.
This is obviously not what biojava is. Indeed biojava is not even an
application you just use it to build applications. Maybe for your use
case you could use biojava to handle the I/O and then do the more
efficient SW using your own code. BioJava is a collection of objects
that are (somewhat) related and interoperable. It doesn't mean you
have to use biojava throughout your application.

- Mark

> On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > Hi Felipe -
> >
> > I agree your method is more efficient but I think it violates the
> > SequenceAlignment interface which would cause compatibility problems.
> > I also wonder what should happen if a user calls the getAlignment()
> > method if you have only calculated a score.
> >
> > instanceof is potentially expensive but it is nothing compared to
> > actually performing the SmithWaterman.
> >
> > Biojava is somewhat memory heavy but this is largely because it is
> > object oriented. Certainly something in C would be lighter and faster
> > but the whole point in using Java is the relative benefits of object
> > oriented design.  While ultra optimized algorithms where once a major
> > feature of bioinformatics this is becoming less necessary as standard
> > desktops are now equivalent to the super computers of 5 years ago.
> >
> > I actually find the SW and NW to be reasonably fast. This is because
> > all the heavy lifting is done in loops that the JVM presumably
> > compiles and executes natively.
> >
> > - Mark
> >
> >
> >
> >
> >
> > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> wrote:
> > > Hello,
> > >
> > > I saw the commit and I think that this solution is not the better.
> > > I think it because you are creating internally two Sequence and probably
> the
> > > programmer will not use others alignment information,  he will use only
> the
> > > score.
> > >
> > > Because it, I think that if you have 2 SymbolList, just do the alignment
> and
> > > return the score, as I did.Otherwise, If the programmer want the "visual
> > > alignment", he should create externally the SimpleSequences, it is, not
> the
> > > method must do it.
> > >
> > > IMHO, one [serious] problem in biojava is the memory consumption, it
> have
> > > not "lightweight" classes or methods that do the things quickly. Because
> it,
> > > may be is a good choice to have a method that simply gives the alignment
> > > score, and not do the others things, like backtracking. Another think,
> the
> > > cost of the "instanceof" is high.
> > >
> > > Thank you,
> > >
> > > Felipe Albrecht
> > >
> > >
> > >
> > >
> > > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > > Hi -
> > > >
> > > > I have just commited changes that let you use SymbolLists in all parts
> > > > of the NW and SW SequenceAlignment objects.
> > > >
> > > > As you suggested I made the matrix a method local variable. I also
> > > > removed calls to the garbage collector.
> > > >
> > > > This can be checked out from SVN.
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > > wrote:
> > > > > If you prefer, I can send a diff and should I do the same thing in
> > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > >
> > > > > Thank  you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber < markjschreiber at gmail.com >
> > > wrote:
> > > > > > Hi Felipe -
> > > > > >
> > > > > > Thanks for the input on this. As a general rule the GC should
> never be
> > > > > > called from code. Generally this degrades performance of the JVM.
> > > > > > Unless there is a very good reason I will remove this. Probably
> you
> > > > > > are right a method parameter may work better.
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> <felipe.albrecht at gmail.com>
> > > > > wrote:
> > > > > > > Hello,
> > > > > >
> > > > > >
> > > > > >
> > > > > > >
> > > > > > > I think that it can be solved by a simple way:
> > > > > > > Implement (or just copy and cut) a pairwiseAlignment utilizing
> > > SymboList
> > > > > as
> > > > > > > parameters and do no creating a alignment, just the calculating
> it
> > > and
> > > > > > > returning the value.
> > > > > > >
> > > > > > > Another thing that is a bit stange for me, is the utilization of
> > > garbage
> > > > > > > collector direcly, that is: The field "scoreMatrix" is a class
> > > field,
> > > > > why at
> > > > > > > the end of pairwiseAlignment it is set to null and the garbage
> > > collector
> > > > > > > run? It is not better (and simpler) to use scoreMatrix as method
> > > > > variable?
> > > > > > >
> > > > > > > I'm annexing the class code with my changes that is doing well
> the
> > > (4^8)
> > > > > *
> > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > >
> > > > > > > Thank you,
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > > >
> > > > > wrote:
> > > > > > > > Hi Felipe -
> > > > > > > >
> > > > > > > > I agree this is a barrier to ease of use. Even if Sequences
> are
> > > > > > > > required internally for some obscure reason there is no reason
> why
> > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > sequences
> > > > > > > > could be given names like 'query' and 'subject' or even 'seq1'
> and
> > > > > > > > 'seq2'.
> > > > > > > >
> > > > > > > > I will take a look at adding some methods.
> > > > > > > >
> > > > > > > > Best regards,
> > > > > > > >
> > > > > > > > - Mark
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > <felipe.albrecht at gmail.com >
> > > > > > > wrote:
> > > > > > > > > Hello all,
> > > > > > > > >
> > > > > > > > > I have a simple question about pairwise alignment classes
> > > > > (SmithWaterman
> > > > > > > and
> > > > > > > > > NeedlemanWunsch):
> > > > > > > > > Why it is necessary two Sequence for alignment and not two
> > > > > SymbolList?
> > > > > > > > >
> > > > > > > > > Example, I have a SymbolList collection to align between
> then,
> > > > > > > > > by this way I need to create some "dummies"  Sequence for to
> do
> > > the
> > > > > > > > > alignment.
> > > > > > > > >
> > > > > > > > > Reading the source, I saw that the unique field that is
> > > exclusive to
> > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > >
> > > > > > > > > It is not possible to override the pairwiseAlignment to
> accept
> > > > > > > SymbolList or
> > > > > > > > > may be a new method that the parameters are 2 SymbolList and
> > > returns
> > > > > the
> > > > > > > > > alignment score?
> > > > > > > > >
> > > > > > > > > Thank you
> > > > > > > > >
> > > > > > > > > Felipe Albrecht
> > > > > > > > > _______________________________________________
> > > > > > > > > biojava-dev mailing list
> > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>


From felipe.albrecht at gmail.com  Fri Jan 25 04:25:23 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 02:25:23 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
Message-ID: <f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>

Hello again :-)

On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hi,
> >
> > is not possible to add into the SequenceAlignment interface something
> like:
> > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > symbolList2)"?
> > Okay, the name is horrible, but you know what it means.
> >
>
> You could but you would break backwards compatibility with anyone who
> implemented this interface previously.  We have sometimes done this in
> biojava but we would need to make sure it will break no ones code.
> Another option would be to extend the interface with another that adds
> this method (not very tidy I know).


