From andreas at sdsc.edu Sat Jul 3 21:55:36 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 3 Jul 2010 18:55:36 -0700 Subject: [Biojava-l] BioJava at ISMB, BOSC, and 3D SIG Message-ID: Hi, Next week the BOSC and ISMB conferences will be in Boston. There will be a couple of opportunities to meet BioJava related people, even if we won't have a BioJava specific talk at BOSC this time. The week will start with the Codefest in the days before BOSC. I have not heard too much about that, so perhaps one of the people who are going there can give us an update about what the plans are? At BOSC, there will be a talk from Jianjiong Gao, who is also on of our Google summer of code students. He will be present about general and kinase specific phosphorylation sites (with Musite). I will give a talk at 3D-SIG about structure alignments (using BioJava). Any other BioJava related events that are planned? Is anybody planning to blog or twitter about the conferences ? If people are interested in a meetup in Boston, drop me a mail and we'll arrange something... Andreas From phidias51 at gmail.com Mon Jul 5 12:38:11 2010 From: phidias51 at gmail.com (Mark Fortner) Date: Mon, 5 Jul 2010 09:38:11 -0700 Subject: [Biojava-l] Anonymous Checkout Problem Message-ID: I was trying an anonymous checkout of the latest BioJava3 code, and partway through the checkout I got this error message and the checkout stopped: svn: Can't read length line in file '/home/svn-repositories/biojava/db/revprops/7760' Has anyone else encountered this problem? Regards, Mark Fortner From pjotr.public23 at thebird.nl Mon Jul 5 14:34:04 2010 From: pjotr.public23 at thebird.nl (Pjotr Prins) Date: Mon, 5 Jul 2010 20:34:04 +0200 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: References: Message-ID: <20100705183404.GA25974@thebird.nl> Yes, it has been like this for more than a week. The svn db is corrupted. Separately, I would suggest to migrate to git. It is really a lot nicer for development than SVN. Talk with the BioRuby or the BioPerl guys at BOSC. We are all convinced, by now. Pj. On Mon, Jul 05, 2010 at 09:38:11AM -0700, Mark Fortner wrote: > I was trying an anonymous checkout of the latest BioJava3 code, and partway > through the checkout I got this error message and the checkout stopped: > svn: Can't read length line in file > '/home/svn-repositories/biojava/db/revprops/7760' > > Has anyone else encountered this problem? > > Regards, > > Mark Fortner > _______________________________________________ > 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 Tue Jul 6 04:29:30 2010 From: ayates at ebi.ac.uk (Andy Yates) Date: Tue, 6 Jul 2010 09:29:30 +0100 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: <20100705183404.GA25974@thebird.nl> References: <20100705183404.GA25974@thebird.nl> Message-ID: I also wish to add my vote to using git rather than open-bio's SVN. Andy On 5 Jul 2010, at 19:34, Pjotr Prins wrote: > Yes, it has been like this for more than a week. The svn db is > corrupted. > > Separately, I would suggest to migrate to git. It is really a lot > nicer for development than SVN. Talk with the BioRuby or the BioPerl > guys at BOSC. We are all convinced, by now. > > Pj. > > On Mon, Jul 05, 2010 at 09:38:11AM -0700, Mark Fortner wrote: >> I was trying an anonymous checkout of the latest BioJava3 code, and partway >> through the checkout I got this error message and the checkout stopped: >> svn: Can't read length line in file >> '/home/svn-repositories/biojava/db/revprops/7760' >> >> Has anyone else encountered this problem? >> >> Regards, >> >> Mark Fortner >> _______________________________________________ >> 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 -- Andrew Yates Ensembl Genomes Engineer EMBL-EBI Tel: +44-(0)1223-492538 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ From andreas.prlic at gmail.com Tue Jul 6 08:11:05 2010 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Tue, 6 Jul 2010 08:11:05 -0400 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: References: Message-ID: <-2603462182192551485@unknownmsgid> Hi Mark, Are you on the latest version of svn? Otherwise the problem is most likely that something goes wrong with the replication to anonymous svn.. An alternative way to get a copy is the github install which either can get obtained as svn or git checkouts... Andreas On 5 Jul 2010, at 12:38, Mark Fortner wrote: > I was trying an anonymous checkout of the latest BioJava3 code, and partway > through the checkout I got this error message and the checkout stopped: > svn: Can't read length line in file > '/home/svn-repositories/biojava/db/revprops/7760' > > Has