From holland at ebi.ac.uk  Mon Mar  3 03:41:58 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 03 Mar 2008 08:41:58 +0000
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <47C839BC.8030506@ebi.ac.uk>
References: <47C839BC.8030506@ebi.ac.uk>
Message-ID: <47CBB9D6.8090705@ebi.ac.uk>

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Arnaud - you are correct.

cheers,
Richard

Arnaud Kerhornou wrote:
> Hi everyone,
> 
> I don't think the RichLocation.Tools.merge(Collection members) method is
> doing it right.
> 
> e.g. Input:
> biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
> Expected output:1157624..1158895
> 
> But I get: join:[1157624..1158420,1158420..1158894]
> 
> I think the code should have the extra line: parent = union;
> just after c=p; statement line 18 (See source code below),
> otherwise it doesn't take into account the newly generated location.
> 
> Is that right ?
> 
> Thanks
> Arnaud
> 
> Source code:
> 
> 1    public static Collection merge(Collection members) {
> 2            // flatten them out first so we don't end up recursing
> 3            List membersList = new ArrayList(flatten(members));
> 4            // all members are now singles so we can use single vs
> single union operations
> 5            if (membersList.size()>1) {
> 6                for (int p = 0; p < (membersList.size()-1); p++) {
> 7                    RichLocation parent =
> (RichLocation)membersList.get(p);
> 8                    for (int c = p+1; c < membersList.size(); c++) {
> 9                        RichLocation child =
> (RichLocation)membersList.get(c);
> 10                       RichLocation union =
> (RichLocation)parent.union(child);
> 11                        // if parent can merge with child
> 12                        if (union.isContiguous()) {
> 13                           // replace parent with union
> 14                            membersList.set(p,union);
> 15                            // remove child
> 16                            membersList.remove(c);
> 17                            // check all children again
> 18                            c=p;
> 19                        }
> 20                    }
> 21                }
> 22            }
> 23            return membersList;
> 24        }
>       _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Tue Mar  4 21:16:13 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 5 Mar 2008 10:16:13 +0800
Subject: [Biojava-l] biojava group on linkedin
Message-ID: <93b45ca50803041816s28728b2eme99edcda863d252d@mail.gmail.com>

Hi -

BioJava is now a group on the networking site, linkedin
(www.linkedin.com). If you have been involved in biojava in some way
and want to join you can find it on the list of available groups when
editing your profile.

Best regards,

- Mark

From markjschreiber at gmail.com  Tue Mar  4 21:20:52 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 5 Mar 2008 10:20:52 +0800
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <47CBB9D6.8090705@ebi.ac.uk>
References: <47C839BC.8030506@ebi.ac.uk> <47CBB9D6.8090705@ebi.ac.uk>
Message-ID: <93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>

Just to follow up...

Has there been a fix checked in for this?

- Mark

On Mon, Mar 3, 2008 at 4:41 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
>  Hash: SHA1
>
>  Arnaud - you are correct.
>
>  cheers,
>  Richard
>
>
>
>  Arnaud Kerhornou wrote:
>  > Hi everyone,
>  >
>  > I don't think the RichLocation.Tools.merge(Collection members) method is
>  > doing it right.
>  >
>  > e.g. Input:
>  > biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
>  > Expected output:1157624..1158895
>  >
>  > But I get: join:[1157624..1158420,1158420..1158894]
>  >
>  > I think the code should have the extra line: parent = union;
>  > just after c=p; statement line 18 (See source code below),
>  > otherwise it doesn't take into account the newly generated location.
>  >
>  > Is that right ?
>  >
>  > Thanks
>  > Arnaud
>  >
>  > Source code:
>  >
>  > 1    public static Collection merge(Collection members) {
>  > 2            // flatten them out first so we don't end up recursing
>  > 3            List membersList = new ArrayList(flatten(members));
>  > 4            // all members are now singles so we can use single vs
>  > single union operations
>  > 5            if (membersList.size()>1) {
>  > 6                for (int p = 0; p < (membersList.size()-1); p++) {
>  > 7                    RichLocation parent =
>  > (RichLocation)membersList.get(p);
>  > 8                    for (int c = p+1; c < membersList.size(); c++) {
>  > 9                        RichLocation child =
>  > (RichLocation)membersList.get(c);
>  > 10                       RichLocation union =
>  > (RichLocation)parent.union(child);
>  > 11                        // if parent can merge with child
>  > 12                        if (union.isContiguous()) {
>  > 13                           // replace parent with union
>  > 14                            membersList.set(p,union);
>  > 15                            // remove child
>  > 16                            membersList.remove(c);
>  > 17                            // check all children again
>  > 18                            c=p;
>  > 19                        }
>  > 20                    }
>  > 21                }
>  > 22            }
>  > 23            return membersList;
>  > 24        }
>  >       _______________________________________________
>  > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>  >
>
>  - --
>  Richard Holland (BioMart)
>  EMBL EBI, Wellcome Trust Genome Campus,
>  Hinxton, Cambridgeshire CB10 1SD, UK
>  Tel. +44 (0)1223 494416
>
>  http://www.biomart.org/
>  http://www.biojava.org/
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>  Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
>  iD8DBQFHy7m04C5LeMEKA/QRAj05AJ9SBrv6yz8qvhwbmTrLZVfmwBuHTACgiq57
>  +J0EpviSyp2Qq00m4A8xLUA=
>  =re75
>  -----END PGP SIGNATURE-----
>
>
> _______________________________________________
>  Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From holland at ebi.ac.uk  Wed Mar  5 03:35:24 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 05 Mar 2008 08:35:24 +0000
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>
References: <47C839BC.8030506@ebi.ac.uk> <47CBB9D6.8090705@ebi.ac.uk>
	<93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>
Message-ID: <47CE5B4C.3080506@ebi.ac.uk>

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Not that I'm aware of.

Mark Schreiber wrote:
> Just to follow up...
> 
> Has there been a fix checked in for this?
> 
> - Mark
> 
> On Mon, Mar 3, 2008 at 4:41 PM, Richard Holland <holland at ebi.ac.uk> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>>  Hash: SHA1
>>
>>  Arnaud - you are correct.
>>
>>  cheers,
>>  Richard
>>
>>
>>
>>  Arnaud Kerhornou wrote:
>>  > Hi everyone,
>>  >
>>  > I don't think the RichLocation.Tools.merge(Collection members) method is
>>  > doing it right.
>>  >
>>  > e.g. Input:
>>  > biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
>>  > Expected output:1157624..1158895
>>  >
>>  > But I get: join:[1157624..1158420,1158420..1158894]
>>  >
>>  > I think the code should have the extra line: parent = union;
>>  > just after c=p; statement line 18 (See source code below),
>>  > otherwise it doesn't take into account the newly generated location.
>>  >
>>  > Is that right ?
>>  >
>>  > Thanks
>>  > Arnaud
>>  >
>>  > Source code:
>>  >
>>  > 1    public static Collection merge(Collection members) {
>>  > 2            // flatten them out first so we don't end up recursing
>>  > 3            List membersList = new ArrayList(flatten(members));
>>  > 4            // all members are now singles so we can use single vs
>>  > single union operations
>>  > 5            if (membersList.size()>1) {
>>  > 6                for (int p = 0; p < (membersList.size()-1); p++) {
>>  > 7                    RichLocation parent =
>>  > (RichLocation)membersList.get(p);
>>  > 8                    for (int c = p+1; c < membersList.size(); c++) {
>>  > 9                        RichLocation child =
>>  > (RichLocation)membersList.get(c);
>>  > 10                       RichLocation union =
>>  > (RichLocation)parent.union(child);
>>  > 11                        // if parent can merge with child
>>  > 12                        if (union.isContiguous()) {
>>  > 13                           // replace parent with union
>>  > 14                            membersList.set(p,union);
>>  > 15                            // remove child
>>  > 16                            membersList.remove(c);
>>  > 17                            // check all children again
>>  > 18                            c=p;
>>  > 19                        }
>>  > 20                    }
>>  > 21                }
>>  > 22            }
>>  > 23            return membersList;
>>  > 24        }
>>  >       _______________________________________________
>>  > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>  >
>>
>>  - --
>>  Richard Holland (BioMart)
>>  EMBL EBI, Wellcome Trust Genome Campus,
>>  Hinxton, Cambridgeshire CB10 1SD, UK
>>  Tel. +44 (0)1223 494416
>>
>>  http://www.biomart.org/
>>  http://www.biojava.org/
>>  -----BEGIN PGP SIGNATURE-----
>>  Version: GnuPG v1.4.2.2 (GNU/Linux)
>>  Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>>  iD8DBQFHy7m04C5LeMEKA/QRAj05AJ9SBrv6yz8qvhwbmTrLZVfmwBuHTACgiq57
>>  +J0EpviSyp2Qq00m4A8xLUA=
>>  =re75
>>  -----END PGP SIGNATURE-----
>>
>>
>> _______________________________________________
>>  Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Thu Mar  6 01:24:32 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 6 Mar 2008 14:24:32 +0800
Subject: [Biojava-l] proposal to drop BioSQL Singapore version support from
	BJ version 1.6 onwards
Message-ID: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>

Hi all -

With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate
ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC
mappings to the BioSQL (Singapore) are now outdated.  We have not been
supporting these for some time.

Unless people are still actively using these mappings I would propose
that we drop them from the upcoming BioJava 1.6.  This would remove
some cruft from the code base and would also mean we can drop about 4
jar files from the lib (commons-pool etc).

Are there any strong arguments for or against?

- Mark

From ayates at ebi.ac.uk  Thu Mar  6 04:10:25 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 6 Mar 2008 09:10:25 +0000
Subject: [Biojava-l] [Biojava-dev] proposal to drop BioSQL Singapore
	version support from BJ version 1.6 onwards
In-Reply-To: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>
References: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>
Message-ID: <E6C0FD35-F40F-4B5A-B8AE-9CB320E43429@ebi.ac.uk>

+1

Maintaining two apis is always a bad idea

On 6 Mar 2008, at 06:24, Mark Schreiber wrote:

> Hi all -
>
> With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate
> ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC
> mappings to the BioSQL (Singapore) are now outdated.  We have not been
> supporting these for some time.
>
> Unless people are still actively using these mappings I would propose
> that we drop them from the upcoming BioJava 1.6.  This would remove
> some cruft from the code base and would also mean we can drop about 4
> jar files from the lib (commons-pool etc).
>
> Are there any strong arguments for or against?
>
> - Mark
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From awollhe at gwdg.de  Thu Mar  6 07:41:59 2008
From: awollhe at gwdg.de (Antje Wollherr)
Date: Thu, 06 Mar 2008 13:41:59 +0100
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
Message-ID: <1204807319.23262.11.camel@antje-desktop>

Hello biojava people,

I am new to this list and also not very familiar with BioJava. I was
trying to parse an EMBL File and extract the dna sequence with
RichSequence.IOTools.readEMBLDNA(br, ns); . 

For most of the embl files this isn't a problem, but the file with
accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
saying the sequence could not be read.

Can somebody tell where the problem is or how it can be solved?
I'm using BioJava 1.5.

Thank you a lot

Antje

Here is the error message:

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

Format_object=org.biojavax.bio.seq.io.EMBLFormat
Accession=AL009126
Id=not set
Comments=Unable to handle contig assemblies just yet
Parse_block=
Stack trace follows ....


