From juberpatel at gmail.com  Mon Nov 10 08:54:43 2008
From: juberpatel at gmail.com (juber patel)
Date: Mon, 10 Nov 2008 19:24:43 +0530
Subject: [Biojava-dev] want to contribute...
Message-ID: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>

Hello people,

i have been lurking for long on this list, hoping that i would be able
to contribute soon.
now that version 3 has been started from the scratch i think this is
the best time to get involved as a programmer.
it may not be easy given my day job, but please give me some ideas. is
there a web page or document about biojava 3 ?

-- 
Juber Patel        http://juberpatel.googlepages.com

From holland at eaglegenomics.com  Mon Nov 10 09:02:19 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 10 Nov 2008 14:02:19 +0000
Subject: [Biojava-dev] want to contribute...
In-Reply-To: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>
References: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>
Message-ID: <a0d826f40811100602q325f8390id297d16f72bbb345@mail.gmail.com>

Thanks for joining in!

The general idea is here:

Right now we could do with an implementation of a decent Blast parser,
that parsed the entire Blast XML format into an appropriate object
model that reflected the XML format.

cheers,
Richard

2008/11/10 juber patel <juberpatel at gmail.com>:
> Hello people,
>
> i have been lurking for long on this list, hoping that i would be able
> to contribute soon.
> now that version 3 has been started from the scratch i think this is
> the best time to get involved as a programmer.
> it may not be easy given my day job, but please give me some ideas. is
> there a web page or document about biojava 3 ?
>
> --
> Juber Patel        http://juberpatel.googlepages.com
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From Ekta.Jain at icr.ac.uk  Tue Nov 11 14:02:55 2008
From: Ekta.Jain at icr.ac.uk (Ekta Jain)
Date: Tue, 11 Nov 2008 19:02:55 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
Message-ID: <s919d703.055@groupwise.icr.ac.uk>

Hello All,

Wondering if BioJava has a PID xml parser ?? PID format is mainly used
for pathway data such as provided from NCI.

Many Thanks

Ekta

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

From holland at eaglegenomics.com  Tue Nov 11 14:40:31 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 11 Nov 2008 19:40:31 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
In-Reply-To: <s919d703.053@groupwise.icr.ac.uk>
References: <s919d703.053@groupwise.icr.ac.uk>
Message-ID: <a0d826f40811111140k6931029emd6510aa80fb86593@mail.gmail.com>

Not that I'm aware of, unless it's very well hidden!

If you end up writing one for yourself, would you consider
contributing it back to BioJava for others to use? Such additions are
always very welcome and appreciated.

cheers,
Richard

2008/11/11 Ekta Jain <Ekta.Jain at icr.ac.uk>:
> Hello All,
>
> Wondering if BioJava has a PID xml parser ?? PID format is mainly used
> for pathway data such as provided from NCI.
>
> Many Thanks
>
> Ekta
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From Ekta.Jain at icr.ac.uk  Tue Nov 11 15:29:07 2008
From: Ekta.Jain at icr.ac.uk (Ekta Jain)
Date: Tue, 11 Nov 2008 20:29:07 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
Message-ID: <s919eb3a.028@groupwise.icr.ac.uk>

Absolutely :). Wil get back to find out how the code can be added to
Biojava once its ready.

Many Thanks

Ekta

>>> "Richard Holland" <holland at eaglegenomics.com> 11/11/08 7:40 PM >>>
Not that I'm aware of, unless it's very well hidden!

If you end up writing one for yourself, would you consider
contributing it back to BioJava for others to use? Such additions are
always very welcome and appreciated.

cheers,
Richard

2008/11/11 Ekta Jain <Ekta.Jain at icr.ac.uk>:
> Hello All,
>
> Wondering if BioJava has a PID xml parser ?? PID format is mainly used
> for pathway data such as provided from NCI.
>
> Many Thanks
>
> Ekta
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
>
> This e-mail message is confidential and for use by the addressee only.
 If the message is received by anyone other than the addressee, please
return the message to the sender by replying to it and then delete the
message from your computer and network.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

From felipe.albrecht at gmail.com  Sat Nov 15 13:02:11 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 16:02:11 -0200
Subject: [Biojava-dev] Does biojava can calculate evalue ?
In-Reply-To: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>

Hello,

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have
a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht

On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

>
> Dear experts,
>
>  I develop a sequence search program. Now , my program can calculate the
> score value ,and I want to provide a expectation value ( like blast evalue)
> to user. I do not know how to do in this step. Can biojava do it ? Thank you
> in advanced.
>
>
> --
>
>
> Student
>
> _______________________________________________
> 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  Sat Nov 15 13:02:11 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 16:02:11 -0200
Subject: [Biojava-dev] Does biojava can calculate evalue ?
In-Reply-To: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>

Hello,

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have
a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht

On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

>
> Dear experts,
>
>  I develop a sequence search program. Now , my program can calculate the
> score value ,and I want to provide a expectation value ( like blast evalue)
> to user. I do not know how to do in this step. Can biojava do it ? Thank you
> in advanced.
>
>
> --
>
>
> Student
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>

From simpleyrx at 163.com  Sat Nov 15 19:22:23 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Sun, 16 Nov 2008 08:22:23 +0800 (CST)
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
References: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>

 
 I am very interested in the code. Could you send a copy of the code to me ?
thank you.

--


Renxiang Yan

  Ph.D. Candidate Student (2007) 
  E-mail: simpleyrx at 163.com
  Mobile phone:+86-13811458000

  Tel. +86-(0)10-62734412

+86-(0)10-80973092 

 

  Address: College of Biological Sciences,
  China Agricultural University,
  No.2, Yuanmingyuan West Rd.,
  Haidian district, 100094
  Beijing, China


??2008-11-16??"Felipe Albrecht" <felipe.albrecht at gmail.com> ??????
Hello, 

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht


On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

Dear experts,

 I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced.


--


Student

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





From simpleyrx at 163.com  Sat Nov 15 19:22:23 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Sun, 16 Nov 2008 08:22:23 +0800 (CST)
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
References: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>

 
 I am very interested in the code. Could you send a copy of the code to me ?
thank you.

--


Renxiang Yan

  Ph.D. Candidate Student (2007) 
  E-mail: simpleyrx at 163.com
  Mobile phone:+86-13811458000

  Tel. +86-(0)10-62734412

+86-(0)10-80973092 

 

  Address: College of Biological Sciences,
  China Agricultural University,
  No.2, Yuanmingyuan West Rd.,
  Haidian district, 100094
  Beijing, China


??2008-11-16??"Felipe Albrecht" <felipe.albrecht at gmail.com> ??????
Hello, 

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht


On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

Dear experts,

 I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced.


--


Student

_______________________________________________
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  Sat Nov 15 19:57:56 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 22:57:56 -0200
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
	<f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<13860930.332041226794943111.JavaMail.coremail@app143.163.com>
Message-ID: <f6b04db30811151657x54545fcbu30467ffe823c1391@mail.gmail.com>

Hello,

I put the source at http://www.pih.bio.br/src/Statistics.java

if you modify this source, send to me the update version to use it.

Felipe Albrecht

2008/11/15 simpleyrx <simpleyrx at 163.com>

>
>  I am very interested in the code. Could you send a copy of the code to me
> ?
> thank you.
>
> --
>
> Renxiang Yan
>   Ph.D. Candidate Student (2007)
>   E-mail: simpleyrx at 163.com
>   Mobile phone:+86-13811458000
>
>   Tel. +86-(0)10-62734412
>
> +86-(0)10-80973092
>
>
>
>   Address: College of Biological Sciences,
>   China Agricultural University,
>   No.2, Yuanmingyuan West Rd.,
>   Haidian district, 100094
>   Beijing, China
>
> ??2008-11-16??"Felipe Albrecht" <felipe.albrecht at gmail.com> ??????
>
> Hello,
>
> I have a source code in java where I calculate the Evalue, H, K and lambda.
> I only tested the source with nucleotidies and the score matrix should have
> a 1 or -1 in your score.
>
> If it is interesting to someone, I can send it.
>
> Thank you,
>
> Felipe Albrecht
>
> On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:
>
>>
>> Dear experts,
>>
>>  I develop a sequence search program. Now , my program can calculate the
>> score value ,and I want to provide a expectation value ( like blast evalue)
>> to user. I do not know how to do in this step. Can biojava do it ? Thank you
>> in advanced.
>>
>>
>> --
>>
>>
>> Student
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> ------------------------------
> [????] ??????????????-???????? <http://popme.163.com/link/003985_1010_7027.html>


From felipe.albrecht at gmail.com  Sat Nov 15 19:57:56 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 22:57:56 -0200
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
	<f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<13860930.332041226794943111.JavaMail.coremail@app143.163.com>
Message-ID: <f6b04db30811151657x54545fcbu30467ffe823c1391@mail.gmail.com>

Hello,

I put the source at http://www.pih.bio.br/src/Statistics.java

if you modify this source, send to me the update version to use it.

Felipe Albrecht

2008/11/15 simpleyrx <simpleyrx at 163.com>

>
>  I am very interested in the code. Could you send a copy of the code to me
> ?
> thank you.
>
> --
>
> Renxiang Yan
>   Ph.D. Candidate Student (2007)
>   E-mail: simpleyrx at 163.com
>   Mobile phone:+86-13811458000
>
>   Tel. +86-(0)10-62734412
>
> +86-(0)10-80973092
>
>
>
>   Address: College of Biological Sciences,
>   China Agricultural University,
>   No.2, Yuanmingyuan West Rd.,
>   Haidian district, 100094
>   Beijing, China
>
> ??2008-11-16??"Felipe Albrecht" <felipe.albrecht at gmail.com> ??????
>
> Hello,
>
> I have a source code in java where I calculate the Evalue, H, K and lambda.
> I only tested the source with nucleotidies and the score matrix should have
> a 1 or -1 in your score.
>
> If it is interesting to someone, I can send it.
>
> Thank you,
>
> Felipe Albrecht
>
> On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:
>
>>
>> Dear experts,
>>
>>  I develop a sequence search program. Now , my program can calculate the
>> score value ,and I want to provide a expectation value ( like blast evalue)
>> to user. I do not know how to do in this step. Can biojava do it ? Thank you
>> in advanced.
>>
>>
>> --
>>
>>
>> Student
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> ------------------------------
> [????] ??????????????-???????? <http://popme.163.com/link/003985_1010_7027.html>


From holland at eaglegenomics.com  Tue Nov 18 22:36:27 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 19 Nov 2008 03:36:27 +0000
Subject: [Biojava-dev] BioJava 3 code usage examples
Message-ID: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>

I've posted some brief HOWTOs here on how to use the new code as it progresses:

  http://biojava.org/wiki/BioJava3:HowTo

Hopefully the examples will make the new approach a bit clearer. The
FASTA parser example does need simplifying even further, through a
standard file parser utility class to go in the core module which has
yet to be written. But the examples on the page are a start and show
you what the convenience methods would have to implement internally
(hint, hint!).

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From me at hongyu.org  Wed Nov 19 00:20:07 2008
From: me at hongyu.org (Hongyu Zhang)
Date: Tue, 18 Nov 2008 21:20:07 -0800 (PST)
Subject: [Biojava-dev] BioJava 3 code usage examples
References: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>
Message-ID: <935207.30877.qm@web51405.mail.re2.yahoo.com>

Hi Richard,

Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
"Sequences are perfectly happy as Strings unless you want to do complex
things like store base quality information, and only at that point
should you want to convert them into more complex object models."

 
The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.

Let me know if I missed something. Thanks!

Best,

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750

From holland at eaglegenomics.com  Wed Nov 19 07:00:17 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 19 Nov 2008 12:00:17 +0000
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <935207.30877.qm@web51405.mail.re2.yahoo.com>
References: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>
	<935207.30877.qm@web51405.mail.re2.yahoo.com>
Message-ID: <a0d826f40811190400m386d97dasd63d2004dd8fdec5@mail.gmail.com>

Hello.

Thanks for your feedback. You are right that we've continued to
provide a Symbol-based alphabet/symbol structure, but it is no longer
a central concept nor is it required to use it.

