From chen_li3 at yahoo.com Sun Jul 2 21:15:03 2006 From: chen_li3 at yahoo.com (chen li) Date: Sun, 2 Jul 2006 18:15:03 -0700 (PDT) Subject: [Biojava-l] reverse and complement of sequence using Java Message-ID: <20060703011503.35259.qmail@web36807.mail.mud.yahoo.com> Dear all, I am newbie to Java and BioJava. I just want to know if there are methods available for reversing or/and complementing a sequence in standard Java library. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mark.schreiber at novartis.com Sun Jul 2 21:31:21 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 3 Jul 2006 09:31:21 +0800 Subject: [Biojava-l] reverse and complement of sequence using Java Message-ID: Take a look at some of the static methods in DNATools and RNATools. - Mark chen li Sent by: biojava-l-bounces at lists.open-bio.org 07/03/2006 09:15 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] reverse and complement of sequence using Java Dear all, I am newbie to Java and BioJava. I just want to know if there are methods available for reversing or/and complementing a sequence in standard Java library. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From richard.holland at ebi.ac.uk Tue Jul 4 06:15:50 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Tue, 04 Jul 2006 11:15:50 +0100 Subject: [Biojava-l] Getting a Slice of an Alignment In-Reply-To: <1151485076.3942.8.camel@texas.ebi.ac.uk> References: <5047818.post@talk.nabble.com> <1151335745.3938.40.camel@texas.ebi.ac.uk> <5049831.post@talk.nabble.com> <1151399858.3938.57.camel@texas.ebi.ac.uk> <5066891.post@talk.nabble.com> <1151421997.3938.91.camel@texas.ebi.ac.uk> <5072893.post@talk.nabble.com> <1151485076.3942.8.camel@texas.ebi.ac.uk> Message-ID: <1152008150.3948.63.camel@texas.ebi.ac.uk> Right... didn't hear anything, but I won't make the change. Here's why... I read the code again this morning, and realised that the vertical slice effect can be achieved using existing methods in the alignment classes. Given an alignment: Alignment algn = .....; And a sub-alignment: Alignment sub = algn.subAlignment(null, new Location(5,10)); The sequences in the sub-alignment can be found like this: Collection labels = sub.getLabels(); For any given label in this collection, the symbol list (for the full sequence can be obtained like this): SymbolList symbols = sub.symbolListForLabel(label); That symbol list will include gaps in appropriate places. To find out the offset of that symbollist within the alignment, you can do this: Location offset = sub.locInAlignment(label); This will return a location with the min and max set to the position of the label in relation to the beginning of the alignment. To explain this, our alignment 'algn' above contains sequence X: SymbolList symbols = algn.symbolListForLabel("X"); // could have used sub instead but same symbollist returned. Location algnOffset = algn.locInAlignment("X"); Location subOffset = sub.locInAlignment("X"); If the sub alignment is over positions 5..10 in the main alignment, and sequence X is 20 bases long and begins 5 bases before the start of the main alignment, then min and max for 'algnOffset' above will equal -5..15, and for 'subOffset' will equal -10..10. You can then use the min and max of 'subOffset' to obtain the chunk of the sequence that actually occurs within the sub alignment: int symStart = -subOffset.getMin(); int symEnd = symStart + subOffset.getMax(); If symStart is <=0, you need to change it to 1 and pad the result with a number of leading gaps equivalent to the negative value. If symStart is beyond the end of the symbol list, or symEnd is <=0, the symbol list does not appear in this alignment. If symEnd is beyond the end of the symbol list, you need to pad the result with trailing gaps equivalent to the difference. You can pass these values to symbol list to get the actual symbols that occur in the sub alignment: SymbolList subSymbols = symbols.subList(symStart, symEnd); Doing this for each label returned by getLabels() in the sub alignment will give you the vertical slice you're looking for. cheers, Richard On Wed, 2006-06-28 at 09:57 +0100, Richard Holland wrote: > Dear list... if I haven't heard any arguments to the contrary by 9am > Monday 3rd July (UK time), I'll make the changes described below. > > cheers, > Richard > > On Tue, 2006-06-27 at 12:57 -0700, Dexter Riley wrote: > > > > Richard Holland-2 wrote: > > > > > > Ah... > > > > > > I just read the source code for the symbolListForLabel() method on sub > > > alignments, and found what may well be a bug. > > > > > > BioJava list people, your help please! In my understanding, > > > symbolListForLabel() should return the symbols from the given label that > > > fall within the alignment. This is the case in all except sub > > > alignments. Sub alignments, for whatever reason, are returning the > > > symbols from the given label that fall within the parent alignment upon > > > which the sub alignment is based, NOT just those that fall within the > > > sub alignment itself. > > > > > > Is this a bug? I think it is. > > > > > > The solution would be for me to alter > > > AbstractULAlignment.SubULAlignment.symbolListForLabel() to restrict the > > > returned symbols to only include those in the area covered by the sub > > > alignment. It would return EMPTY_SEQUENCE if the label didn't cover the > > > area of the sub alignment, and it would return a truncated symbol list > > > if it only partially covered it. > > > > > > Would this be acceptable? > > > > > > If so, once this change was made, it would fix Ed's problems below as > > > subAlignment() would start returning vertical slices as I think it > > > should probably have done so from the start, rather than the horizontal > > > slices it is returning at present. > > > > > > cheers, > > > Richard > > > > > > > I think that would provide just the functionality I was looking for! Thanks > > very much for all your help. > > All the best, > > Ed -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From edbeaty at charter.net Tue Jul 4 12:46:48 2006 From: edbeaty at charter.net (Dexter Riley) Date: Tue, 4 Jul 2006 09:46:48 -0700 (PDT) Subject: [Biojava-l] Getting a Slice of an Alignment In-Reply-To: <1152008150.3948.63.camel@texas.ebi.ac.uk> References: <5047818.post@talk.nabble.com> <1151335745.3938.40.camel@texas.ebi.ac.uk> <5049831.post@talk.nabble.com> <1151399858.3938.57.camel@texas.ebi.ac.uk> <5066891.post@talk.nabble.com> <1151421997.3938.91.camel@texas.ebi.ac.uk> <5072893.post@talk.nabble.com> <1151485076.3942.8.camel@texas.ebi.ac.uk> <1152008150.3948.63.camel@texas.ebi.ac.uk> Message-ID: <5170318.post@talk.nabble.com> I will give this a try. If this provides the "alignment slice" functionality we discussed, I think a function to perform this would be a useful addition to the API (either of Alignment or of the appropriate utility class). Thanks, Ed -- View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5170318 Sent from the BioJava forum at Nabble.com. From mark.schreiber at novartis.com Tue Jul 4 21:00:36 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 5 Jul 2006 09:00:36 +0800 Subject: [Biojava-l] Getting a Slice of an Alignment Message-ID: The method would be useful but Alignment is an interface so you can't add it there. Typically in biojava we use a Tools class that contains static methods to do common things. For example DNATools, DistributionTools, RichSequence.IOTools. As you can see the last case is an inner class of the RichSequence interface. This is probably a tidier approach. - Mark Dexter Riley Sent by: biojava-l-bounces at lists.open-bio.org 07/05/2006 12:46 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] Getting a Slice of an Alignment I will give this a try. If this provides the "alignment slice" functionality we discussed, I think a function to perform this would be a useful addition to the API (either of Alignment or of the appropriate utility class). Thanks, Ed -- View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5170318 Sent from the BioJava forum at Nabble.com. _______________________________________________ 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 Thu Jul 6 14:44:42 2006 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 6 Jul 2006 19:44:42 +0100 Subject: [Biojava-l] biojava wiki and Jmol Message-ID: Hi! I will commit some new protein structure functionality to CVS soon (structure alignments). For this it would be nice if I could show some examples in 3D with the Jmol applet in the BioJava Wiki pages. Could somebody with admin rights install the Jmol-wiki extension for MediaWiki? - not sure who to contact about that... instructions would be here: http://wiki.jmol.org/index.php/MediaWiki#Installation Thanks! :-) Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From arareko at campus.iztacala.unam.mx Thu Jul 6 17:45:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 06 Jul 2006 16:45:34 -0500 Subject: [Biojava-l] biojava wiki and Jmol In-Reply-To: References: Message-ID: <44AD847E.9030306@campus.iztacala.unam.mx> Hi Andreas, I have admin privileges for the open-bio.org webserver. Unless Mark Schreiber (who appears to be the website admin for BioJava) has other opinion, I can help you with this and get the extension installed and configured for the wiki. Regards, Mauricio. Andreas Prlic wrote: > Hi! > > I will commit some new protein structure functionality to CVS soon > (structure alignments). > For this it would be nice if I could show some examples in 3D with the > Jmol applet in > the BioJava Wiki pages. > > Could somebody with admin rights install the Jmol-wiki extension for > MediaWiki? - not sure who to contact about that... > instructions would be here: > http://wiki.jmol.org/index.php/MediaWiki#Installation > > Thanks! :-) > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From mark.schreiber at novartis.com Thu Jul 6 20:56:04 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 7 Jul 2006 08:56:04 +0800 Subject: [Biojava-l] biojava wiki and Jmol Message-ID: Be my guest!! Mauricio Herrera Cuadra Sent by: biojava-l-bounces at lists.open-bio.org 07/07/2006 05:45 AM To: Andreas Prlic cc: biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] biojava wiki and Jmol Hi Andreas, I have admin privileges for the open-bio.org webserver. Unless Mark Schreiber (who appears to be the website admin for BioJava) has other opinion, I can help you with this and get the extension installed and configured for the wiki. Regards, Mauricio. Andreas Prlic wrote: > Hi! > > I will commit some new protein structure functionality to CVS soon > (structure alignments). > For this it would be nice if I could show some examples in 3D with the > Jmol