	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
	at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
	at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
	... 2 more



From holland at ebi.ac.uk  Thu Mar  6 08:29:30 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 06 Mar 2008 13:29:30 +0000
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
In-Reply-To: <1204807319.23262.11.camel@antje-desktop>
References: <1204807319.23262.11.camel@antje-desktop>
Message-ID: <47CFF1BA.7060003@ebi.ac.uk>

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The error message says it all:

 Comments=Unable to handle contig assemblies just yet

BioJava does not yet support EMBL contig files such as AL009126.

cheers,
Richard

Antje Wollherr wrote:
> Hello biojava people,
> 
> I am new to this list and also not very familiar with BioJava. I was
> trying to parse an EMBL File and extract the dna sequence with
> RichSequence.IOTools.readEMBLDNA(br, ns); . 
> 
> For most of the embl files this isn't a problem, but the file with
> accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
> saying the sequence could not be read.
> 
> Can somebody tell where the problem is or how it can be solved?
> I'm using BioJava 1.5.
> 
> Thank you a lot
> 
> Antje
> 
> Here is the error message:
> 
>  Exception Has Occurred During Parsing. 
> Please submit the details that follow to biojava-l at biojava.org or post a
> bug report to http://bugzilla.open-bio.org/ 
> 
> Format_object=org.biojavax.bio.seq.io.EMBLFormat
> Accession=AL009126
> Id=not set
> Comments=Unable to handle contig assemblies just yet
> Parse_block=
> Stack trace follows ....
> 
> 
> 	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
> 	at
> org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> 	at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> 	... 2 more
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From awollhe at gwdg.de  Thu Mar  6 08:57:39 2008
From: awollhe at gwdg.de (Antje Wollherr)
Date: Thu, 06 Mar 2008 14:57:39 +0100
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
In-Reply-To: <47CFF1BA.7060003@ebi.ac.uk>
References: <1204807319.23262.11.camel@antje-desktop>
	<47CFF1BA.7060003@ebi.ac.uk>
Message-ID: <1204811859.24352.16.camel@antje-desktop>

Hallo Richard,

thank you for the fast response. Now I understand, what the error
message means. Sorry for asking stupid questions but sometimes  I don't
see the wood for the trees. ;)

Cheers,

Antje


On Thu, 2008-03-06 at 13:29 +0000, Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> The error message says it all:
> 
>  Comments=Unable to handle contig assemblies just yet
> 
> BioJava does not yet support EMBL contig files such as AL009126.
> 
> cheers,
> Richard
> 
> Antje Wollherr wrote:
> > Hello biojava people,
> > 
> > I am new to this list and also not very familiar with BioJava. I was
> > trying to parse an EMBL File and extract the dna sequence with
> > RichSequence.IOTools.readEMBLDNA(br, ns); . 
> > 
> > For most of the embl files this isn't a problem, but the file with
> > accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
> > saying the sequence could not be read.
> > 
> > Can somebody tell where the problem is or how it can be solved?
> > I'm using BioJava 1.5.
> > 
> > Thank you a lot
> > 
> > Antje
> > 
> > Here is the error message:
> > 
> >  Exception Has Occurred During Parsing. 
> > Please submit the details that follow to biojava-l at biojava.org or post a
> > bug report to http://bugzilla.open-bio.org/ 
> > 
> > Format_object=org.biojavax.bio.seq.io.EMBLFormat
> > Accession=AL009126
> > Id=not set
> > Comments=Unable to handle contig assemblies just yet
> > Parse_block=
> > Stack trace follows ....
> > 
> > 
> > 	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
> > 	at
> > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> > 	at
> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> > 	... 2 more
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > 
> 
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
> 
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
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> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> 
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> DJIY1k+vicFOMoX4GCwdwGs=
> =8JwO
> -----END PGP SIGNATURE-----
> 
-- 
Antje Wollherr, Diplom-Bioinformatikerin
G?ttinger Genomlabor
Institut f?r Mikrobiologie und Genetik
Grisebachstra?e 8
37077 G?ttingen

Email: awollhe at gwdg.de
Tel.: 0551 393843
Fax: 0551 394195


From alex.johansson1 at gmail.com  Fri Mar  7 15:22:45 2008
From: alex.johansson1 at gmail.com (alex johansson)
Date: Fri, 7 Mar 2008 21:22:45 +0100
Subject: [Biojava-l] Dp newbie question!!
Message-ID: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>

Hi,

Iam a Cell biology student with a growing interest in biojava, although i
have a very basic biojava experience but the cookbook
examples makes it easy to get around with api. My question is very basic and
might sound very stupid, i followed the cookbook example on creating a HMMER
like profileHMM and made a profile with a set 12 training sequences (19bp)
and tested it with a test sequence with motif occuring twice.Below is the
output from the program:

Log Odds = 43.786769243019506
m-1 m-2 m-3 m-4 m-5 m-6 d-7 m-8 m-9 m-10 m-11 m-12 m-13 m-14 m-15 m-16 m-17
d-18 i-18 d-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19
i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 m-20 i-20

My Question is how to interpret these results?how do i know if the motif is
occuring twice and its location in the test sequence?? I know that 'm'
stands for match and 'i' and 'd' stands for insert and delete transitions in
the path from start to end.

I'd certainly appreciate if the biojava gurus out there could spend some of
their valuable time in explaining this.

Thank you for your time,

Cheers,
Alex J

From markjschreiber at gmail.com  Sat Mar  8 09:41:44 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 8 Mar 2008 22:41:44 +0800
Subject: [Biojava-l] Dp newbie question!!
In-Reply-To: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>
References: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>
Message-ID: <93b45ca50803080641v51a8111egbd3a8c34a8941c86@mail.gmail.com>

Hi Alex -

Good to know that the cookbook is helpful in getting you started.  You
are correct about the state path of matches and deletes etc.

The limitation of the model you probably used is that it doesn't loop
back on itself and can by definition find only one match to a repeated
motif.  There are two ways to deal with this. One would be to wire up
the model (set the transition alphabets and probs) so that the model
can repeat (or at least repeat the motif part).  The other would be to
apply the model to a sliding window.  The second approach requires
less understanding of the DP package but is much less efficient and if
you interested in interpreting the forwards and backwards probs it
would be a bit hard to correct for the sliding window.

Hope this helps.

- Mark

On Sat, Mar 8, 2008 at 4:22 AM, alex johansson
<alex.johansson1 at gmail.com> wrote:
> Hi,
>
> Iam a Cell biology student with a growing interest in biojava, although i
> have a very basic biojava experience but the cookbook
> examples makes it easy to get around with api. My question is very basic and
> might sound very stupid, i followed the cookbook example on creating a HMMER
> like profileHMM and made a profile with a set 12 training sequences (19bp)
> and tested it with a test sequence with motif occuring twice.Below is the
> output from the program:
>
> Log Odds = 43.786769243019506
> m-1 m-2 m-3 m-4 m-5 m-6 d-7 m-8 m-9 m-10 m-11 m-12 m-13 m-14 m-15 m-16 m-17
> d-18 i-18 d-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19
> i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 m-20 i-20
>
> My Question is how to interpret these results?how do i know if the motif is
> occuring twice and its location in the test sequence?? I know that 'm'
> stands for match and 'i' and 'd' stands for insert and delete transitions in
> the path from start to end.
>
> I'd certainly appreciate if the biojava gurus out there could spend some of
> their valuable time in explaining this.
>
> Thank you for your time,
>
> Cheers,
> Alex J
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From pwrose at ucsd.edu  Tue Mar 11 18:34:33 2008
From: pwrose at ucsd.edu (Peter Rose)
Date: Tue, 11 Mar 2008 15:34:33 -0700
Subject: [Biojava-l] [Job] Scientific Software Developer - RCSB PDB La Jolla,
	CA
Message-ID: <006701c883c8$14b0fb60$3e12f220$@edu>

The RCSB Protein Data Bank at the University of California San Diego has an
open position for a junior Scientific Software Developer:

http://joblink.ucsd.edu/bulletin/job.html?cat=new&job_id=45537

Please contact Dr. Peter Rose at pwrose at sdsc.edu or Dr. Phil Bourne at
bourne at sdsc.edu about this position. 





From pwrose at ucsd.edu  Wed Mar 12 20:21:48 2008
From: pwrose at ucsd.edu (Peter Rose)
Date: Wed, 12 Mar 2008 17:21:48 -0700
Subject: [Biojava-l] [Job] Lead Web Architect - RCSB PDB at UCSD, La Jolla,
	CA
Message-ID: <001901c884a0$3a4826e0$aed874a0$@edu>

The RCSB Protein Data Bank has an exciting position for a Lead Web Architect
to help shape the future presentation layer of the website.

A detailed description of the job is available:
http://joblink.ucsd.edu/bulletin/job.html?cat=new&job_id=44789

Please contact Dr. Peter Rose at pwrose at sdsc.edu or Dr. Phil Bourne at
bourne at sdsc.edu about this position.




From adf at ncgr.org  Thu Mar 13 15:06:40 2008
From: adf at ncgr.org (Andrew Farmer)
Date: Thu, 13 Mar 2008 13:06:40 -0600
Subject: [Biojava-l] using phred calls with ChromatogramGraphic produced
	from ab1 files
Message-ID: <47D97B40.2040100@ncgr.org>

Hi all-
I have been trying to use the ChromatogramGraphic class to display ABI 
chromatogram data, whilst relating this to alignments of sequences 
called from these trace files with phred. For example, if the user 
clicks a putatively polymorphic base in an alignment viewer, to scroll 
and highlight the region of the ChromatogramGraphic corresponding to the 
ase call. However, I seem to be having some difficulty in establishing 
correspondences between the phred base calls and the information shown 
in the graphic.

As far as I understand what is being displayed by ChromatogramGraphic, 
it is drawing "callboxes" around peaks corresponding to calls that are 
stored by Chromatogram, which in turn is storing information about the 
base calls that was encoded in the ABI file. These tend to differ 
substantially (e.g. in lower-quality areas) from the calls made by 
phred- e.g. an untrimmed phred-called sequence might have 1300 bases to 
the abi-called version's 900 bases. So, I am trying to find some way to 
get the ChromatogramGraphic callboxes to reflect the calls made by phred.

Has anyone else encountered this type of situation before? It appears 
that phred's phd output encodes a trace offset for each of its calls, so 
I would guess that one could conceivably overlay the phred calls into a 
chromatogram produced by the abi parser in order to get the callboxes to 
reflect phred's interpretation of the trace data.

I could be way off-base (no pun intended) in my interpretation, and 
would appreciate any insights from the gurus out there. And if this is 
more or less correct, and there is not yet a canned solution, any advice 
on how to go about coding it in a way that could be contributed back to 
the project would be great.

Thanks in advance
-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
---

From adf at ncgr.org  Thu Mar 13 19:27:46 2008
From: adf at ncgr.org (Andrew Farmer)
Date: Thu, 13 Mar 2008 17:27:46 -0600
Subject: [Biojava-l] jRe: using phred calls with ChromatogramGraphic
 produced from ab1 files
In-Reply-To: <Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
References: <47D97B40.2040100@ncgr.org>
	<Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
Message-ID: <47D9B872.4040308@ncgr.org>

Eric-
thanks very much for your insights, the phred -c trick might in fact be 
exactly what I need. If not, I will check out the other code you have 
sent and follow up off-list if I have further questions.


Andrew


Eric Haugen wrote:
> 
> Hi Andrew,
> 
> It looks like what I did three years ago was turn off the 
> ChromatogramGraphic's call boxes:
> 
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS, 
> Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, 
> Boolean.FALSE );
> 
> then set the range based on the chromat positions in the phred file:
> 
> graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, 
> startIndex );
> graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> 
> and finally just draw Phred's base calls myself based on the chromat 
> position scale.
> 
> I don't know if you'll find it useful, but I've attached 
> PhdSequence.java and support code which I use as an alternative to 
> PhredSequence currently in biojava, which I think ignores chromat 
> positions.
> 
> But the easiest solution may be to have "phred -c" convert your ABI 
> chromats to SCF files containing the phred base calls.
> 
> -- 
> Eric Haugen
> Software Engineer
> University of Washington Genome Center
> ehaugen at u.washington.edu
> (206) 616-7582
> 
> On Thu, 13 Mar 2008, Andrew Farmer wrote:
> 
>> Hi all-
>> I have been trying to use the ChromatogramGraphic class to display ABI 
>> chromatogram data, whilst relating this to alignments of sequences 
>> called from these trace files with phred. For example, if the user 
>> clicks a putatively polymorphic base in an alignment viewer, to scroll 
>> and highlight the region of the ChromatogramGraphic corresponding to 
>> the ase call. However, I seem to be having some difficulty in 
>> establishing correspondences between the phred base calls and the 
>> information shown in the graphic.
>>
>> As far as I understand what is being displayed by ChromatogramGraphic, 
>> it is drawing "callboxes" around peaks corresponding to calls that are 
>> stored by Chromatogram, which in turn is storing information about the 
>> base calls that was encoded in the ABI file. These tend to differ 
>> substantially (e.g. in lower-quality areas) from the calls made by 
>> phred- e.g. an untrimmed phred-called sequence might have 1300 bases 
>> to the abi-called version's 900 bases. So, I am trying to find some 
>> way to get the ChromatogramGraphic callboxes to reflect the calls made 
>> by phred.
>>
>> Has anyone else encountered this type of situation before? It appears 
>> that phred's phd output encodes a trace offset for each of its calls, 
>> so I would guess that one could conceivably overlay the phred calls 
>> into a chromatogram produced by the abi parser in order to get the 
>> callboxes to reflect phred's interpretation of the trace data.
>>
>> I could be way off-base (no pun intended) in my interpretation, and 
>> would appreciate any insights from the gurus out there. And if this is 
>> more or less correct, and there is not yet a canned solution, any 
>> advice on how to go about coding it in a way that could be contributed 
>> back to the project would be great.
>>
>> Thanks in advance
>> -- 
>>
>> Andrew Farmer
>> adf at ncgr.org
>> (505) 995-4464
>> Database Administrator/Software Developer
>> National Center for Genome Resources
>>
>> ---
>> "To live in the presence of great truths and eternal laws,
>> to be led by permanent ideals-
>> that is what keeps a man patient when the world ignores him,
>> and calm and unspoiled when the world praises him."
>> -Balzac
>> ---
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>

-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
---

From markjschreiber at gmail.com  Fri Mar 14 08:48:59 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 14 Mar 2008 20:48:59 +0800
Subject: [Biojava-l] jRe: using phred calls with ChromatogramGraphic
	produced from ab1 files
In-Reply-To: <47D9B872.4040308@ncgr.org>
References: <47D97B40.2040100@ncgr.org>
	<Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
	<47D9B872.4040308@ncgr.org>
Message-ID: <93b45ca50803140548y1fc37831m1f071c7bc4f95370@mail.gmail.com>

Some code examples like this would be great on the biojava.org
cookbook.  If people could add their GUI code that would be excellent.