You'll notice that when FASTA is read using the new parser, it reads
the sequence from the FASTA file as a simple String (actually, a
CharSequence). If you want to work with it as a String/CharSequence
and don't want to convert it into Symbols/Lists, you can do so. This
is the big change from the existing BioJava way of doing things, which
automatically converts everything into the BioJava object model
instead of giving the user the choice of what to do with it. This
change is consistent with the part of the design document you quote in
your email.

So, this is giving users the choice of whether they want to work with
the sequences directly as Strings/CharSequences, or whether they want
to convert them into Symbols/Lists. Users can then tailor their choice
depending on locally observed speed/memory usage issues should they so
wish.

cheers,
Richard


2008/11/19 Hongyu Zhang <me at hongyu.org>:
> Hi Richard,
>
> Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
> "Sequences are perfectly happy as Strings unless you want to do complex
> things like store base quality information, and only at that point
> should you want to convert them into more complex object models."
>
>
> The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.
>
> Let me know if I missed something. Thanks!
>
> Best,
>
> Hongyu Zhang, Ph.D.
> Ceres Inc., Thousand Oaks, CA
> Cell: 805-405-5394
> Fax: 866-447-8750
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From me at hongyu.org  Thu Nov 20 17:26:07 2008
From: me at hongyu.org (Hongyu Zhang)
Date: Thu, 20 Nov 2008 14:26:07 -0800 (PST)
Subject: [Biojava-dev] BioJava 3 code usage examples
Message-ID: <644724.10477.qm@web51411.mail.re2.yahoo.com>

Hi Richard,

I spent some time reading the codes today. I found that you had packed the biojava3
modules in a different style from the old version. I guess that some of the
reasons are related to the new design philosophy and some are related to the
maven software (I am new to maven). The things that are not clear to me are:

1) It doesn't seem that you want to avoid name conflicts with the old version
because you are continuing using the package name "org.biojava.*"
instead of "org.biojava3.*"

2) The old biojava version arranges sequence related classes in a hierarchical fashion,
while in the new version you put the FASTA parsing classes directly under a first level
node "org.biojava.fasta" rather than under the
"org.biojava.seq" as before. There are tens of popular file formats
in the bioinformatics world, so will all of them crowd the first level nodes under
the root package?

3) The source files are now in much deeper paths now, for example for
the FASTA parser, the path is "src/main/java/org/biojava/fasta",
as opposed to the common style "src/org/biojava/fasta", so I am
wondering why it is necessary to add "main/java" in the middle of the
path.

4) It is interesting to see that you put the source codes of all the
sub-packages separately, so whenever I need to browse the codes of some related classes
in Windows explorer or Unix shell, I really need to go up and down by clicking or typing many more times.
Netbean IDE alleviated this problem a little bit. I understand the idea of seperating independent packages in the new design, but I am wondering whether the current very fine seperation of classes went too far.

I am not familiar with the new design, so forgive my ignorance. Thanks for your
time.

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750




________________________________
From: Hongyu Zhang <me at hongyu.org>
To: holland at eaglegenomics.com
Sent: Wednesday, November 19, 2008 10:55:06 AM
Subject: Re: [Biojava-dev] BioJava 3 code usage examples


Thanks for the quick response, Richard. I will dive deeper into your codes. 

 Best,

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750




________________________________
From: Richard Holland <holland at eaglegenomics.com>
To: Hongyu Zhang <me at hongyu.org>
Cc: biojava-dev <biojava-dev at lists.open-bio.org>
Sent: Wednesday, November 19, 2008 4:00:17 AM
Subject: Re: [Biojava-dev] BioJava 3 code usage examples

Hello.

Thanks for your feedback. You are right that we've continued to
provide a Symbol-based alphabet/symbol structure, but it is no longer
a central concept nor is it required to use it.

You'll notice that when FASTA is read using the new parser, it reads
the sequence from the FASTA file as a simple String (actually, a
CharSequence). If you want to work with it as a String/CharSequence
and don't want to convert it into Symbols/Lists, you can do so. This
is the big change from the existing BioJava way of doing things, which
automatically converts everything into the BioJava object model
instead of giving the user the choice of what to do with it. This
change is consistent with the part of the design document you quote in
your email.

So, this is giving users the choice of whether they want to work with
the sequences directly as Strings/CharSequences, or whether they want
to convert them into Symbols/Lists. Users can then tailor their choice
depending on locally observed speed/memory usage issues should they so
wish.

cheers,
Richard


2008/11/19 Hongyu Zhang <me at hongyu.org>:
> Hi Richard,
>
> Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
> "Sequences are perfectly happy as Strings unless you want to do complex
> things like store base quality information, and only at that point
> should you want to convert them into more complex object models."
>
>
> The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.
>
> Let me know if I missed something. Thanks!
>
> Best,
>
> Hongyu Zhang, Ph.D.
> Ceres Inc., Thousand Oaks, CA
> Cell: 805-405-5394
> Fax: 866-447-8750
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From holland at eaglegenomics.com  Thu Nov 20 20:02:37 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 20 Nov 2008 20:02:37 -0500
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <644724.10477.qm@web51411.mail.re2.yahoo.com>
References: <644724.10477.qm@web51411.mail.re2.yahoo.com>
Message-ID: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>

Hello. Thanks for spending the time looking into the code. It's a bit
like a virtual code review session for me... you've made some very
useful comments.

> 1) It doesn't seem that you want to avoid name conflicts with the old
> version because you are continuing using the package name "org.biojava.*"
> instead of "org.biojava3.*"

Yes, I agree, I think they should be changed to org.biojava3. I will
do this when I get 5 minutes spare. They should be in org.biojava3
because one of the stated goals was to be able to write a
biojava-biojava3 mapper module if someone needed that to happen, and
the use of org.biojava in the new code would preclude that.

> 2) The old biojava version arranges sequence related classes in a
> hierarchical fashion, while in the new version you put the FASTA parsing
> classes directly under a first level node "org.biojava.fasta" rather than
> under the "org.biojava.seq" as before. There are tens of popular file
> formats in the bioinformatics world, so will all of them crowd the first
> level nodes under the root package?

That's also a good suggestion. I'll move it. It makes no difference to
the physical structure of the project on disk, but it would make class
and package browsing easier to do, especially in JavaDocs.

> 3) The source files are now in much deeper paths now, for example for the
> FASTA parser, the path is "src/main/java/org/biojava/fasta", as opposed to
> the common style "src/org/biojava/fasta", so I am wondering why it is
> necessary to add "main/java" in the middle of the path.

This is because of Maven. The src folder contains both source code and
test code, and within each you can have multiple programming
languages. The default behaviour, to store source code in a main
folder and test code in a test folder, and under each have a subfolder
for the programming language, seems sensible to me so I went with it.
It also allows the inclusion of resource folders at the same level as
the java folder, the contents of which automatically get built into
the resulting jars as top-level classpath elements.

> 4) It is interesting to see that you put the source codes of all the
> sub-packages separately, so whenever I need to browse the codes of some
> related classes in Windows explorer or Unix shell, I really need to go up
> and down by clicking or typing many more times. Netbean IDE alleviated this
> problem a little bit. I understand the idea of seperating independent
> packages in the new design, but I am wondering whether the current very fine
> seperation of classes went too far.

I did this for clarity's sake as to which source code related to which
module - you can see really easily if they're separated, whereas if
they were all in one tree, it would be hard to know which module a
particular class ended up in. Also if you have one source tree, you
have to remember to update the Maven configs to split different bits
of it into different jars. By simply keeping them separate, this
happens automatically.

Thanks again for your feedback!

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From mark.schreiber at novartis.com  Thu Nov 20 22:40:53 2008
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 21 Nov 2008 11:40:53 +0800
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>
Message-ID: <OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>

biojava-dev-bounces at lists.open-bio.org wrote on 11/21/2008 09:02:37 AM:

> Hello. Thanks for spending the time looking into the code. It's a bit
> like a virtual code review session for me... you've made some very
> useful comments.
> 
> > 1) It doesn't seem that you want to avoid name conflicts with the old
> > version because you are continuing using the package name 
"org.biojava.*"
> > instead of "org.biojava3.*"
> 
> Yes, I agree, I think they should be changed to org.biojava3. I will
> do this when I get 5 minutes spare. They should be in org.biojava3
> because one of the stated goals was to be able to write a
> biojava-biojava3 mapper module if someone needed that to happen, and
> the use of org.biojava in the new code would preclude that.
> 

I think it would be a very good idea to differentiate this from old code 
via the packages. Strictly speaking you are supposed to use a domain that 
you own. I don't know if biojava3.org is available or if open-bio wants to 
obtain it. It's not critical but it would prevent possible issues.

Alternatives would be to use org.biojava.v3.*

or you could use the open-bio domain as in org.open-bio.biojava3

- Mark

_________________________

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From holland at eaglegenomics.com  Thu Nov 20 22:57:24 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 20 Nov 2008 22:57:24 -0500
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>
References: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>
	<OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>
Message-ID: <a0d826f40811201957x441b495bia8b56c2df953e6dc@mail.gmail.com>

I like the domain registration idea better. I'll find out what the
folks at open-bio think.

cheers,
Richard

2008/11/20  <mark.schreiber at novartis.com>:
>
> biojava-dev-bounces at lists.open-bio.org wrote on 11/21/2008 09:02:37 AM:
>
>> Hello. Thanks for spending the time looking into the code. It's a bit
>> like a virtual code review session for me... you've made some very
>> useful comments.
>>
>> > 1) It doesn't seem that you want to avoid name conflicts with the old
>> > version because you are continuing using the package name
>> > "org.biojava.*"
>> > instead of "org.biojava3.*"
>>
>> Yes, I agree, I think they should be changed to org.biojava3. I will
>> do this when I get 5 minutes spare. They should be in org.biojava3
>> because one of the stated goals was to be able to write a
>> biojava-biojava3 mapper module if someone needed that to happen, and
>> the use of org.biojava in the new code would preclude that.
>>
>
> I think it would be a very good idea to differentiate this from old code via
> the packages. Strictly speaking you are supposed to use a domain that you
> own. I don't know if biojava3.org is available or if open-bio wants to
> obtain it. It's not critical but it would prevent possible issues.
>
> Alternatives would be to use org.biojava.v3.*
>
> or you could use the open-bio domain as in org.open-bio.biojava3
>
> - Mark
>
> _________________________
>
> CONFIDENTIALITY NOTICE
>
> The information contained in this e-mail message is intended only for the
> exclusive use of the individual or entity named above and may contain
> information that is privileged, confidential or exempt from disclosure under
> applicable law. If the reader of this message is not the intended recipient,
> or the employee or agent responsible for delivery of the message to the
> intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If you
> have received this communication in error, please notify the sender
> immediately by e-mail and delete the material from any computer.  Thank you.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 05:48:59 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:48:59 -0500
Subject: [Biojava-dev] [Bug 2679] New: NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
Message-ID: <bug-2679-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679

           Summary: NEXUS parse fails on extraneous comma (TREES/TRANSLATE)
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P1
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keesey at gmail.com


If the last item in a TRANSLATE command of a TREES node ends with a comma, the
parser fails with the following exception:

Error: org.biojava.bio.seq.io.ParseException: Found unexpected token = in TREES
block

A properly-formatted NEXUS file should not have a comma here, but there are
many files which do. The parser should see the semicolon and assume the command
is is ended.

Example TREES block (from TREEBase, accession M474):

BEGIN TREES;

[! 1 trees. TreeBASE accession#: Tree1118 ]
        TRANSLATE
                1       'Nyctereutes_procyonoides',
                2       'Urocyon_cinereoargenteus',
                3       'Pseudalopex_gymnocercus',
                4       'Chrysocyon_brachyurus',
                5       'Pseudalopex_sechurae',
                6       'Pseudalopex_culpaeus',
                7       'Pseudalopex_vetulus',
                8       'Atelocynus_microtis',
                9       'Pseudalopex_griseus',
                10      'Dusicyon_australis',
                11      'Urocyon_littoralis',
                12      'Vulpes_bengalensis',
                13      'Speothos_venaticus',
                14      'Otocyon_megalotis',
                15      'Vulpes_ferrilata',
                16      'Vulpes_rueppelli',
                17      'Canis_mesomelas',
                18      'Cerdocyon_thous',
                19      'Alopex_lagopus',
                20      'Vulpes_pallida',
                21      'Canis_simensis',
                22      'Vulpes_corsac',
                23      'Canis_latrans',
                24      'Lycaon_pictus',
                25      'Canis_adustus',
                26      'Vulpes_vulpes',
                27      'Vulpes_chama',
                28      'Vulpes_velox',
                29      'Vulpes_zerda',
                30      'Canis_aureus',
                31      'Cuon_alpinus',
                32      'Pseudalopex',
                33      'Canis_rufus',
                34      'Vulpes_cana',
                35      'Canis_lupus',
                36      'Canidae',
                37      'Canis',
        ;
        TREE 'Fig._9' =  [&R]
(((((((19,28),((22,15),(16,26))),(34,29)),(12,27,20)),(2,11)),14),((8,(((25,30),17),(23,(35,33),21)),18,4,31,(10,((6,9,3,5),7)),24,13),1));


END;


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 05:49:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:49:45 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211049.mALAnjes020244@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #1 from keesey at gmail.com  2008-11-21 05:49 EST -------
The next comment is the full NEXUS file from the example.