applet in > the BioJava Wiki pages. > > Could somebody with admin rights install the Jmol-wiki extension for > MediaWiki? - not sure who to contact about that... > instructions would be here: > http://wiki.jmol.org/index.php/MediaWiki#Installation > > Thanks! :-) > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Thu Jul 6 22:29:57 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 7 Jul 2006 10:29:57 +0800 Subject: [Biojava-l] submission of bug reports and requests for enhancement Message-ID: Hello all - Biojava now has a working bug reporting and tracking system based on bugzilla. You can submit and track bugs or requests for enhancement at http://bugzilla.open-bio.org/ (I will add this link to the biojava wiki). >From now on this should be the prefered way to report a bug in biojava. This is so we don't forget about the bugs that we haven't dealt with and the new features people want that we should add. By default bugs will be 'assigned' to biojava-dev but from time to time I may reassign really bad ones to the appropriate person to clear them more quickly. Please make use of this so we can make biojava better. Thanks, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From arareko at campus.iztacala.unam.mx Fri Jul 7 10:23:05 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 07 Jul 2006 09:23:05 -0500 Subject: [Biojava-l] biojava wiki and Jmol In-Reply-To: References: Message-ID: <44AE6E49.9030107@campus.iztacala.unam.mx> Mark and Andreas, The Jmol extension is installed now and should be working. I configured it with all the steps from the installation page. For the moment, I've only added *.cml files to the allowed extensions to upload. If you want to upload other types of files, please let me know and I'll perform the necessary steps. Andreas - please try to upload some files and play with the Jmol wiki tags to see if everything works as it should. Regards, Mauricio. PS. I'm Cc'ing this to some BioPerl friends to see if someone gets interested in having this for our wiki also ;) mark.schreiber at novartis.com wrote: > Be my guest!! > > > Mauricio Herrera Cuadra > Sent by: biojava-l-bounces at lists.open-bio.org > 07/07/2006 05:45 AM > > > To: Andreas Prlic > cc: biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark > Schreiber/GP/Novartis) > Subject: Re: [Biojava-l] biojava wiki and Jmol > > > Hi Andreas, > > I have admin privileges for the open-bio.org webserver. Unless Mark > Schreiber (who appears to be the website admin for BioJava) has other > opinion, I can help you with this and get the extension installed and > configured for the wiki. > > Regards, > Mauricio. > > Andreas Prlic wrote: >> Hi! >> >> I will commit some new protein structure functionality to CVS soon >> (structure alignments). >> For this it would be nice if I could show some examples in 3D with the >> Jmol applet in >> the BioJava Wiki pages. >> >> Could somebody with admin rights install the Jmol-wiki extension for >> MediaWiki? - not sure who to contact about that... >> instructions would be here: >> http://wiki.jmol.org/index.php/MediaWiki#Installation >> >> Thanks! :-) >> Andreas >> >> ----------------------------------------------------------------------- >> >> Andreas Prlic Wellcome Trust Sanger Institute >> Hinxton, Cambridge CB10 1SA, UK >> +44 (0) 1223 49 6891 >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From michael.tran at acpfg.com.au Tue Jul 4 21:21:56 2006 From: michael.tran at acpfg.com.au (Michael Tran) Date: Wed, 5 Jul 2006 10:51:56 +0930 Subject: [Biojava-l] API for global alignments References: Message-ID: Hi Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file. The BioJava API 1.4 doesn't seem to have this. org.biojava.bio.alignment Interfaces AlignmentElement ARAlignment EditableAlignment QualitativeAlignment UnequalLengthAlignment Classes AbstractULAlignment FlexibleAlignment SimpleAlignmentElement Exceptions IllegalAlignmentEditException Any help appreciated. Cheers, MT -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4762 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/biojava-l/attachments/20060705/7fca4da5/attachment.bin From chen_li3 at yahoo.com Sun Jul 9 13:42:30 2006 From: chen_li3 at yahoo.com (chen li) Date: Sun, 9 Jul 2006 10:42:30 -0700 (PDT) Subject: [Biojava-l] some source code In-Reply-To: Message-ID: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> Hi all, It sounds like stupid but I just wonder if it is possible to read some source codes for a specific method from a class, for instance, the source code for reverse method in DNAtools. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mark.schreiber at novartis.com Sun Jul 9 21:40:46 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 10 Jul 2006 09:40:46 +0800 Subject: [Biojava-l] some source code Message-ID: You can get the source code from here. http://biojava.org/wiki/BioJava:Download chen li Sent by: biojava-l-bounces at lists.open-bio.org 07/10/2006 01:42 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] some source code Hi all, It sounds like stupid but I just wonder if it is possible to read some source codes for a specific method from a class, for instance, the source code for reverse method in DNAtools. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From debesis at gmail.com Tue Jul 11 08:06:25 2006 From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=) Date: Tue, 11 Jul 2006 15:06:25 +0300 Subject: [Biojava-l] blast parser Message-ID: Hi, i'm trying to parse blast output text with BlastLikeSaxParser and I get an exception: Exception in thread "main" org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.14 is not supported by the biojava blast-like parsing framework Do you know any working parser for the newest version of blast? Thanks in advance, Valdemaras Rep?ys ** From online1 at dewkid.com Tue Jul 11 15:24:28 2006 From: online1 at dewkid.com (Dewkid) Date: Tue, 11 Jul 2006 12:24:28 -0700 (PDT) Subject: [Biojava-l] blast parser In-Reply-To: References: Message-ID: <5276129.post@talk.nabble.com> I'm new to this list, but I also ran into this problem. The easy solution, is to call the setModeLazy method in your BlastLikeSaxParser object, and it will ignore the version. Near as I can tell, the parser works just fine this way. Still, I'm anxious to see this parser updated to support the newer blast versions! -- View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 Sent from the BioJava forum at Nabble.com. From k_stellar at msn.com Tue Jul 11 17:43:30 2006 From: k_stellar at msn.com (Kikia Carter) Date: Tue, 11 Jul 2006 17:43:30 -0400 Subject: [Biojava-l] SCF Chromatogram Read Error Message-ID: I am having the following problem when trying to create a chromatogram from an SCF file: java.lang.IndexOutOfBoundsException at java.io.FileInputStream.readBytes(Native Method) at java.io.FileInputStream.read(FileInputStream.java:194) at java.io.DataInputStream.read(DataInputStream.java:224) at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) at org.biojava.bio.program.scf.SCF.load(SCF.java:122) at org.biojava.bio.program.scf.SCF.load(SCF.java:117) at org.biojava.bio.program.scf.SCF.create(SCF.java:104) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) Can anyone offer advice on this problem? Thanks in advance! _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar ? get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ From mark.schreiber at novartis.com Tue Jul 11 22:32:00 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 12 Jul 2006 10:32:00 +0800 Subject: [Biojava-l] blast parser Message-ID: Hi - Essentially someone needs to do some testing with the new versions of blast. If the parser seems to produce the correct results then we can add version 2.x.x to the 'certified' list. As always we need volunteers. Also if people notice it doesn't work then perhaps submit a bug report detailing the version etc. Thanks, - Mark Dewkid Sent by: biojava-l-bounces at lists.open-bio.org 07/12/2006 03:24 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] blast parser I'm new to this list, but I also ran into this problem. The easy solution, is to call the setModeLazy method in your BlastLikeSaxParser object, and it will ignore the version. Near as I can tell, the parser works just fine this way. Still, I'm anxious to see this parser updated to support the newer blast versions! -- View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Tue Jul 11 22:36:06 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 12 Jul 2006 10:36:06 +0800 Subject: [Biojava-l] SCF Chromatogram Read Error Message-ID: Hi Kikia - This might be a bug. To be sure we need more details. Please submit a bug report to http://bugzilla.open-bio.org/ (under biojava) with as much detail as possible. Try and include some sample code so we can recreate the error. Best regards, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 "Kikia Carter" Sent by: biojava-l-bounces at lists.open-bio.org 07/12/2006 05:43 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] SCF Chromatogram Read Error I am having the following problem when trying to create a chromatogram from an SCF file: java.lang.IndexOutOfBoundsException at java.io.FileInputStream.readBytes(Native Method) at java.io.FileInputStream.read(FileInputStream.java:194) at java.io.DataInputStream.read(DataInputStream.java:224) at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) at org.biojava.bio.program.scf.SCF.load(SCF.java:122) at org.biojava.bio.program.scf.SCF.load(SCF.java:117) at org.biojava.bio.program.scf.SCF.create(SCF.java:104) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) Can anyone offer advice on this problem? Thanks in advance! _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar ? get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From debesis at gmail.com Wed Jul 12 03:39:12 2006 From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=) Date: Wed, 12 Jul 2006 10:39:12 +0300 Subject: [Biojava-l] blast parser In-Reply-To: References: Message-ID: Thanks for the help. It really works fine with lazy mode on when parsing blastpgp output (i tried versions 2.2.14 & 2.2.10). The thing is I need a psiblast-on-the-web parser, the text output from the web and command line differs slightly and web output does not parse. I think I have no choise but to write my own parser.. Valdemaras Rep?ys On 7/12/06, mark.schreiber at novartis.com wrote: > > Hi - > > Essentially someone needs to do some testing with the new versions of > blast. If the parser seems to produce the correct results then we can add > version 2.x.x to the 'certified' list. > > As always we need volunteers. Also if people notice it doesn't work then > perhaps submit a bug