- Mark

On Fri, Mar 14, 2008 at 7:27 AM, Andrew Farmer <adf at ncgr.org> wrote:
> Eric-
> thanks very much for your insights, the phred -c trick might in fact be
> exactly what I need. If not, I will check out the other code you have
> sent and follow up off-list if I have further questions.
>
>
> Andrew
>
>
> Eric Haugen wrote:
> >
> > Hi Andrew,
> >
> > It looks like what I did three years ago was turn off the
> > ChromatogramGraphic's call boxes:
> >
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS,
> > Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER,
> > Boolean.FALSE );
> >
> > then set the range based on the chromat positions in the phred file:
> >
> > graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE,
> > startIndex );
> > graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> >
> > and finally just draw Phred's base calls myself based on the chromat
> > position scale.
> >
> > I don't know if you'll find it useful, but I've attached
> > PhdSequence.java and support code which I use as an alternative to
> > PhredSequence currently in biojava, which I think ignores chromat
> > positions.
> >
> > But the easiest solution may be to have "phred -c" convert your ABI
> > chromats to SCF files containing the phred base calls.
> >
> > --
> > Eric Haugen
> > Software Engineer
> > University of Washington Genome Center
> > ehaugen at u.washington.edu
> > (206) 616-7582
> >
> > On Thu, 13 Mar 2008, Andrew Farmer wrote:
> >
> >> Hi all-
> >> I have been trying to use the ChromatogramGraphic class to display ABI
> >> chromatogram data, whilst relating this to alignments of sequences
> >> called from these trace files with phred. For example, if the user
> >> clicks a putatively polymorphic base in an alignment viewer, to scroll
> >> and highlight the region of the ChromatogramGraphic corresponding to
> >> the ase call. However, I seem to be having some difficulty in
> >> establishing correspondences between the phred base calls and the
> >> information shown in the graphic.
> >>
> >> As far as I understand what is being displayed by ChromatogramGraphic,
> >> it is drawing "callboxes" around peaks corresponding to calls that are
> >> stored by Chromatogram, which in turn is storing information about the
> >> base calls that was encoded in the ABI file. These tend to differ
> >> substantially (e.g. in lower-quality areas) from the calls made by
> >> phred- e.g. an untrimmed phred-called sequence might have 1300 bases
> >> to the abi-called version's 900 bases. So, I am trying to find some
> >> way to get the ChromatogramGraphic callboxes to reflect the calls made
> >> by phred.
> >>
> >> Has anyone else encountered this type of situation before? It appears
> >> that phred's phd output encodes a trace offset for each of its calls,
> >> so I would guess that one could conceivably overlay the phred calls
> >> into a chromatogram produced by the abi parser in order to get the
> >> callboxes to reflect phred's interpretation of the trace data.
> >>
> >> I could be way off-base (no pun intended) in my interpretation, and
> >> would appreciate any insights from the gurus out there. And if this is
> >> more or less correct, and there is not yet a canned solution, any
> >> advice on how to go about coding it in a way that could be contributed
> >> back to the project would be great.
> >>
> >> Thanks in advance
> >> --
> >>
> >> Andrew Farmer
> >> adf at ncgr.org
> >> (505) 995-4464
> >> Database Administrator/Software Developer
> >> National Center for Genome Resources
> >>
> >> ---
> >> "To live in the presence of great truths and eternal laws,
> >> to be led by permanent ideals-
> >> that is what keeps a man patient when the world ignores him,
> >> and calm and unspoiled when the world praises him."
> >> -Balzac
> >> ---
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
>
> --
>
> Andrew Farmer
> adf at ncgr.org
> (505) 995-4464
> Database Administrator/Software Developer
> National Center for Genome Resources
>
> ---
> "To live in the presence of great truths and eternal laws,
> to be led by permanent ideals-
> that is what keeps a man patient when the world ignores him,
> and calm and unspoiled when the world praises him."
> -Balzac
> ---
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From yangkuan81 at gmail.com  Sun Mar 23 02:42:14 2008
From: yangkuan81 at gmail.com (Kuan Yang)
Date: Sun, 23 Mar 2008 02:42:14 -0400
Subject: [Biojava-l] About ORFs
Message-ID: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>

Hi Guys,

I am new to biojava and don't know how to do a lot of things with it.
One of them is how to get ORF prediction with it. Any help will be
appreciated.
BTW, Is there a detailed manual for it?

Thanks

Kuan

From yangkuan81 at gmail.com  Sun Mar 23 04:17:52 2008
From: yangkuan81 at gmail.com (Kuan Yang)
Date: Sun, 23 Mar 2008 04:17:52 -0400
Subject: [Biojava-l] How to translate RNA into Proteins with different codon
	tables?
Message-ID: <a68367020803230117s4967436doe30073131063d0f8@mail.gmail.com>

Hi all,

Sorry, another question, how to translate a RNA into Protein with
different codon table?
All I can find is the "translate" method that uses the standard codon table (1).

Thanks you so much in advance!!!

Kuan

From markjschreiber at gmail.com  Sun Mar 23 08:46:44 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sun, 23 Mar 2008 20:46:44 +0800
Subject: [Biojava-l] About ORFs
In-Reply-To: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>
References: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>
Message-ID: <93b45ca50803230546w5a8d61b3y7f184d95f0e0c45b@mail.gmail.com>

Hi -

For a 'manual' of biojava, take a look at the documentation section of
the biojava wiki (www.biojava.org). Specifically the tutorial
(http://biojava.org/wiki/BioJava:Tutorial) and the cookbook
(http://biojava.org/wiki/BioJava:CookBook).

There is more than one way to get an ORF prediction. One way would be
to do a six frame translation
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames) a
more sophisticated way would be to make a Hidden Markov Model that
distinguishes coding ORFs from non coding ORFs. You could do this
using the DP package. There is no specific tutorial but you can get
some hints from the Dynamic Programming part of the cookbook.

One of the interesting things about BioJava is that it is much more
low level than something like EMBOSS. Rather than doing lots of things
it enables you to write your own programs to do things.

Hope this helps. Welcome to BioJava.

- Mark

On Sun, Mar 23, 2008 at 2:42 PM, Kuan Yang <yangkuan81 at gmail.com> wrote:
> Hi Guys,
>
> I am new to biojava and don't know how to do a lot of things with it.
> One of them is how to get ORF prediction with it. Any help will be
> appreciated.
> BTW, Is there a detailed manual for it?
>
> Thanks
>
> Kuan
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From martin.jones at ed.ac.uk  Thu Mar 27 09:45:50 2008
From: martin.jones at ed.ac.uk (Martin Jones)
Date: Thu, 27 Mar 2008 13:45:50 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank file
Message-ID: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>

Hi,

I'm just getting started with BioJava so this may be a simple
question.  I'm reading a RichSequence from a GenBank file and want to
get the gene name of each CDS feature.  The following code gets hold
of the features I'm interested in

for (Object o : mySeq.getFeatureSet()){
      RichFeature f = (RichFeature) o;
      if (f.getType().equals("CDS")){
            //get gene name here
      }
}

but I'm not sure how best to get the gene name.  The following seems to work:

for (Object o2 : f.getNoteSet()){
     Note n = (Note) o2;
     if (n.getTerm().getName().equals("gene")){
                 System.out.println("gene name is " + n.getValue());
     }
}

but seems overly verbose - ideally I'd like to be able to pass the
Feature to another part of my program,  but writing the above whenever
I want to get the name seems like overkill.  Is there a shorter way -
something along the lines of

String name = f.getNoteByName("gene").getValue();

Thanks in advance for any help.

PS one more question - is there a reason why e.g.  getNoteSet returns
a Set rather than a Set<Feature>, which makes it necessary to do all
the type casts?

Thanks,

Martin

From holland at ebi.ac.uk  Thu Mar 27 10:11:26 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 27 Mar 2008 14:11:26 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
Message-ID: <47EBAB0E.3020305@ebi.ac.uk>

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

Hello,

Your code for getting the Note named "gene" is correct. I agree, a
shorthand way of doing this would be lovely, but doesn't currently
exist. (Such a method would have to do the same thing internally
anyway). If you'd like to write one and add it in then you'd be most
welcome! :)

At the time that the BioJavaX extensions were written compatibility with
Java 1.4 was still required and so we could not make use of any new Java
features that were introduced in Java 1.5. Set<Feature>, being an
example of Generics, is one of these.

Future versions of BioJava will require the user to install Java 1.6 or
later and so we will be able to use these newer features in both new and
existing code, depending on feasibility (for instance it is not always
possible to convert older code to use Generics in a sensible manner, and
it is not always possible to write Generics code that can interface
sensibly with older non-Generics modules).

cheers,
Richard



Martin Jones wrote:
> Hi,
> 
> I'm just getting started with BioJava so this may be a simple
> question.  I'm reading a RichSequence from a GenBank file and want to
> get the gene name of each CDS feature.  The following code gets hold
> of the features I'm interested in
> 
> for (Object o : mySeq.getFeatureSet()){
>       RichFeature f = (RichFeature) o;
>       if (f.getType().equals("CDS")){
>             //get gene name here
>       }
> }
> 
> but I'm not sure how best to get the gene name.  The following seems to work:
> 
> for (Object o2 : f.getNoteSet()){
>      Note n = (Note) o2;
>      if (n.getTerm().getName().equals("gene")){
>                  System.out.println("gene name is " + n.getValue());
>      }
> }
> 
> but seems overly verbose - ideally I'd like to be able to pass the
> Feature to another part of my program,  but writing the above whenever
> I want to get the name seems like overkill.  Is there a shorter way -
> something along the lines of
> 
> String name = f.getNoteByName("gene").getValue();
> 
> Thanks in advance for any help.
> 
> PS one more question - is there a reason why e.g.  getNoteSet returns
> a Set rather than a Set<Feature>, which makes it necessary to do all
> the type casts?
> 
> Thanks,
> 
> Martin
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From su24 at st-andrews.ac.uk  Thu Mar 27 13:46:38 2008
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Thu, 27 Mar 2008 17:46:38 +0000
Subject: [Biojava-l] Problem
Message-ID: <1206639998.47ebdd7e5f32c@webmail.st-andrews.ac.uk>


Dear All,

I am attempting to split up a Fasta file of an entire genomes amino acid
sequences into separate files for each individual gene. I am simply reading the
Fasta file of the entire genome as a Sequence Db and then iterating around it
creating a new file for each Sequence and writing it out to that file. However
out of a Fasta file containing 13465 genes only 12945 are written out to their
own individual files. This does not occur in files which lack the termination
symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if you
could suggest any reason why this might occur as I am completely mystified.

Thanking you in advance,

Saif


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Dyers Brae
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk


From su24 at st-andrews.ac.uk  Thu Mar 27 13:46:40 2008
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Thu, 27 Mar 2008 17:46:40 +0000
Subject: [Biojava-l] Problem
Message-ID: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>


Dear All,

I am attempting to split up a Fasta file of an entire genomes amino acid
sequences into separate files for each individual gene. I am simply reading the
Fasta file of the entire genome as a Sequence Db and then iterating around it
creating a new file for each Sequence and writing it out to that file. However
out of a Fasta file containing 13465 genes only 12945 are written out to their
own individual files. This does not occur in files which lack the termination
symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if you
could suggest any reason why this might occur as I am completely mystified.