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 05:50:10 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:50:10 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211050.mALAoAwx020305@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #2 from keesey at gmail.com  2008-11-21 05:50 EST -------
#NEXUS
[File created by TreeBASE:  1/29/99  19:24:10]
[Matrix accession#: M474]
BEGIN DATA;
DIMENSIONS  NTAX=34 NCHAR=223;

[!This data set was downloaded from TreeBASE, a prototype relational database
of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard
University, and UC Davis. Please do not remove this acknowledgment from the
Nexus file. 
TreeBASE ?? 1994-1999.

Study reference: 
Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building larger
phylogenies using supertrees: a complete phylogeny of the extant Carnivora
(Mammalia). Biological Reviews, in press. 

Study accession number = S355
Matrix accession number = M474
]
FORMAT MISSING = ? GAP = -   INTERLEAVE ;
MATRIX

'Vulpes_zerda'                
1?000111000????0000?1100000000?1001???????001100000?????10000000000000111000??????1000000????????111
'Vulpes_vulpes'               
1?110000000?00??????1100000000?1001???????110000000?1???10000000000000110101??????1100000???0000?110
'Vulpes_velox'                
1?111000000????0000?1100000000?1001???????110000000?????10000000000000110110??????1100000????????110
'Vulpes_rueppelli'            
1???????????????????1100000000?1001???????110000000?????10000000000000110101??????1100000????????110
'Vulpes_pallida'              
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_ferrilata'            
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_corsac'               
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000????????110
'Vulpes_chama'                
1???????????????????1100000000?1001???????110000000?????10000000000000110000??????1100000????????100
'Vulpes_cana'                 
1???????????????????1100000000?1001???????110000000?????10000000000000111000??????1100000????????111
'Vulpes_bengalensis'          
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Urocyon_littoralis'          
1??????????????????????????????1001???????001110000???????????????????????????????1010000???????????
'Urocyon_cinereoargenteus'    
1?000110000?????????1010000000?1001?0?000?001110000?????00000000000000000000??????1010000?0?1000?000
'Speothos_venaticus'          
1?000100111?????????0001100110?0000?????????????????????11100011100000000000?1100?0001000???????????
'Pseudalopex_vetulus'         
1???????????????????0001111000?1000???????001001010??????????????????????????0000?0001000???????????
'Pseudalopex_sechurae'        
1???????????????????0001111000?1010???????001001010??????????????????????????0010?0001101???????????
'Pseudalopex_gymnocercus'     
1???????????????????0001111000?1010???????001001010?????11111000000000000000?0010?0001101???????????
'Pseudalopex_griseus'         
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0010?0001101???????????
'Pseudalopex_culpaeus'        
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0011?0001101???????????
'Otocyon_megalotis'           
1?000111000?????????1010000000?0000???????100000000?????11000000000000000000??????1000000???????????
'Nyctereutes_procyonoides'    
1?100000000?????????0001100101?0000???????100000000?1???10000000000000100000????????????????????????
'Lycaon_pictus'               
1??????????????1000????????????0000???000???????????????11100011100000000000??????0001000???1110????
'Dusicyon_australis'          
1???????????????????0001110000?1000???????001001010??????????????????????????0011?0001100???????????
'Cuon_alpinus'                
1??????????????????????????????0000?????????????????????11100010010000000000??????0001000???????????
'Chrysocyon_brachyurus'       
1?000100110?????????0001000000?0000???????001001100?????11100011000000000000?0000?0001000???????????
'Cerdocyon_thous'             
1?000100111?????????0001100101?1000?????????????????????11110000000000000000?1000?0001000???????????
'Canis_simensis'              
1??????????????????????????????1100???111?001000001???0?11100010011011000000??????0001110???????????
'Canis_rufus'                 
1??????????????????????????????1100???????001000001???0???????????????????????????0001110???????????
'Canis_mesomelas'             
1???????????10?1100????????????1100???100?001000001???0?11100010010000000000??????0001110???????????
'Canis_lupus'                 
1?000100100?11?1111????????????1100?1?111?001000001?0?1?11100010011010000000??????0001110?1?1111????
'Canis_latrans'               
1???????????11?1111????????????1100?1?111?001000001???1?11100010011011000000??????0001110?1?1111????
'Canis_aureus'                
1??????????????1110????????????1100???110?001000001???0?11100010011100000000??????0001110???1100????
'Canis_adustus'               
1??????????????1000????????????1100???000?001000001???0?11100010011100000000??????0001110???????????
'Atelocynus_microtis'         
1???????????????????0001100110?1000???????001001100??????????????????????????1100?0001000???????????
'Alopex_lagopus'              
1?111000000????????????????????1000???????110000000?????10000000000000110110??????1000000????????110


'Vulpes_zerda'                
0000?11111000?11110000?00000010??????????10000?01???????????????????100000?????0001?1000001010000000
'Vulpes_vulpes'               
1011?11110100?11101101?00000010????????????????01?0000110???00001???100010?????0001?1000001000000000
'Vulpes_velox'                
1100?11110111?11101110?00000011????????????????01???????????00001???100010?????0001?1000001000000000
'Vulpes_rueppelli'            
1011?11110110?11101101?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_pallida'              
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_ferrilata'            
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_corsac'               
1010?11110100?11101100?????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_chama'                
0000?11100000?11101000?00000010????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_cana'                 
0000?11111000?11110000?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_bengalensis'          
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Urocyon_littoralis'          
?????????????????????????????????????????11000?01???????????????????100100?????0010?1000001000010000
'Urocyon_cinereoargenteus'    
0000?10000000?10000000?00000000??????????11000?01???????????????????100100?????0010?1000001000010000
'Speothos_venaticus'          
???????????????????????11001000??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Pseudalopex_vetulus'         
???????????????????????11110000??????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_sechurae'        
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_gymnocercus'     
?????????????????????????????????????????00101?01?1100000???????????101000?????0100?1000000000001110
'Pseudalopex_griseus'         
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001100
'Pseudalopex_culpaeus'        
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001110
'Otocyon_megalotis'           
?????11000000?11000000?00000000????????????????00?0000001???????????100000?????0000?0000000000000000
'Nyctereutes_procyonoides'    
???????????????????????00000000????????????????01?0000001???????????100000?????0000?0000000000000000
'Lycaon_pictus'               
???????????????????????11001100??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Dusicyon_australis'          
?????????????????????????????????????????00101?01???????????????????100000?????0000?1000000000001000
'Cuon_alpinus'                
???????????????????????????????????????????????10???????????????????000001?????0000?0000000000000000
'Chrysocyon_brachyurus'       
???????????????????????11100000??????????00100?01?0000100???????????100000?????0000?0000000000000000
'Cerdocyon_thous'             
???????????????????????11110000????????????????01???????????????????100000?????0000?1000000000001000
'Canis_simensis'              
?????????????????????????????????????????00110?01???????????????????110000?????1000?1110000000000000
'Canis_rufus'                 
??????????????????????????????????100?10?00110?01?????????1?11100?1?110000???1?1000?1100110000000000
'Canis_mesomelas'             
???????????????????????11001000?1?011?11?00110?01?1110000???11010???110000?0???1000?1111000000000000
'Canis_lupus'                 
?????00000000?00000000?11001100?1?100????00110?01?1001000?1?11100?1?110000???1?1000?1100110000000000
'Canis_latrans'               
???????????????????????11001100???010?00?00110?01?1001000???10000?1?110000???1?1000?1100100000000000
'Canis_aureus'                
??????????????????????????????????011?11?00110?01???????????11010?0?110000?1?0?1000?1110000000000000
'Canis_adustus'               
?????????????????????????????????????????00110?01?1110000???11010???110000?1???1000?1111000000000000
'Atelocynus_microtis'         
?????????????????????????????????????????00100?01???????????????????100000?????0000?1000000000001000
'Alopex_lagopus'              
1100?11111111?11101110?00000011?0??????????????01?0000110???00001???100000?????0000?1000001000000000


'Vulpes_zerda'                 ?????????11000000000000
'Vulpes_vulpes'                ?????????11000000000000
'Vulpes_velox'                 ?????????11000000000000
'Vulpes_rueppelli'             ???????????????????????
'Vulpes_pallida'               ?????????11000000000000
'Vulpes_ferrilata'             ????????????????????0??
'Vulpes_corsac'                ?????????11000000000000
'Vulpes_chama'                 ?????????11000000000000
'Vulpes_cana'                  ???????????????????0???
'Vulpes_bengalensis'           ?????????11000000000000
'Urocyon_littoralis'           ???????????????????????
'Urocyon_cinereoargenteus'     ???0?????10100000000000
'Speothos_venaticus'           ?????????00010001101101
'Pseudalopex_vetulus'          ?????????00010001101000
'Pseudalopex_sechurae'         ?????????00010001000000
'Pseudalopex_gymnocercus'      ?????????00010001000000
'Pseudalopex_griseus'          ?????????00010001000000
'Pseudalopex_culpaeus'         ?????????00010001110000
'Otocyon_megalotis'            ?1???????10100000000000
'Nyctereutes_procyonoides'     ?????????00010001101110
'Lycaon_pictus'                ?0???????00011010000000
'Dusicyon_australis'           ?????????00010001110000
'Cuon_alpinus'                 ?????????00011010000000
'Chrysocyon_brachyurus'        ?????????00010001101000
'Cerdocyon_thous'              ?????????00010001101110
'Canis_simensis'               ?????????00011100000000
'Canis_rufus'                  ?????1?1?00011100000000
'Canis_mesomelas'              ?????????00011100000000
'Canis_lupus'                  ?1?1?1?1?00011100000000
'Canis_latrans'                ???1?1?0?00011100000000
'Canis_aureus'                 ?????????00011100000000
'Canis_adustus'                ?????????00011100000000
'Atelocynus_microtis'          ?????????00010001101101
'Alopex_lagopus'               ?????????11000000000000
;
END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;
BEGIN TREEBASE;
END;

BEGIN TREES;

[! 1 trees. TreeBASE accession#: Tree1118 ]
        TRANSLATE
                1       'Nyctereutes_procyonoides',
                2       'Urocyon_cinereoargenteus',
                3       'Pseudalopex_gymnocercus',
                4       'Chrysocyon_brachyurus',
                5       'Pseudalopex_sechurae',
                6       'Pseudalopex_culpaeus',
                7       'Pseudalopex_vetulus',
                8       'Atelocynus_microtis',
                9       'Pseudalopex_griseus',
                10      'Dusicyon_australis',
                11      'Urocyon_littoralis',
                12      'Vulpes_bengalensis',
                13      'Speothos_venaticus',
                14      'Otocyon_megalotis',
                15      'Vulpes_ferrilata',
                16      'Vulpes_rueppelli',
                17      'Canis_mesomelas',
                18      'Cerdocyon_thous',
                19      'Alopex_lagopus',
                20      'Vulpes_pallida',
                21      'Canis_simensis',
                22      'Vulpes_corsac',
                23      'Canis_latrans',
                24      'Lycaon_pictus',
                25      'Canis_adustus',
                26      'Vulpes_vulpes',
                27      'Vulpes_chama',
                28      'Vulpes_velox',
                29      'Vulpes_zerda',
                30      'Canis_aureus',
                31      'Cuon_alpinus',
                32      'Pseudalopex',
                33      'Canis_rufus',
                34      'Vulpes_cana',
                35      'Canis_lupus',
                36      'Canidae',
                37      'Canis',
        ;
        TREE 'Fig._9' =  [&R]
(((((((19,28),((22,15),(16,26))),(34,29)),(12,27,20)),(2,11)),14),((8,(((25,30),17),(23,(35,33),21)),18,4,31,(10,((6,9,3,5),7)),24,13),1));