If I'm correct, the SequenceAlignment is an abstract class, so, we can
define there with an empty implementation, and SmithWaterman and others
classes implements it. Anyone that implemented SequenceAlignment will not
see anything different.



>
> >
> > > While ultra optimized algorithms where once a major
> > > feature of bioinformatics this is becoming less necessary as standard
> > > desktops are now equivalent to the super computers of 5 years ago.
> >
> > Okay, but do not forget that the bioinformatics data size is growing
> faster
> > than the computer processing and main memory capacity.
> >
> > What im trying to say is that the actual methods are fast [and light]
> enough
> > for do 1, 10, 100, 1000 pairwise alignments, but not for 10k, 100k or in
> my
> > case, 65k * 65k.
>
> One could also argue that Smith Waterman is not ideal for large
> sequences. I think it is o(NM) or something.


I'm not comparing  two sequences with 65k * 65k  bases, but doing the
alignment of 65k little sequences between then.

>
>
> > Really, I dont see problems of having optimized functions for specifics
> > operations, as unix phylosofies: "do small programs for specifics
> things,
> > for big things join then" (Something like it :-) ).
> >
>
> Yes, this would be an argument for workflow or service oriented
> architecture built from multiple inter operable biojava sub-projects.
> This is obviously not what biojava is. Indeed biojava is not even an
> application you just use it to build applications. Maybe for your use
> case you could use biojava to handle the I/O and then do the more
> efficient SW using your own code. BioJava is a collection of objects
> that are (somewhat) related and interoperable. It doesn't mean you
> have to use biojava throughout your application.


Okay, now I understood, biojava is not a library for bioinformatics
applications, but for interconnect bioinformatics applications. So, biojava
in the actual way is not appropriate for the application that I am
developing. I will develop some "optimized" classes and functions for my use
and when it will be ready I will announce in this mailing list and ask if
want to merge in biojava. If biojava team needs somebody to improve some
biojava functions, specially sequences and sequences IO, can ask me.

Thank you

Felipe Albrecht




>
>
> - Mark
>
> > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > Hi Felipe -
> > >
> > > I agree your method is more efficient but I think it violates the
> > > SequenceAlignment interface which would cause compatibility problems.
> > > I also wonder what should happen if a user calls the getAlignment()
> > > method if you have only calculated a score.
> > >
> > > instanceof is potentially expensive but it is nothing compared to
> > > actually performing the SmithWaterman.
> > >
> > > Biojava is somewhat memory heavy but this is largely because it is
> > > object oriented. Certainly something in C would be lighter and faster
> > > but the whole point in using Java is the relative benefits of object
> > > oriented design.  While ultra optimized algorithms where once a major
> > > feature of bioinformatics this is becoming less necessary as standard
> > > desktops are now equivalent to the super computers of 5 years ago.
> > >
> > > I actually find the SW and NW to be reasonably fast. This is because
> > > all the heavy lifting is done in loops that the JVM presumably
> > > compiles and executes natively.
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > >
> > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > wrote:
> > > > Hello,
> > > >
> > > > I saw the commit and I think that this solution is not the better.
> > > > I think it because you are creating internally two Sequence and
> probably
> > the
> > > > programmer will not use others alignment information,  he will use
> only
> > the
> > > > score.
> > > >
> > > > Because it, I think that if you have 2 SymbolList, just do the
> alignment
> > and
> > > > return the score, as I did.Otherwise, If the programmer want the
> "visual
> > > > alignment", he should create externally the SimpleSequences, it is,
> not
> > the
> > > > method must do it.
> > > >
> > > > IMHO, one [serious] problem in biojava is the memory consumption, it
>
> > have
> > > > not "lightweight" classes or methods that do the things quickly.
> Because
> > it,
> > > > may be is a good choice to have a method that simply gives the
> alignment
> > > > score, and not do the others things, like backtracking. Another
> think,
> > the
> > > > cost of the "instanceof" is high.
> > > >
> > > > Thank you,
> > > >
> > > > Felipe Albrecht
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com >
> > wrote:
> > > > > Hi -
> > > > >
> > > > > I have just commited changes that let you use SymbolLists in all
> parts
> > > > > of the NW and SW SequenceAlignment objects.
> > > > >
> > > > > As you suggested I made the matrix a method local variable. I also
> > > > > removed calls to the garbage collector.
> > > > >
> > > > > This can be checked out from SVN.
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > > > wrote:
> > > > > > If you prefer, I can send a diff and should I do the same thing
> in
> > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > >
> > > > > > Thank  you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> markjschreiber at gmail.com >
> > > > wrote:
> > > > > > > Hi Felipe -
> > > > > > >
> > > > > > > Thanks for the input on this. As a general rule the GC should
> > never be
> > > > > > > called from code. Generally this degrades performance of the
> JVM.
> > > > > > > Unless there is a very good reason I will remove this.
> Probably
> > you
> > > > > > > are right a method parameter may work better.
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > <felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > Hello,
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > >
> > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> utilizing
> > > > SymboList
> > > > > > as
> > > > > > > > parameters and do no creating a alignment, just the
> calculating
> > it
> > > > and
> > > > > > > > returning the value.
> > > > > > > >
> > > > > > > > Another thing that is a bit stange for me, is the
> utilization of
> > > > garbage
> > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> class
> > > > field,
> > > > > > why at
> > > > > > > > the end of pairwiseAlignment it is set to null and the
> garbage
> > > > collector
> > > > > > > > run? It is not better (and simpler) to use scoreMatrix as
> method
> > > > > > variable?
> > > > > > > >
> > > > > > > > I'm annexing the class code with my changes that is doing
> well
> > the
> > > > (4^8)
> > > > > > *
> > > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > > >
> > > > > > > > Thank you,
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > markjschreiber at gmail.com
> > > > >
> > > > > > wrote:
> > > > > > > > > Hi Felipe -
> > > > > > > > >
> > > > > > > > > I agree this is a barrier to ease of use. Even if
> Sequences
> > are
> > > > > > > > > required internally for some obscure reason there is no
> reason
> > why
> > > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > > sequences
> > > > > > > > > could be given names like 'query' and 'subject' or even
> 'seq1'
> > and
> > > > > > > > > 'seq2'.
> > > > > > > > >
> > > > > > > > > I will take a look at adding some methods.
> > > > > > > > >
> > > > > > > > > Best regards,
> > > > > > > > >
> > > > > > > > > - Mark
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > < felipe.albrecht at gmail.com >
> > > > > > > > wrote:
> > > > > > > > > > Hello all,
> > > > > > > > > >
> > > > > > > > > > I have a simple question about pairwise alignment
> classes
> > > > > > (SmithWaterman
> > > > > > > > and
> > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > Why it is necessary two Sequence for alignment and not
> two
> > > > > > SymbolList?
> > > > > > > > > >
> > > > > > > > > > Example, I have a SymbolList collection to align between
> > then,
> > > > > > > > > > by this way I need to create some "dummies"  Sequence
> for to
> > do
> > > > the
> > > > > > > > > > alignment.
> > > > > > > > > >
> > > > > > > > > > Reading the source, I saw that the unique field that is
> > > > exclusive to
> > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > > >
> > > > > > > > > > It is not possible to override the pairwiseAlignment to
> > accept
> > > > > > > > SymbolList or
> > > > > > > > > > may be a new method that the parameters are 2 SymbolList
> and
> > > > returns
> > > > > > the
> > > > > > > > > > alignment score?
> > > > > > > > > >
> > > > > > > > > > Thank you
> > > > > > > > > >
> > > > > > > > > > Felipe Albrecht
> > > > > > > > > > _______________________________________________
> > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>