report detailing the version etc. > > Thanks, > > - Mark > > > > > > Dewkid > Sent by: biojava-l-bounces at lists.open-bio.org > 07/12/2006 03:24 AM > > > To: biojava-l at lists.open-bio.org > cc: (bcc: Mark Schreiber/GP/Novartis) > Subject: Re: [Biojava-l] blast parser > > > > I'm new to this list, but I also ran into this problem. The easy > solution, > is to call the setModeLazy method in your BlastLikeSaxParser object, and > it > will ignore the version. Near as I can tell, the parser works just fine > this way. > > Still, I'm anxious to see this parser updated to support the newer blast > versions! > -- > View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 > > Sent from the BioJava forum at Nabble.com. > > _______________________________________________ > 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 richard.holland at ebi.ac.uk Wed Jul 12 07:02:58 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 12 Jul 2006 12:02:58 +0100 Subject: [Biojava-l] API for global alignments In-Reply-To: References: Message-ID: <1152702178.3943.9.camel@texas.ebi.ac.uk> 1.4 doesn't have anything for this, but 1.5 will do (the code is already in the head branch of CVS). Needleman-Wunsch and Smith-Waterman implementations are both in the org.biojava.bio.alignment package. cheers, Richard On Wed, 2006-07-05 at 10:51 +0930, Michael Tran wrote: > Hi > > Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file. > > The BioJava API 1.4 doesn't seem to have this. > > org.biojava.bio.alignment > Interfaces > AlignmentElement > ARAlignment > EditableAlignment > QualitativeAlignment > UnequalLengthAlignment > Classes > AbstractULAlignment > FlexibleAlignment > SimpleAlignmentElement > Exceptions > IllegalAlignmentEditException > > Any help appreciated. > > Cheers, > > MT > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From richard.holland at ebi.ac.uk Wed Jul 12 06:59:21 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 12 Jul 2006 11:59:21 +0100 Subject: [Biojava-l] some source code In-Reply-To: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> References: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> Message-ID: <1152701961.3943.4.camel@texas.ebi.ac.uk> Check out the source from CVS, then find the source file for the class you are looking for in the 'src' folder. (in this instance, DNATools.java). The methods are inside the source for the class. cheers, Richard On Sun, 2006-07-09 at 10:42 -0700, chen li wrote: > Hi all, > > It sounds like stupid but I just wonder if it is > possible to read some source codes for a specific > method from a class, for instance, the source code for > reverse method in DNAtools. > > > Thanks, > > Li > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From ady at sanger.ac.uk Wed Jul 12 08:45:25 2006 From: ady at sanger.ac.uk (Andy Yates) Date: Wed, 12 Jul 2006 13:45:25 +0100 Subject: [Biojava-l] SCF Chromatogram Read Error In-Reply-To: References: Message-ID: <44B4EEE5.6020009@sanger.ac.uk> Hi Kikia, Have you tried the latest version of the chromatogram parser code from CVS. It didn't make it into the 1.4 release of biojava which is why you may be having a problem. If not then I guess it is a proper bug. The src can be accessed @ http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/program/scf/SCF.java?cvsroot=biojava Cheers, Andy Yates Kikia Carter wrote: > I am having the following problem when trying to create a chromatogram > from an SCF file: > java.lang.IndexOutOfBoundsException > at java.io.FileInputStream.readBytes(Native Method) > at java.io.FileInputStream.read(FileInputStream.java:194) > at java.io.DataInputStream.read(DataInputStream.java:224) > at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) > at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) > at org.biojava.bio.program.scf.SCF.load(SCF.java:122) > at org.biojava.bio.program.scf.SCF.load(SCF.java:117) > at org.biojava.bio.program.scf.SCF.create(SCF.java:104) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) > > > Can anyone offer advice on this problem? Thanks in advance! > > _________________________________________________________________ > FREE pop-up blocking with the new MSN Toolbar ? get it now! > http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From dreher at mpiib-berlin.mpg.de Thu Jul 13 14:46:00 2006 From: dreher at mpiib-berlin.mpg.de (Felix Dreher) Date: Thu, 13 Jul 2006 20:46:00 +0200 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI Message-ID: <44B694E8.9060207@mpiib-berlin.mpg.de> Hello, I have a problem with the parsing of Genbank-Sequences from NCBI. The probably most important line of the log (see below) is the following: Error while trying to call new class org.biojavax.SimpleDocRef(class java.util.ArrayList,class java.lang.String,class java.lang.String) This exception is thrown when I run the following code (with the latest CVS version): GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); RichSequence rs = ncbi.getRichSequence("110002612"); If I use the CVS version of March 2006, a different exception is thrown. This is said to be fixed (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI ASN.1 daily update files Richard Holland Fri, 02 Jun 2006 02:16:07 -0700) Any help would be highly appreciated! Best regards, Felix current exception: 2006-07-13 20:28:04,446 ERROR [main] Error: org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) at rnaiserver.calculation.TestRun.main(TestRun.java:40) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) ... 2 more Caused by: java.lang.RuntimeException: Error while trying to call new class org.biojavax.SimpleDocRef(class java.util.ArrayList,class java.lang.String,class java.lang.String) at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) ... 3 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) ... 6 more Caused by: org.hibernate.exception.GenericJDBCException: could not execute query at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2148) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) at org.hibernate.loader.Loader.list(Loader.java:2024) at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) at org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) ... 11 more Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) at org.hibernate.loader.Loader.doQuery(Loader.java:662) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) at org.hibernate.loader.Loader.doList(Loader.java:2145) ... 19 more 'old' exception with Biojava-live from March 2006: 2006-07-13 20:22:08,425 ERROR [main] Error: org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) at rnaiserver.calculation.TestRun.main(TestRun.java:40) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) ... 2 more Caused by: java.lang.IllegalArgumentException: Authors string cannot be null at org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) ... 3 more From richard.holland at ebi.ac.uk Fri Jul 14 04:56:11 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Fri, 14 Jul 2006 09:56:11 +0100 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <44B694E8.9060207@mpiib-berlin.mpg.de> References: <44B694E8.9060207@mpiib-berlin.mpg.de> Message-ID: <1152867372.3943.66.camel@texas.ebi.ac.uk> This exception happens whenever the Genbank record has a reference that either does not have any author or consortium tags, or has no location. Are you sure you're using the latest version from CVS? The code I've got here works just fine and it's the same as what's in CVS. cheers, Richard On Thu, 2006-07-13 at 20:46 +0200, Felix Dreher wrote: > Hello, > > I have a problem with the parsing of Genbank-Sequences from NCBI. > > The probably most important line of the log (see below) is the following: > Error while trying to call new class org.biojavax.SimpleDocRef(class > java.util.ArrayList,class java.lang.String,class java.lang.String) > > This exception is thrown when I run the following code (with the latest > CVS version): > > GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); > ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); > RichSequence rs = ncbi.getRichSequence("110002612"); > > > If I use the CVS version of March 2006, a different exception is thrown. > This is said to be fixed > (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI > ASN.1 daily update files > Richard Holland > Fri, 02 Jun 2006 02:16:07 -0700) > > > > Any help would be highly appreciated! > Best regards, > Felix > > > > current exception: > > 2006-07-13 20:28:04,446 ERROR [main] > Error: > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) > at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) > at rnaiserver.calculation.TestRun.main(TestRun.java:40) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) > ... 2 more > Caused by: java.lang.RuntimeException: Error while trying to call new > class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,class java.lang.String) > at > org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > ... 3 more > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:585) > at > org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) > ... 6 more > Caused by: org.hibernate.exception.GenericJDBCException: could not > execute query > at > org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > at org.hibernate.loader.Loader.doList(Loader.java:2148) > at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) > at org.hibernate.loader.Loader.list(Loader.java:2024) > at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) > at > org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) > at > org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) > at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) > at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) > at > org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) > ... 11 more > Caused by: org.postgresql.util.PSQLException: ERROR: current transaction > is aborted, commands ignored until end of transaction block > at > org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) > at > org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) > at > org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) > at > org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) > at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) > at org.hibernate.loader.Loader.doQuery(Loader.java:662) > at > org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) > at org.hibernate.loader.Loader.doList(Loader.java:2145) > ... 19 more > > > > > > > 'old' exception with Biojava-live from March 2006: > > 2006-07-13 20:22:08,425 ERROR [main] > Error: > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) > at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) > at rnaiserver.calculation.TestRun.main(TestRun.java:40) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) > ... 