END;


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 05:51:52 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:51:52 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211051.mALApqKl020508@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #3 from keesey at gmail.com  2008-11-21 05:51 EST -------
version is 1.6 (no place to specifiy that)


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From bugzilla-daemon at portal.open-bio.org  Tue Nov 25 18:31:57 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 25 Nov 2008 18:31:57 -0500
Subject: [Biojava-dev] [Bug 2687] New: UniProt: Tags in feature continuation
	lines may be lost.
Message-ID: <bug-2687-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2687

           Summary: UniProt: Tags in feature continuation lines may be lost.
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: jan at biochemfusion.com


Using BioJava 1.6.1 on Windows XP to read in a UniProt file and write it back
out. Main code that does this:

        BufferedReader br = new BufferedReader(new FileReader(args[0]));
        SimpleNamespace ns = new SimpleNamespace("biojava");

        RichSequenceIterator rsi = RichSequence.IOTools.readUniProt(br, ns);
        RichSequence rs = rsi.nextRichSequence();
        RichSequence.IOTools.writeUniProt(System.out, rs, ns);

When reading in this heavily abridged version of FA9_BOVIN from www.uniprot.org
it works:

ID   FA9_BOVIN               Reviewed;         416 AA.
AC   P00741;
FT   CHAIN         1    416       Coagulation factor IX.
FT   CARBOHYD     53     53       O-linked (Glc...).
FT                                /FTId=CAR_000008.
FT                                Extra information.
SQ   SEQUENCE   416 AA;  46785 MW;  34A7DFE916330662 CRC64;
     YNSGKLEEFV RGNLERECKE EKCSFEEARE VFENTEKTTE FWKQYVDGDQ CESNPCLNGG
     MCKDDINSYE CWCQAGFEGT NCELDATCSI KNGRCKQFCK RDTDNKVVCS CTDGYRLAED
     QKSCEPAVPF PCGRVSVSHI SKKLTRAETI FSNTNYENSS EAEIIWDNVT QSNQSFDEFS
     RVVGGEDAER GQFPWQVLLH GEIAAFCGGS IVNEKWVVTA AHCIKPGVKI TVVAGEHNTE
     KPEPTEQKRN VIRAIPYHSY NASINKYSHD IALLELDEPL ELNSYVTPIC IADRDYTNIF
     SKFGYGYVSG WGKVFNRGRS ASILQYLKVP LVDRATCLRS TKFSIYSHMF CAGYHEGGKD
     SCQGDSGGPH VTEVEGTSFL TGIISWGEEC AMKGKYGIYT KVSRYVNWIK EKTKLT
//

However, when the extra information has been tagged with a slash it is lost:

ID   FA9_BOVIN               Reviewed;         416 AA.
AC   P00741;
FT   CHAIN         1    416       Coagulation factor IX.
FT   CARBOHYD     53     53       O-linked (Glc...).
FT                                /FTId=CAR_000008.
FT                                /NB=Extra information.
SQ   SEQUENCE   416 AA;  46785 MW;  34A7DFE916330662 CRC64;
     YNSGKLEEFV RGNLERECKE EKCSFEEARE VFENTEKTTE FWKQYVDGDQ CESNPCLNGG
     MCKDDINSYE CWCQAGFEGT NCELDATCSI KNGRCKQFCK RDTDNKVVCS CTDGYRLAED
     QKSCEPAVPF PCGRVSVSHI SKKLTRAETI FSNTNYENSS EAEIIWDNVT QSNQSFDEFS
     RVVGGEDAER GQFPWQVLLH GEIAAFCGGS IVNEKWVVTA AHCIKPGVKI TVVAGEHNTE
     KPEPTEQKRN VIRAIPYHSY NASINKYSHD IALLELDEPL ELNSYVTPIC IADRDYTNIF
     SKFGYGYVSG WGKVFNRGRS ASILQYLKVP LVDRATCLRS TKFSIYSHMF CAGYHEGGKD
     SCQGDSGGPH VTEVEGTSFL TGIISWGEEC AMKGKYGIYT KVSRYVNWIK EKTKLT
//

BioPerl 1.5.2 copes with both situtations without problems.


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From bugzilla-daemon at portal.open-bio.org  Tue Nov 25 18:35:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 25 Nov 2008 18:35:42 -0500
Subject: [Biojava-dev] [Bug 2687] UniProt: Tags in feature continuation
	lines may be lost.
In-Reply-To: <bug-2687-485@http.bugzilla.open-bio.org/>
Message-ID: <200811252335.mAPNZg6D004170@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2687





------- Comment #1 from jan at biochemfusion.com  2008-11-25 18:35 EST -------
To clarify: In the first case the information in all feature lines is correctly
preserved. In the second case the last FT line "/NB=Extra information." is
lost.


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From holland at eaglegenomics.com  Wed Nov 26 11:04:56 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 26 Nov 2008 16:04:56 +0000
Subject: [Biojava-dev] BugZilla!
Message-ID: <492D73A8.4020401@eaglegenomics.com>

Hi all,

There's been a few new bugs reported on BugZilla recently. Whilst the
development of the new BJ features is fun, it's really important to
maintain the existing code and keep on top of the issues reported.

If there's anyone with a few minutes spare, or would like to learn
BioJava and don't know where to start - then zapping a few virtual
creepy crawlies is an excellent way to get involved and make a contribution.

Here's the list of the currently outstanding problems:

http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED

If you see one you think you can fix, or might like to try to
investigate, go for it! All you have to do is assign the bug to yourself
in order to take ownership of it so that people don't end up working on
the same thing without knowing.

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From bugzilla-daemon at portal.open-bio.org  Wed Nov 26 12:44:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 26 Nov 2008 12:44:45 -0500
Subject: [Biojava-dev] [Bug 2603] StringIndexOutOfBoundsException while
	parsing blastresult
In-Reply-To: <bug-2603-485@http.bugzilla.open-bio.org/>
Message-ID: <200811261744.mAQHijbY009725@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2603


tbanks at agr.gc.ca changed:

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




------- Comment #7 from tbanks at agr.gc.ca  2008-11-26 12:44 EST -------
Fixed.  The change to the blast result format (sometime around v2.2.15) made
the parser unable to determine where the end of one result finished and the
next began.  Now the code can recognize the two ways a result can end; the
start of a new result or the statistics for the blast and database.


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From mark.schreiber at novartis.com  Wed Nov 26 21:33:05 2008
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 27 Nov 2008 10:33:05 +0800
Subject: [Biojava-dev] [Biojava-l] BugZilla!
In-Reply-To: <492D73A8.4020401@eaglegenomics.com>
Message-ID: <OF05FA111C.951667E1-ON4825750E.000D7781-4825750E.000E04E1@ah.novartis.com>

Hi -

I would concur with this. BioJava is volunteer based and requires people 
to volunteer before things happen.

In my experience bug reports get resolved most rapidly if the person 
reporting the bug can do as much of their own investigation as possible. 
Have a good look at the stack trace and try using a debugger. You can 
rapidly narrow down the underlying cause. Even if you are not confident 
about the best way to fix the problem, armed with all the relevant 
information someone more experienced will be able to tell you if you are 
on the right track.

Unit tests are also good here. For one thing they will set-up a situation 
to replicate your bug. They will also provide a way to make sure the bug 
doesn't happen again in future releases.  Finally, the more unit tests 
there are the more confident you can be that your proposed bug fix won't 
break anything else.

Helping fix stuff in BioJava will definitely improve you're programming 
skills and greatly increase your knowledge of how the API works so by 
helping others you are probably helping yourself more.

- Mark

biojava-l-bounces at lists.open-bio.org wrote on 11/27/2008 12:04:56 AM:

> Hi all,
> 
> There's been a few new bugs reported on BugZilla recently. Whilst the
> development of the new BJ features is fun, it's really important to
> maintain the existing code and keep on top of the issues reported.
> 
> If there's anyone with a few minutes spare, or would like to learn
> BioJava and don't know where to start - then zapping a few virtual
> creepy crawlies is an excellent way to get involved and make a 
contribution.
> 
> Here's the list of the currently outstanding problems:
> 
> http://bugzilla.open-bio.org/buglist.cgi?
> product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED
> 
> If you see one you think you can fix, or might like to try to
> investigate, go for it! All you have to do is assign the bug to yourself
> in order to take ownership of it so that people don't end up working on
> the same thing without knowing.
> 
> cheers,
> Richard
> 
> -- 
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> M: +44 7500 438846 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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From talk2ali at gmail.com  Fri Nov 21 20:38:26 2008
From: talk2ali at gmail.com (Muhammad Ali)
Date: Fri, 21 Nov 2008 20:38:26 -0500
Subject: [Biojava-dev] NCBI Blast XML Parser update
In-Reply-To: <59a41c430808191936sb139efcwff92065cffe8f49@mail.gmail.com>
References: <e1a332c90808190610l481cfbd6x8e664aaaedf5629b@mail.gmail.com>
	<59a41c430808191936sb139efcwff92065cffe8f49@mail.gmail.com>
Message-ID: <e1a332c90811211738g7f6d95c0lfb566fed926754a6@mail.gmail.com>

Hi,

Sorry for the delay, I got caught up with my other project. Anyway,
I'm here now and I've attached the patch file with this email. Please
take a look and let me know if changes are required.

With regards to testing, there is a BlastParser.java file in the
/demos/blastxml folder that I've been using to test on my end. It
takes a Blast output file as its input. If you want, I can provide
some Blast output file with multiple iteration entries for use as a
sample input file for testing.

I think I'll do without SVN write access. I don't expect to be working
on other parts of biojava right now, unless someone else in my lab
complains about something else being broken ;). But if I do make any
local patches, I'll definitely try and get them back to you guys.

Cheers,
Ali.

On Tue, Aug 19, 2008 at 9:36 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Ali,
>
> that's good news, can you send your patch to this list, so we can have
> a look? At this stage it would be also great to provide a new Junit
> test that makes sure that the parsing works ok and to demonstrate the
> new feature. If you provide more patches in the future we can also set
> up write access to the SVN repository.
>
> Andreas
>
> On Tue, Aug 19, 2008 at 6:10 AM, Muhammad Ali <talk2ali at gmail.com> wrote:
>> Hello,
>>
>> The current version of the BlastXMLParser (used for parsing NCBI BLAST
>> output files) is not handling multiple Iteration entries in the file
>> correctly. It lumps them all together, resulting in a loss of
>> search-specific parameters. The end result is a single
>> SeqSimilaritySearchResult object. The expected output should be one
>> SeqSimilaritySearchResult for each Iteration entry in the file.
>>
>> I've fixed this issue on my locally checked out copy by modifying a
>> few files in the  org.biojava.bio.program.sax.blastxml package. I'm
>> interested in submitting the updated code back to the main repository.
>> Can someone tell me how I can go about doing so?
>>
>> Also the javadocs for the BlastXMLParser seem to be outdated. They
>> mention malformed XML being generated by NCBI, but that doesn't seem
>> to be the case anymore.
>>
>> Thanks,
>> Ali.
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
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From juberpatel at gmail.com  Mon Nov 10 13:54:43 2008
From: juberpatel at gmail.com (juber patel)
Date: Mon, 10 Nov 2008 19:24:43 +0530
Subject: [Biojava-dev] want to contribute...
Message-ID: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>

Hello people,

i have been lurking for long on this list, hoping that i would be able
to contribute soon.
now that version 3 has been started from the scratch i think this is
the best time to get involved as a programmer.
it may not be easy given my day job, but please give me some ideas. is
there a web page or document about biojava 3 ?

-- 
Juber Patel        http://juberpatel.googlepages.com


From holland at eaglegenomics.com  Mon Nov 10 14:02:19 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 10 Nov 2008 14:02:19 +0000
Subject: [Biojava-dev] want to contribute...
In-Reply-To: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>
References: <f8e28e170811100554t12d7d7e3q956353c7a0d4017e@mail.gmail.com>
Message-ID: <a0d826f40811100602q325f8390id297d16f72bbb345@mail.gmail.com>

Thanks for joining in!