From markjschreiber at gmail.com  Fri Jan 25 05:40:20 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 25 Jan 2008 13:40:20 +0800
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
	<f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
Message-ID: <93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>

On Jan 25, 2008 12:25 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello again :-)
>
>
> On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> >
> > On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > > Hi,
> > >
> > > is not possible to add into the SequenceAlignment interface something
> like:
> > > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > > symbolList2)"?
> > > Okay, the name is horrible, but you know what it means.
> > >

> If I'm correct, the SequenceAlignment is an abstract class, so, we can
> define there with an empty implementation, and SmithWaterman and others
> classes implements it. Anyone that implemented SequenceAlignment will not
> see anything different.

OK in that case adding the method would be OK, even desirable.
Probably this would be the best way to merge in your code.

> Okay, now I understood, biojava is not a library for bioinformatics
> applications, but for interconnect bioinformatics applications. So, biojava

Actually it is a library for bioinformatics that you use to build
bioinformatics applications.  It is possibly not as loosely coupled as
you might like for your purpose. It is definitely not as loosely
coupled as the Unix collection of executables or an SOA system.  Due
to heavy use of interfaces and abstract classes there is some
possibility for custom code.  For example you can recode the
SmithWaterman object to be optimal for your needs and then create an
application where you use your class in place of the normal biojava
SmithWaterman.

> in the actual way is not appropriate for the application that I am
> developing. I will develop some "optimized" classes and functions for my use
> and when it will be ready I will announce in this mailing list and ask if
> want to merge in biojava. If biojava team needs somebody to improve some
> biojava functions, specially sequences and sequences IO, can ask me.

Code improvements and optimizations are always welcome especially if
current interfaces can be preserved (that way the end user gets the
improvement without having to change their code).  I always advise
potential optimizers to use a profiler because it is sometimes hard to
predict how the JVM will behave, for example JIT compiling may mean
parts of code that are theoretically CPU intensive may not be the CPU
bottleneck when the JVM compiles them.