2 more > Caused by: java.lang.IllegalArgumentException: Authors string cannot be null > at > org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) > ... 3 more > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From dreher at mpiib-berlin.mpg.de Fri Jul 14 12:45:54 2006 From: dreher at mpiib-berlin.mpg.de (Felix Dreher) Date: Fri, 14 Jul 2006 18:45:54 +0200 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <1152867372.3943.66.camel@texas.ebi.ac.uk> References: <44B694E8.9060207@mpiib-berlin.mpg.de> <1152867372.3943.66.camel@texas.ebi.ac.uk> Message-ID: <44B7CA42.90700@mpiib-berlin.mpg.de> Hello, as I found out in the mean-time, the download from NCBI was not the original problem. By changing the IDE (from Studio Creator to Netbeans), I got a more informative error message... :-) It seems to have to do with specific Genbank sequence characteristics and trying to change the feature set of the sequences. So the problem is not really critical, but anyway maybe someone knows what's going wrong?! The code I use is shown below. What I do is create a GI-number list with efetch (outside of Java), download the respective sequences from NCBI, filter them by CDS, and store them in a local BioSQL-database. So all features and annotations that have nothing to do with the CDS get discarded. After the successful filtering of one sequence, the following exception was thrown (in addition to the stack-trace in my last post). This was the case for quite a number of GI-numbers (unfortunately right now I can't tell exactly which numbers, because our in-house server is down for backup-purposes and I can't verify the GI-numbers. But I could do that next week). When the filtering was commented out, the download of sequences was functioning without errors. Regards, Felix java.sql.BatchUpdateException: *Batch entry 0 update reference set title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences, *authors=Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., Marra,M.A. and Mammalian Gene Collection Program Team (consortium), location=Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002), crc=ffffffffc6201355fae78655, dbxref_id=11 where reference_id=61 was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2497) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1298) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:347) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2559) at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:58) at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:195) ... 18 more Source code: static private int[] numbers = {109732075, 109732055, 109731929, 109731809, 109731807, 109731805}; //and so on static private GenbankRichSequenceDB gbDb= new GenbankRichSequenceDB(); static private FeatureFilter ffCDS = new FeatureFilter.ByType("CDS"); public static void main(String[] args) { for(int i=0; i This exception happens whenever the Genbank record has a reference that > either does not have any author or consortium tags, or has no location. > > Are you sure you're using the latest version from CVS? The code I've got > here works just fine and it's the same as what's in CVS. > > cheers, > Richard > > On Thu, 2006-07-13 at 20:46 +0200, Felix Dreher wrote: > >> Hello, >> >> I have a problem with the parsing of Genbank-Sequences from NCBI. >> >> The probably most important line of the log (see below) is the following: >> Error while trying to call new class org.biojavax.SimpleDocRef(class >> java.util.ArrayList,class java.lang.String,class java.lang.String) >> >> This exception is thrown when I run the following code (with the latest >> CVS version): >> >> GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); >> ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); >> RichSequence rs = ncbi.getRichSequence("110002612"); >> >> >> If I use the CVS version of March 2006, a different exception is thrown. >> This is said to be fixed >> (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI >> ASN.1 daily update files >> Richard Holland >> Fri, 02 Jun 2006 02:16:07 -0700) >> >> >> >> Any help would be highly appreciated! >> Best regards, >> Felix >> >> >> >> current exception: >> >> 2006-07-13 20:28:04,446 ERROR [main] >> Error: >> org.biojava.bio.BioException: Failed to read Genbank sequence >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) >> at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) >> at rnaiserver.calculation.TestRun.main(TestRun.java:40) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) >> ... 2 more >> Caused by: java.lang.RuntimeException: Error while trying to call new >> class org.biojavax.SimpleDocRef(class java.util.ArrayList,class >> java.lang.String,class java.lang.String) >> at >> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) >> at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) >> at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) >> ... 3 more >> Caused by: java.lang.reflect.InvocationTargetException >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> at java.lang.reflect.Method.invoke(Method.java:585) >> at >> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) >> ... 6 more >> Caused by: org.hibernate.exception.GenericJDBCException: could not >> execute query >> at >> org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) >> at >> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) >> at >> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) >> at org.hibernate.loader.Loader.doList(Loader.java:2148) >> at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) >> at org.hibernate.loader.Loader.list(Loader.java:2024) >> at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) >> at >> org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) >> at >> org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) >> at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) >> at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) >> at >> org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) >> ... 11 more >> Caused by: org.postgresql.util.PSQLException: ERROR: current transaction >> is aborted, commands ignored until end of transaction block >> at >> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) >> at >> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) >> at >> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) >> at >> org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) >> at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) >> at org.hibernate.loader.Loader.doQuery(Loader.java:662) >> at >> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) >> at org.hibernate.loader.Loader.doList(Loader.java:2145) >> ... 19 more >> >> >> >> >> >> >> 'old' exception with Biojava-live from March 2006: >> >> 2006-07-13 20:22:08,425 ERROR [main] >> Error: >> org.biojava.bio.BioException: Failed to read Genbank sequence >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) >> at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) >> at rnaiserver.calculation.TestRun.main(TestRun.java:40) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) >> ... 2 more >> Caused by: java.lang.IllegalArgumentException: Authors string cannot be null >> at >> org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) >> at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) >> ... 3 more >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> From heatkent at gmail.com Fri Jul 14 17:41:37 2006 From: heatkent at gmail.com (Heather Kent) Date: Fri, 14 Jul 2006 16:41:37 -0500 Subject: [Biojava-l] SCF and ABI chromatogram read error Message-ID: Hi! im also having a problem creating a chromatogram object from abi or scf files. The abi files i have are sequences that have been processed for heterozygotes so there are symbols for incompletely specified bases in the sequence (for instance r or y). The ABI and SCF parsers in biojava apear to only parse the DNA atomic symbols or a gap symbol. Right now im in the middle of trying to override the decodeDNAToken method in the ABIFParser.java class. I'll create my own finite alphabet with the other symbols i need the parser to recognize. Am i heading in the right direction here or is there an easier way?? The SCF parser is set up the same way so i'll have to override it too.... any help would be appreciated!! thanx heather From chen_li3 at yahoo.com Sat Jul 15 15:04:08 2006 From: chen_li3 at yahoo.com (chen li) Date: Sat, 15 Jul 2006 12:04:08 -0700 (PDT) Subject: [Biojava-l] how to avoid duplicate codes Message-ID: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> Hi guys, I am a newie in java and biojava. I just write a small program for my study java purpose. What bother me is that method do_revSeq() and do_revComSeq () look like duplicate. I have problems to chain method do_revSeq() and do_comSeq to get the revComSeq. Any ideas on how to improve/correct it? Thanks, Li public class SeqReader { private String my_seq; private String my_revSeq; private String my_comSeq; private String my_reComSeq; public SeqReader() { my_seq="aatT ccGG"; } private String do_seq() { return my_seq.replace(" ", "");//sequence clean up } public String do_revSeq() { my_revSeq=new StringBuilder(do_seq()).reverse().toString().toUpperCase(); return my_revSeq; } public String do_comSeq() { my_comSeq=do_seq().toLowerCase().replace('a', 'T').replace('t', 'A').replace('c', 'G').replace('g', 'C'); return my_comSeq; } public String do_revComSeq () { my_reComSeq=new StringBuilder(do_comSeq()).reverse().toString().toUpperCase(); return my_reComSeq; } public void print_results() { System.out.println(do_seq()); System.out.println(do_revSeq()); System.out.println( do_comSeq()); System.out.println(do_revComSeq ()); } } __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From richard.holland at ebi.ac.uk Mon Jul 17 04:30:24 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 17 Jul 2006 09:30:24 +0100 Subject: [Biojava-l] how to avoid duplicate codes In-Reply-To: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> References: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> Message-ID: <1153125024.3957.1.camel@texas.ebi.ac.uk> There is nothing wrong with the way you are approaching the bioinformatics part of the problem - the solution you have already is just fine. However, there are a few technical issues with the Java code you have written, but that is for your Java tutor to solve, not us! :) Good luck. cheers, Richard On Sat, 2006-07-15 at 12:04 -0700, chen li wrote: > Hi guys, > > I am a newie in java and biojava. I just write a small > program for my study java purpose. What bother me > is that method