The general idea is here:

Right now we could do with an implementation of a decent Blast parser,
that parsed the entire Blast XML format into an appropriate object
model that reflected the XML format.

cheers,
Richard

2008/11/10 juber patel <juberpatel at gmail.com>:
> Hello people,
>
> i have been lurking for long on this list, hoping that i would be able
> to contribute soon.
> now that version 3 has been started from the scratch i think this is
> the best time to get involved as a programmer.
> it may not be easy given my day job, but please give me some ideas. is
> there a web page or document about biojava 3 ?
>
> --
> Juber Patel        http://juberpatel.googlepages.com
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From Ekta.Jain at icr.ac.uk  Tue Nov 11 19:02:55 2008
From: Ekta.Jain at icr.ac.uk (Ekta Jain)
Date: Tue, 11 Nov 2008 19:02:55 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
Message-ID: <s919d703.055@groupwise.icr.ac.uk>

Hello All,

Wondering if BioJava has a PID xml parser ?? PID format is mainly used
for pathway data such as provided from NCI.

Many Thanks

Ekta

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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From holland at eaglegenomics.com  Tue Nov 11 19:40:31 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 11 Nov 2008 19:40:31 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
In-Reply-To: <s919d703.053@groupwise.icr.ac.uk>
References: <s919d703.053@groupwise.icr.ac.uk>
Message-ID: <a0d826f40811111140k6931029emd6510aa80fb86593@mail.gmail.com>

Not that I'm aware of, unless it's very well hidden!

If you end up writing one for yourself, would you consider
contributing it back to BioJava for others to use? Such additions are
always very welcome and appreciated.

cheers,
Richard

2008/11/11 Ekta Jain <Ekta.Jain at icr.ac.uk>:
> Hello All,
>
> Wondering if BioJava has a PID xml parser ?? PID format is mainly used
> for pathway data such as provided from NCI.
>
> Many Thanks
>
> Ekta
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From Ekta.Jain at icr.ac.uk  Tue Nov 11 20:29:07 2008
From: Ekta.Jain at icr.ac.uk (Ekta Jain)
Date: Tue, 11 Nov 2008 20:29:07 +0000
Subject: [Biojava-dev] Does BioJava have a PID parser?
Message-ID: <s919eb3a.028@groupwise.icr.ac.uk>

Absolutely :). Wil get back to find out how the code can be added to
Biojava once its ready.

Many Thanks

Ekta

>>> "Richard Holland" <holland at eaglegenomics.com> 11/11/08 7:40 PM >>>
Not that I'm aware of, unless it's very well hidden!

If you end up writing one for yourself, would you consider
contributing it back to BioJava for others to use? Such additions are
always very welcome and appreciated.

cheers,
Richard

2008/11/11 Ekta Jain <Ekta.Jain at icr.ac.uk>:
> Hello All,
>
> Wondering if BioJava has a PID xml parser ?? PID format is mainly used
> for pathway data such as provided from NCI.
>
> Many Thanks
>
> Ekta
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
>
> This e-mail message is confidential and for use by the addressee only.
 If the message is received by anyone other than the addressee, please
return the message to the sender by replying to it and then delete the
message from your computer and network.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.


From felipe.albrecht at gmail.com  Sat Nov 15 18:02:11 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 16:02:11 -0200
Subject: [Biojava-dev] Does biojava can calculate evalue ?
In-Reply-To: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>

Hello,

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have
a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht

On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

>
> Dear experts,
>
>  I develop a sequence search program. Now , my program can calculate the
> score value ,and I want to provide a expectation value ( like blast evalue)
> to user. I do not know how to do in this step. Can biojava do it ? Thank you
> in advanced.
>
>
> --
>
>
> Student
>
> _______________________________________________
> 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  Sat Nov 15 18:02:11 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 16:02:11 -0200
Subject: [Biojava-dev] Does biojava can calculate evalue ?
In-Reply-To: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>

Hello,

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have
a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht

On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

>
> Dear experts,
>
>  I develop a sequence search program. Now , my program can calculate the
> score value ,and I want to provide a expectation value ( like blast evalue)
> to user. I do not know how to do in this step. Can biojava do it ? Thank you
> in advanced.
>
>
> --
>
>
> Student
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


From simpleyrx at 163.com  Sun Nov 16 00:22:23 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Sun, 16 Nov 2008 08:22:23 +0800 (CST)
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
References: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>

 
 I am very interested in the code. Could you send a copy of the code to me ?
thank you.

--


Renxiang Yan

  Ph.D. Candidate Student (2007) 
  E-mail: simpleyrx at 163.com
  Mobile phone:+86-13811458000

  Tel. +86-(0)10-62734412

+86-(0)10-80973092 

 

  Address: College of Biological Sciences,
  China Agricultural University,
  No.2, Yuanmingyuan West Rd.,
  Haidian district, 100094
  Beijing, China


?2008-11-16?"Felipe Albrecht" <felipe.albrecht at gmail.com> ???
Hello, 

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht


On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

Dear experts,

 I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced.


--


Student

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






From simpleyrx at 163.com  Sun Nov 16 00:22:23 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Sun, 16 Nov 2008 08:22:23 +0800 (CST)
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
References: <f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
Message-ID: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>

 
 I am very interested in the code. Could you send a copy of the code to me ?
thank you.

--


Renxiang Yan

  Ph.D. Candidate Student (2007) 
  E-mail: simpleyrx at 163.com
  Mobile phone:+86-13811458000

  Tel. +86-(0)10-62734412

+86-(0)10-80973092 

 

  Address: College of Biological Sciences,
  China Agricultural University,
  No.2, Yuanmingyuan West Rd.,
  Haidian district, 100094
  Beijing, China


?2008-11-16?"Felipe Albrecht" <felipe.albrecht at gmail.com> ???
Hello, 

I have a source code in java where I calculate the Evalue, H, K and lambda.
I only tested the source with nucleotidies and the score matrix should have a 1 or -1 in your score.

If it is interesting to someone, I can send it.

Thank you,

Felipe Albrecht


On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:

Dear experts,

 I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced.


--


Student

_______________________________________________
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  Sun Nov 16 00:57:56 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 22:57:56 -0200
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
	<f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<13860930.332041226794943111.JavaMail.coremail@app143.163.com>
Message-ID: <f6b04db30811151657x54545fcbu30467ffe823c1391@mail.gmail.com>

Hello,

I put the source at http://www.pih.bio.br/src/Statistics.java

if you modify this source, send to me the update version to use it.

Felipe Albrecht

2008/11/15 simpleyrx <simpleyrx at 163.com>

>
>  I am very interested in the code. Could you send a copy of the code to me
> ?
> thank you.
>
> --
>
> Renxiang Yan
>   Ph.D. Candidate Student (2007)
>   E-mail: simpleyrx at 163.com
>   Mobile phone:+86-13811458000
>
>   Tel. +86-(0)10-62734412
>
> +86-(0)10-80973092
>
>
>
>   Address: College of Biological Sciences,
>   China Agricultural University,
>   No.2, Yuanmingyuan West Rd.,
>   Haidian district, 100094
>   Beijing, China
>
> ?2008-11-16?"Felipe Albrecht" <felipe.albrecht at gmail.com> ???
>
> Hello,
>
> I have a source code in java where I calculate the Evalue, H, K and lambda.
> I only tested the source with nucleotidies and the score matrix should have
> a 1 or -1 in your score.
>
> If it is interesting to someone, I can send it.
>
> Thank you,
>
> Felipe Albrecht
>
> On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:
>
>>
>> Dear experts,
>>
>>  I develop a sequence search program. Now , my program can calculate the
>> score value ,and I want to provide a expectation value ( like blast evalue)
>> to user. I do not know how to do in this step. Can biojava do it ? Thank you
>> in advanced.
>>
>>
>> --
>>
>>
>> Student
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> ------------------------------
> [??] ???????-???? <http://popme.163.com/link/003985_1010_7027.html>



From felipe.albrecht at gmail.com  Sun Nov 16 00:57:56 2008
From: felipe.albrecht at gmail.com (Felipe Albrecht)
Date: Sat, 15 Nov 2008 22:57:56 -0200
Subject: [Biojava-dev] Reply:Re:  Does biojava can calculate evalue ?
In-Reply-To: <13860930.332041226794943111.JavaMail.coremail@app143.163.com>
References: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com>
	<f6b04db30811151002r5ca1d2ecwde3a3268150cc6f0@mail.gmail.com>
	<13860930.332041226794943111.JavaMail.coremail@app143.163.com>
Message-ID: <f6b04db30811151657x54545fcbu30467ffe823c1391@mail.gmail.com>

Hello,

I put the source at http://www.pih.bio.br/src/Statistics.java

if you modify this source, send to me the update version to use it.

Felipe Albrecht

2008/11/15 simpleyrx <simpleyrx at 163.com>

>
>  I am very interested in the code. Could you send a copy of the code to me
> ?
> thank you.
>
> --
>
> Renxiang Yan
>   Ph.D. Candidate Student (2007)
>   E-mail: simpleyrx at 163.com
>   Mobile phone:+86-13811458000
>
>   Tel. +86-(0)10-62734412
>
> +86-(0)10-80973092
>
>
>
>   Address: College of Biological Sciences,
>   China Agricultural University,
>   No.2, Yuanmingyuan West Rd.,
>   Haidian district, 100094
>   Beijing, China
>
> ?2008-11-16?"Felipe Albrecht" <felipe.albrecht at gmail.com> ???
>
> Hello,
>
> I have a source code in java where I calculate the Evalue, H, K and lambda.
> I only tested the source with nucleotidies and the score matrix should have
> a 1 or -1 in your score.
>
> If it is interesting to someone, I can send it.
>
> Thank you,
>
> Felipe Albrecht
>
> On Sat, Aug 30, 2008 at 12:48 PM, simpleyrx <simpleyrx at 163.com> wrote:
>
>>
>> Dear experts,
>>
>>  I develop a sequence search program. Now , my program can calculate the
>> score value ,and I want to provide a expectation value ( like blast evalue)
>> to user. I do not know how to do in this step. Can biojava do it ? Thank you
>> in advanced.
>>
>>
>> --
>>
>>
>> Student
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> ------------------------------
> [??] ???????-???? <http://popme.163.com/link/003985_1010_7027.html>



From holland at eaglegenomics.com  Wed Nov 19 03:36:27 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 19 Nov 2008 03:36:27 +0000
Subject: [Biojava-dev] BioJava 3 code usage examples
Message-ID: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>

I've posted some brief HOWTOs here on how to use the new code as it progresses:

  http://biojava.org/wiki/BioJava3:HowTo

Hopefully the examples will make the new approach a bit clearer. The
FASTA parser example does need simplifying even further, through a
standard file parser utility class to go in the core module which has
yet to be written. But the examples on the page are a start and show
you what the convenience methods would have to implement internally
(hint, hint!).

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From me at hongyu.org  Wed Nov 19 05:20:07 2008
From: me at hongyu.org (Hongyu Zhang)
Date: Tue, 18 Nov 2008 21:20:07 -0800 (PST)
Subject: [Biojava-dev] BioJava 3 code usage examples
References: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>
Message-ID: <935207.30877.qm@web51405.mail.re2.yahoo.com>

Hi Richard,

Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
"Sequences are perfectly happy as Strings unless you want to do complex
things like store base quality information, and only at that point
should you want to convert them into more complex object models."

 
The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.

Let me know if I missed something. Thanks!

Best,

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750


From holland at eaglegenomics.com  Wed Nov 19 12:00:17 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 19 Nov 2008 12:00:17 +0000
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <935207.30877.qm@web51405.mail.re2.yahoo.com>
References: <a0d826f40811181936r31daab3av965e232cdec0c68c@mail.gmail.com>
	<935207.30877.qm@web51405.mail.re2.yahoo.com>
Message-ID: <a0d826f40811190400m386d97dasd63d2004dd8fdec5@mail.gmail.com>

Hello.

Thanks for your feedback. You are right that we've continued to
provide a Symbol-based alphabet/symbol structure, but it is no longer
a central concept nor is it required to use it.