- Mark

>
> Thank you
>
> Felipe Albrecht
>
>
>
>
>
> >
> >
> >
> >
> >
> > - Mark
> >
> > > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > > > Hi Felipe -
> > > >
> > > > I agree your method is more efficient but I think it violates the
> > > > SequenceAlignment interface which would cause compatibility problems.
> > > > I also wonder what should happen if a user calls the getAlignment()
> > > > method if you have only calculated a score.
> > > >
> > > > instanceof is potentially expensive but it is nothing compared to
> > > > actually performing the SmithWaterman.
> > > >
> > > > Biojava is somewhat memory heavy but this is largely because it is
> > > > object oriented. Certainly something in C would be lighter and faster
> > > > but the whole point in using Java is the relative benefits of object
> > > > oriented design.  While ultra optimized algorithms where once a major
> > > > feature of bioinformatics this is becoming less necessary as standard
> > > > desktops are now equivalent to the super computers of 5 years ago.
> > > >
> > > > I actually find the SW and NW to be reasonably fast. This is because
> > > > all the heavy lifting is done in loops that the JVM presumably
> > > > compiles and executes natively.
> > > >
> > > > - Mark
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com >
> > > wrote:
> > > > > Hello,
> > > > >
> > > > > I saw the commit and I think that this solution is not the better.
> > > > > I think it because you are creating internally two Sequence and
> probably
> > > the
> > > > > programmer will not use others alignment information,  he will use
> only
> > > the
> > > > > score.
> > > > >
> > > > > Because it, I think that if you have 2 SymbolList, just do the
> alignment
> > > and
> > > > > return the score, as I did.Otherwise, If the programmer want the
> "visual
> > > > > alignment", he should create externally the SimpleSequences, it is,
> not
> > > the
> > > > > method must do it.
> > > > >
> > > > > IMHO, one [serious] problem in biojava is the memory consumption, it
> > > have
> > > > > not "lightweight" classes or methods that do the things quickly.
> Because
> > > it,
> > > > > may be is a good choice to have a method that simply gives the
> alignment
> > > > > score, and not do the others things, like backtracking. Another
> think,
> > > the
> > > > > cost of the "instanceof" is high.
> > > > >
> > > > > Thank you,
> > > > >
> > > > > Felipe Albrecht
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 24, 2008 11:35 AM, Mark Schreiber < markjschreiber at gmail.com
> >
> > > wrote:
> > > > > > Hi -
> > > > > >
> > > > > > I have just commited changes that let you use SymbolLists in all
> parts
> > > > > > of the NW and SW SequenceAlignment objects.
> > > > > >
> > > > > > As you suggested I made the matrix a method local variable. I also
> > > > > > removed calls to the garbage collector.
> > > > > >
> > > > > > This can be checked out from SVN.
> > > > > >
> > > > > > - Mark
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <
> felipe.albrecht at gmail.com >
> > > > > wrote:
> > > > > > > If you prefer, I can send a diff and should I do the same thing
> in
> > > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > > >
> > > > > > > Thank  you,
> > > > > > >
> > > > > > > Felipe Albrecht
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> markjschreiber at gmail.com >
> > > > > wrote:
> > > > > > > > Hi Felipe -
> > > > > > > >
> > > > > > > > Thanks for the input on this. As a general rule the GC should
> > > never be
> > > > > > > > called from code. Generally this degrades performance of the
> JVM.
> > > > > > > > Unless there is a very good reason I will remove this.
> Probably
> > > you
> > > > > > > > are right a method parameter may work better.
> > > > > > > >
> > > > > > > > - Mark
> > > > > > > >
> > > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > > <felipe.albrecht at gmail.com >
> > > > > > > wrote:
> > > > > > > > > Hello,
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > >
> > > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> utilizing
> > > > > SymboList
> > > > > > > as
> > > > > > > > > parameters and do no creating a alignment, just the
> calculating
> > > it
> > > > > and
> > > > > > > > > returning the value.
> > > > > > > > >
> > > > > > > > > Another thing that is a bit stange for me, is the
> utilization of
> > > > > garbage
> > > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> class
> > > > > field,
> > > > > > > why at
> > > > > > > > > the end of pairwiseAlignment it is set to null and the
> garbage
> > > > > collector
> > > > > > > > > run? It is not better (and simpler) to use scoreMatrix as
> method
> > > > > > > variable?
> > > > > > > > >
> > > > > > > > > I'm annexing the class code with my changes that is doing
> well
> > > the
> > > > > (4^8)
> > > > > > > *
> > > > > > > > > (4^8) SymbolList pairwise alignments that I am needing :-)
> > > > > > > > >
> > > > > > > > > Thank you,
> > > > > > > > >
> > > > > > > > > Felipe Albrecht
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > > markjschreiber at gmail.com
> > > > > >
> > > > > > > wrote:
> > > > > > > > > > Hi Felipe -
> > > > > > > > > >
> > > > > > > > > > I agree this is a barrier to ease of use. Even if
> Sequences
> > > are
> > > > > > > > > > required internally for some obscure reason there is no
> reason
> > > why
> > > > > > > > > > dummy Sequences cannot be made inside the aligner.  These
> > > > > sequences
> > > > > > > > > > could be given names like 'query' and 'subject' or even
> 'seq1'
> > > and
> > > > > > > > > > 'seq2'.
> > > > > > > > > >
> > > > > > > > > > I will take a look at adding some methods.
> > > > > > > > > >
> > > > > > > > > > Best regards,
> > > > > > > > > >
> > > > > > > > > > - Mark
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > > < felipe.albrecht at gmail.com >
> > > > > > > > > wrote:
> > > > > > > > > > > Hello all,
> > > > > > > > > > >
> > > > > > > > > > > I have a simple question about pairwise alignment
> classes
> > > > > > > (SmithWaterman
> > > > > > > > > and
> > > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > > Why it is necessary two Sequence for alignment and not
> two
> > > > > > > SymbolList?
> > > > > > > > > > >
> > > > > > > > > > > Example, I have a SymbolList collection to align between
> > > then,
> > > > > > > > > > > by this way I need to create some "dummies"  Sequence
> for to
> > > do
> > > > > the
> > > > > > > > > > > alignment.
> > > > > > > > > > >
> > > > > > > > > > > Reading the source, I saw that the unique field that is
> > > > > exclusive to
> > > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > > but if I need only the alignment result, it is useless.
> > > > > > > > > > >
> > > > > > > > > > > It is not possible to override the pairwiseAlignment to
> > > accept
> > > > > > > > > SymbolList or
> > > > > > > > > > > may be a new method that the parameters are 2 SymbolList
> and
> > > > > returns
> > > > > > > the
> > > > > > > > > > > alignment score?
> > > > > > > > > > >
> > > > > > > > > > > Thank you
> > > > > > > > > > >
> > > > > > > > > > > Felipe Albrecht
> > > > > > > > > > > _______________________________________________
> > > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>