Thanking you in advance,

Saif


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Dyers Brae
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk


From holland at ebi.ac.uk  Thu Mar 27 14:16:41 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 27 Mar 2008 18:16:41 -0000 (GMT)
Subject: [Biojava-l] Problem
In-Reply-To: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>
References: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>
Message-ID: <42786.80.42.15.154.1206641801.squirrel@webmail.ebi.ac.uk>

I'm afraid we can't be much help unless we can see the actual code you
have written to do this job!

cheers,
Richard

On Thu, March 27, 2008 5:46 pm, Saif Ur-Rehman wrote:
>
> Dear All,
>
> I am attempting to split up a Fasta file of an entire genomes amino acid
> sequences into separate files for each individual gene. I am simply
> reading the
> Fasta file of the entire genome as a Sequence Db and then iterating around
> it
> creating a new file for each Sequence and writing it out to that file.
> However
> out of a Fasta file containing 13465 genes only 12945 are written out to
> their
> own individual files. This does not occur in files which lack the
> termination
> symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if
> you
> could suggest any reason why this might occur as I am completely
> mystified.
>
> Thanking you in advance,
>
> Saif
>
>
> -------------------------------------------------------------------------------
> Saif Ur-Rehman
> Research Student
> The Centre for Evolution, Genes & Genomics (CEGG)
> Dyers Brae
> School of Biology
> The University of St Andrews
> St Andrews,
> Fife
> Scotland,UK
>
> ------------------------------------------------------------------
> University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


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


From markjschreiber at gmail.com  Thu Mar 27 21:55:38 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 28 Mar 2008 09:55:38 +0800
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
In-Reply-To: <47EBAB0E.3020305@ebi.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
	<47EBAB0E.3020305@ebi.ac.uk>
Message-ID: <93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>

These are good points.  Can we generify interfaces without breaking them?
Certainly the addition of generics to the biojavax packages would remove a
lot of nasty casting.  Adding convenience methods would certainly also help
biojavax code does get a bit verbose.  Again this would break interfaces
unless we put them in some kind of tools class.

These are certainly good points to remember for future designs (eg biojava2)
usability should be a test criteria as well. BioJavaX gives excellent ORM
with BioSQL and great capture of detail in it's parsers but the coding style
is a bit unwieldy. 2 out of 3 is not bad though : )

- Mark

On Thu, Mar 27, 2008 at 10:11 PM, Richard Holland <holland at ebi.ac.uk> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello,
>
> Your code for getting the Note named "gene" is correct. I agree, a
> shorthand way of doing this would be lovely, but doesn't currently
> exist. (Such a method would have to do the same thing internally
> anyway). If you'd like to write one and add it in then you'd be most
> welcome! :)
>
> At the time that the BioJavaX extensions were written compatibility with
> Java 1.4 was still required and so we could not make use of any new Java
> features that were introduced in Java 1.5. Set<Feature>, being an
> example of Generics, is one of these.
>
> Future versions of BioJava will require the user to install Java 1.6 or
> later and so we will be able to use these newer features in both new and
> existing code, depending on feasibility (for instance it is not always
> possible to convert older code to use Generics in a sensible manner, and
> it is not always possible to write Generics code that can interface
> sensibly with older non-Generics modules).
>
> cheers,
> Richard
>
>
>
> Martin Jones wrote:
> > Hi,
> >
> > I'm just getting started with BioJava so this may be a simple
> > question.  I'm reading a RichSequence from a GenBank file and want to
> > get the gene name of each CDS feature.  The following code gets hold
> > of the features I'm interested in
> >
> > for (Object o : mySeq.getFeatureSet()){
> >       RichFeature f = (RichFeature) o;
> >       if (f.getType().equals("CDS")){
> >             //get gene name here
> >       }
> > }
> >
> > but I'm not sure how best to get the gene name.  The following seems to
> work:
> >
> > for (Object o2 : f.getNoteSet()){
> >      Note n = (Note) o2;
> >      if (n.getTerm().getName().equals("gene")){
> >                  System.out.println("gene name is " + n.getValue());
> >      }
> > }
> >
> > but seems overly verbose - ideally I'd like to be able to pass the
> > Feature to another part of my program,  but writing the above whenever
> > I want to get the name seems like overkill.  Is there a shorter way -
> > something along the lines of
> >
> > String name = f.getNoteByName("gene").getValue();
> >
> > Thanks in advance for any help.
> >
> > PS one more question - is there a reason why e.g.  getNoteSet returns
> > a Set rather than a Set<Feature>, which makes it necessary to do all
> > the type casts?
> >
> > Thanks,
> >
> > Martin
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFH66sO4C5LeMEKA/QRAmq9AJ4qyMw4eGVYIMZjVf5jcADVRQmzpQCeOXej
> mak90aLUhSF60DrWeRtM8o0=
> =0EOE
> -----END PGP SIGNATURE-----
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From ayates at ebi.ac.uk  Fri Mar 28 05:17:54 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 28 Mar 2008 09:17:54 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>
	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
Message-ID: <47ECB7C2.3070800@ebi.ac.uk>

As with most things the answer is a yes & no. It shouldn't break 
interfaces as in the contract setup between the interface & a consumer 
since generics are erased after compilation.

However if we're looking at class incompatibility errors then it's quite 
likely that the new interface will have a different signature to the 
original one & may cause runtime errors in classes which haven't been 
recompiled against the new interface. A solution in some other projects 
is to have to sets of interfaces; one with generics & one without but 
that can be quite a nightmare to maintain.

Andy

Mark Schreiber wrote:
> These are good points.  Can we generify interfaces without breaking them?
> Certainly the addition of generics to the biojavax packages would remove a
> lot of nasty casting.  Adding convenience methods would certainly also help
> biojavax code does get a bit verbose.  Again this would break interfaces
> unless we put them in some kind of tools class.
> 
> These are certainly good points to remember for future designs (eg biojava2)
> usability should be a test criteria as well. BioJavaX gives excellent ORM
> with BioSQL and great capture of detail in it's parsers but the coding style
> is a bit unwieldy. 2 out of 3 is not bad though : )
> 
> - Mark
> 
> On Thu, Mar 27, 2008 at 10:11 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> 
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hello,
>>
>> Your code for getting the Note named "gene" is correct. I agree, a
>> shorthand way of doing this would be lovely, but doesn't currently
>> exist. (Such a method would have to do the same thing internally
>> anyway). If you'd like to write one and add it in then you'd be most
>> welcome! :)
>>
>> At the time that the BioJavaX extensions were written compatibility with
>> Java 1.4 was still required and so we could not make use of any new Java
>> features that were introduced in Java 1.5. Set<Feature>, being an
>> example of Generics, is one of these.
>>
>> Future versions of BioJava will require the user to install Java 1.6 or
>> later and so we will be able to use these newer features in both new and
>> existing code, depending on feasibility (for instance it is not always
>> possible to convert older code to use Generics in a sensible manner, and
>> it is not always possible to write Generics code that can interface
>> sensibly with older non-Generics modules).
>>
>> cheers,
>> Richard
>>
>>
>>
>> Martin Jones wrote:
>>> Hi,
>>>
>>> I'm just getting started with BioJava so this may be a simple
>>> question.  I'm reading a RichSequence from a GenBank file and want to
>>> get the gene name of each CDS feature.  The following code gets hold
>>> of the features I'm interested in
>>>
>>> for (Object o : mySeq.getFeatureSet()){
>>>       RichFeature f = (RichFeature) o;
>>>       if (f.getType().equals("CDS")){
>>>             //get gene name here
>>>       }
>>> }
>>>
>>> but I'm not sure how best to get the gene name.  The following seems to
>> work:
>>> for (Object o2 : f.getNoteSet()){
>>>      Note n = (Note) o2;
>>>      if (n.getTerm().getName().equals("gene")){
>>>                  System.out.println("gene name is " + n.getValue());
>>>      }
>>> }
>>>
>>> but seems overly verbose - ideally I'd like to be able to pass the
>>> Feature to another part of my program,  but writing the above whenever
>>> I want to get the name seems like overkill.  Is there a shorter way -
>>> something along the lines of
>>>
>>> String name = f.getNoteByName("gene").getValue();
>>>
>>> Thanks in advance for any help.
>>>
>>> PS one more question - is there a reason why e.g.  getNoteSet returns
>>> a Set rather than a Set<Feature>, which makes it necessary to do all
>>> the type casts?
>>>
>>> Thanks,
>>>
>>> Martin
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>> - --
>> Richard Holland (BioMart)
>> EMBL EBI, Wellcome Trust Genome Campus,
>> Hinxton, Cambridgeshire CB10 1SD, UK
>> Tel. +44 (0)1223 494416
>>
>> http://www.biomart.org/
>> http://www.biojava.org/
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.2.2 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>> iD8DBQFH66sO4C5LeMEKA/QRAmq9AJ4qyMw4eGVYIMZjVf5jcADVRQmzpQCeOXej
>> mak90aLUhSF60DrWeRtM8o0=
>> =0EOE
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From ap3 at sanger.ac.uk  Fri Mar 28 06:50:34 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Fri, 28 Mar 2008 10:50:34 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
In-Reply-To: <47ECB7C2.3070800@ebi.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>
	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
	<47ECB7C2.3070800@ebi.ac.uk>
Message-ID: <7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>


>> These are good points.  Can we generify interfaces without  
>> breaking them?



I don;t think that adding generics will break anything, e.g.

old code:

public interface MyTest {
	public Set getFeatures()
}

then some code that uses this:

public void myFoo(){

	MyTest test = new MyTestImpl();

	Set features = test.getFeatures();
}

this call will not break, even if we change the MyTest interface to:

	public Set<Feature> getFeatures()

MyTestImpl will get some warnings (in my eclipse), to ensure the type  
safety, but that is all.

Andreas





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

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

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




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

From holland at ebi.ac.uk  Fri Mar 28 07:47:38 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 28 Mar 2008 11:47:38 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>	<47ECB7C2.3070800@ebi.ac.uk>
	<7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>
Message-ID: <47ECDADA.4050800@ebi.ac.uk>

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

I was more worried about breaking concepts than breaking code.

For instance, the concept of a SymbolList can be almost completely
replaced by the use of a standard genericised colleciton, e.g.
List<DNASymbol> or List<RNASymbol> .

Likewise, the concept of a SequenceIterator is really just an
Iterator<Sequence> (or maybe Iterator<? extends Sequence> ? ).

cheers,
Richard

Andreas Prlic wrote:
> 
>>> These are good points.  Can we generify interfaces without breaking
>>> them?
> 
> 
> 
> I don;t think that adding generics will break anything, e.g.
> 
> old code:
> 
> public interface MyTest {
>     public Set getFeatures()
> }
> 
> then some code that uses this:
> 
> public void myFoo(){
> 
>     MyTest test = new MyTestImpl();
> 
>     Set features = test.getFeatures();
> }
> 
> this call will not break, even if we change the MyTest interface to:
> 
>     public Set<Feature> getFeatures()
> 
> MyTestImpl will get some warnings (in my eclipse), to ensure the type
> safety, but that is all.
> 
> Andreas
> 
> 
> 
> 
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                               Hinxton, Cambridge CB10 1SA, UK
>                               +44 (0) 1223 49 6891
> 
> -----------------------------------------------------------------------
> 
> 
> 
> 
> --The Wellcome Trust Sanger Institute is operated by Genome
> ResearchLimited, a charity registered in England with number 1021457 and
> acompany registered in England with number 2742969, whose
> registeredoffice is 215 Euston Road, London, NW1
> 2BE._______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From philipheller at comcast.net  Fri Mar 28 11:46:33 2008
From: philipheller at comcast.net (philipheller at comcast.net)
Date: Fri, 28 Mar 2008 15:46:33 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
Message-ID: <032820081546.8495.47ED12D9000D53B70000212F22007507849D0A04040A089F070407089F@comcast.net>

An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20080328/94cc7ae0/attachment.pl>

From markjschreiber at gmail.com  Sat Mar  1 02:30:42 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 1 Mar 2008 10:30:42 +0800
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <47C839BC.8030506@ebi.ac.uk>
References: <47C839BC.8030506@ebi.ac.uk>
Message-ID: <93b45ca50802291830l58628d0bqbed7a1feb0e85e89@mail.gmail.com>

Hi -

This could be a corner case. Can you provide the code that actually
generates this error?