You'll notice that when FASTA is read using the new parser, it reads
the sequence from the FASTA file as a simple String (actually, a
CharSequence). If you want to work with it as a String/CharSequence
and don't want to convert it into Symbols/Lists, you can do so. This
is the big change from the existing BioJava way of doing things, which
automatically converts everything into the BioJava object model
instead of giving the user the choice of what to do with it. This
change is consistent with the part of the design document you quote in
your email.

So, this is giving users the choice of whether they want to work with
the sequences directly as Strings/CharSequences, or whether they want
to convert them into Symbols/Lists. Users can then tailor their choice
depending on locally observed speed/memory usage issues should they so
wish.

cheers,
Richard


2008/11/19 Hongyu Zhang <me at hongyu.org>:
> Hi Richard,
>
> Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
> "Sequences are perfectly happy as Strings unless you want to do complex
> things like store base quality information, and only at that point
> should you want to convert them into more complex object models."
>
>
> The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.
>
> Let me know if I missed something. Thanks!
>
> Best,
>
> Hongyu Zhang, Ph.D.
> Ceres Inc., Thousand Oaks, CA
> Cell: 805-405-5394
> Fax: 866-447-8750
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From me at hongyu.org  Thu Nov 20 22:26:07 2008
From: me at hongyu.org (Hongyu Zhang)
Date: Thu, 20 Nov 2008 14:26:07 -0800 (PST)
Subject: [Biojava-dev] BioJava 3 code usage examples
Message-ID: <644724.10477.qm@web51411.mail.re2.yahoo.com>

Hi Richard,

I spent some time reading the codes today. I found that you had packed the biojava3
modules in a different style from the old version. I guess that some of the
reasons are related to the new design philosophy and some are related to the
maven software (I am new to maven). The things that are not clear to me are:

1) It doesn't seem that you want to avoid name conflicts with the old version
because you are continuing using the package name "org.biojava.*"
instead of "org.biojava3.*"

2) The old biojava version arranges sequence related classes in a hierarchical fashion,
while in the new version you put the FASTA parsing classes directly under a first level
node "org.biojava.fasta" rather than under the
"org.biojava.seq" as before. There are tens of popular file formats
in the bioinformatics world, so will all of them crowd the first level nodes under
the root package?

3) The source files are now in much deeper paths now, for example for
the FASTA parser, the path is "src/main/java/org/biojava/fasta",
as opposed to the common style "src/org/biojava/fasta", so I am
wondering why it is necessary to add "main/java" in the middle of the
path.

4) It is interesting to see that you put the source codes of all the
sub-packages separately, so whenever I need to browse the codes of some related classes
in Windows explorer or Unix shell, I really need to go up and down by clicking or typing many more times.
Netbean IDE alleviated this problem a little bit. I understand the idea of seperating independent packages in the new design, but I am wondering whether the current very fine seperation of classes went too far.

I am not familiar with the new design, so forgive my ignorance. Thanks for your
time.

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750




________________________________
From: Hongyu Zhang <me at hongyu.org>
To: holland at eaglegenomics.com
Sent: Wednesday, November 19, 2008 10:55:06 AM
Subject: Re: [Biojava-dev] BioJava 3 code usage examples


Thanks for the quick response, Richard. I will dive deeper into your codes. 

 Best,

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750




________________________________
From: Richard Holland <holland at eaglegenomics.com>
To: Hongyu Zhang <me at hongyu.org>
Cc: biojava-dev <biojava-dev at lists.open-bio.org>
Sent: Wednesday, November 19, 2008 4:00:17 AM
Subject: Re: [Biojava-dev] BioJava 3 code usage examples

Hello.

Thanks for your feedback. You are right that we've continued to
provide a Symbol-based alphabet/symbol structure, but it is no longer
a central concept nor is it required to use it.

You'll notice that when FASTA is read using the new parser, it reads
the sequence from the FASTA file as a simple String (actually, a
CharSequence). If you want to work with it as a String/CharSequence
and don't want to convert it into Symbols/Lists, you can do so. This
is the big change from the existing BioJava way of doing things, which
automatically converts everything into the BioJava object model
instead of giving the user the choice of what to do with it. This
change is consistent with the part of the design document you quote in
your email.

So, this is giving users the choice of whether they want to work with
the sequences directly as Strings/CharSequences, or whether they want
to convert them into Symbols/Lists. Users can then tailor their choice
depending on locally observed speed/memory usage issues should they so
wish.

cheers,
Richard


2008/11/19 Hongyu Zhang <me at hongyu.org>:
> Hi Richard,
>
> Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
> "Sequences are perfectly happy as Strings unless you want to do complex
> things like store base quality information, and only at that point
> should you want to convert them into more complex object models."
>
>
> The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.
>
> Let me know if I missed something. Thanks!
>
> Best,
>
> Hongyu Zhang, Ph.D.
> Ceres Inc., Thousand Oaks, CA
> Cell: 805-405-5394
> Fax: 866-447-8750
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From holland at eaglegenomics.com  Fri Nov 21 01:02:37 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 20 Nov 2008 20:02:37 -0500
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <644724.10477.qm@web51411.mail.re2.yahoo.com>
References: <644724.10477.qm@web51411.mail.re2.yahoo.com>
Message-ID: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>

Hello. Thanks for spending the time looking into the code. It's a bit
like a virtual code review session for me... you've made some very
useful comments.

> 1) It doesn't seem that you want to avoid name conflicts with the old
> version because you are continuing using the package name "org.biojava.*"
> instead of "org.biojava3.*"

Yes, I agree, I think they should be changed to org.biojava3. I will
do this when I get 5 minutes spare. They should be in org.biojava3
because one of the stated goals was to be able to write a
biojava-biojava3 mapper module if someone needed that to happen, and
the use of org.biojava in the new code would preclude that.

> 2) The old biojava version arranges sequence related classes in a
> hierarchical fashion, while in the new version you put the FASTA parsing
> classes directly under a first level node "org.biojava.fasta" rather than
> under the "org.biojava.seq" as before. There are tens of popular file
> formats in the bioinformatics world, so will all of them crowd the first
> level nodes under the root package?

That's also a good suggestion. I'll move it. It makes no difference to
the physical structure of the project on disk, but it would make class
and package browsing easier to do, especially in JavaDocs.

> 3) The source files are now in much deeper paths now, for example for the
> FASTA parser, the path is "src/main/java/org/biojava/fasta", as opposed to
> the common style "src/org/biojava/fasta", so I am wondering why it is
> necessary to add "main/java" in the middle of the path.

This is because of Maven. The src folder contains both source code and
test code, and within each you can have multiple programming
languages. The default behaviour, to store source code in a main
folder and test code in a test folder, and under each have a subfolder
for the programming language, seems sensible to me so I went with it.
It also allows the inclusion of resource folders at the same level as
the java folder, the contents of which automatically get built into
the resulting jars as top-level classpath elements.

> 4) It is interesting to see that you put the source codes of all the
> sub-packages separately, so whenever I need to browse the codes of some
> related classes in Windows explorer or Unix shell, I really need to go up
> and down by clicking or typing many more times. Netbean IDE alleviated this
> problem a little bit. I understand the idea of seperating independent
> packages in the new design, but I am wondering whether the current very fine
> seperation of classes went too far.

I did this for clarity's sake as to which source code related to which
module - you can see really easily if they're separated, whereas if
they were all in one tree, it would be hard to know which module a
particular class ended up in. Also if you have one source tree, you
have to remember to update the Maven configs to split different bits
of it into different jars. By simply keeping them separate, this
happens automatically.

Thanks again for your feedback!

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From mark.schreiber at novartis.com  Fri Nov 21 03:40:53 2008
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 21 Nov 2008 11:40:53 +0800
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>
Message-ID: <OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>

biojava-dev-bounces at lists.open-bio.org wrote on 11/21/2008 09:02:37 AM:

> Hello. Thanks for spending the time looking into the code. It's a bit
> like a virtual code review session for me... you've made some very
> useful comments.
> 
> > 1) It doesn't seem that you want to avoid name conflicts with the old
> > version because you are continuing using the package name 
"org.biojava.*"
> > instead of "org.biojava3.*"
> 
> Yes, I agree, I think they should be changed to org.biojava3. I will
> do this when I get 5 minutes spare. They should be in org.biojava3
> because one of the stated goals was to be able to write a
> biojava-biojava3 mapper module if someone needed that to happen, and
> the use of org.biojava in the new code would preclude that.
> 

I think it would be a very good idea to differentiate this from old code 
via the packages. Strictly speaking you are supposed to use a domain that 
you own. I don't know if biojava3.org is available or if open-bio wants to 
obtain it. It's not critical but it would prevent possible issues.

Alternatives would be to use org.biojava.v3.*

or you could use the open-bio domain as in org.open-bio.biojava3

- Mark

_________________________

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The information contained in this e-mail message is intended only for the 
exclusive use of the individual or entity named above and may contain 
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under applicable law. If the reader of this message is not the intended 
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From holland at eaglegenomics.com  Fri Nov 21 03:57:24 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 20 Nov 2008 22:57:24 -0500
Subject: [Biojava-dev] BioJava 3 code usage examples
In-Reply-To: <OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>
References: <a0d826f40811201702t52ba7eceh784cd9a7d276c7a6@mail.gmail.com>
	<OFDCFF6259.03F448B2-ON48257508.0013E5A9-48257508.001438AC@ah.novartis.com>
Message-ID: <a0d826f40811201957x441b495bia8b56c2df953e6dc@mail.gmail.com>

I like the domain registration idea better. I'll find out what the
folks at open-bio think.

cheers,
Richard

2008/11/20  <mark.schreiber at novartis.com>:
>
> biojava-dev-bounces at lists.open-bio.org wrote on 11/21/2008 09:02:37 AM:
>
>> Hello. Thanks for spending the time looking into the code. It's a bit
>> like a virtual code review session for me... you've made some very
>> useful comments.
>>
>> > 1) It doesn't seem that you want to avoid name conflicts with the old
>> > version because you are continuing using the package name
>> > "org.biojava.*"
>> > instead of "org.biojava3.*"
>>
>> Yes, I agree, I think they should be changed to org.biojava3. I will
>> do this when I get 5 minutes spare. They should be in org.biojava3
>> because one of the stated goals was to be able to write a
>> biojava-biojava3 mapper module if someone needed that to happen, and
>> the use of org.biojava in the new code would preclude that.
>>
>
> I think it would be a very good idea to differentiate this from old code via
> the packages. Strictly speaking you are supposed to use a domain that you
> own. I don't know if biojava3.org is available or if open-bio wants to
> obtain it. It's not critical but it would prevent possible issues.
>
> Alternatives would be to use org.biojava.v3.*
>
> or you could use the open-bio domain as in org.open-bio.biojava3
>
> - Mark
>
> _________________________
>
> CONFIDENTIALITY NOTICE
>
> The information contained in this e-mail message is intended only for the
> exclusive use of the individual or entity named above and may contain
> information that is privileged, confidential or exempt from disclosure under
> applicable law. If the reader of this message is not the intended recipient,
> or the employee or agent responsible for delivery of the message to the
> intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If you
> have received this communication in error, please notify the sender
> immediately by e-mail and delete the material from any computer.  Thank you.
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 10:48:59 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:48:59 -0500
Subject: [Biojava-dev] [Bug 2679] New: NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
Message-ID: <bug-2679-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679

           Summary: NEXUS parse fails on extraneous comma (TREES/TRANSLATE)
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P1
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keesey at gmail.com


If the last item in a TRANSLATE command of a TREES node ends with a comma, the
parser fails with the following exception:

Error: org.biojava.bio.seq.io.ParseException: Found unexpected token = in TREES
block

A properly-formatted NEXUS file should not have a comma here, but there are
many files which do. The parser should see the semicolon and assume the command
is is ended.