anyone else encountered this problem? > > Regards, > > Mark Fortner > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From er.indupandey at gmail.com Sat Jul 17 06:41:03 2010 From: er.indupandey at gmail.com (indu pandey) Date: Sat, 17 Jul 2010 03:41:03 -0700 Subject: [Biojava-l] regarding code Message-ID: hi everyone i am tryin to run this code from my application through jFrame.I want to pass this accession number through textarea for which i am usin g string data type as: private void jButtonActionPerformed(java.awt.evet.ActionEvent evt) { string input=jTextArea1.getText(); String out= readg(input); jTextArea2.SetText(out); } public String readg( String in) { RichSequence rs = *null*; String Seq=""; GenbankRichSequenceDB grsdb = *new* GenbankRichSequenceDB(); *try*{ *// Demonstration of use with GenBank accession number* rs = grsdb.getRichSequence(in); SymbolList sl = rs.getInternalSymbolList(); Seq=sl.seqString(); } *catch*(BioException be){ be.printStackTrace(); System .exit(-1); } return (Seq); } ny one tell me why this code is not working. thanx indu From holland at eaglegenomics.com Sat Jul 17 10:12:57 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 17 Jul 2010 15:12:57 +0100 Subject: [Biojava-l] regarding code In-Reply-To: References: Message-ID: <40900395-3F5E-4544-84A1-0D7A0ABA2B4D@eaglegenomics.com> It would be helpful if you could paste the full stack trace of the error message you are getting. Without that, it is impossible to help! Richard. On 17 Jul 2010, at 11:41, indu pandey wrote: > hi everyone > i am tryin to run this code from my application through jFrame.I want to > pass this accession number through textarea for which i am usin g string > data type as: > > private void jButtonActionPerformed(java.awt.evet.ActionEvent evt) > { > string input=jTextArea1.getText(); > String out= readg(input); > jTextArea2.SetText(out); > } > public String readg( String in) > { > RichSequence rs = *null*; > String Seq=""; > > GenbankRichSequenceDB grsdb = *new* GenbankRichSequenceDB(); > > *try*{ > > *// Demonstration of use with GenBank accession number* > > rs = grsdb.getRichSequence(in); > > SymbolList sl = rs.getInternalSymbolList(); > > Seq=sl.seqString(); > } > > *catch*(BioException be){ > > be.printStackTrace(); > > System .exit(-1); > > } > return (Seq); > > } > > ny one tell me why this code is not working. > thanx > indu > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From koen.bruynseels at cropdesign.com Sat Jul 17 12:17:09 2010 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Sat, 17 Jul 2010 18:17:09 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 07/09/2010 and will not return until 07/26/2010. I will respond to your message when I return. From jdlkem at gmail.com Sat Jul 17 12:43:11 2010 From: jdlkem at gmail.com (jdlkem) Date: Sat, 17 Jul 2010 12:43:11 -0400 Subject: [Biojava-l] jboss tools 3.1 Message-ID: Hey all, So I've been having some trouble with the freemarker plugin that comes with jboss tools for eclipse ( http://www.jboss.org/tools/download/installation/update_3_1.html). I know that it gets installed, but nothing happens to my *.ftl files, nor am I able to create new *.ftl files. Any ideas? From sheoran143 at gmail.com Sat Jul 17 19:05:44 2010 From: sheoran143 at gmail.com (Deepak Sheoran) Date: Sat, 17 Jul 2010 18:05:44 -0500 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: References: Message-ID: <4C423748.5080305@gmail.com> The problem which I think Indu Pandey is having is with following method from latest version of biojava: public RichSequence getRichSequence(String id) throws IllegalIDException, BioException { try { // Build the query object String queryText = "from Sequence where name = ?"; **************///// instead of "name" it should be "accession" Object query = this.createQuery.invoke(this.session, new Object[]{queryText}); // Set the parameters query = this.setParameter.invoke(query, new Object[]{new Integer(0), id}); // Get the results List result = (List)this.list.invoke(query,(Object[]) null); // If the result doesn't just have a single entry, throw an exception if (result.size()==0) throw new IllegalIDException("Id not found: "+id); else if (result.size()>1) throw new IllegalIDException("Multiple records found with that id - use getRichSequences: "+id); // Return the found object, if found - null if not. return (RichSequence)result.get(0); } catch (Exception e) { // Throw the exception with our nice message throw new RuntimeException("Error while trying to load by id: "+id,e); } } Either biojava or Indu should change this method from