From felipe.albrecht at gmail.com  Fri Jan 25 06:39:45 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Fri, 25 Jan 2008 04:39:45 -0200
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801232350g5996fe1bp1bb6f5c4b92bc734@mail.gmail.com>
	<f6b04db30801240505t5efee4aew873b8f451ea96ed7@mail.gmail.com>
	<93b45ca50801240535v15688c02n17c8bac9d4c962a7@mail.gmail.com>
	<f6b04db30801241140m7033ccard4008d4a10931fb7@mail.gmail.com>
	<93b45ca50801241726h25c44621s42c9d89c85de5dc4@mail.gmail.com>
	<f6b04db30801241806x75b96189t34a6db754e73c1de@mail.gmail.com>
	<93b45ca50801241943l10e634fal3d10bfc739af5a1d@mail.gmail.com>
	<f6b04db30801242025xa513a7dtab2fdd4221e764a4@mail.gmail.com>
	<93b45ca50801242140j299b91e7td9fb295a7393ced9@mail.gmail.com>
Message-ID: <f6b04db30801242239l5b11f0f3o5e9e1c253264a79a@mail.gmail.com>

Okay, I agree with what you said.

I was looking the SequenceAlignment source and I realize a strange thing.
At formatOutput method, the editDistance is multiplied by -1,
if you use a NeedlemanWunsch pairwiseAlignment method, the editDistance
is returned without any multiplication.
That is, the score/editDistance of formatOutput is different from there that
is given by NeedlemanWunsch pairwiseAlignment.

What is the correct?