Example TREES block (from TREEBase, accession M474):

BEGIN TREES;

[! 1 trees. TreeBASE accession#: Tree1118 ]
        TRANSLATE
                1       'Nyctereutes_procyonoides',
                2       'Urocyon_cinereoargenteus',
                3       'Pseudalopex_gymnocercus',
                4       'Chrysocyon_brachyurus',
                5       'Pseudalopex_sechurae',
                6       'Pseudalopex_culpaeus',
                7       'Pseudalopex_vetulus',
                8       'Atelocynus_microtis',
                9       'Pseudalopex_griseus',
                10      'Dusicyon_australis',
                11      'Urocyon_littoralis',
                12      'Vulpes_bengalensis',
                13      'Speothos_venaticus',
                14      'Otocyon_megalotis',
                15      'Vulpes_ferrilata',
                16      'Vulpes_rueppelli',
                17      'Canis_mesomelas',
                18      'Cerdocyon_thous',
                19      'Alopex_lagopus',
                20      'Vulpes_pallida',
                21      'Canis_simensis',
                22      'Vulpes_corsac',
                23      'Canis_latrans',
                24      'Lycaon_pictus',
                25      'Canis_adustus',
                26      'Vulpes_vulpes',
                27      'Vulpes_chama',
                28      'Vulpes_velox',
                29      'Vulpes_zerda',
                30      'Canis_aureus',
                31      'Cuon_alpinus',
                32      'Pseudalopex',
                33      'Canis_rufus',
                34      'Vulpes_cana',
                35      'Canis_lupus',
                36      'Canidae',
                37      'Canis',
        ;
        TREE 'Fig._9' =  [&R]
(((((((19,28),((22,15),(16,26))),(34,29)),(12,27,20)),(2,11)),14),((8,(((25,30),17),(23,(35,33),21)),18,4,31,(10,((6,9,3,5),7)),24,13),1));


END;


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 10:49:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:49:45 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211049.mALAnjes020244@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #1 from keesey at gmail.com  2008-11-21 05:49 EST -------
The next comment is the full NEXUS file from the example.


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 10:50:10 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:50:10 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211050.mALAoAwx020305@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #2 from keesey at gmail.com  2008-11-21 05:50 EST -------
#NEXUS
[File created by TreeBASE:  1/29/99  19:24:10]
[Matrix accession#: M474]
BEGIN DATA;
DIMENSIONS  NTAX=34 NCHAR=223;

[!This data set was downloaded from TreeBASE, a prototype relational database
of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard
University, and UC Davis. Please do not remove this acknowledgment from the
Nexus file. 
TreeBASE ?? 1994-1999.

Study reference: 
Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building larger
phylogenies using supertrees: a complete phylogeny of the extant Carnivora
(Mammalia). Biological Reviews, in press. 

Study accession number = S355
Matrix accession number = M474
]
FORMAT MISSING = ? GAP = -   INTERLEAVE ;
MATRIX

'Vulpes_zerda'                
1?000111000????0000?1100000000?1001???????001100000?????10000000000000111000??????1000000????????111
'Vulpes_vulpes'               
1?110000000?00??????1100000000?1001???????110000000?1???10000000000000110101??????1100000???0000?110
'Vulpes_velox'                
1?111000000????0000?1100000000?1001???????110000000?????10000000000000110110??????1100000????????110
'Vulpes_rueppelli'            
1???????????????????1100000000?1001???????110000000?????10000000000000110101??????1100000????????110
'Vulpes_pallida'              
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_ferrilata'            
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_corsac'               
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000????????110
'Vulpes_chama'                
1???????????????????1100000000?1001???????110000000?????10000000000000110000??????1100000????????100
'Vulpes_cana'                 
1???????????????????1100000000?1001???????110000000?????10000000000000111000??????1100000????????111
'Vulpes_bengalensis'          
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Urocyon_littoralis'          
1??????????????????????????????1001???????001110000???????????????????????????????1010000???????????
'Urocyon_cinereoargenteus'    
1?000110000?????????1010000000?1001?0?000?001110000?????00000000000000000000??????1010000?0?1000?000
'Speothos_venaticus'          
1?000100111?????????0001100110?0000?????????????????????11100011100000000000?1100?0001000???????????
'Pseudalopex_vetulus'         
1???????????????????0001111000?1000???????001001010??????????????????????????0000?0001000???????????
'Pseudalopex_sechurae'        
1???????????????????0001111000?1010???????001001010??????????????????????????0010?0001101???????????
'Pseudalopex_gymnocercus'     
1???????????????????0001111000?1010???????001001010?????11111000000000000000?0010?0001101???????????
'Pseudalopex_griseus'         
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0010?0001101???????????
'Pseudalopex_culpaeus'        
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0011?0001101???????????
'Otocyon_megalotis'           
1?000111000?????????1010000000?0000???????100000000?????11000000000000000000??????1000000???????????
'Nyctereutes_procyonoides'    
1?100000000?????????0001100101?0000???????100000000?1???10000000000000100000????????????????????????
'Lycaon_pictus'               
1??????????????1000????????????0000???000???????????????11100011100000000000??????0001000???1110????
'Dusicyon_australis'          
1???????????????????0001110000?1000???????001001010??????????????????????????0011?0001100???????????
'Cuon_alpinus'                
1??????????????????????????????0000?????????????????????11100010010000000000??????0001000???????????
'Chrysocyon_brachyurus'       
1?000100110?????????0001000000?0000???????001001100?????11100011000000000000?0000?0001000???????????
'Cerdocyon_thous'             
1?000100111?????????0001100101?1000?????????????????????11110000000000000000?1000?0001000???????????
'Canis_simensis'              
1??????????????????????????????1100???111?001000001???0?11100010011011000000??????0001110???????????
'Canis_rufus'                 
1??????????????????????????????1100???????001000001???0???????????????????????????0001110???????????
'Canis_mesomelas'             
1???????????10?1100????????????1100???100?001000001???0?11100010010000000000??????0001110???????????
'Canis_lupus'                 
1?000100100?11?1111????????????1100?1?111?001000001?0?1?11100010011010000000??????0001110?1?1111????
'Canis_latrans'               
1???????????11?1111????????????1100?1?111?001000001???1?11100010011011000000??????0001110?1?1111????
'Canis_aureus'                
1??????????????1110????????????1100???110?001000001???0?11100010011100000000??????0001110???1100????
'Canis_adustus'               
1??????????????1000????????????1100???000?001000001???0?11100010011100000000??????0001110???????????
'Atelocynus_microtis'         
1???????????????????0001100110?1000???????001001100??????????????????????????1100?0001000???????????
'Alopex_lagopus'              
1?111000000????????????????????1000???????110000000?????10000000000000110110??????1000000????????110


'Vulpes_zerda'                
0000?11111000?11110000?00000010??????????10000?01???????????????????100000?????0001?1000001010000000
'Vulpes_vulpes'               
1011?11110100?11101101?00000010????????????????01?0000110???00001???100010?????0001?1000001000000000
'Vulpes_velox'                
1100?11110111?11101110?00000011????????????????01???????????00001???100010?????0001?1000001000000000
'Vulpes_rueppelli'            
1011?11110110?11101101?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_pallida'              
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_ferrilata'            
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_corsac'               
1010?11110100?11101100?????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_chama'                
0000?11100000?11101000?00000010????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_cana'                 
0000?11111000?11110000?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_bengalensis'          
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Urocyon_littoralis'          
?????????????????????????????????????????11000?01???????????????????100100?????0010?1000001000010000
'Urocyon_cinereoargenteus'    
0000?10000000?10000000?00000000??????????11000?01???????????????????100100?????0010?1000001000010000
'Speothos_venaticus'          
???????????????????????11001000??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Pseudalopex_vetulus'         
???????????????????????11110000??????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_sechurae'        
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_gymnocercus'     
?????????????????????????????????????????00101?01?1100000???????????101000?????0100?1000000000001110
'Pseudalopex_griseus'         
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001100
'Pseudalopex_culpaeus'        
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001110
'Otocyon_megalotis'           
?????11000000?11000000?00000000????????????????00?0000001???????????100000?????0000?0000000000000000
'Nyctereutes_procyonoides'    
???????????????????????00000000????????????????01?0000001???????????100000?????0000?0000000000000000
'Lycaon_pictus'               
???????????????????????11001100??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Dusicyon_australis'          
?????????????????????????????????????????00101?01???????????????????100000?????0000?1000000000001000
'Cuon_alpinus'                
???????????????????????????????????????????????10???????????????????000001?????0000?0000000000000000
'Chrysocyon_brachyurus'       
???????????????????????11100000??????????00100?01?0000100???????????100000?????0000?0000000000000000
'Cerdocyon_thous'             
???????????????????????11110000????????????????01???????????????????100000?????0000?1000000000001000
'Canis_simensis'              
?????????????????????????????????????????00110?01???????????????????110000?????1000?1110000000000000
'Canis_rufus'                 
??????????????????????????????????100?10?00110?01?????????1?11100?1?110000???1?1000?1100110000000000
'Canis_mesomelas'             
???????????????????????11001000?1?011?11?00110?01?1110000???11010???110000?0???1000?1111000000000000
'Canis_lupus'                 
?????00000000?00000000?11001100?1?100????00110?01?1001000?1?11100?1?110000???1?1000?1100110000000000
'Canis_latrans'               
???????????????????????11001100???010?00?00110?01?1001000???10000?1?110000???1?1000?1100100000000000
'Canis_aureus'                
??????????????????????????????????011?11?00110?01???????????11010?0?110000?1?0?1000?1110000000000000
'Canis_adustus'               
?????????????????????????????????????????00110?01?1110000???11010???110000?1???1000?1111000000000000
'Atelocynus_microtis'         
?????????????????????????????????????????00100?01???????????????????100000?????0000?1000000000001000
'Alopex_lagopus'              
1100?11111111?11101110?00000011?0??????????????01?0000110???00001???100000?????0000?1000001000000000


'Vulpes_zerda'                 ?????????11000000000000
'Vulpes_vulpes'                ?????????11000000000000
'Vulpes_velox'                 ?????????11000000000000
'Vulpes_rueppelli'             ???????????????????????
'Vulpes_pallida'               ?????????11000000000000
'Vulpes_ferrilata'             ????????????????????0??
'Vulpes_corsac'                ?????????11000000000000
'Vulpes_chama'                 ?????????11000000000000
'Vulpes_cana'                  ???????????????????0???
'Vulpes_bengalensis'           ?????????11000000000000
'Urocyon_littoralis'           ???????????????????????
'Urocyon_cinereoargenteus'     ???0?????10100000000000
'Speothos_venaticus'           ?????????00010001101101
'Pseudalopex_vetulus'          ?????????00010001101000
'Pseudalopex_sechurae'         ?????????00010001000000
'Pseudalopex_gymnocercus'      ?????????00010001000000
'Pseudalopex_griseus'          ?????????00010001000000
'Pseudalopex_culpaeus'         ?????????00010001110000
'Otocyon_megalotis'            ?1???????10100000000000
'Nyctereutes_procyonoides'     ?????????00010001101110
'Lycaon_pictus'                ?0???????00011010000000
'Dusicyon_australis'           ?????????00010001110000
'Cuon_alpinus'                 ?????????00011010000000
'Chrysocyon_brachyurus'        ?????????00010001101000
'Cerdocyon_thous'              ?????????00010001101110
'Canis_simensis'               ?????????00011100000000
'Canis_rufus'                  ?????1?1?00011100000000
'Canis_mesomelas'              ?????????00011100000000
'Canis_lupus'                  ?1?1?1?1?00011100000000
'Canis_latrans'                ???1?1?0?00011100000000
'Canis_aureus'                 ?????????00011100000000
'Canis_adustus'                ?????????00011100000000
'Atelocynus_microtis'          ?????????00010001101101
'Alopex_lagopus'               ?????????11000000000000
;
END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;
BEGIN TREEBASE;
END;

BEGIN TREES;