having "name" to "accession" because in biosql.bioentry table "name" and "accession" are not same, in most case they are equal, but its not necessary. Thus even if you are querying the database with a valid accession number you won't get any record back in some cases. Also we should update the documentation which indicate that it query "name" column from bioentry table and not the accession column. Deepak Sheoran On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: > Send Biojava-l mailing list submissions to > biojava-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > biojava-l-request at lists.open-bio.org > > You can reach the person managing the list at > biojava-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. regarding code (indu pandey) > 2. Re: regarding code (Richard Holland) > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From jbdundas at gmail.com Sun Jul 18 01:14:17 2010 From: jbdundas at gmail.com (jitesh dundas) Date: Sun, 18 Jul 2010 10:44:17 +0530 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: <4C423748.5080305@gmail.com> References: <4C423748.5080305@gmail.com> Message-ID: Thanks Deepak for updating us. I have just starting updating the latest version on my laptop.I am going through the code and I will update you what is wrong with this code. Your point though,seems valid. Thanks, JD On 7/18/10, Deepak Sheoran wrote: > The problem which I think Indu Pandey is having is with following > method from latest version of biojava: > > public RichSequence getRichSequence(String id) throws > IllegalIDException, BioException { > try { > // Build the query object > String queryText = "from Sequence where name = ?"; > **************///// instead of "name" it should be "accession" > Object query = this.createQuery.invoke(this.session, new > Object[]{queryText}); > // Set the parameters > query = this.setParameter.invoke(query, new Object[]{new > Integer(0), id}); > // Get the results > List result = (List)this.list.invoke(query,(Object[]) null); > // If the result doesn't just have a single entry, throw an > exception > if (result.size()==0) throw new IllegalIDException("Id not > found: "+id); > else if (result.size()>1) throw new > IllegalIDException("Multiple records found with that id - use > getRichSequences: "+id); > // Return the found object, if found - null if not. > return (RichSequence)result.get(0); > } catch (Exception e) { > // Throw the exception with our nice message > throw new RuntimeException("Error while trying to load by > id: "+id,e); > } > } > > Either biojava or Indu should change this method from having "name" to > "accession" because in biosql.bioentry table "name" and "accession" are > not same, in most case they are equal, but its not necessary. Thus even > if you are querying the database with a valid accession number you won't > get any record back in some cases. Also we should update the > documentation which indicate that it query "name" column from bioentry > table and not the accession column. > > Deepak Sheoran > > > > > > > On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: >> Send Biojava-l mailing list submissions to >> biojava-l at lists.open-bio.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> or, via email, send a message with subject or body 'help' to >> biojava-l-request at lists.open-bio.org >> >> You can reach the person managing the list at >> biojava-l-owner at lists.open-bio.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Biojava-l digest..." >> >> >> Today's Topics: >> >> 1. regarding code (indu pandey) >> 2. Re: regarding code (Richard Holland) >> >> >> _______________________________________________ >> 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 holland at eaglegenomics.com Sun Jul 18 06:00:32 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Sun, 18 Jul 2010 11:00:32 +0100 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: <4C423748.5080305@gmail.com> References: <4C423748.5080305@gmail.com> Message-ID: How about 'name = ? or accession = ?' - solves both in that case. On 18 Jul 2010, at 00:05, Deepak Sheoran wrote: > The problem which I think Indu Pandey is having is with following method from latest version of biojava: > > public RichSequence getRichSequence(String id) throws IllegalIDException, BioException { > try { > // Build the query object > String queryText = "from Sequence where name = ?"; **************///// instead of "name" it should be "accession" > Object query = this.createQuery.invoke(this.session, new Object[]{queryText}); > // Set the parameters > query = this.setParameter.invoke(query, new Object[]{new