- Mark

On Sat, Mar 1, 2008 at 12:58 AM, Arnaud Kerhornou <arnaud at ebi.ac.uk> wrote:
> Hi everyone,
>
> I don't think the RichLocation.Tools.merge(Collection members) method is
> doing it right.
>
> e.g. Input:
> biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
> Expected output:1157624..1158895
>
> But I get: join:[1157624..1158420,1158420..1158894]
>
> I think the code should have the extra line: parent = union;
> just after c=p; statement line 18 (See source code below),
> otherwise it doesn't take into account the newly generated location.
>
> Is that right ?
>
> Thanks
> Arnaud
>
> Source code:
>
> 1    public static Collection merge(Collection members) {
> 2            // flatten them out first so we don't end up recursing
> 3            List membersList = new ArrayList(flatten(members));
> 4            // all members are now singles so we can use single vs
> single union operations
> 5            if (membersList.size()>1) {
> 6                for (int p = 0; p < (membersList.size()-1); p++) {
> 7                    RichLocation parent = (RichLocation)membersList.get(p);
> 8                    for (int c = p+1; c < membersList.size(); c++) {
> 9                        RichLocation child =
> (RichLocation)membersList.get(c);
> 10                       RichLocation union =
> (RichLocation)parent.union(child);
> 11                        // if parent can merge with child
> 12                        if (union.isContiguous()) {
> 13                           // replace parent with union
> 14                            membersList.set(p,union);
> 15                            // remove child
> 16                            membersList.remove(c);
> 17                            // check all children again
> 18                            c=p;
> 19                        }
> 20                    }
> 21                }
> 22            }
> 23            return membersList;
> 24        }
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From holland at ebi.ac.uk  Mon Mar  3 08:41:58 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 03 Mar 2008 08:41:58 +0000
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <47C839BC.8030506@ebi.ac.uk>
References: <47C839BC.8030506@ebi.ac.uk>
Message-ID: <47CBB9D6.8090705@ebi.ac.uk>

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

Arnaud - you are correct.

cheers,
Richard

Arnaud Kerhornou wrote:
> Hi everyone,
> 
> I don't think the RichLocation.Tools.merge(Collection members) method is
> doing it right.
> 
> e.g. Input:
> biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
> Expected output:1157624..1158895
> 
> But I get: join:[1157624..1158420,1158420..1158894]
> 
> I think the code should have the extra line: parent = union;
> just after c=p; statement line 18 (See source code below),
> otherwise it doesn't take into account the newly generated location.
> 
> Is that right ?
> 
> Thanks
> Arnaud
> 
> Source code:
> 
> 1    public static Collection merge(Collection members) {
> 2            // flatten them out first so we don't end up recursing
> 3            List membersList = new ArrayList(flatten(members));
> 4            // all members are now singles so we can use single vs
> single union operations
> 5            if (membersList.size()>1) {
> 6                for (int p = 0; p < (membersList.size()-1); p++) {
> 7                    RichLocation parent =
> (RichLocation)membersList.get(p);
> 8                    for (int c = p+1; c < membersList.size(); c++) {
> 9                        RichLocation child =
> (RichLocation)membersList.get(c);
> 10                       RichLocation union =
> (RichLocation)parent.union(child);
> 11                        // if parent can merge with child
> 12                        if (union.isContiguous()) {
> 13                           // replace parent with union
> 14                            membersList.set(p,union);
> 15                            // remove child
> 16                            membersList.remove(c);
> 17                            // check all children again
> 18                            c=p;
> 19                        }
> 20                    }
> 21                }
> 22            }
> 23            return membersList;
> 24        }
>       _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Wed Mar  5 02:16:13 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 5 Mar 2008 10:16:13 +0800
Subject: [Biojava-l] biojava group on linkedin
Message-ID: <93b45ca50803041816s28728b2eme99edcda863d252d@mail.gmail.com>

Hi -

BioJava is now a group on the networking site, linkedin
(www.linkedin.com). If you have been involved in biojava in some way
and want to join you can find it on the list of available groups when
editing your profile.

Best regards,

- Mark


From markjschreiber at gmail.com  Wed Mar  5 02:20:52 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 5 Mar 2008 10:20:52 +0800
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <47CBB9D6.8090705@ebi.ac.uk>
References: <47C839BC.8030506@ebi.ac.uk> <47CBB9D6.8090705@ebi.ac.uk>
Message-ID: <93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>

Just to follow up...

Has there been a fix checked in for this?

- Mark

On Mon, Mar 3, 2008 at 4:41 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
>  Hash: SHA1
>
>  Arnaud - you are correct.
>
>  cheers,
>  Richard
>
>
>
>  Arnaud Kerhornou wrote:
>  > Hi everyone,
>  >
>  > I don't think the RichLocation.Tools.merge(Collection members) method is
>  > doing it right.
>  >
>  > e.g. Input:
>  > biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
>  > Expected output:1157624..1158895
>  >
>  > But I get: join:[1157624..1158420,1158420..1158894]
>  >
>  > I think the code should have the extra line: parent = union;
>  > just after c=p; statement line 18 (See source code below),
>  > otherwise it doesn't take into account the newly generated location.
>  >
>  > Is that right ?
>  >
>  > Thanks
>  > Arnaud
>  >
>  > Source code:
>  >
>  > 1    public static Collection merge(Collection members) {
>  > 2            // flatten them out first so we don't end up recursing
>  > 3            List membersList = new ArrayList(flatten(members));
>  > 4            // all members are now singles so we can use single vs
>  > single union operations
>  > 5            if (membersList.size()>1) {
>  > 6                for (int p = 0; p < (membersList.size()-1); p++) {
>  > 7                    RichLocation parent =
>  > (RichLocation)membersList.get(p);
>  > 8                    for (int c = p+1; c < membersList.size(); c++) {
>  > 9                        RichLocation child =
>  > (RichLocation)membersList.get(c);
>  > 10                       RichLocation union =
>  > (RichLocation)parent.union(child);
>  > 11                        // if parent can merge with child
>  > 12                        if (union.isContiguous()) {
>  > 13                           // replace parent with union
>  > 14                            membersList.set(p,union);
>  > 15                            // remove child
>  > 16                            membersList.remove(c);
>  > 17                            // check all children again
>  > 18                            c=p;
>  > 19                        }
>  > 20                    }
>  > 21                }
>  > 22            }
>  > 23            return membersList;
>  > 24        }
>  >       _______________________________________________
>  > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>  >
>
>  - --
>  Richard Holland (BioMart)
>  EMBL EBI, Wellcome Trust Genome Campus,
>  Hinxton, Cambridgeshire CB10 1SD, UK
>  Tel. +44 (0)1223 494416
>
>  http://www.biomart.org/
>  http://www.biojava.org/
>  -----BEGIN PGP SIGNATURE-----
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>
>  iD8DBQFHy7m04C5LeMEKA/QRAj05AJ9SBrv6yz8qvhwbmTrLZVfmwBuHTACgiq57
>  +J0EpviSyp2Qq00m4A8xLUA=
>  =re75
>  -----END PGP SIGNATURE-----
>
>
> _______________________________________________
>  Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From holland at ebi.ac.uk  Wed Mar  5 08:35:24 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 05 Mar 2008 08:35:24 +0000
Subject: [Biojava-l] RichLocation.Tools.merge(Collection members) method
In-Reply-To: <93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>
References: <47C839BC.8030506@ebi.ac.uk> <47CBB9D6.8090705@ebi.ac.uk>
	<93b45ca50803041820i38b06a68m9308e00eefb2824c@mail.gmail.com>
Message-ID: <47CE5B4C.3080506@ebi.ac.uk>

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

Not that I'm aware of.

Mark Schreiber wrote:
> Just to follow up...
> 
> Has there been a fix checked in for this?
> 
> - Mark
> 
> On Mon, Mar 3, 2008 at 4:41 PM, Richard Holland <holland at ebi.ac.uk> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>>  Hash: SHA1
>>
>>  Arnaud - you are correct.
>>
>>  cheers,
>>  Richard
>>
>>
>>
>>  Arnaud Kerhornou wrote:
>>  > Hi everyone,
>>  >
>>  > I don't think the RichLocation.Tools.merge(Collection members) method is
>>  > doing it right.
>>  >
>>  > e.g. Input:
>>  > biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
>>  > Expected output:1157624..1158895
>>  >
>>  > But I get: join:[1157624..1158420,1158420..1158894]
>>  >
>>  > I think the code should have the extra line: parent = union;
>>  > just after c=p; statement line 18 (See source code below),
>>  > otherwise it doesn't take into account the newly generated location.
>>  >
>>  > Is that right ?
>>  >
>>  > Thanks
>>  > Arnaud
>>  >
>>  > Source code:
>>  >
>>  > 1    public static Collection merge(Collection members) {
>>  > 2            // flatten them out first so we don't end up recursing
>>  > 3            List membersList = new ArrayList(flatten(members));
>>  > 4            // all members are now singles so we can use single vs
>>  > single union operations
>>  > 5            if (membersList.size()>1) {
>>  > 6                for (int p = 0; p < (membersList.size()-1); p++) {
>>  > 7                    RichLocation parent =
>>  > (RichLocation)membersList.get(p);
>>  > 8                    for (int c = p+1; c < membersList.size(); c++) {
>>  > 9                        RichLocation child =
>>  > (RichLocation)membersList.get(c);
>>  > 10                       RichLocation union =
>>  > (RichLocation)parent.union(child);
>>  > 11                        // if parent can merge with child
>>  > 12                        if (union.isContiguous()) {
>>  > 13                           // replace parent with union
>>  > 14                            membersList.set(p,union);
>>  > 15                            // remove child
>>  > 16                            membersList.remove(c);
>>  > 17                            // check all children again
>>  > 18                            c=p;
>>  > 19                        }
>>  > 20                    }
>>  > 21                }
>>  > 22            }
>>  > 23            return membersList;
>>  > 24        }
>>  >       _______________________________________________
>>  > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>  >
>>
>>  - --
>>  Richard Holland (BioMart)
>>  EMBL EBI, Wellcome Trust Genome Campus,
>>  Hinxton, Cambridgeshire CB10 1SD, UK
>>  Tel. +44 (0)1223 494416
>>
>>  http://www.biomart.org/
>>  http://www.biojava.org/
>>  -----BEGIN PGP SIGNATURE-----
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>>  Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>>  iD8DBQFHy7m04C5LeMEKA/QRAj05AJ9SBrv6yz8qvhwbmTrLZVfmwBuHTACgiq57
>>  +J0EpviSyp2Qq00m4A8xLUA=
>>  =re75
>>  -----END PGP SIGNATURE-----
>>
>>
>> _______________________________________________
>>  Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From markjschreiber at gmail.com  Thu Mar  6 06:24:32 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 6 Mar 2008 14:24:32 +0800
Subject: [Biojava-l] proposal to drop BioSQL Singapore version support from
	BJ version 1.6 onwards
Message-ID: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>

Hi all -

With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate
ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC
mappings to the BioSQL (Singapore) are now outdated.  We have not been
supporting these for some time.

Unless people are still actively using these mappings I would propose
that we drop them from the upcoming BioJava 1.6.  This would remove
some cruft from the code base and would also mean we can drop about 4
jar files from the lib (commons-pool etc).

Are there any strong arguments for or against?

- Mark


From ayates at ebi.ac.uk  Thu Mar  6 09:10:25 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 6 Mar 2008 09:10:25 +0000
Subject: [Biojava-l] [Biojava-dev] proposal to drop BioSQL Singapore
	version support from BJ version 1.6 onwards
In-Reply-To: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>
References: <93b45ca50803052224y5434d6d9t35fa180f33db35ca@mail.gmail.com>
Message-ID: <E6C0FD35-F40F-4B5A-B8AE-9CB320E43429@ebi.ac.uk>

+1

Maintaining two apis is always a bad idea

On 6 Mar 2008, at 06:24, Mark Schreiber wrote:

> Hi all -
>
> With the formal release of BioSQL v1.0 (Tokyo) and the new Hibernate
> ORM mapping to BioSQL offered in BioJava 1.5 (BioJavaX) the older JDBC
> mappings to the BioSQL (Singapore) are now outdated.  We have not been
> supporting these for some time.
>
> Unless people are still actively using these mappings I would propose
> that we drop them from the upcoming BioJava 1.6.  This would remove
> some cruft from the code base and would also mean we can drop about 4
> jar files from the lib (commons-pool etc).
>
> Are there any strong arguments for or against?
>
> - Mark
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From awollhe at gwdg.de  Thu Mar  6 12:41:59 2008
From: awollhe at gwdg.de (Antje Wollherr)
Date: Thu, 06 Mar 2008 13:41:59 +0100
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
Message-ID: <1204807319.23262.11.camel@antje-desktop>

Hello biojava people,

I am new to this list and also not very familiar with BioJava. I was
trying to parse an EMBL File and extract the dna sequence with
RichSequence.IOTools.readEMBLDNA(br, ns); . 

For most of the embl files this isn't a problem, but the file with
accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
saying the sequence could not be read.

Can somebody tell where the problem is or how it can be solved?
I'm using BioJava 1.5.

Thank you a lot

Antje

Here is the error message:

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

Format_object=org.biojavax.bio.seq.io.EMBLFormat
Accession=AL009126
Id=not set
Comments=Unable to handle contig assemblies just yet
Parse_block=
Stack trace follows ....