[! 1 trees. TreeBASE accession#: Tree1118 ]
        TRANSLATE
                1       'Nyctereutes_procyonoides',
                2       'Urocyon_cinereoargenteus',
                3       'Pseudalopex_gymnocercus',
                4       'Chrysocyon_brachyurus',
                5       'Pseudalopex_sechurae',
                6       'Pseudalopex_culpaeus',
                7       'Pseudalopex_vetulus',
                8       'Atelocynus_microtis',
                9       'Pseudalopex_griseus',
                10      'Dusicyon_australis',
                11      'Urocyon_littoralis',
                12      'Vulpes_bengalensis',
                13      'Speothos_venaticus',
                14      'Otocyon_megalotis',
                15      'Vulpes_ferrilata',
                16      'Vulpes_rueppelli',
                17      'Canis_mesomelas',
                18      'Cerdocyon_thous',
                19      'Alopex_lagopus',
                20      'Vulpes_pallida',
                21      'Canis_simensis',
                22      'Vulpes_corsac',
                23      'Canis_latrans',
                24      'Lycaon_pictus',
                25      'Canis_adustus',
                26      'Vulpes_vulpes',
                27      'Vulpes_chama',
                28      'Vulpes_velox',
                29      'Vulpes_zerda',
                30      'Canis_aureus',
                31      'Cuon_alpinus',
                32      'Pseudalopex',
                33      'Canis_rufus',
                34      'Vulpes_cana',
                35      'Canis_lupus',
                36      'Canidae',
                37      'Canis',
        ;
        TREE 'Fig._9' =  [&R]
(((((((19,28),((22,15),(16,26))),(34,29)),(12,27,20)),(2,11)),14),((8,(((25,30),17),(23,(35,33),21)),18,4,31,(10,((6,9,3,5),7)),24,13),1));


END;


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From bugzilla-daemon at portal.open-bio.org  Fri Nov 21 10:51:52 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 21 Nov 2008 05:51:52 -0500
Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma
	(TREES/TRANSLATE)
In-Reply-To: <bug-2679-485@http.bugzilla.open-bio.org/>
Message-ID: <200811211051.mALApqKl020508@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2679





------- Comment #3 from keesey at gmail.com  2008-11-21 05:51 EST -------
version is 1.6 (no place to specifiy that)


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From bugzilla-daemon at portal.open-bio.org  Tue Nov 25 23:31:57 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 25 Nov 2008 18:31:57 -0500
Subject: [Biojava-dev] [Bug 2687] New: UniProt: Tags in feature continuation
	lines may be lost.
Message-ID: <bug-2687-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2687

           Summary: UniProt: Tags in feature continuation lines may be lost.
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: jan at biochemfusion.com


Using BioJava 1.6.1 on Windows XP to read in a UniProt file and write it back
out. Main code that does this:

        BufferedReader br = new BufferedReader(new FileReader(args[0]));
        SimpleNamespace ns = new SimpleNamespace("biojava");

        RichSequenceIterator rsi = RichSequence.IOTools.readUniProt(br, ns);
        RichSequence rs = rsi.nextRichSequence();
        RichSequence.IOTools.writeUniProt(System.out, rs, ns);

When reading in this heavily abridged version of FA9_BOVIN from www.uniprot.org
it works:

ID   FA9_BOVIN               Reviewed;         416 AA.
AC   P00741;
FT   CHAIN         1    416       Coagulation factor IX.
FT   CARBOHYD     53     53       O-linked (Glc...).
FT                                /FTId=CAR_000008.
FT                                Extra information.
SQ   SEQUENCE   416 AA;  46785 MW;  34A7DFE916330662 CRC64;
     YNSGKLEEFV RGNLERECKE EKCSFEEARE VFENTEKTTE FWKQYVDGDQ CESNPCLNGG
     MCKDDINSYE CWCQAGFEGT NCELDATCSI KNGRCKQFCK RDTDNKVVCS CTDGYRLAED
     QKSCEPAVPF PCGRVSVSHI SKKLTRAETI FSNTNYENSS EAEIIWDNVT QSNQSFDEFS
     RVVGGEDAER GQFPWQVLLH GEIAAFCGGS IVNEKWVVTA AHCIKPGVKI TVVAGEHNTE
     KPEPTEQKRN VIRAIPYHSY NASINKYSHD IALLELDEPL ELNSYVTPIC IADRDYTNIF
     SKFGYGYVSG WGKVFNRGRS ASILQYLKVP LVDRATCLRS TKFSIYSHMF CAGYHEGGKD
     SCQGDSGGPH VTEVEGTSFL TGIISWGEEC AMKGKYGIYT KVSRYVNWIK EKTKLT
//

However, when the extra information has been tagged with a slash it is lost:

ID   FA9_BOVIN               Reviewed;         416 AA.
AC   P00741;
FT   CHAIN         1    416       Coagulation factor IX.
FT   CARBOHYD     53     53       O-linked (Glc...).
FT                                /FTId=CAR_000008.
FT                                /NB=Extra information.
SQ   SEQUENCE   416 AA;  46785 MW;  34A7DFE916330662 CRC64;
     YNSGKLEEFV RGNLERECKE EKCSFEEARE VFENTEKTTE FWKQYVDGDQ CESNPCLNGG
     MCKDDINSYE CWCQAGFEGT NCELDATCSI KNGRCKQFCK RDTDNKVVCS CTDGYRLAED
     QKSCEPAVPF PCGRVSVSHI SKKLTRAETI FSNTNYENSS EAEIIWDNVT QSNQSFDEFS
     RVVGGEDAER GQFPWQVLLH GEIAAFCGGS IVNEKWVVTA AHCIKPGVKI TVVAGEHNTE
     KPEPTEQKRN VIRAIPYHSY NASINKYSHD IALLELDEPL ELNSYVTPIC IADRDYTNIF
     SKFGYGYVSG WGKVFNRGRS ASILQYLKVP LVDRATCLRS TKFSIYSHMF CAGYHEGGKD
     SCQGDSGGPH VTEVEGTSFL TGIISWGEEC AMKGKYGIYT KVSRYVNWIK EKTKLT
//

BioPerl 1.5.2 copes with both situtations without problems.


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From bugzilla-daemon at portal.open-bio.org  Tue Nov 25 23:35:42 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 25 Nov 2008 18:35:42 -0500
Subject: [Biojava-dev] [Bug 2687] UniProt: Tags in feature continuation
	lines may be lost.
In-Reply-To: <bug-2687-485@http.bugzilla.open-bio.org/>
Message-ID: <200811252335.mAPNZg6D004170@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2687





------- Comment #1 from jan at biochemfusion.com  2008-11-25 18:35 EST -------
To clarify: In the first case the information in all feature lines is correctly
preserved. In the second case the last FT line "/NB=Extra information." is
lost.


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From holland at eaglegenomics.com  Wed Nov 26 16:04:56 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 26 Nov 2008 16:04:56 +0000
Subject: [Biojava-dev] BugZilla!
Message-ID: <492D73A8.4020401@eaglegenomics.com>

Hi all,

There's been a few new bugs reported on BugZilla recently. Whilst the
development of the new BJ features is fun, it's really important to
maintain the existing code and keep on top of the issues reported.

If there's anyone with a few minutes spare, or would like to learn
BioJava and don't know where to start - then zapping a few virtual
creepy crawlies is an excellent way to get involved and make a contribution.

Here's the list of the currently outstanding problems:

http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED

If you see one you think you can fix, or might like to try to
investigate, go for it! All you have to do is assign the bug to yourself
in order to take ownership of it so that people don't end up working on
the same thing without knowing.

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From bugzilla-daemon at portal.open-bio.org  Wed Nov 26 17:44:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 26 Nov 2008 12:44:45 -0500
Subject: [Biojava-dev] [Bug 2603] StringIndexOutOfBoundsException while
	parsing blastresult
In-Reply-To: <bug-2603-485@http.bugzilla.open-bio.org/>
Message-ID: <200811261744.mAQHijbY009725@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2603


tbanks at agr.gc.ca changed:

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




------- Comment #7 from tbanks at agr.gc.ca  2008-11-26 12:44 EST -------
Fixed.  The change to the blast result format (sometime around v2.2.15) made
the parser unable to determine where the end of one result finished and the
next began.  Now the code can recognize the two ways a result can end; the
start of a new result or the statistics for the blast and database.


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From mark.schreiber at novartis.com  Thu Nov 27 02:33:05 2008
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 27 Nov 2008 10:33:05 +0800
Subject: [Biojava-dev] [Biojava-l] BugZilla!
In-Reply-To: <492D73A8.4020401@eaglegenomics.com>
Message-ID: <OF05FA111C.951667E1-ON4825750E.000D7781-4825750E.000E04E1@ah.novartis.com>

Hi -

I would concur with this. BioJava is volunteer based and requires people 
to volunteer before things happen.

In my experience bug reports get resolved most rapidly if the person 
reporting the bug can do as much of their own investigation as possible. 
Have a good look at the stack trace and try using a debugger. You can 
rapidly narrow down the underlying cause. Even if you are not confident 
about the best way to fix the problem, armed with all the relevant 
information someone more experienced will be able to tell you if you are 
on the right track.

Unit tests are also good here. For one thing they will set-up a situation 
to replicate your bug. They will also provide a way to make sure the bug 
doesn't happen again in future releases.  Finally, the more unit tests 
there are the more confident you can be that your proposed bug fix won't 
break anything else.

Helping fix stuff in BioJava will definitely improve you're programming 
skills and greatly increase your knowledge of how the API works so by 
helping others you are probably helping yourself more.

- Mark

biojava-l-bounces at lists.open-bio.org wrote on 11/27/2008 12:04:56 AM:

> Hi all,
> 
> There's been a few new bugs reported on BugZilla recently. Whilst the
> development of the new BJ features is fun, it's really important to
> maintain the existing code and keep on top of the issues reported.
> 
> If there's anyone with a few minutes spare, or would like to learn
> BioJava and don't know where to start - then zapping a few virtual
> creepy crawlies is an excellent way to get involved and make a 
contribution.
> 
> Here's the list of the currently outstanding problems:
> 
> http://bugzilla.open-bio.org/buglist.cgi?
> product=BioJava&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED
> 
> If you see one you think you can fix, or might like to try to
> investigate, go for it! All you have to do is assign the bug to yourself
> in order to take ownership of it so that people don't end up working on
> the same thing without knowing.
> 
> cheers,
> Richard
> 
> -- 
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> M: +44 7500 438846 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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From talk2ali at gmail.com  Sat Nov 22 01:38:26 2008
From: talk2ali at gmail.com (Muhammad Ali)
Date: Fri, 21 Nov 2008 20:38:26 -0500
Subject: [Biojava-dev] NCBI Blast XML Parser update
In-Reply-To: <59a41c430808191936sb139efcwff92065cffe8f49@mail.gmail.com>
References: <e1a332c90808190610l481cfbd6x8e664aaaedf5629b@mail.gmail.com>
	<59a41c430808191936sb139efcwff92065cffe8f49@mail.gmail.com>
Message-ID: <e1a332c90811211738g7f6d95c0lfb566fed926754a6@mail.gmail.com>

Hi,

Sorry for the delay, I got caught up with my other project. Anyway,
I'm here now and I've attached the patch file with this email. Please
take a look and let me know if changes are required.

With regards to testing, there is a BlastParser.java file in the
/demos/blastxml folder that I've been using to test on my end. It
takes a Blast output file as its input. If you want, I can provide
some Blast output file with multiple iteration entries for use as a
sample input file for testing.

I think I'll do without SVN write access. I don't expect to be working
on other parts of biojava right now, unless someone else in my lab
complains about something else being broken ;). But if I do make any
local patches, I'll definitely try and get them back to you guys.

Cheers,
Ali.

On Tue, Aug 19, 2008 at 9:36 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Ali,
>
> that's good news, can you send your patch to this list, so we can have
> a look? At this stage it would be also great to provide a new Junit
> test that makes sure that the parsing works ok and to demonstrate the
> new feature. If you provide more patches in the future we can also set
> up write access to the SVN repository.
>
> Andreas
>
> On Tue, Aug 19, 2008 at 6:10 AM, Muhammad Ali <talk2ali at gmail.com> wrote:
>> Hello,
>>
>> The current version of the BlastXMLParser (used for parsing NCBI BLAST
>> output files) is not handling multiple Iteration entries in the file
>> correctly. It lumps them all together, resulting in a loss of
>> search-specific parameters. The end result is a single
>> SeqSimilaritySearchResult object. The expected output should be one
>> SeqSimilaritySearchResult for each Iteration entry in the file.
>>
>> I've fixed this issue on my locally checked out copy by modifying a
>> few files in the  org.biojava.bio.program.sax.blastxml package. I'm
>> interested in submitting the updated code back to the main repository.
>> Can someone tell me how I can go about doing so?
>>
>> Also the javadocs for the BlastXMLParser seem to be outdated. They
>> mention malformed XML being generated by NCBI, but that doesn't seem
>> to be the case anymore.
>>
>> Thanks,
>> Ali.
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
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