Integer(0), id}); > // Get the results > List result = (List)this.list.invoke(query,(Object[]) null); > // If the result doesn't just have a single entry, throw an exception > if (result.size()==0) throw new IllegalIDException("Id not found: "+id); > else if (result.size()>1) throw new IllegalIDException("Multiple records found with that id - use getRichSequences: "+id); > // Return the found object, if found - null if not. > return (RichSequence)result.get(0); > } catch (Exception e) { > // Throw the exception with our nice message > throw new RuntimeException("Error while trying to load by id: "+id,e); > } > } > > Either biojava or Indu should change this method from having "name" to "accession" because in biosql.bioentry table "name" and "accession" are not same, in most case they are equal, but its not necessary. Thus even if you are querying the database with a valid accession number you won't get any record back in some cases. Also we should update the documentation which indicate that it query "name" column from bioentry table and not the accession column. > > Deepak Sheoran > > > > > > > On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: >> Send Biojava-l mailing list submissions to >> >> biojava-l at lists.open-bio.org >> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> or, via email, send a message with subject or body 'help' to >> >> biojava-l-request at lists.open-bio.org >> >> >> You can reach the person managing the list at >> >> biojava-l-owner at lists.open-bio.org >> >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Biojava-l digest..." >> >> >> Today's Topics: >> >> 1. regarding code (indu pandey) >> 2. Re: regarding code (Richard Holland) >> >> >> _______________________________________________ >> Biojava-l mailing list - >> Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From indranikundusaha at gmail.com Sun Jul 25 23:58:30 2010 From: indranikundusaha at gmail.com (Indrani Kundu Saha) Date: Sun, 25 Jul 2010 23:58:30 -0400 Subject: [Biojava-l] Looking for summer project Message-ID: Hi, I am doing MS in computer engineering focusing on algorithm and machine learning. I am looking for project to which I can contribute. Could someone please direct me to some open projects? Regards, Indrani From andreas at sdsc.edu Sun Jul 4 01:55:36 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 3 Jul 2010 18:55:36 -0700 Subject: [Biojava-l] BioJava at ISMB, BOSC, and 3D SIG Message-ID: Hi, Next week the BOSC and ISMB conferences will be in Boston. There will be a couple of opportunities to meet BioJava related people, even if we won't have a BioJava specific talk at BOSC this time. The week will start with the Codefest in the days before BOSC. I have not heard too much about that, so perhaps one of the people who are going there can give us an update about what the plans are? At BOSC, there will be a talk from Jianjiong Gao, who is also on of our Google summer of code students. He will be present about general and kinase specific phosphorylation sites (with Musite). I will give a talk at 3D-SIG about structure alignments (using BioJava). Any other BioJava related events that are planned? Is anybody planning to blog or twitter about the conferences ? If people are interested in a meetup in Boston, drop me a mail and we'll arrange something... Andreas From phidias51 at gmail.com Mon Jul 5 16:38:11 2010 From: phidias51 at gmail.com (Mark Fortner) Date: Mon, 5 Jul 2010 09:38:11 -0700 Subject: [Biojava-l] Anonymous Checkout Problem Message-ID: I was trying an anonymous checkout of the latest BioJava3 code, and partway through the checkout I got this error message and the checkout stopped: svn: Can't read length line in file '/home/svn-repositories/biojava/db/revprops/7760' Has anyone else encountered this problem? Regards, Mark Fortner From pjotr.public23 at thebird.nl Mon Jul 5 18:34:04 2010 From: pjotr.public23 at thebird.nl (Pjotr Prins) Date: Mon, 5 Jul 2010 20:34:04 +0200 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: References: Message-ID: <20100705183404.GA25974@thebird.nl> Yes, it has been like this for more than a week. The svn db is corrupted. Separately, I would suggest to migrate to git. It is really a lot nicer for development than SVN. Talk with the BioRuby or the BioPerl guys at BOSC. We are all convinced, by now. Pj. On Mon, Jul 05, 2010 at 09:38:11AM -0700, Mark Fortner wrote: > I was trying an anonymous checkout of the latest BioJava3 code, and partway > through the checkout I got this error message and the checkout stopped: > svn: Can't read length line in file > '/home/svn-repositories/biojava/db/revprops/7760' > > Has