Thank you again

Felipe Albrecht

On Jan 25, 2008 3:40 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> On Jan 25, 2008 12:25 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello again :-)
> >
> >
> > On Jan 25, 2008 1:43 AM, Mark Schreiber <markjschreiber at gmail.com>
> wrote:
> > >
> > > On Jan 25, 2008 10:06 AM, Felipe Albrecht <felipe.albrecht at gmail.com>
> > wrote:
> > > > Hi,
> > > >
> > > > is not possible to add into the SequenceAlignment interface
> something
> > like:
> > > > "double doAlignmentAndGetTheScore(SymbolList symbolList1, SymbolList
> > > > symbolList2)"?
> > > > Okay, the name is horrible, but you know what it means.
> > > >
>
> > If I'm correct, the SequenceAlignment is an abstract class, so, we can
> > define there with an empty implementation, and SmithWaterman and others
> > classes implements it. Anyone that implemented SequenceAlignment will
> not
> > see anything different.
>
> OK in that case adding the method would be OK, even desirable.
> Probably this would be the best way to merge in your code.
>
> > Okay, now I understood, biojava is not a library for bioinformatics
> > applications, but for interconnect bioinformatics applications. So,
> biojava
>
> Actually it is a library for bioinformatics that you use to build
> bioinformatics applications.  It is possibly not as loosely coupled as
> you might like for your purpose. It is definitely not as loosely
> coupled as the Unix collection of executables or an SOA system.  Due
> to heavy use of interfaces and abstract classes there is some
> possibility for custom code.  For example you can recode the
> SmithWaterman object to be optimal for your needs and then create an
> application where you use your class in place of the normal biojava
> SmithWaterman.
>
> > in the actual way is not appropriate for the application that I am
> > developing. I will develop some "optimized" classes and functions for my
> use
> > and when it will be ready I will announce in this mailing list and ask
> if
> > want to merge in biojava. If biojava team needs somebody to improve some
> > biojava functions, specially sequences and sequences IO, can ask me.
>
> Code improvements and optimizations are always welcome especially if
> current interfaces can be preserved (that way the end user gets the
> improvement without having to change their code).  I always advise
> potential optimizers to use a profiler because it is sometimes hard to
> predict how the JVM will behave, for example JIT compiling may mean
> parts of code that are theoretically CPU intensive may not be the CPU
> bottleneck when the JVM compiles them.
>
> - Mark
>
> >
> > Thank you
> >
> > Felipe Albrecht
> >
> >
> >
> >
> >
> > >
> > >
> > >
> > >
> > >
> > > - Mark
> > >
> > > > On Jan 24, 2008 11:26 PM, Mark Schreiber <markjschreiber at gmail.com>
> > wrote:
> > > > > Hi Felipe -
> > > > >
> > > > > I agree your method is more efficient but I think it violates the
> > > > > SequenceAlignment interface which would cause compatibility
> problems.
> > > > > I also wonder what should happen if a user calls the
> getAlignment()
> > > > > method if you have only calculated a score.
> > > > >
> > > > > instanceof is potentially expensive but it is nothing compared to
> > > > > actually performing the SmithWaterman.
> > > > >
> > > > > Biojava is somewhat memory heavy but this is largely because it is
> > > > > object oriented. Certainly something in C would be lighter and
> faster
> > > > > but the whole point in using Java is the relative benefits of
> object
> > > > > oriented design.  While ultra optimized algorithms where once a
> major
> > > > > feature of bioinformatics this is becoming less necessary as
> standard
> > > > > desktops are now equivalent to the super computers of 5 years ago.
> > > > >
> > > > > I actually find the SW and NW to be reasonably fast. This is
> because
> > > > > all the heavy lifting is done in loops that the JVM presumably
> > > > > compiles and executes natively.
> > > > >
> > > > > - Mark
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Jan 25, 2008 3:40 AM, Felipe Albrecht <
> felipe.albrecht at gmail.com >
> > > > wrote:
> > > > > > Hello,
> > > > > >
> > > > > > I saw the commit and I think that this solution is not the
> better.
> > > > > > I think it because you are creating internally two Sequence and
> > probably
> > > > the
> > > > > > programmer will not use others alignment information,  he will
> use
> > only
> > > > the
> > > > > > score.
> > > > > >
> > > > > > Because it, I think that if you have 2 SymbolList, just do the
> > alignment
> > > > and
> > > > > > return the score, as I did.Otherwise, If the programmer want the
> > "visual
> > > > > > alignment", he should create externally the SimpleSequences, it
> is,
> > not
> > > > the
> > > > > > method must do it.
> > > > > >
> > > > > > IMHO, one [serious] problem in biojava is the memory
> consumption, it
> > > > have
> > > > > > not "lightweight" classes or methods that do the things quickly.
> > Because
> > > > it,
> > > > > > may be is a good choice to have a method that simply gives the
> > alignment
> > > > > > score, and not do the others things, like backtracking. Another
> > think,
> > > > the
> > > > > > cost of the "instanceof" is high.
> > > > > >
> > > > > > Thank you,
> > > > > >
> > > > > > Felipe Albrecht
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Jan 24, 2008 11:35 AM, Mark Schreiber <
> markjschreiber at gmail.com
> > >
> > > > wrote:
> > > > > > > Hi -
> > > > > > >
> > > > > > > I have just commited changes that let you use SymbolLists in
> all
> > parts
> > > > > > > of the NW and SW SequenceAlignment objects.
> > > > > > >
> > > > > > > As you suggested I made the matrix a method local variable. I
> also
> > > > > > > removed calls to the garbage collector.
> > > > > > >
> > > > > > > This can be checked out from SVN.
> > > > > > >
> > > > > > > - Mark
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Jan 24, 2008 9:05 PM, Felipe Albrecht <
> > felipe.albrecht at gmail.com >
> > > > > > wrote:
> > > > > > > > If you prefer, I can send a diff and should I do the same
> thing
> > in
> > > > > > > > SequenceAlignment and NeedlemanWunsch classes?
> > > > > > > >
> > > > > > > > Thank  you,
> > > > > > > >
> > > > > > > > Felipe Albrecht
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Jan 24, 2008 5:50 AM, Mark Schreiber <
> > markjschreiber at gmail.com >
> > > > > > wrote:
> > > > > > > > > Hi Felipe -
> > > > > > > > >
> > > > > > > > > Thanks for the input on this. As a general rule the GC
> should
> > > > never be
> > > > > > > > > called from code. Generally this degrades performance of
> the
> > JVM.
> > > > > > > > > Unless there is a very good reason I will remove this.
> > Probably
> > > > you
> > > > > > > > > are right a method parameter may work better.
> > > > > > > > >
> > > > > > > > > - Mark
> > > > > > > > >
> > > > > > > > > On Jan 24, 2008 1:47 PM, Felipe Albrecht
> > > > <felipe.albrecht at gmail.com >
> > > > > > > > wrote:
> > > > > > > > > > Hello,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > I think that it can be solved by a simple way:
> > > > > > > > > > Implement (or just copy and cut) a pairwiseAlignment
> > utilizing
> > > > > > SymboList
> > > > > > > > as
> > > > > > > > > > parameters and do no creating a alignment, just the
> > calculating
> > > > it
> > > > > > and
> > > > > > > > > > returning the value.
> > > > > > > > > >
> > > > > > > > > > Another thing that is a bit stange for me, is the
> > utilization of
> > > > > > garbage
> > > > > > > > > > collector direcly, that is: The field "scoreMatrix" is a
> > class
> > > > > > field,
> > > > > > > > why at
> > > > > > > > > > the end of pairwiseAlignment it is set to null and the
> > garbage
> > > > > > collector
> > > > > > > > > > run? It is not better (and simpler) to use scoreMatrix
> as
> > method
> > > > > > > > variable?
> > > > > > > > > >
> > > > > > > > > > I'm annexing the class code with my changes that is
> doing
> > well
> > > > the
> > > > > > (4^8)
> > > > > > > > *
> > > > > > > > > > (4^8) SymbolList pairwise alignments that I am needing
> :-)
> > > > > > > > > >
> > > > > > > > > > Thank you,
> > > > > > > > > >
> > > > > > > > > > Felipe Albrecht
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >  On Jan 23, 2008 6:50 AM, Mark Schreiber <
> > > > markjschreiber at gmail.com
> > > > > > >
> > > > > > > > wrote:
> > > > > > > > > > > Hi Felipe -
> > > > > > > > > > >
> > > > > > > > > > > I agree this is a barrier to ease of use. Even if
> > Sequences
> > > > are
> > > > > > > > > > > required internally for some obscure reason there is
> no
> > reason
> > > > why
> > > > > > > > > > > dummy Sequences cannot be made inside the aligner.
>  These
> > > > > > sequences
> > > > > > > > > > > could be given names like 'query' and 'subject' or
> even
> > 'seq1'
> > > > and
> > > > > > > > > > > 'seq2'.
> > > > > > > > > > >
> > > > > > > > > > > I will take a look at adding some methods.
> > > > > > > > > > >
> > > > > > > > > > > Best regards,
> > > > > > > > > > >
> > > > > > > > > > > - Mark
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Jan 23, 2008 2:58 PM, Felipe Albrecht
> > > > > > < felipe.albrecht at gmail.com >
> > > > > > > > > > wrote:
> > > > > > > > > > > > Hello all,
> > > > > > > > > > > >
> > > > > > > > > > > > I have a simple question about pairwise alignment
> > classes
> > > > > > > > (SmithWaterman
> > > > > > > > > > and
> > > > > > > > > > > > NeedlemanWunsch):
> > > > > > > > > > > > Why it is necessary two Sequence for alignment and
> not
> > two
> > > > > > > > SymbolList?
> > > > > > > > > > > >
> > > > > > > > > > > > Example, I have a SymbolList collection to align
> between
> > > > then,
> > > > > > > > > > > > by this way I need to create some "dummies"
>  Sequence
> > for to
> > > > do
> > > > > > the
> > > > > > > > > > > > alignment.
> > > > > > > > > > > >
> > > > > > > > > > > > Reading the source, I saw that the unique field that
> is
> > > > > > exclusive to
> > > > > > > > > > > > Sequence is the name, for the alignment output,
> > > > > > > > > > > > but if I need only the alignment result, it is
> useless.
> > > > > > > > > > > >
> > > > > > > > > > > > It is not possible to override the pairwiseAlignment
> to
> > > > accept
> > > > > > > > > > SymbolList or
> > > > > > > > > > > > may be a new method that the parameters are 2
> SymbolList
> > and
> > > > > > returns
> > > > > > > > the
> > > > > > > > > > > > alignment score?
> > > > > > > > > > > >
> > > > > > > > > > > > Thank you
> > > > > > > > > > > >
> > > > > > > > > > > > Felipe Albrecht
> > > > > > > > > > > > _______________________________________________
> > > > > > > > > > > > biojava-dev mailing list
> > > > > > > > > > > > biojava-dev at lists.open-bio.org
> > > > > > > > > > > >
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>