	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
	at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
	at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
	... 2 more




From holland at ebi.ac.uk  Thu Mar  6 13:29:30 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 06 Mar 2008 13:29:30 +0000
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
In-Reply-To: <1204807319.23262.11.camel@antje-desktop>
References: <1204807319.23262.11.camel@antje-desktop>
Message-ID: <47CFF1BA.7060003@ebi.ac.uk>

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

The error message says it all:

 Comments=Unable to handle contig assemblies just yet

BioJava does not yet support EMBL contig files such as AL009126.

cheers,
Richard

Antje Wollherr wrote:
> Hello biojava people,
> 
> I am new to this list and also not very familiar with BioJava. I was
> trying to parse an EMBL File and extract the dna sequence with
> RichSequence.IOTools.readEMBLDNA(br, ns); . 
> 
> For most of the embl files this isn't a problem, but the file with
> accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
> saying the sequence could not be read.
> 
> Can somebody tell where the problem is or how it can be solved?
> I'm using BioJava 1.5.
> 
> Thank you a lot
> 
> Antje
> 
> Here is the error message:
> 
>  Exception Has Occurred During Parsing. 
> Please submit the details that follow to biojava-l at biojava.org or post a
> bug report to http://bugzilla.open-bio.org/ 
> 
> Format_object=org.biojavax.bio.seq.io.EMBLFormat
> Accession=AL009126
> Id=not set
> Comments=Unable to handle contig assemblies just yet
> Parse_block=
> Stack trace follows ....
> 
> 
> 	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
> 	at
> org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> 	at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> 	... 2 more
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From awollhe at gwdg.de  Thu Mar  6 13:57:39 2008
From: awollhe at gwdg.de (Antje Wollherr)
Date: Thu, 06 Mar 2008 14:57:39 +0100
Subject: [Biojava-l] Problem with EMBL and RichStreamReader
In-Reply-To: <47CFF1BA.7060003@ebi.ac.uk>
References: <1204807319.23262.11.camel@antje-desktop>
	<47CFF1BA.7060003@ebi.ac.uk>
Message-ID: <1204811859.24352.16.camel@antje-desktop>

Hallo Richard,

thank you for the fast response. Now I understand, what the error
message means. Sorry for asking stupid questions but sometimes  I don't
see the wood for the trees. ;)

Cheers,

Antje


On Thu, 2008-03-06 at 13:29 +0000, Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> The error message says it all:
> 
>  Comments=Unable to handle contig assemblies just yet
> 
> BioJava does not yet support EMBL contig files such as AL009126.
> 
> cheers,
> Richard
> 
> Antje Wollherr wrote:
> > Hello biojava people,
> > 
> > I am new to this list and also not very familiar with BioJava. I was
> > trying to parse an EMBL File and extract the dna sequence with
> > RichSequence.IOTools.readEMBLDNA(br, ns); . 
> > 
> > For most of the embl files this isn't a problem, but the file with
> > accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
> > saying the sequence could not be read.
> > 
> > Can somebody tell where the problem is or how it can be solved?
> > I'm using BioJava 1.5.
> > 
> > Thank you a lot
> > 
> > Antje
> > 
> > Here is the error message:
> > 
> >  Exception Has Occurred During Parsing. 
> > Please submit the details that follow to biojava-l at biojava.org or post a
> > bug report to http://bugzilla.open-bio.org/ 
> > 
> > Format_object=org.biojavax.bio.seq.io.EMBLFormat
> > Accession=AL009126
> > Id=not set
> > Comments=Unable to handle contig assemblies just yet
> > Parse_block=
> > Stack trace follows ....
> > 
> > 
> > 	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
> > 	at
> > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> > 	at
> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> > 	... 2 more
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > 
> 
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
> 
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
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> 
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> DJIY1k+vicFOMoX4GCwdwGs=
> =8JwO
> -----END PGP SIGNATURE-----
> 
-- 
Antje Wollherr, Diplom-Bioinformatikerin
G?ttinger Genomlabor
Institut f?r Mikrobiologie und Genetik
Grisebachstra?e 8
37077 G?ttingen

Email: awollhe at gwdg.de
Tel.: 0551 393843
Fax: 0551 394195



From alex.johansson1 at gmail.com  Fri Mar  7 20:22:45 2008
From: alex.johansson1 at gmail.com (alex johansson)
Date: Fri, 7 Mar 2008 21:22:45 +0100
Subject: [Biojava-l] Dp newbie question!!
Message-ID: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>

Hi,

Iam a Cell biology student with a growing interest in biojava, although i
have a very basic biojava experience but the cookbook
examples makes it easy to get around with api. My question is very basic and
might sound very stupid, i followed the cookbook example on creating a HMMER
like profileHMM and made a profile with a set 12 training sequences (19bp)
and tested it with a test sequence with motif occuring twice.Below is the
output from the program:

Log Odds = 43.786769243019506
m-1 m-2 m-3 m-4 m-5 m-6 d-7 m-8 m-9 m-10 m-11 m-12 m-13 m-14 m-15 m-16 m-17
d-18 i-18 d-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19
i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 m-20 i-20

My Question is how to interpret these results?how do i know if the motif is
occuring twice and its location in the test sequence?? I know that 'm'
stands for match and 'i' and 'd' stands for insert and delete transitions in
the path from start to end.

I'd certainly appreciate if the biojava gurus out there could spend some of
their valuable time in explaining this.

Thank you for your time,

Cheers,
Alex J


From markjschreiber at gmail.com  Sat Mar  8 14:41:44 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 8 Mar 2008 22:41:44 +0800
Subject: [Biojava-l] Dp newbie question!!
In-Reply-To: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>
References: <33380be30803071222l13357a33l4bf2c9e009d3d7fc@mail.gmail.com>
Message-ID: <93b45ca50803080641v51a8111egbd3a8c34a8941c86@mail.gmail.com>

Hi Alex -

Good to know that the cookbook is helpful in getting you started.  You
are correct about the state path of matches and deletes etc.

The limitation of the model you probably used is that it doesn't loop
back on itself and can by definition find only one match to a repeated
motif.  There are two ways to deal with this. One would be to wire up
the model (set the transition alphabets and probs) so that the model
can repeat (or at least repeat the motif part).  The other would be to
apply the model to a sliding window.  The second approach requires
less understanding of the DP package but is much less efficient and if
you interested in interpreting the forwards and backwards probs it
would be a bit hard to correct for the sliding window.

Hope this helps.

- Mark

On Sat, Mar 8, 2008 at 4:22 AM, alex johansson
<alex.johansson1 at gmail.com> wrote:
> Hi,
>
> Iam a Cell biology student with a growing interest in biojava, although i
> have a very basic biojava experience but the cookbook
> examples makes it easy to get around with api. My question is very basic and
> might sound very stupid, i followed the cookbook example on creating a HMMER
> like profileHMM and made a profile with a set 12 training sequences (19bp)
> and tested it with a test sequence with motif occuring twice.Below is the
> output from the program:
>
> Log Odds = 43.786769243019506
> m-1 m-2 m-3 m-4 m-5 m-6 d-7 m-8 m-9 m-10 m-11 m-12 m-13 m-14 m-15 m-16 m-17
> d-18 i-18 d-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19
> i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 m-20 i-20
>
> My Question is how to interpret these results?how do i know if the motif is
> occuring twice and its location in the test sequence?? I know that 'm'
> stands for match and 'i' and 'd' stands for insert and delete transitions in
> the path from start to end.
>
> I'd certainly appreciate if the biojava gurus out there could spend some of
> their valuable time in explaining this.
>
> Thank you for your time,
>
> Cheers,
> Alex J
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From pwrose at ucsd.edu  Tue Mar 11 22:34:33 2008
From: pwrose at ucsd.edu (Peter Rose)
Date: Tue, 11 Mar 2008 15:34:33 -0700
Subject: [Biojava-l] [Job] Scientific Software Developer - RCSB PDB La Jolla,
	CA
Message-ID: <006701c883c8$14b0fb60$3e12f220$@edu>

The RCSB Protein Data Bank at the University of California San Diego has an
open position for a junior Scientific Software Developer:

http://joblink.ucsd.edu/bulletin/job.html?cat=new&job_id=45537

Please contact Dr. Peter Rose at pwrose at sdsc.edu or Dr. Phil Bourne at
bourne at sdsc.edu about this position. 






From pwrose at ucsd.edu  Thu Mar 13 00:21:48 2008
From: pwrose at ucsd.edu (Peter Rose)
Date: Wed, 12 Mar 2008 17:21:48 -0700
Subject: [Biojava-l] [Job] Lead Web Architect - RCSB PDB at UCSD, La Jolla,
	CA
Message-ID: <001901c884a0$3a4826e0$aed874a0$@edu>

The RCSB Protein Data Bank has an exciting position for a Lead Web Architect
to help shape the future presentation layer of the website.

A detailed description of the job is available:
http://joblink.ucsd.edu/bulletin/job.html?cat=new&job_id=44789

Please contact Dr. Peter Rose at pwrose at sdsc.edu or Dr. Phil Bourne at
bourne at sdsc.edu about this position.





From adf at ncgr.org  Thu Mar 13 19:06:40 2008
From: adf at ncgr.org (Andrew Farmer)
Date: Thu, 13 Mar 2008 13:06:40 -0600
Subject: [Biojava-l] using phred calls with ChromatogramGraphic produced
	from ab1 files
Message-ID: <47D97B40.2040100@ncgr.org>

Hi all-
I have been trying to use the ChromatogramGraphic class to display ABI 
chromatogram data, whilst relating this to alignments of sequences 
called from these trace files with phred. For example, if the user 
clicks a putatively polymorphic base in an alignment viewer, to scroll 
and highlight the region of the ChromatogramGraphic corresponding to the 
ase call. However, I seem to be having some difficulty in establishing 
correspondences between the phred base calls and the information shown 
in the graphic.

As far as I understand what is being displayed by ChromatogramGraphic, 
it is drawing "callboxes" around peaks corresponding to calls that are 
stored by Chromatogram, which in turn is storing information about the 
base calls that was encoded in the ABI file. These tend to differ 
substantially (e.g. in lower-quality areas) from the calls made by 
phred- e.g. an untrimmed phred-called sequence might have 1300 bases to 
the abi-called version's 900 bases. So, I am trying to find some way to 
get the ChromatogramGraphic callboxes to reflect the calls made by phred.

Has anyone else encountered this type of situation before? It appears 
that phred's phd output encodes a trace offset for each of its calls, so 
I would guess that one could conceivably overlay the phred calls into a 
chromatogram produced by the abi parser in order to get the callboxes to 
reflect phred's interpretation of the trace data.

I could be way off-base (no pun intended) in my interpretation, and 
would appreciate any insights from the gurus out there. And if this is 
more or less correct, and there is not yet a canned solution, any advice 
on how to go about coding it in a way that could be contributed back to 
the project would be great.

Thanks in advance
-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
---


From adf at ncgr.org  Thu Mar 13 23:27:46 2008
From: adf at ncgr.org (Andrew Farmer)
Date: Thu, 13 Mar 2008 17:27:46 -0600
Subject: [Biojava-l] jRe: using phred calls with ChromatogramGraphic
 produced from ab1 files
In-Reply-To: <Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
References: <47D97B40.2040100@ncgr.org>
	<Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
Message-ID: <47D9B872.4040308@ncgr.org>

Eric-
thanks very much for your insights, the phred -c trick might in fact be 
exactly what I need. If not, I will check out the other code you have 
sent and follow up off-list if I have further questions.


Andrew


Eric Haugen wrote:
> 
> Hi Andrew,
> 
> It looks like what I did three years ago was turn off the 
> ChromatogramGraphic's call boxes:
> 
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS, 
> Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, 
> Boolean.FALSE );
> 
> then set the range based on the chromat positions in the phred file:
> 
> graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE, 
> startIndex );
> graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> 
> and finally just draw Phred's base calls myself based on the chromat 
> position scale.
> 
> I don't know if you'll find it useful, but I've attached 
> PhdSequence.java and support code which I use as an alternative to 
> PhredSequence currently in biojava, which I think ignores chromat 
> positions.
> 
> But the easiest solution may be to have "phred -c" convert your ABI 
> chromats to SCF files containing the phred base calls.
> 
> -- 
> Eric Haugen
> Software Engineer
> University of Washington Genome Center
> ehaugen at u.washington.edu
> (206) 616-7582
> 
> On Thu, 13 Mar 2008, Andrew Farmer wrote:
> 
>> Hi all-
>> I have been trying to use the ChromatogramGraphic class to display ABI 
>> chromatogram data, whilst relating this to alignments of sequences 
>> called from these trace files with phred. For example, if the user 
>> clicks a putatively polymorphic base in an alignment viewer, to scroll 
>> and highlight the region of the ChromatogramGraphic corresponding to 
>> the ase call. However, I seem to be having some difficulty in 
>> establishing correspondences between the phred base calls and the 
>> information shown in the graphic.
>>
>> As far as I understand what is being displayed by ChromatogramGraphic, 
>> it is drawing "callboxes" around peaks corresponding to calls that are 
>> stored by Chromatogram, which in turn is storing information about the 
>> base calls that was encoded in the ABI file. These tend to differ 
>> substantially (e.g. in lower-quality areas) from the calls made by 
>> phred- e.g. an untrimmed phred-called sequence might have 1300 bases 
>> to the abi-called version's 900 bases. So, I am trying to find some 
>> way to get the ChromatogramGraphic callboxes to reflect the calls made 
>> by phred.
>>
>> Has anyone else encountered this type of situation before? It appears 
>> that phred's phd output encodes a trace offset for each of its calls, 
>> so I would guess that one could conceivably overlay the phred calls 
>> into a chromatogram produced by the abi parser in order to get the 
>> callboxes to reflect phred's interpretation of the trace data.
>>
>> I could be way off-base (no pun intended) in my interpretation, and 
>> would appreciate any insights from the gurus out there. And if this is 
>> more or less correct, and there is not yet a canned solution, any 
>> advice on how to go about coding it in a way that could be contributed 
>> back to the project would be great.
>>
>> Thanks in advance
>> -- 
>>
>> Andrew Farmer
>> adf at ncgr.org
>> (505) 995-4464
>> Database Administrator/Software Developer
>> National Center for Genome Resources
>>
>> ---
>> "To live in the presence of great truths and eternal laws,
>> to be led by permanent ideals-
>> that is what keeps a man patient when the world ignores him,
>> and calm and unspoiled when the world praises him."
>> -Balzac
>> ---
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>

-- 

Andrew Farmer
adf at ncgr.org
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

---
"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
that is what keeps a man patient when the world ignores him,
and calm and unspoiled when the world praises him."
-Balzac
---


From markjschreiber at gmail.com  Fri Mar 14 12:48:59 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 14 Mar 2008 20:48:59 +0800
Subject: [Biojava-l] jRe: using phred calls with ChromatogramGraphic
	produced from ab1 files
In-Reply-To: <47D9B872.4040308@ncgr.org>
References: <47D97B40.2040100@ncgr.org>
	<Pine.WNT.4.64.0803131521440.892@csp26f1_uwgc.clients.nebula2.washington.edu>
	<47D9B872.4040308@ncgr.org>
Message-ID: <93b45ca50803140548y1fc37831m1f071c7bc4f95370@mail.gmail.com>

Some code examples like this would be great on the biojava.org
cookbook.  If people could add their GUI code that would be excellent.