do_revSeq() and do_revComSeq () look > like duplicate. I have problems to chain method > do_revSeq() and do_comSeq to get the revComSeq. Any > ideas on how to improve/correct it? > > Thanks, > > Li > > public class SeqReader > { > private String my_seq; > private String my_revSeq; > private String my_comSeq; > private String my_reComSeq; > > public SeqReader() > { > my_seq="aatT ccGG"; > } > > private String do_seq() > { > return my_seq.replace(" ", "");//sequence > clean up > } > > public String do_revSeq() > { > my_revSeq=new > StringBuilder(do_seq()).reverse().toString().toUpperCase(); > return my_revSeq; > } > > public String do_comSeq() > { > > my_comSeq=do_seq().toLowerCase().replace('a', > 'T').replace('t', 'A').replace('c', 'G').replace('g', > 'C'); > return my_comSeq; > > } > > public String do_revComSeq () > { > my_reComSeq=new > StringBuilder(do_comSeq()).reverse().toString().toUpperCase(); > return my_reComSeq; > } > > public void print_results() > { > System.out.println(do_seq()); > System.out.println(do_revSeq()); > System.out.println( do_comSeq()); > System.out.println(do_revComSeq ()); > } > } > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From richard.holland at ebi.ac.uk Mon Jul 17 04:51:17 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 17 Jul 2006 09:51:17 +0100 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <44B7CA42.90700@mpiib-berlin.mpg.de> References: <44B694E8.9060207@mpiib-berlin.mpg.de> <1152867372.3943.66.camel@texas.ebi.ac.uk> <44B7CA42.90700@mpiib-berlin.mpg.de> Message-ID: <1153126277.3957.8.camel@texas.ebi.ac.uk> There is a hint in the exception stack trace you sent: > Call getNextException to see the cause. Posting the results from that call might help explain it a bit better. Also, you didn't include in your example code any of the calls you make to persist the sequence to BioSQL - including establishing the connection to BioSQL, etc. Judging from the stacktrace, this is a problem at the BJX/BioSQL level, so I need to see the entire example, not just the bits that are doing the filtering. cheers, Richard -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From heatkent at gmail.com Wed Jul 19 09:50:47 2006 From: heatkent at gmail.com (Heather Kent) Date: Wed, 19 Jul 2006 08:50:47 -0500 Subject: [Biojava-l] SCF and ABI chromatogram read error Message-ID: I have a parser that will read abi files with ambiguity symbols now, heather From ramyaraghukumar at gmail.com Sun Jul 23 18:02:02 2006 From: ramyaraghukumar at gmail.com (Ramya Raghukumar) Date: Sun, 23 Jul 2006 17:02:02 -0500 Subject: [Biojava-l] Help needed for a GUI Message-ID: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> Hello, I am new to BioJava and am exploring its features. I am planning to build a simple editor for alignments(something like a wordpad, but to handle alignments).Does Biojava support this? Could someone please show me some pointers for this? I did search in "Google Scholar" for hints, but could not find any. Also I tried to display an alignment on a GUI, but did not succeed. Any suggestions would be of help. Thanks for the time, ramya From richard.holland at ebi.ac.uk Mon Jul 24 04:27:58 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 24 Jul 2006 09:27:58 +0100 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> References: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> Message-ID: <1153729678.4138.9.camel@localhost.localdomain> Google Scholar won't be much help with any programming problems as it only catalogs published papers, of which there are not many which discuss Biojava, and even less which include sample code. You're better off searching vanilla-Google, which gives lots of hits if you search for "biojava alignment viewer". Most of the hits Google returns will be to the BioJava mailing list archive. Here is a thread from that archive that discusses exactly what you ask: http://lists.open-bio.org/pipermail/biojava-l/2003-May/003800.html cheers, Richard On Sun, 2006-07-23 at 17:02 -0500, Ramya Raghukumar wrote: > Hello, > > I am new to BioJava and am exploring its features. I am planning to build a > simple editor for alignments(something like a wordpad, but to handle > alignments).Does Biojava support this? Could someone please show me some > pointers for this? > > I did search in "Google Scholar" for hints, but could not find any. Also I > tried to display an alignment on a GUI, but did not succeed. > > Any suggestions would be of help. > > Thanks for the time, > ramya > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From Russell.Smithies at agresearch.co.nz Mon Jul 24 17:14:51 2006 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 25 Jul 2006 09:14:51 +1200 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <1153729678.4138.9.camel@localhost.localdomain> Message-ID: Give Krugle a go too http://www.krugle.com It's still in beta but very good as it searches source code. Russell > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of > Richard Holland > Sent: Monday, 24 July 2006 8:28 p.m. > To: Ramya Raghukumar > Cc: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] Help needed for a GUI > > Google Scholar won't be much help with any programming > problems as it only catalogs published papers, of which there > are not many which discuss Biojava, and even less which > include sample code. You're better off searching > vanilla-Google, which gives lots of hits if you search for > "biojava alignment viewer". > > Most of the hits Google returns will be to the BioJava > mailing list archive. Here is a thread from that archive that > discusses exactly what you ask: > > http://lists.open-bio.org/pipermail/biojava-l/2003-May/003800.html > > cheers, > Richard > > On Sun, 2006-07-23 at 17:02 -0500, Ramya Raghukumar wrote: > > Hello, > > > > I am new to BioJava and am exploring its features. I am planning to > > build a simple editor for alignments(something like a > wordpad, but to > > handle alignments).Does Biojava support this? Could someone please > > show me some pointers for this? > > > > I did search in "Google Scholar" for hints, but could not find any. > > Also I tried to display an alignment on a GUI, but did not succeed. > > > > Any suggestions would be of help. > > > > Thanks for the time, > > ramya > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- > Richard Holland (BioMart Team) > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > UNITED KINGDOM > Tel: +44-(0)1223-494416 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From christoph.gille at charite.de Mon Jul 24 17:16:20 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 24 Jul 2006 23:16:20 +0200 (CEST) Subject: [Biojava-l] Help needed for a GUI Message-ID: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> >I am new to BioJava and am exploring its features. I am planning to build a >simple editor for alignments(something like a wordpad, but to handle >alignments).Does Biojava support this? Could someone please show me some >pointers for this? Using the classes /interfaces - MultiLineRenderer - FeatureRenderer - SequenceRenderer - SequencePanel - FeatureBlockSequenceRenderer one can easily display a gapped sequence with annotations. Perhaps one could place several SequencePanels over each other and put everything in one scroll-panel? Will this wordpad-like program be part of a larger application? From russ at kepler-eng.com Mon Jul 24 17:38:20 2006 From: russ at kepler-eng.com (Russ Kepler) Date: Mon, 24 Jul 2006 15:38:20 -0600 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> References: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> Message-ID: <200607241538.20730.russ@kepler-eng.com> On Monday 24 July 2006 03:16 pm, Dr. Christoph Gille wrote: > >I am new to BioJava and am exploring its features. I am planning to build > > a simple editor for alignments(something like a wordpad, but to handle > > alignments).Does Biojava support this? Could someone please show me some > > pointers for this? > > Using the classes /interfaces > - MultiLineRenderer > - FeatureRenderer > - SequenceRenderer > - SequencePanel > - FeatureBlockSequenceRenderer > one can easily display a gapped sequence with annotations. > Perhaps one could place several SequencePanels over each other and put > everything in one scroll-panel? Better to put the alignment into a TranslatedSequencePanel, and populate the panel with AlignmentRenderers, one per aligned sequence. The AlignmentRenderer accepts a label that it uses to extract the "current" sequence from the alignment that the TranslatedSequencePanel has. Below the AlignmentRenderer are the MultiLineRenderers, etc. From mark.schreiber at novartis.com Mon Jul 24 21:26:20 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 25 Jul 2006 09:26:20 +0800 Subject: [Biojava-l] Help needed for a GUI Message-ID: General Plea - Could someone add some examples of these to the biojava cook book in the wiki. I'm not really familiar with the GUI classes so I wouldn't be the best person to put up demo code. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Russ Kepler Sent by: biojava-l-bounces at lists.open-bio.org 07/25/2006 05:38 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] Help needed for a GUI On Monday 24 July 2006 03:16 pm, Dr. Christoph Gille wrote: > >I am new to BioJava and am exploring its features. I am planning to build > > a simple editor for alignments(something like a wordpad, but to handle > > alignments).Does Biojava support this? Could someone please show me some > > pointers for this? > > Using the classes /interfaces > - MultiLineRenderer > - FeatureRenderer > - SequenceRenderer > - SequencePanel > - FeatureBlockSequenceRenderer > one can easily display a gapped sequence with annotations. > Perhaps one could place several SequencePanels over each other and put > everything in one scroll-panel? Better to put the alignment into a TranslatedSequencePanel, and populate the panel with AlignmentRenderers, one per aligned sequence. The AlignmentRenderer accepts a label that it uses to extract the "current" sequence from the alignment that the TranslatedSequencePanel has. Below the AlignmentRenderer are the MultiLineRenderers, etc. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From bornmand at BATTELLE.ORG Tue Jul 25 16:16:55 2006 From: bornmand at BATTELLE.ORG (Bornman, Daniel M) Date: Tue, 25 Jul 2006 16:16:55 -0400 Subject: [Biojava-l] Setup problems on Linux Message-ID: Dear Listers, I am having problems getting my biojava-1.4 set up on my linux machine. I have java2-sdk-1.4.2 working just fine. I also have a working install of biojava on my windows machine so I'm surprised to have ran into such a problem. I put all the .jar files in a directory '/usr/local/biojava' and set the permissions to each of the .jar files to 755. I am using a bash shell so I inluded a command in my bash_profile to inlcude the jar files in the CLASSPATH variable. (i.e. export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah blah blah...) Also, mozilla browser forced the jar files to be saved with a .zip extension. So I downloaded a .zip version and a .jar version of each of the jar files and tried each of these extensions set in the bash_profile with no luck. Argh! Does someone have an idea of what I can try next??? Thank You, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 From mark.schreiber at novartis.com Tue Jul 25 23:33:33 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 26 Jul 2006 11:33:33 +0800 Subject: [Biojava-l] Setup problems on Linux Message-ID: What is the specific problem? I assume you are getting some sort of ClassNotFound exception but it's hard to know what is going wrong without an example. To make sure your CLASSPATH variable is actually being set you could try echo $CLASSPATH What comes back should be what you set it to. If you get a blank line for some reason it is not set. Note that you also need to set the classpath to include the classes or jar of any program you compiled yourself. Hence if you compiled a program called Main.class from a package called examples and it is in /usr/home/me/myprogram/classes/examples you need to append /usr/home/me/myprogram/classes to your classpath. There are lots of ways to do this. One of my favourites is to make a script to setup the classpath and execute the program all in one go. something like #! /bin/bash #basic biojava export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah #classes for my program export CLASSPATH=$CLASSPATH:/usr/home/me/myprogram/classes/ #run the program java examples.Main Make this shell script executable and run it. You may find that as you get more java experience you will end up with some projects having huge numbers of jar dependencies and possibly projects that require different versions of jars, for example some programs might be fine with biojava1.4 some may need biojava-live. By setting your classpath in the script you keep everything seperate and don't end up with a mammoth environment variable with possible naming collisions. Another way to do it is to put commonly used CLASSPATHs in your .bashrc with different names. eg #default export CLASSPATH=/usr/jars/default.jar export CLASSPATH_BIOJAVA=/usr/biojava/biojava.jar:/usr/biojava/blah export CLASSPATH_MYAPP=/usr/home/me/app/build/myapp.jar:/usr/jar/someotherstuff.jar #extends CLASSPATH_BIOJAVA export CLASSPATH_BIOJAVA_DEMOS=$CLASSPATH_BIOJAVA:/usr/biojava/demos/classes and then from the java command line you can do this neat trick java myproject.Main (runs Main.class from the myproject package with the default classpath) java -cp $CLASSPATH_MYAPP myapp.MainApp (runs MainApp.class from the myapp package with the MYAPP classpath) java -cp $CLASSPATH_BIOJAVA_DEMOS demo.Demo1 (runs Demo1.class from the demo package with the BIOJAVA_DEMO classpath) Hope this helps, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 "Bornman, Daniel M" Sent by: biojava-l-bounces at lists.open-bio.org 07/26/2006 04:16 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Setup problems on Linux Dear Listers, I am having problems getting my biojava-1.4 set up on my linux machine. I have java2-sdk-1.4.2 working just fine. I also have a working install of biojava on my windows machine so I'm surprised to have ran into such a problem. I put all the .jar files in a directory '/usr/local/biojava' and set the permissions to each of the .jar files to 755. I am using a bash shell so I inluded a command in my bash_profile to inlcude the jar files in the CLASSPATH variable. (i.e. export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah blah blah...) Also, mozilla browser forced the jar files to be saved with a .zip extension. So I downloaded a .zip version and a .jar version of each of the jar files and tried each of these extensions set in the bash_profile with no luck. Argh! Does someone have an idea of what I can try next??? Thank You, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Wed Jul 26 03:02:25 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 26 Jul 2006 15:02:25 +0800 Subject: [Biojava-l] [Off Topic] Research Investigator position at NITD in Singapore Message-ID: Dear All - Apologies for the off topic post... A bioinformatics position has become available at NITD in Singapore (Details below). If you wish to apply, please use the URL Listed below. DO NOT reply to this email, all applications must be via the website. Research Investigator Bioinformatics Job ID 18053BR The successful candidate will provide general bioinformatics support to the research institute (malaria project), using both remote and locally available research tools and databases. Requirements: * PhD in Biology plus post graduate qualification in Bioinformatics, Statistics, Computer Science or Information Science, with at least 2 years' relevant postdoc or industry experience. * Demonstrable experience in systems biology or integrative bioinformatics is essential * Must have programming skills in one or more of Java, Perl, Python or C/C++, and proficiency in working with a Linux/Unix operating system. * Knowledge of malarial biology will be an advantage. * Experience in in-silico drug target identification and validation, and in use and management of databases. * Able to work effectively with multidisciplinary and remote teams and possess excellent communication skills. Successful candidate will be offered up to 5-year contract and relocation assistance to work in Singapore. For more details and to apply, please visit our careers website www.novartis.com/careers quoting the appropriate Job ID or selecting country (Singapore) to view all job postings in Singapore. Regards, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From czaleski at albany.edu Wed Jul 26 12:59:48 2006 From: czaleski at albany.edu (czaleski) Date: Wed, 26 Jul 2006 09:59:48 -0700 (PDT) Subject: [Biojava-l] Am I misunderstanding? Message-ID: <5507066.post@talk.nabble.com> I'm worried I may be misunderstanding the intended usage of BioJava. What made me question this was a simple example... I followed the tutorial, and examples in the cookbook. I make a Sequence via the DNATools.createDNASequence(str, str) method. This returns a Sequence object. Sequence is an Interface, so there must be an implementation I don't see... however by following the examples, it shouldn't be necessary to worry about it. According to the tutorial there are 2 global pieces of annotation that have their own accessors - name and URN. The name gets set when I called createDNASequence, but how do I set the URN? There is no method declared on Sequence, or anything it inherits to be able to set the URN. This seems weird. So I start to dig through the source code. I find that createDNASequence(str, str) eventually ends up returning a SimpleSequence impl object, and sure enough, SimpleSequence implements setURN(str); So... in my code... if I want to set the URN, I need to create SimpleSequence objects explicitly instead of referencing them as Sequence objects. Like this: SimpleSequence simpSeq = (SimpleSequence)DNATools.createDNASequence(seq, name); This seems like an unintentional use of the package, and I only even came to this possibility by having to search through the source sode. If this is true and you are you not supposed to use the .impl classes directly, then how would I perform the simple task of setting the URN? Am I misunderstanding? Thanks much. -- View this message in context: http://www.nabble.com/Am-I-misunderstanding--tf2004940.html#a5507066 Sent from the BioJava forum at Nabble.com. From bornmand at BATTELLE.ORG Wed Jul 26 13:26:42 2006 From: bornmand at BATTELLE.ORG (Bornman, Daniel M) Date: Wed, 26 Jul 2006 13:26:42 -0400 Subject: [Biojava-l] MultiAlignClustalW tutorial example Message-ID: All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 From guedes at unisul.br Wed Jul 26 15:37:06 2006 From: guedes at unisul.br (Dickson S. Guedes) Date: Wed, 26 Jul 2006 16:37:06 -0300 Subject: [Biojava-l] RES: MultiAlignClustalW tutorial example In-Reply-To: Message-ID: <200607261936.k6QJaqA7004999@relay.unisul.br> Hi Daniel, The algorithm for MultAlignTest is: - Instantiate a ClustalWAlign class with some name; - Add the sequences to be aligned to this class; - Call the "doMultAlign()" method who make multi-align; To see the results, you may get a Iterator with the aligned sequences like this session code: SequenceIterator it = alSequences.getIterator(); while (it.hasNext()) { Sequence seq = it.nextSequence(); System.out.println(seq.getName() + ": " + seq.seqString()); } System.out.print("GUIDE TREE:" + alSequences.getGuideTree()); You sad "cannot get any output from this external process.". Well, In ClustalWAlign.java there are a session code: Process proc = rt.exec(strComando); InputStream stdin = proc.getInputStream(); BufferedReader br = new BufferedReader(new InputStreamReader(stdin)); while ( (br.readLine()) != null) { // do nothing only read "stdout" from ClustalW // you can put a System.out.print here to prints // the output from ClustalW to console. } exitVal = proc.waitFor(); The loop while hide the output of process but files will be created at path in the "clustalwPath" constant. The String "strComando" is an array with the arguments to run ClustalW by command-line, and contains the follow structure: String [] strComando = { clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align" }; The First Element is: clustalwPath+"ClustalW.EXE" clustalwPath is a constant point to Clustal Executable directory and "ClustalW.EXE" is a String with the name of executable, this value must be changed in other platforms, sorry but I've used this code in Windows. :( Well, another change that must be made is at the end of array if you need more than default multi-alignment (in Windows I can see a list of arguments by type at command line "ClustalW /help"): ... "/align" }; You can add more command-line arguments to something like this: ... "/align", "/tossgaps", "/another_clustal_argument1", "/another_clustal_argument2" . . . }; Yes, the class ClustalWAlign.java need little changes to be portable, and I will make it, or apologize who can do. ;) Have you any other questions about? If yes, send me a e-mail and I'll try to help you. Thanks, Dickson S. Guedes - ATI - Assessoria de Tecnologia da Informa??o UNISUL - Universidade do Sul de Santa Catarina +55 (0xx48) 3621-3200 - http://www.unisul.br -----Mensagem original----- De: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de Bornman, Daniel M Enviada em: quarta-feira, 26 de julho de 2006 14:27 Para: biojava-l at lists.open-bio.org Assunto: [Biojava-l] MultiAlignClustalW tutorial example All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From guedes at unisul.br Wed Jul 26 14:42:21 2006 From: guedes at unisul.br (Dickson S. Guedes) Date: Wed, 26 Jul 2006 15:42:21 -0300 Subject: [Biojava-l] RES: MultiAlignClustalW tutorial example In-Reply-To: Message-ID: <200607261842.k6QIg7A7072533@relay.unisul.br> Hi Daniel, I've developed this code to my environment, but I can help you to do something like it. Please wait a few minutes, because I?m at lunch now and will send another e-mail with more explanation about. []?s Dickson S. Guedes - ATI - Assessoria de Tecnologia da Informa??o UNISUL - Universidade do Sul de Santa Catarina +55 (0xx48) 3621-3200 - http://www.unisul.br -----Mensagem original----- De: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de Bornman, Daniel M Enviada em: quarta-feira, 26 de julho de 2006 14:27 Para: biojava-l at lists.open-bio.org Assunto: [Biojava-l] MultiAlignClustalW tutorial example All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Wed Jul 26 20:58:36 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Thu, 27 Jul 2006 08:58:36 +0800 Subject: [Biojava-l] Am I misunderstanding? Message-ID: Hi - You are correct that when a method says it returns a Sequence it returns an instance of Sequence. It can infact return any instance of Sequence so it is not entirely safe to cast it to SimpleSequence although in this case you are ok. In previous versions of BioJava SimpleSequence was not in an impl package. I think the whole thing came up as a debate surrounding how modifiable sequences should be. As a preference we prefer people build sequences through one of the Tools methods you used or through a SequenceBuilder. There are good reasons why you may want to modify a SimpleSequence and you should regardless of it being in an impl package if you need to. Retrospectively this is probably not the best design. Also when RichSequences become available (in biojava 1.5 or now if you download from CVS) we have deprecated the URN for 3 reasons. 1. Its not clear what should go in there. Possibly an LSID but no-one can agree. 2. BioSQL doesn't store it (not directly anyway). 3. The presence of the BioEntry interface somewhat removes the need for it. Hope this helps, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 czaleski Sent by: biojava-l-bounces at lists.open-bio.org 07/27/2006 12:59 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Am I misunderstanding? I'm worried I may be misunderstanding the intended usage of BioJava. What made me question this was a simple example... I followed the tutorial, and examples in the cookbook. I make a Sequence via the DNATools.createDNASequence(str, str) method. This returns a Sequence object. Sequence is an Interface, so there must be an implementation I don't see... however by following the examples, it shouldn't be necessary to worry about it. According to the tutorial there are 2 global pieces of annotation that have their own accessors - name and URN. The name gets set when I called createDNASequence, but how do I set the URN? There is no method declared on Sequence, or anything it inherits to be able to set the URN. This seems weird. So I start to dig through the source code. I find that createDNASequence(str, str) eventually ends up returning a SimpleSequence impl object, and sure enough, SimpleSequence implements setURN(str); So... in my code... if I want to set the URN, I need to create SimpleSequence objects explicitly instead of referencing them as Sequence objects. Like this: SimpleSequence simpSeq = (SimpleSequence)DNATools.createDNASequence(seq, name); This seems like an unintentional use of the package, and I only even came to this possibility by having to search through the source sode. If this is true and you are you not supposed to use the .impl classes directly, then how would I perform the simple task of setting the URN? Am I misunderstanding? Thanks much. -- View this message in context: http://www.nabble.com/Am-I-misunderstanding--tf2004940.html#a5507066 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From t.juettemann at sms.ed.ac.uk Thu Jul 27 12:49:49 2006 From: t.juettemann at sms.ed.ac.uk (=?ISO-8859-1?Q?Thomas_J=FCttemann?=) Date: Thu, 27 Jul 2006 17:49:49 +0100 Subject: [Biojava-l] installation - java newbie Message-ID: <44C8EEAD.9040306@sms.ed.ac.uk> Hi all! I recently started using Java, today I tried to install BioJava 1.4. As suggested in the "Getting Started" section I put the jar-file into the "ext" directory (D:\Program Files\Java\jre1.5.0_07\lib\ext). When then trying to import org.biojava.bio.*; Eclipse tells me that it can't resolve it. I also tried to use set CLASSPATH, but didn't work. I'm trying this on a windows machine, but have to say I am not that experienced with Windows administration. I tried: set CLASSPATH D:\biojava-1.4\biojava.jar; but when I do: echo %CLASSPATH% the result is: .;C:\Program Files\QuickTime\QTSystem\QTJava.zip The "biojava.jar" is in 2 directories at the moment, one in D:\biojava-1.4 and one in D:\Program Files\Java\jre1.5.0_07\lib\ext Any hints? Apologies if I am blinded by the obvious! Cheers, Thomas From mheusel at gmail.com Thu Jul 27 14:48:22 2006 From: mheusel at gmail.com (Martin Heusel) Date: Thu, 27 Jul 2006 20:48:22 +0200 Subject: [Biojava-l] installation - java newbie In-Reply-To: <44C8EEAD.9040306@sms.ed.ac.uk> References: <44C8EEAD.9040306@sms.ed.ac.uk> Message-ID: <6127fc200607271148p22a69813p1571cb8cb196ca48@mail.gmail.com> On 27/07/06, Thomas J?ttemann wrote: > import org.biojava.bio.*; > > Eclipse tells me that it can't resolve it. Hi Thomas, you can set the classpath/add Jars in Eclipse by right-clicking on the project root and then Properties->Java Build Path->Libraries->Add External Jars.. hth bye Martin -- + In theory, there is no difference between theory and practice. + But, in practice, there is. ~ Jan L. A. van de Snepscheut From clarelz2003 at yahoo.com Sat Jul 29 23:00:57 2006 From: clarelz2003 at yahoo.com (clare) Date: Sat, 29 Jul 2006 20:00:57 -0700 (PDT) Subject: [Biojava-l] the biojava error message Message-ID: <5560299.post@talk.nabble.com> Hi,i'm a newman for bioJava. when i run bioJava , it always show me the biojava error message: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/db/SequenceDB I do not know what's that. Is there anybody could help me to deal with this problem? thank you! -- View this message in context: http://www.nabble.com/the-biojava-error-message-tf2022250.html#a5560299 Sent from the BioJava forum at Nabble.com. From mark.schreiber at novartis.com Sun Jul 30 21:25:34 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 31 Jul 2006 09:25:34 +0800 Subject: [Biojava-l] the biojava error message Message-ID: This is a problem with biojava not being on your classpath.. Take a look at http://biojava.org/wiki/BioJava:GetStarted - Mark clare Sent by: biojava-l-bounces at lists.open-bio.org 07/30/2006 11:00 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] the biojava error message Hi,i'm a newman for bioJava. when i run bioJava , it always show me the biojava error message: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/db/SequenceDB I do not know what's that. Is there anybody could help me to deal with this problem? thank you! -- View this message in context: http://www.nabble.com/the-biojava-error-message-tf2022250.html#a5560299 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andreas.draeger at uni-tuebingen.de Mon Jul 31 09:08:29 2006 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Mon, 31 Jul 2006 15:08:29 +0200 Subject: [Biojava-l] Citation Message-ID: <44CE00CD.3020107@uni-tuebingen.de> Hello, I think it would be great to have a BibTeX entry on the BioJava Wiki and I would like to suggest to write such an entry. That would make citations of the BioJava project much easier. Is there anybody who could write this? Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From richard.holland at ebi.ac.uk Mon Jul 31 11:31:57 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 31 Jul 2006 16:31:57 +0100 Subject: [Biojava-l] Citation In-Reply-To: <44CE00CD.3020107@uni-tuebingen.de> References: <44CE00CD.3020107@uni-tuebingen.de> Message-ID: <1154359918.4151.19.camel@localhost.localdomain> Sounds like a good idea, but I have no idea how to do it. Sorry I can't be more help! On Mon, 2006-07-31 at 15:08 +0200, Andreas Dr?ger wrote: > Hello, > > I think it would be great to have a BibTeX entry on the BioJava Wiki and > I would like to suggest to write such an entry. That would make > citations of the BioJava project much easier. Is there anybody who could > write this? > > Cheers > Andreas > -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From fpepin at cs.mcgill.ca Mon Jul 31 13:52:58 2006 From: fpepin at cs.mcgill.ca (Francois Pepin) Date: Mon, 31 Jul 2006 13:52:58 -0400 Subject: [Biojava-l] Citation In-Reply-To: <44CE00CD.3020107@uni-tuebingen.de> References: <44CE00CD.3020107@uni-tuebingen.de> Message-ID: <1154368378.29618.11.camel@elm.mcb.mcgill.ca> Hi Andreas, Are you asking about getting a specific citation for it, or just to format it in bibtex? Bibtex formatting is easy (jabref is an excellent program for it), and I'd be happy to form one up if there is a specific citation to use. For the 2000 article in ACM SIGBIO (they have a bibtex citation off their website): @article{biojava, author = {Matthew Pocock and Thomas Down and Tim Hubbard}, title = {BioJava: open source components for bioinformatics}, journal = {SIGBIO Newsl.}, volume = {20}, number = {2}, year = {2000}, issn = {0163-5697}, pages = {10--12}, doi = {http://doi.acm.org/10.1145/360262.360266}, publisher = {ACM Press}, address = {New York, NY, USA}, } Another article from pubmed (generated by jabref using the pubmed it): @ARTICLE{Mangalam2002, author = {Harry Mangalam}, title = {The Bio* toolkits--a brief overview.}, journal = {Brief Bioinform}, year = {2002}, volume = {3}, pages = {296--302}, number = {3}, month = {Sep}, abstract = {Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.