anyone else encountered this problem? > > Regards, > > Mark Fortner > _______________________________________________ > 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 Tue Jul 6 08:29:30 2010 From: ayates at ebi.ac.uk (Andy Yates) Date: Tue, 6 Jul 2010 09:29:30 +0100 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: <20100705183404.GA25974@thebird.nl> References: <20100705183404.GA25974@thebird.nl> Message-ID: I also wish to add my vote to using git rather than open-bio's SVN. Andy On 5 Jul 2010, at 19:34, Pjotr Prins wrote: > Yes, it has been like this for more than a week. The svn db is > corrupted. > > Separately, I would suggest to migrate to git. It is really a lot > nicer for development than SVN. Talk with the BioRuby or the BioPerl > guys at BOSC. We are all convinced, by now. > > Pj. > > On Mon, Jul 05, 2010 at 09:38:11AM -0700, Mark Fortner wrote: >> I was trying an anonymous checkout of the latest BioJava3 code, and partway >> through the checkout I got this error message and the checkout stopped: >> svn: Can't read length line in file >> '/home/svn-repositories/biojava/db/revprops/7760' >> >> Has anyone else encountered this problem? >> >> Regards, >> >> Mark Fortner >> _______________________________________________ >> 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 -- Andrew Yates Ensembl Genomes Engineer EMBL-EBI Tel: +44-(0)1223-492538 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ From andreas.prlic at gmail.com Tue Jul 6 12:11:05 2010 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Tue, 6 Jul 2010 08:11:05 -0400 Subject: [Biojava-l] Anonymous Checkout Problem In-Reply-To: References: Message-ID: <-2603462182192551485@unknownmsgid> Hi Mark, Are you on the latest version of svn? Otherwise the problem is most likely that something goes wrong with the replication to anonymous svn.. An alternative way to get a copy is the github install which either can get obtained as svn or git checkouts... Andreas On 5 Jul 2010, at 12:38, Mark Fortner wrote: > I was trying an anonymous checkout of the latest BioJava3 code, and partway > through the checkout I got this error message and the checkout stopped: > svn: Can't read length line in file > '/home/svn-repositories/biojava/db/revprops/7760' > > Has anyone else encountered this problem? > > Regards, > > Mark Fortner > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From er.indupandey at gmail.com Sat Jul 17 10:41:03 2010 From: er.indupandey at gmail.com (indu pandey) Date: Sat, 17 Jul 2010 03:41:03 -0700 Subject: [Biojava-l] regarding code Message-ID: hi everyone i am tryin to run this code from my application through jFrame.I want to pass this accession number through textarea for which i am usin g string data type as: private void jButtonActionPerformed(java.awt.evet.ActionEvent evt) { string input=jTextArea1.getText(); String out= readg(input); jTextArea2.SetText(out); } public String readg( String in) { RichSequence rs = *null*; String Seq=""; GenbankRichSequenceDB grsdb = *new* GenbankRichSequenceDB(); *try*{ *// Demonstration of use with GenBank accession number* rs = grsdb.getRichSequence(in); SymbolList sl = rs.getInternalSymbolList(); Seq=sl.seqString(); } *catch*(BioException be){ be.printStackTrace(); System .exit(-1); } return (Seq); } ny one tell me why this code is not working. thanx indu From holland at eaglegenomics.com Sat Jul 17 14:12:57 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 17 Jul 2010 15:12:57 +0100 Subject: [Biojava-l] regarding code In-Reply-To: References: Message-ID: <40900395-3F5E-4544-84A1-0D7A0ABA2B4D@eaglegenomics.com> It would be helpful if you could paste the full stack trace of the error message you are getting. Without that, it is impossible to help! Richard. On 17 Jul 2010, at 11:41, indu pandey wrote: > hi everyone > i am tryin to run this code from my application through jFrame.I want to > pass this accession number through textarea for which i am usin g string > data type as: > > private void jButtonActionPerformed(java.awt.evet.ActionEvent evt) > { > string input=jTextArea1.getText(); > String out= readg(input); > jTextArea2.SetText(out); > } > public String readg( String in) > { > RichSequence rs = *null*; > String Seq=""; > > GenbankRichSequenceDB grsdb = *new* GenbankRichSequenceDB(); > > *try*{ > > *// Demonstration of use with GenBank accession number* > > rs = grsdb.getRichSequence(in); > > SymbolList sl = rs.getInternalSymbolList(); > > Seq=sl.seqString(); > } > > *catch*(BioException be){ > > be.printStackTrace(); > > System .exit(-1); > > } > return (Seq); > > } > > ny