From ap3 at sanger.ac.uk  Fri Jan 25 09:49:22 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Fri, 25 Jan 2008 09:49:22 +0000
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>
	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>
	<8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
Message-ID: <80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>


> DAS looks just wonderful, and I am very glad to be made aware of it ?
> it seems like a much better solution than my initial, highly naive
> reaction (accessing public SQL connections).

don;t think that this is naive. There is also ensembldb.ensembl.org
which is a public mysql server if you prefer sql....

>
> As I understand it, the easiest way to access DAS services in Java is
> via an API such as JAX-WS?   Jumping into the Javadocs, and looking
> over a JAX-WS tutorial that I found here:
> http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
> is a lot to this.

I have not tried JAX-WS yet, so I can not comment on that, but if you  
want a library
that makes it easier to talk to DAS servers, you can use my
DAS client library at: http://www.spice-3d.org/dasobert/

Andreas


> ---------------------------------------------------------------------- 
> -


Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



From ayates at ebi.ac.uk  Fri Jan 25 09:58:37 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 25 Jan 2008 09:58:37 +0000
Subject: [Biojava-dev] Direct access to public genome databases
In-Reply-To: <80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>
References: <Pine.GSO.4.44.0801231955420.23135-100000@shell3.shore.net>	<Pine.LNX.4.64.0801240829490.13550@deskpro349.dynamic.sanger.ac.uk>	<8adccabf0801241217gfa82d47r2728b08c6bcde862@mail.gmail.com>
	<80544F81-E3DE-4212-8C62-2CA4865E4758@sanger.ac.uk>
Message-ID: <4799B2CD.3010603@ebi.ac.uk>



Andreas Prlic wrote:
> 
>> DAS looks just wonderful, and I am very glad to be made aware of it ?
>> it seems like a much better solution than my initial, highly naive
>> reaction (accessing public SQL connections).
> 
> don;t think that this is naive. There is also ensembldb.ensembl.org
> which is a public mysql server if you prefer sql....

I have to agree. There's a lot to be said about using a database 
directly (in fact my group does just that). But it is potentially a more 
fragile solution than using a public api.

>>
>> As I understand it, the easiest way to access DAS services in Java is
>> via an API such as JAX-WS?   Jumping into the Javadocs, and looking
>> over a JAX-WS tutorial that I found here:
>> http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
>> is a lot to this.
> 
> I have not tried JAX-WS yet, so I can not comment on that, but if you 
> want a library
> that makes it easier to talk to DAS servers, you can use my
> DAS client library at: http://www.spice-3d.org/dasobert/

I would stay away from JAX-WS. It's a web services framework which is 
more for SOAP access than anything else. Even when using it for SOAP 
remoting I've found it less than intuitive (maybe later version have 
gotten better about this especially with the Java6 compiler api 
hopefully removing any need for explicit annotation processing). Chances 
are it would be easier to use JAX-WS when the REST service support comes 
in but until then I would say stay away from it.

Andreas' library is a far superior solution :)

Andy


From bugzilla-daemon at portal.open-bio.org  Fri Jan 25 12:28:08 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 25 Jan 2008 07:28:08 -0500
Subject: [Biojava-dev] [Bug 2432] non conventional fasta header &&
	RichSequence.IOTools
In-Reply-To: <bug-2432-485@http.bugzilla.open-bio.org/>
Message-ID: <200801251228.m0PCS8A5003219@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2432


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from mark.schreiber at novartis.com  2008-01-25 07:28 EST -------
I have added a class called FastaHeader. This class lets you specify which
fields you want to see in the fasta header output. There are overloaded
writeFasta methods in RichSequence.IOTools that let you use this class easily.