- Mark

On Fri, Mar 14, 2008 at 7:27 AM, Andrew Farmer <adf at ncgr.org> wrote:
> Eric-
> thanks very much for your insights, the phred -c trick might in fact be
> exactly what I need. If not, I will check out the other code you have
> sent and follow up off-list if I have further questions.
>
>
> Andrew
>
>
> Eric Haugen wrote:
> >
> > Hi Andrew,
> >
> > It looks like what I did three years ago was turn off the
> > ChromatogramGraphic's call boxes:
> >
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS,
> > Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER,
> > Boolean.FALSE );
> >
> > then set the range based on the chromat positions in the phred file:
> >
> > graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE,
> > startIndex );
> > graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> >
> > and finally just draw Phred's base calls myself based on the chromat
> > position scale.
> >
> > I don't know if you'll find it useful, but I've attached
> > PhdSequence.java and support code which I use as an alternative to
> > PhredSequence currently in biojava, which I think ignores chromat
> > positions.
> >
> > But the easiest solution may be to have "phred -c" convert your ABI
> > chromats to SCF files containing the phred base calls.
> >
> > --
> > Eric Haugen
> > Software Engineer
> > University of Washington Genome Center
> > ehaugen at u.washington.edu
> > (206) 616-7582
> >
> > On Thu, 13 Mar 2008, Andrew Farmer wrote:
> >
> >> Hi all-
> >> I have been trying to use the ChromatogramGraphic class to display ABI
> >> chromatogram data, whilst relating this to alignments of sequences
> >> called from these trace files with phred. For example, if the user
> >> clicks a putatively polymorphic base in an alignment viewer, to scroll
> >> and highlight the region of the ChromatogramGraphic corresponding to
> >> the ase call. However, I seem to be having some difficulty in
> >> establishing correspondences between the phred base calls and the
> >> information shown in the graphic.
> >>
> >> As far as I understand what is being displayed by ChromatogramGraphic,
> >> it is drawing "callboxes" around peaks corresponding to calls that are
> >> stored by Chromatogram, which in turn is storing information about the
> >> base calls that was encoded in the ABI file. These tend to differ
> >> substantially (e.g. in lower-quality areas) from the calls made by
> >> phred- e.g. an untrimmed phred-called sequence might have 1300 bases
> >> to the abi-called version's 900 bases. So, I am trying to find some
> >> way to get the ChromatogramGraphic callboxes to reflect the calls made
> >> by phred.
> >>
> >> Has anyone else encountered this type of situation before? It appears
> >> that phred's phd output encodes a trace offset for each of its calls,
> >> so I would guess that one could conceivably overlay the phred calls
> >> into a chromatogram produced by the abi parser in order to get the
> >> callboxes to reflect phred's interpretation of the trace data.
> >>
> >> I could be way off-base (no pun intended) in my interpretation, and
> >> would appreciate any insights from the gurus out there. And if this is
> >> more or less correct, and there is not yet a canned solution, any
> >> advice on how to go about coding it in a way that could be contributed
> >> back to the project would be great.
> >>
> >> Thanks in advance
> >> --
> >>
> >> Andrew Farmer
> >> adf at ncgr.org
> >> (505) 995-4464
> >> Database Administrator/Software Developer
> >> National Center for Genome Resources
> >>
> >> ---
> >> "To live in the presence of great truths and eternal laws,
> >> to be led by permanent ideals-
> >> that is what keeps a man patient when the world ignores him,
> >> and calm and unspoiled when the world praises him."
> >> -Balzac
> >> ---
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
>
> --
>
> Andrew Farmer
> adf at ncgr.org
> (505) 995-4464
> Database Administrator/Software Developer
> National Center for Genome Resources
>
> ---
> "To live in the presence of great truths and eternal laws,
> to be led by permanent ideals-
> that is what keeps a man patient when the world ignores him,
> and calm and unspoiled when the world praises him."
> -Balzac
> ---
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From yangkuan81 at gmail.com  Sun Mar 23 06:42:14 2008
From: yangkuan81 at gmail.com (Kuan Yang)
Date: Sun, 23 Mar 2008 02:42:14 -0400
Subject: [Biojava-l] About ORFs
Message-ID: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>

Hi Guys,

I am new to biojava and don't know how to do a lot of things with it.
One of them is how to get ORF prediction with it. Any help will be
appreciated.
BTW, Is there a detailed manual for it?

Thanks

Kuan


From yangkuan81 at gmail.com  Sun Mar 23 08:17:52 2008
From: yangkuan81 at gmail.com (Kuan Yang)
Date: Sun, 23 Mar 2008 04:17:52 -0400
Subject: [Biojava-l] How to translate RNA into Proteins with different codon
	tables?
Message-ID: <a68367020803230117s4967436doe30073131063d0f8@mail.gmail.com>

Hi all,

Sorry, another question, how to translate a RNA into Protein with
different codon table?
All I can find is the "translate" method that uses the standard codon table (1).

Thanks you so much in advance!!!

Kuan


From markjschreiber at gmail.com  Sun Mar 23 12:46:44 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sun, 23 Mar 2008 20:46:44 +0800
Subject: [Biojava-l] About ORFs
In-Reply-To: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>
References: <a68367020803222342k2573811fi85892733ad8fb2d0@mail.gmail.com>
Message-ID: <93b45ca50803230546w5a8d61b3y7f184d95f0e0c45b@mail.gmail.com>

Hi -

For a 'manual' of biojava, take a look at the documentation section of
the biojava wiki (www.biojava.org). Specifically the tutorial
(http://biojava.org/wiki/BioJava:Tutorial) and the cookbook
(http://biojava.org/wiki/BioJava:CookBook).

There is more than one way to get an ORF prediction. One way would be
to do a six frame translation
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames) a
more sophisticated way would be to make a Hidden Markov Model that
distinguishes coding ORFs from non coding ORFs. You could do this
using the DP package. There is no specific tutorial but you can get
some hints from the Dynamic Programming part of the cookbook.

One of the interesting things about BioJava is that it is much more
low level than something like EMBOSS. Rather than doing lots of things
it enables you to write your own programs to do things.

Hope this helps. Welcome to BioJava.

- Mark

On Sun, Mar 23, 2008 at 2:42 PM, Kuan Yang <yangkuan81 at gmail.com> wrote:
> Hi Guys,
>
> I am new to biojava and don't know how to do a lot of things with it.
> One of them is how to get ORF prediction with it. Any help will be
> appreciated.
> BTW, Is there a detailed manual for it?
>
> Thanks
>
> Kuan
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From martin.jones at ed.ac.uk  Thu Mar 27 13:45:50 2008
From: martin.jones at ed.ac.uk (Martin Jones)
Date: Thu, 27 Mar 2008 13:45:50 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank file
Message-ID: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>

Hi,

I'm just getting started with BioJava so this may be a simple
question.  I'm reading a RichSequence from a GenBank file and want to
get the gene name of each CDS feature.  The following code gets hold
of the features I'm interested in

for (Object o : mySeq.getFeatureSet()){
      RichFeature f = (RichFeature) o;
      if (f.getType().equals("CDS")){
            //get gene name here
      }
}

but I'm not sure how best to get the gene name.  The following seems to work:

for (Object o2 : f.getNoteSet()){
     Note n = (Note) o2;
     if (n.getTerm().getName().equals("gene")){
                 System.out.println("gene name is " + n.getValue());
     }
}

but seems overly verbose - ideally I'd like to be able to pass the
Feature to another part of my program,  but writing the above whenever
I want to get the name seems like overkill.  Is there a shorter way -
something along the lines of

String name = f.getNoteByName("gene").getValue();

Thanks in advance for any help.

PS one more question - is there a reason why e.g.  getNoteSet returns
a Set rather than a Set<Feature>, which makes it necessary to do all
the type casts?

Thanks,

Martin


From holland at ebi.ac.uk  Thu Mar 27 14:11:26 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 27 Mar 2008 14:11:26 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
Message-ID: <47EBAB0E.3020305@ebi.ac.uk>

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

Hello,

Your code for getting the Note named "gene" is correct. I agree, a
shorthand way of doing this would be lovely, but doesn't currently
exist. (Such a method would have to do the same thing internally
anyway). If you'd like to write one and add it in then you'd be most
welcome! :)

At the time that the BioJavaX extensions were written compatibility with
Java 1.4 was still required and so we could not make use of any new Java
features that were introduced in Java 1.5. Set<Feature>, being an
example of Generics, is one of these.

Future versions of BioJava will require the user to install Java 1.6 or
later and so we will be able to use these newer features in both new and
existing code, depending on feasibility (for instance it is not always
possible to convert older code to use Generics in a sensible manner, and
it is not always possible to write Generics code that can interface
sensibly with older non-Generics modules).

cheers,
Richard



Martin Jones wrote:
> Hi,
> 
> I'm just getting started with BioJava so this may be a simple
> question.  I'm reading a RichSequence from a GenBank file and want to
> get the gene name of each CDS feature.  The following code gets hold
> of the features I'm interested in
> 
> for (Object o : mySeq.getFeatureSet()){
>       RichFeature f = (RichFeature) o;
>       if (f.getType().equals("CDS")){
>             //get gene name here
>       }
> }
> 
> but I'm not sure how best to get the gene name.  The following seems to work:
> 
> for (Object o2 : f.getNoteSet()){
>      Note n = (Note) o2;
>      if (n.getTerm().getName().equals("gene")){
>                  System.out.println("gene name is " + n.getValue());
>      }
> }
> 
> but seems overly verbose - ideally I'd like to be able to pass the
> Feature to another part of my program,  but writing the above whenever
> I want to get the name seems like overkill.  Is there a shorter way -
> something along the lines of
> 
> String name = f.getNoteByName("gene").getValue();
> 
> Thanks in advance for any help.
> 
> PS one more question - is there a reason why e.g.  getNoteSet returns
> a Set rather than a Set<Feature>, which makes it necessary to do all
> the type casts?
> 
> Thanks,
> 
> Martin
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From su24 at st-andrews.ac.uk  Thu Mar 27 17:46:38 2008
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Thu, 27 Mar 2008 17:46:38 +0000
Subject: [Biojava-l] Problem
Message-ID: <1206639998.47ebdd7e5f32c@webmail.st-andrews.ac.uk>


Dear All,

I am attempting to split up a Fasta file of an entire genomes amino acid
sequences into separate files for each individual gene. I am simply reading the
Fasta file of the entire genome as a Sequence Db and then iterating around it
creating a new file for each Sequence and writing it out to that file. However
out of a Fasta file containing 13465 genes only 12945 are written out to their
own individual files. This does not occur in files which lack the termination
symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if you
could suggest any reason why this might occur as I am completely mystified.

Thanking you in advance,

Saif


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Dyers Brae
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk



From su24 at st-andrews.ac.uk  Thu Mar 27 17:46:40 2008
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Thu, 27 Mar 2008 17:46:40 +0000
Subject: [Biojava-l] Problem
Message-ID: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>


Dear All,

I am attempting to split up a Fasta file of an entire genomes amino acid
sequences into separate files for each individual gene. I am simply reading the
Fasta file of the entire genome as a Sequence Db and then iterating around it
creating a new file for each Sequence and writing it out to that file. However
out of a Fasta file containing 13465 genes only 12945 are written out to their
own individual files. This does not occur in files which lack the termination
symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if you
could suggest any reason why this might occur as I am completely mystified.