one tell me why this code is not working. > thanx > indu > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From koen.bruynseels at cropdesign.com Sat Jul 17 16:17:09 2010 From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com) Date: Sat, 17 Jul 2010 18:17:09 +0200 Subject: [Biojava-l] Koen Bruynseels is out of the office. Message-ID: I will be out of the office starting 07/09/2010 and will not return until 07/26/2010. I will respond to your message when I return. From jdlkem at gmail.com Sat Jul 17 16:43:11 2010 From: jdlkem at gmail.com (jdlkem) Date: Sat, 17 Jul 2010 12:43:11 -0400 Subject: [Biojava-l] jboss tools 3.1 Message-ID: Hey all, So I've been having some trouble with the freemarker plugin that comes with jboss tools for eclipse ( http://www.jboss.org/tools/download/installation/update_3_1.html). I know that it gets installed, but nothing happens to my *.ftl files, nor am I able to create new *.ftl files. Any ideas? From sheoran143 at gmail.com Sat Jul 17 23:05:44 2010 From: sheoran143 at gmail.com (Deepak Sheoran) Date: Sat, 17 Jul 2010 18:05:44 -0500 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: References: Message-ID: <4C423748.5080305@gmail.com> The problem which I think Indu Pandey is having is with following method from latest version of biojava: public RichSequence getRichSequence(String id) throws IllegalIDException, BioException { try { // Build the query object String queryText = "from Sequence where name = ?"; **************///// instead of "name" it should be "accession" Object query = this.createQuery.invoke(this.session, new Object[]{queryText}); // Set the parameters query = this.setParameter.invoke(query, new Object[]{new Integer(0), id}); // Get the results List result = (List)this.list.invoke(query,(Object[]) null); // If the result doesn't just have a single entry, throw an exception if (result.size()==0) throw new IllegalIDException("Id not found: "+id); else if (result.size()>1) throw new IllegalIDException("Multiple records found with that id - use getRichSequences: "+id); // Return the found object, if found - null if not. return (RichSequence)result.get(0); } catch (Exception e) { // Throw the exception with our nice message throw new RuntimeException("Error while trying to load by id: "+id,e); } } Either biojava or Indu should change this method from having "name" to "accession" because in biosql.bioentry table "name" and "accession" are not same, in most case they are equal, but its not necessary. Thus even if you are querying the database with a valid accession number you won't get any record back in some cases. Also we should update the documentation which indicate that it query "name" column from bioentry table and not the accession column. Deepak Sheoran On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: > Send Biojava-l mailing list submissions to > biojava-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > biojava-l-request at lists.open-bio.org > > You can reach the person managing the list at > biojava-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. regarding code (indu pandey) > 2. Re: regarding code (Richard Holland) > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From jbdundas at gmail.com Sun Jul 18 05:14:17 2010 From: jbdundas at gmail.com (jitesh dundas) Date: Sun, 18 Jul 2010 10:44:17 +0530 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: <4C423748.5080305@gmail.com> References: <4C423748.5080305@gmail.com> Message-ID: Thanks Deepak for updating us. I have just starting updating the latest version on my laptop.I am going through the code and I will update you what is wrong with this code. Your point though,seems valid. Thanks, JD On 7/18/10, Deepak Sheoran wrote: > The problem which I think Indu Pandey is having is with following > method from latest version of biojava: > > public RichSequence getRichSequence(String id) throws > IllegalIDException, BioException { > try { > // Build the query object > String queryText = "from Sequence where name = ?"; > **************///// instead of "name" it should be "accession" > Object query = this.createQuery.invoke(this.session, new > Object[]{queryText}); > // Set the parameters > query = this.setParameter.invoke(query, new Object[]{new > Integer(0), id}); > // Get the results > List result = (List)this.list.invoke(query,(Object[]) null); > // If the result doesn't just have a single entry, throw an > exception > if (result.size()==0) throw new IllegalIDException("Id not > found: "+id); > else if (result.size()>1) throw new > IllegalIDException("Multiple records found with that id - use > getRichSequences: "+id); > // Return the found object, if found - null if not. > return (RichSequence)result.get(0); > } catch (Exception e) { > // Throw the exception with our nice message > throw new RuntimeException("Error while trying to load by > id: "+id,e); > } > } > > Either biojava or Indu should change this method from having "name" to > "accession" because in biosql.bioentry table "name" and "accession" are > not same, in most case they are equal, but its not necessary. Thus even > if you are querying the database with a valid accession number you won't > get any record back in some cases. Also we should update the > documentation which indicate that it query "name" column from bioentry > table and not the accession column. > > Deepak Sheoran > > > > > > > On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: >> Send Biojava-l mailing list submissions to >> biojava-l at lists.open-bio.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> or, via email, send a message with subject or body 'help' to >> biojava-l-request at lists.open-bio.org >> >> You can reach the person managing the list at >> biojava-l-owner at lists.open-bio.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Biojava-l digest..." >> >> >> Today's Topics: >> >> 1. regarding code (indu pandey) >> 2. Re: regarding code (Richard Holland) >> >> >> _______________________________________________ >> 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 holland at eaglegenomics.com Sun Jul 18 10:00:32 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Sun, 18 Jul 2010 11:00:32 +0100 Subject: [Biojava-l] regarding code (Richard Holland) In-Reply-To: <4C423748.5080305@gmail.com> References: <4C423748.5080305@gmail.com> Message-ID: How about 'name = ? or accession = ?' - solves both in that case. On 18 Jul 2010, at 00:05, Deepak Sheoran wrote: > The problem which I think Indu Pandey is having is with following method from latest version of biojava: > > public RichSequence getRichSequence(String id) throws IllegalIDException, BioException { > try { > // Build the query object > String queryText = "from Sequence where name = ?"; **************///// instead of "name" it should be "accession" > Object query = this.createQuery.invoke(this.session, new Object[]{queryText}); > // Set the parameters > query = this.setParameter.invoke(query, new Object[]{new Integer(0), id}); > // Get the results > List result = (List)this.list.invoke(query,(Object[]) null); > // If the result doesn't just have a single entry, throw an exception > if (result.size()==0) throw new IllegalIDException("Id not found: "+id); > else if (result.size()>1) throw new IllegalIDException("Multiple records found with that id - use getRichSequences: "+id); > // Return the found object, if found - null if not. > return (RichSequence)result.get(0); > } catch (Exception e) { > // Throw the exception with our nice message > throw new RuntimeException("Error while trying to load by id: "+id,e); > } > } > > Either biojava or Indu should change this method from having "name" to "accession" because in biosql.bioentry table "name" and "accession" are not same, in most case they are equal, but its not necessary. Thus even if you are querying the database with a valid accession number you won't get any record back in some cases. Also we should update the documentation which indicate that it query "name" column from bioentry table and not the accession column. > > Deepak Sheoran > > > > > > > On 7/17/2010 11:00 AM, biojava-l-request at lists.open-bio.org wrote: >> Send Biojava-l mailing list submissions to >> >> biojava-l at lists.open-bio.org >> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> or, via email, send a message with subject or body 'help' to >> >> biojava-l-request at lists.open-bio.org >> >> >> You can reach the person managing the list at >> >> biojava-l-owner at lists.open-bio.org >> >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Biojava-l digest..." >> >> >> Today's Topics: >> >> 1. regarding code (indu pandey) >> 2. Re: regarding code (Richard Holland) >> >> >> _______________________________________________ >> Biojava-l mailing list - >> Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From indranikundusaha at gmail.com Mon Jul 26 03:58:30 2010 From: indranikundusaha at gmail.com (Indrani Kundu Saha) Date: Sun, 25 Jul 2010 23:58:30 -0400 Subject: [Biojava-l] Looking for summer project Message-ID: Hi, I am doing MS in computer engineering focusing on algorithm and machine learning. I am looking for project to which I can contribute. Could someone please direct me to some open projects? Regards, Indrani