For example the following test program reads in a fasta file from Genbank with
a full header and outputs it with only the accession number and description
after the '>'

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

package io;

import java.io.BufferedReader;
import java.io.FileReader;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.biojavax.bio.seq.io.FastaHeader;
import static org.biojavax.bio.seq.RichSequence.IOTools;

/**
 *
 * @author Mark
 */
public class WriteFasta {
    public static void main(String[] args) throws Exception{ 
        BufferedReader br = new BufferedReader(
                new FileReader("files/dna.fasta"));
        RichSequenceIterator iter = IOTools.readFastaDNA(br, null);
        //IOTools.writeFasta(System.out, iter, null);

        FastaHeader header = new FastaHeader();
        header.setShowDescription(true);
        header.setShowIdentifier(false);
        header.setShowNamespace(false);
        header.setShowName(false);
        header.setShowVersion(false);

        IOTools.writeFasta(System.out, iter, null, header);
    }
}


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
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From miwalsh125 at gmail.com  Tue Jan 29 15:22:07 2008
From: miwalsh125 at gmail.com (michael walsh)
Date: Tue, 29 Jan 2008 10:22:07 -0500
Subject: [Biojava-dev] Genbank Feature extraction question.
Message-ID: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>

BioJava,

I am writing a program that extracts features from a Genbank file using
BioJava The program needs to extract the feature locations from the file.
This is easy enough to do but the location information returned by the
program does not specify whether or not the location is on the complementary
strand of DNA.

This is some of my code:
FeatureHolder fltrHold = seq.filter(codeFltr);//codeFltr is a filter that
retrieves coding features only.
        //iterate over the Features in fh
        for (Iterator i = fltrHold.features(); i.hasNext(); ){
            Feature f = (Feature)i.next();
            System.out.println(f.getLocation().toString());

An example of the output of the print command is:
join:[32775..32948,31801..32052]

However, the entry in the Genbank file reads:
complement(join(31801..32052,32775..32948))

Is there any way to get my program to output the fact that a features
location is on the complementary strand of DNA?

Any help that anyone can give me would be greatly appreciated.

Sincerely,

M Walsh


From holland at ebi.ac.uk  Wed Jan 30 08:53:29 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 30 Jan 2008 08:53:29 +0000
Subject: [Biojava-dev] Genbank Feature extraction question.
In-Reply-To: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>
References: <e882126a0801290722l1f93379at2295a823a475e602@mail.gmail.com>
Message-ID: <47A03B09.1030905@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

If you are using the BioJavaX parsers as opposed to the older deprecated
ones, then yes, the information is there.

Your parser will be returning instances of RichSequence (there will be a
nextRichSequence or getRichSequence method depending on the way in which
you are using the parser and/or iterator).

Features on a RichSequence are all instances of RichFeature.

Locations for RichFeatures are all instances of RichLocation.

If you cast appropriately (or locate and find the getRich* equivalents
of the get* methods you already using on the non-Rich interfaces) then
you will find that RichLocation does have a getStrand method which will
give you the information you need.

cheers,
Richard

michael walsh wrote:
> BioJava,
> 
> I am writing a program that extracts features from a Genbank file using
> BioJava The program needs to extract the feature locations from the file.
> This is easy enough to do but the location information returned by the
> program does not specify whether or not the location is on the complementary
> strand of DNA.
> 
> This is some of my code:
> FeatureHolder fltrHold = seq.filter(codeFltr);//codeFltr is a filter that
> retrieves coding features only.
>         //iterate over the Features in fh
>         for (Iterator i = fltrHold.features(); i.hasNext(); ){
>             Feature f = (Feature)i.next();
>             System.out.println(f.getLocation().toString());
> 
> An example of the output of the print command is:
> join:[32775..32948,31801..32052]
> 
> However, the entry in the Genbank file reads:
> complement(join(31801..32052,32775..32948))
> 
> Is there any way to get my program to output the fact that a features
> location is on the complementary strand of DNA?
> 
> Any help that anyone can give me would be greatly appreciated.
> 
> Sincerely,
> 
> M Walsh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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From felipe.albrecht at gmail.com  Thu Jan 24 05:47:37 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Thu, 24 Jan 2008 05:47:37 -0000
Subject: [Biojava-dev] Pairwise Alignment methods
In-Reply-To: <93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
References: <f6b04db30801222258s5c79e58at3f29abfc7f685969@mail.gmail.com>
	<93b45ca50801230050t582784b9l732e08311406cc29@mail.gmail.com>
Message-ID: <f6b04db30801232147o16af026bi8104b19de05ba7f5@mail.gmail.com>

Hello,

I think that it can be solved by a simple way:
Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList as
parameters and do no creating a alignment, just the calculating it and
returning the value.

Another thing that is a bit stange for me, is the utilization of garbage
collector direcly, that is: The field "scoreMatrix" is a class field, why at
the end of pairwiseAlignment it is set to null and the garbage collector
run? It is not better (and simpler) to use scoreMatrix as method variable?

I'm annexing the class code with my changes that is doing well the (4^8) *
(4^8) SymbolList pairwise alignments that I am needing :-)

Thank you,

Felipe Albrecht



On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> I agree this is a barrier to ease of use. Even if Sequences are
> required internally for some obscure reason there is no reason why
> dummy Sequences cannot be made inside the aligner.  These sequences
> could be given names like 'query' and 'subject' or even 'seq1' and
> 'seq2'.
>
> I will take a look at adding some methods.
>
> Best regards,
>
> - Mark
>
> On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello all,
> >
> > I have a simple question about pairwise alignment classes (SmithWaterman
> and
> > NeedlemanWunsch):
> > Why it is necessary two Sequence for alignment and not two SymbolList?
> >
> > Example, I have a SymbolList collection to align between then,
> > by this way I need to create some "dummies"  Sequence for to do the
> > alignment.
> >
> > Reading the source, I saw that the unique field that is exclusive to
> > Sequence is the name, for the alignment output,
> > but if I need only the alignment result, it is useless.
> >
> > It is not possible to override the pairwiseAlignment to accept
> SymbolList or
> > may be a new method that the parameters are 2 SymbolList and returns the
> > alignment score?
> >
> > Thank you
> >
> > Felipe Albrecht
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
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