Thanking you in advance,

Saif


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Dyers Brae
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk



From holland at ebi.ac.uk  Thu Mar 27 18:16:41 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Thu, 27 Mar 2008 18:16:41 -0000 (GMT)
Subject: [Biojava-l] Problem
In-Reply-To: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>
References: <1206640000.47ebdd802a753@webmail.st-andrews.ac.uk>
Message-ID: <42786.80.42.15.154.1206641801.squirrel@webmail.ebi.ac.uk>

I'm afraid we can't be much help unless we can see the actual code you
have written to do this job!

cheers,
Richard

On Thu, March 27, 2008 5:46 pm, Saif Ur-Rehman wrote:
>
> Dear All,
>
> I am attempting to split up a Fasta file of an entire genomes amino acid
> sequences into separate files for each individual gene. I am simply
> reading the
> Fasta file of the entire genome as a Sequence Db and then iterating around
> it
> creating a new file for each Sequence and writing it out to that file.
> However
> out of a Fasta file containing 13465 genes only 12945 are written out to
> their
> own individual files. This does not occur in files which lack the
> termination
> symbol i.e do not use the Alphabet ("PROTEIN_TERM"). I was wondering if
> you
> could suggest any reason why this might occur as I am completely
> mystified.
>
> Thanking you in advance,
>
> Saif
>
>
> -------------------------------------------------------------------------------
> Saif Ur-Rehman
> Research Student
> The Centre for Evolution, Genes & Genomics (CEGG)
> Dyers Brae
> School of Biology
> The University of St Andrews
> St Andrews,
> Fife
> Scotland,UK
>
> ------------------------------------------------------------------
> University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


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



From markjschreiber at gmail.com  Fri Mar 28 01:55:38 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 28 Mar 2008 09:55:38 +0800
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
In-Reply-To: <47EBAB0E.3020305@ebi.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>
	<47EBAB0E.3020305@ebi.ac.uk>
Message-ID: <93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>

These are good points.  Can we generify interfaces without breaking them?
Certainly the addition of generics to the biojavax packages would remove a
lot of nasty casting.  Adding convenience methods would certainly also help
biojavax code does get a bit verbose.  Again this would break interfaces
unless we put them in some kind of tools class.

These are certainly good points to remember for future designs (eg biojava2)
usability should be a test criteria as well. BioJavaX gives excellent ORM
with BioSQL and great capture of detail in it's parsers but the coding style
is a bit unwieldy. 2 out of 3 is not bad though : )

- Mark

On Thu, Mar 27, 2008 at 10:11 PM, Richard Holland <holland at ebi.ac.uk> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello,
>
> Your code for getting the Note named "gene" is correct. I agree, a
> shorthand way of doing this would be lovely, but doesn't currently
> exist. (Such a method would have to do the same thing internally
> anyway). If you'd like to write one and add it in then you'd be most
> welcome! :)
>
> At the time that the BioJavaX extensions were written compatibility with
> Java 1.4 was still required and so we could not make use of any new Java
> features that were introduced in Java 1.5. Set<Feature>, being an
> example of Generics, is one of these.
>
> Future versions of BioJava will require the user to install Java 1.6 or
> later and so we will be able to use these newer features in both new and
> existing code, depending on feasibility (for instance it is not always
> possible to convert older code to use Generics in a sensible manner, and
> it is not always possible to write Generics code that can interface
> sensibly with older non-Generics modules).
>
> cheers,
> Richard
>
>
>
> Martin Jones wrote:
> > Hi,
> >
> > I'm just getting started with BioJava so this may be a simple
> > question.  I'm reading a RichSequence from a GenBank file and want to
> > get the gene name of each CDS feature.  The following code gets hold
> > of the features I'm interested in
> >
> > for (Object o : mySeq.getFeatureSet()){
> >       RichFeature f = (RichFeature) o;
> >       if (f.getType().equals("CDS")){
> >             //get gene name here
> >       }
> > }
> >
> > but I'm not sure how best to get the gene name.  The following seems to
> work:
> >
> > for (Object o2 : f.getNoteSet()){
> >      Note n = (Note) o2;
> >      if (n.getTerm().getName().equals("gene")){
> >                  System.out.println("gene name is " + n.getValue());
> >      }
> > }
> >
> > but seems overly verbose - ideally I'd like to be able to pass the
> > Feature to another part of my program,  but writing the above whenever
> > I want to get the name seems like overkill.  Is there a shorter way -
> > something along the lines of
> >
> > String name = f.getNoteByName("gene").getValue();
> >
> > Thanks in advance for any help.
> >
> > PS one more question - is there a reason why e.g.  getNoteSet returns
> > a Set rather than a Set<Feature>, which makes it necessary to do all
> > the type casts?
> >
> > Thanks,
> >
> > Martin
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFH66sO4C5LeMEKA/QRAmq9AJ4qyMw4eGVYIMZjVf5jcADVRQmzpQCeOXej
> mak90aLUhSF60DrWeRtM8o0=
> =0EOE
> -----END PGP SIGNATURE-----
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From ayates at ebi.ac.uk  Fri Mar 28 09:17:54 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 28 Mar 2008 09:17:54 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>
	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
Message-ID: <47ECB7C2.3070800@ebi.ac.uk>

As with most things the answer is a yes & no. It shouldn't break 
interfaces as in the contract setup between the interface & a consumer 
since generics are erased after compilation.

However if we're looking at class incompatibility errors then it's quite 
likely that the new interface will have a different signature to the 
original one & may cause runtime errors in classes which haven't been 
recompiled against the new interface. A solution in some other projects 
is to have to sets of interfaces; one with generics & one without but 
that can be quite a nightmare to maintain.

Andy

Mark Schreiber wrote:
> These are good points.  Can we generify interfaces without breaking them?
> Certainly the addition of generics to the biojavax packages would remove a
> lot of nasty casting.  Adding convenience methods would certainly also help
> biojavax code does get a bit verbose.  Again this would break interfaces
> unless we put them in some kind of tools class.
> 
> These are certainly good points to remember for future designs (eg biojava2)
> usability should be a test criteria as well. BioJavaX gives excellent ORM
> with BioSQL and great capture of detail in it's parsers but the coding style
> is a bit unwieldy. 2 out of 3 is not bad though : )
> 
> - Mark
> 
> On Thu, Mar 27, 2008 at 10:11 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> 
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hello,
>>
>> Your code for getting the Note named "gene" is correct. I agree, a
>> shorthand way of doing this would be lovely, but doesn't currently
>> exist. (Such a method would have to do the same thing internally
>> anyway). If you'd like to write one and add it in then you'd be most
>> welcome! :)
>>
>> At the time that the BioJavaX extensions were written compatibility with
>> Java 1.4 was still required and so we could not make use of any new Java
>> features that were introduced in Java 1.5. Set<Feature>, being an
>> example of Generics, is one of these.
>>
>> Future versions of BioJava will require the user to install Java 1.6 or
>> later and so we will be able to use these newer features in both new and
>> existing code, depending on feasibility (for instance it is not always
>> possible to convert older code to use Generics in a sensible manner, and
>> it is not always possible to write Generics code that can interface
>> sensibly with older non-Generics modules).
>>
>> cheers,
>> Richard
>>
>>
>>
>> Martin Jones wrote:
>>> Hi,
>>>
>>> I'm just getting started with BioJava so this may be a simple
>>> question.  I'm reading a RichSequence from a GenBank file and want to
>>> get the gene name of each CDS feature.  The following code gets hold
>>> of the features I'm interested in
>>>
>>> for (Object o : mySeq.getFeatureSet()){
>>>       RichFeature f = (RichFeature) o;
>>>       if (f.getType().equals("CDS")){
>>>             //get gene name here
>>>       }
>>> }
>>>
>>> but I'm not sure how best to get the gene name.  The following seems to
>> work:
>>> for (Object o2 : f.getNoteSet()){
>>>      Note n = (Note) o2;
>>>      if (n.getTerm().getName().equals("gene")){
>>>                  System.out.println("gene name is " + n.getValue());
>>>      }
>>> }
>>>
>>> but seems overly verbose - ideally I'd like to be able to pass the
>>> Feature to another part of my program,  but writing the above whenever
>>> I want to get the name seems like overkill.  Is there a shorter way -
>>> something along the lines of
>>>
>>> String name = f.getNoteByName("gene").getValue();
>>>
>>> Thanks in advance for any help.
>>>
>>> PS one more question - is there a reason why e.g.  getNoteSet returns
>>> a Set rather than a Set<Feature>, which makes it necessary to do all
>>> the type casts?
>>>
>>> Thanks,
>>>
>>> Martin
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>> - --
>> Richard Holland (BioMart)
>> EMBL EBI, Wellcome Trust Genome Campus,
>> Hinxton, Cambridgeshire CB10 1SD, UK
>> Tel. +44 (0)1223 494416
>>
>> http://www.biomart.org/
>> http://www.biojava.org/
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.2.2 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>> iD8DBQFH66sO4C5LeMEKA/QRAmq9AJ4qyMw4eGVYIMZjVf5jcADVRQmzpQCeOXej
>> mak90aLUhSF60DrWeRtM8o0=
>> =0EOE
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From ap3 at sanger.ac.uk  Fri Mar 28 10:50:34 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Fri, 28 Mar 2008 10:50:34 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
In-Reply-To: <47ECB7C2.3070800@ebi.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>
	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>
	<47ECB7C2.3070800@ebi.ac.uk>
Message-ID: <7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>


>> These are good points.  Can we generify interfaces without  
>> breaking them?



I don;t think that adding generics will break anything, e.g.

old code:

public interface MyTest {
	public Set getFeatures()
}

then some code that uses this:

public void myFoo(){

	MyTest test = new MyTestImpl();

	Set features = test.getFeatures();
}

this call will not break, even if we change the MyTest interface to:

	public Set<Feature> getFeatures()

MyTestImpl will get some warnings (in my eclipse), to ensure the type  
safety, but that is all.

Andreas





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

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

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




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


From holland at ebi.ac.uk  Fri Mar 28 11:47:38 2008
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 28 Mar 2008 11:47:38 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
 file
In-Reply-To: <7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>
References: <eb55ec040803270645l4de4dfd6kceeebc0a24390ff2@mail.gmail.com>	<47EBAB0E.3020305@ebi.ac.uk>	<93b45ca50803271855r12190578l137c4bcc723bfb9b@mail.gmail.com>	<47ECB7C2.3070800@ebi.ac.uk>
	<7E037431-F0AB-48CD-A628-A2236E8BA95D@sanger.ac.uk>
Message-ID: <47ECDADA.4050800@ebi.ac.uk>

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

I was more worried about breaking concepts than breaking code.

For instance, the concept of a SymbolList can be almost completely
replaced by the use of a standard genericised colleciton, e.g.
List<DNASymbol> or List<RNASymbol> .

Likewise, the concept of a SequenceIterator is really just an
Iterator<Sequence> (or maybe Iterator<? extends Sequence> ? ).

cheers,
Richard

Andreas Prlic wrote:
> 
>>> These are good points.  Can we generify interfaces without breaking
>>> them?
> 
> 
> 
> I don;t think that adding generics will break anything, e.g.
> 
> old code:
> 
> public interface MyTest {
>     public Set getFeatures()
> }
> 
> then some code that uses this:
> 
> public void myFoo(){
> 
>     MyTest test = new MyTestImpl();
> 
>     Set features = test.getFeatures();
> }
> 
> this call will not break, even if we change the MyTest interface to:
> 
>     public Set<Feature> getFeatures()
> 
> MyTestImpl will get some warnings (in my eclipse), to ensure the type
> safety, but that is all.
> 
> Andreas
> 
> 
> 
> 
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                               Hinxton, Cambridge CB10 1SA, UK
>                               +44 (0) 1223 49 6891
> 
> -----------------------------------------------------------------------
> 
> 
> 
> 
> --The Wellcome Trust Sanger Institute is operated by Genome
> ResearchLimited, a charity registered in England with number 1021457 and
> acompany registered in England with number 2742969, whose
> registeredoffice is 215 Euston Road, London, NW1
> 2BE._______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

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

http://www.biomart.org/
http://www.biojava.org/
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From philipheller at comcast.net  Fri Mar 28 15:46:33 2008
From: philipheller at comcast.net (philipheller at comcast.net)
Date: Fri, 28 Mar 2008 15:46:33 +0000
Subject: [Biojava-l] how to get properties of a Feature from a GenBank
	file
Message-ID: <032820081546.8495.47ED12D9000D53B70000212F22007507849D0A04040A089F070407089F@comcast.net>

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