}, keywords = {Computational Biology; Computer Systems; Humans; Internet; Programming Languages; Software; User-Computer Interface}, pmid = {12230038} } Is there another article that is the current biojava citation? Francois On Mon, 2006-07-31 at 15:08 +0200, Andreas Dr?ger wrote: > Hello, > > I think it would be great to have a BibTeX entry on the BioJava Wiki and > I would like to suggest to write such an entry. That would make > citations of the BioJava project much easier. Is there anybody who could > write this? > > Cheers > Andreas > From mjoss at bio.mq.edu.au Mon Jul 31 17:50:47 2006 From: mjoss at bio.mq.edu.au (Michael Joss) Date: Tue, 01 Aug 2006 07:50:47 +1000 Subject: [Biojava-l] Problem Inserting Genbank File Message-ID: <44CF07D70200004E00003B08@gwc2cn06.its.mq.edu.au> Hi all, I am pretty new to this whole BioJava/BioJavaX thing. I thought I would start with something reasonably basic. At least what I thought would be. I wanted to open a Genbank file and save it into a BioSQL DB. I have got the BioSQL Database all running and BioJava and BioJavaX seem to be working ok ( I might have messed up some stuff along the way but it does appear to be working). I can open the file and can convert it to fasta etc .. all the code was found in various examples. When I use session.saveOrUpdate: BufferedReader br = new BufferedReader(new FileReader("C:/CODE/AY928791.GBANK")); // a namespace to override that in the file Namespace ns = RichObjectFactory.getDefaultNamespace(); // we are reading DNA sequences RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(br,ns); while (seqs.hasNext()) { RichSequence rs = seqs.nextRichSequence(); session.saveOrUpdate("Sequence",rs); } I get an error saying it can't insert a taxon, the taxon and taxon_name tables seem to be populated correctly and I am not sure how to work out why its attempting to insert a taxon that is already there? I just don't know enough about .. well anything.. but hibernate in particular. Any ideas? If you need anything else please let me know? The file is simply a single genbank record with locus the same name as the file. I tried a few others and got the same result. I am using the latest CVS of BioJavaX and BioJava 1.4 and Hibernate 3.1. Cheers Joss 6860 [main] DEBUG org.hibernate.engine.Cascade - processing cascade ACTION_SAVE_UPDATE for: Sequence 6860 [main] DEBUG org.hibernate.engine.CascadingAction - cascading to saveOrUpdate: Taxon 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - transient instance of: Taxon 6860 [main] DEBUG org.hibernate.event.def.DefaultSaveOrUpdateEventListener - saving transient instance 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - saving [Taxon#] 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - executing insertions 6860 [main] DEBUG org.hibernate.event.def.WrapVisitor - Wrapped collection in role: Taxon.nameSet 6875 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Inserting entity: Taxon (native id) 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - about to open PreparedStatement (open PreparedStatements: 0, globally: 0) 6875 [main] DEBUG org.hibernate.SQL - insert into taxon (ncbi_taxon_id, node_rank, genetic_code, mito_genetic_code, left_value, right_value, parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?) 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - preparing statement 6891 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Dehydrating entity: [Taxon#] 6891 [main] DEBUG org.hibernate.type.IntegerType - binding '36865' to parameter: 1 6891 [main] DEBUG org.hibernate.type.StringType - binding null to parameter: 2 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 3 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 4 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 5 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 6 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 7 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - about to close PreparedStatement (open PreparedStatements: 1, globally: 1) 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - closing statement 6953 [main] DEBUG org.hibernate.util.JDBCExceptionReporter - could not insert: [Taxon] [insert into taxon (ncbi_taxon_id, node_rank, genetic_code, mito_genetic_code, left_value, right_value, parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?)] java.sql.SQLException: Duplicate entry '36865' for key 2 From chen_li3 at yahoo.com Mon Jul 3 01:15:03 2006 From: chen_li3 at yahoo.com (chen li) Date: Sun, 2 Jul 2006 18:15:03 -0700 (PDT) Subject: [Biojava-l] reverse and complement of sequence using Java Message-ID: <20060703011503.35259.qmail@web36807.mail.mud.yahoo.com> Dear all, I am newbie to Java and BioJava. I just want to know if there are methods available for reversing or/and complementing a sequence in standard Java library. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mark.schreiber at novartis.com Mon Jul 3 01:31:21 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 3 Jul 2006 09:31:21 +0800 Subject: [Biojava-l] reverse and complement of sequence using Java Message-ID: Take a look at some of the static methods in DNATools and RNATools. - Mark chen li Sent by: biojava-l-bounces at lists.open-bio.org 07/03/2006 09:15 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] reverse and complement of sequence using Java Dear all, I am newbie to Java and BioJava. I just want to know if there are methods available for reversing or/and complementing a sequence in standard Java library. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From richard.holland at ebi.ac.uk Tue Jul 4 10:15:50 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Tue, 04 Jul 2006 11:15:50 +0100 Subject: [Biojava-l] Getting a Slice of an Alignment In-Reply-To: <1151485076.3942.8.camel@texas.ebi.ac.uk> References: <5047818.post@talk.nabble.com> <1151335745.3938.40.camel@texas.ebi.ac.uk> <5049831.post@talk.nabble.com> <1151399858.3938.57.camel@texas.ebi.ac.uk> <5066891.post@talk.nabble.com> <1151421997.3938.91.camel@texas.ebi.ac.uk> <5072893.post@talk.nabble.com> <1151485076.3942.8.camel@texas.ebi.ac.uk> Message-ID: <1152008150.3948.63.camel@texas.ebi.ac.uk> Right... didn't hear anything, but I won't make the change. Here's why... I read the code again this morning, and realised that the vertical slice effect can be achieved using existing methods in the alignment classes. Given an alignment: Alignment algn = .....; And a sub-alignment: Alignment sub = algn.subAlignment(null, new Location(5,10)); The sequences in the sub-alignment can be found like this: Collection labels = sub.getLabels(); For any given label in this collection, the symbol list (for the full sequence can be obtained like this): SymbolList symbols = sub.symbolListForLabel(label); That symbol list will include gaps in appropriate places. To find out the offset of that symbollist within the alignment, you can do this: Location offset = sub.locInAlignment(label); This will return a location with the min and max set to the position of the label in relation to the beginning of the alignment. To explain this, our alignment 'algn' above contains sequence X: SymbolList symbols = algn.symbolListForLabel("X"); // could have used sub instead but same symbollist returned. Location algnOffset = algn.locInAlignment("X"); Location subOffset = sub.locInAlignment("X"); If the sub alignment is over positions 5..10 in the main alignment, and sequence X is 20 bases long and begins 5 bases before the start of the main alignment, then min and max for 'algnOffset' above will equal -5..15, and for 'subOffset' will equal -10..10. You can then use the min and max of 'subOffset' to obtain the chunk of the sequence that actually occurs within the sub alignment: int symStart = -subOffset.getMin(); int symEnd = symStart + subOffset.getMax(); If symStart is <=0, you need to change it to 1 and pad the result with a number of leading gaps equivalent to the negative value. If symStart is beyond the end of the symbol list, or symEnd is <=0, the symbol list does not appear in this alignment. If symEnd is beyond the end of the symbol list, you need to pad the result with trailing gaps equivalent to the difference. You can pass these values to symbol list to get the actual symbols that occur in the sub alignment: SymbolList subSymbols = symbols.subList(symStart, symEnd); Doing this for each label returned by getLabels() in the sub alignment will give you the vertical slice you're looking for. cheers, Richard On Wed, 2006-06-28 at 09:57 +0100, Richard Holland wrote: > Dear list... if I haven't heard any arguments to the contrary by 9am > Monday 3rd July (UK time), I'll make the changes described below. > > cheers, > Richard > > On Tue, 2006-06-27 at 12:57 -0700, Dexter Riley wrote: > > > > Richard Holland-2 wrote: > > > > > > Ah... > > > > > > I just read the source code for the symbolListForLabel() method on sub > > > alignments, and found what may well be a bug. > > > > > > BioJava list people, your help please! In my understanding, > > > symbolListForLabel() should return the symbols from the given label that > > > fall within the alignment. This is the case in all except sub > > > alignments. Sub alignments, for whatever reason, are returning the > > > symbols from the given label that fall within the parent alignment upon > > > which the sub alignment is based, NOT just those that fall within the > > > sub alignment itself. > > > > > > Is this a bug? I think it is. > > > > > > The solution would be for me to alter > > > AbstractULAlignment.SubULAlignment.symbolListForLabel() to restrict the > > > returned symbols to only include those in the area covered by the sub > > > alignment. It would return EMPTY_SEQUENCE if the label didn't cover the > > > area of the sub alignment, and it would return a truncated symbol list > > > if it only partially covered it. > > > > > > Would this be acceptable? > > > > > > If so, once this change was made, it would fix Ed's problems below as > > > subAlignment() would start returning vertical slices as I think it > > > should probably have done so from the start, rather than the horizontal > > > slices it is returning at present. > > > > > > cheers, > > > Richard > > > > > > > I think that would provide just the functionality I was looking for! Thanks > > very much for all your help. > > All the best, > > Ed -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From edbeaty at charter.net Tue Jul 4 16:46:48 2006 From: edbeaty at charter.net (Dexter Riley) Date: Tue, 4 Jul 2006 09:46:48 -0700 (PDT) Subject: [Biojava-l] Getting a Slice of an Alignment In-Reply-To: <1152008150.3948.63.camel@texas.ebi.ac.uk> References: <5047818.post@talk.nabble.com> <1151335745.3938.40.camel@texas.ebi.ac.uk> <5049831.post@talk.nabble.com> <1151399858.3938.57.camel@texas.ebi.ac.uk> <5066891.post@talk.nabble.com> <1151421997.3938.91.camel@texas.ebi.ac.uk> <5072893.post@talk.nabble.com> <1151485076.3942.8.camel@texas.ebi.ac.uk> <1152008150.3948.63.camel@texas.ebi.ac.uk> Message-ID: <5170318.post@talk.nabble.com> I will give this a try. If this provides the "alignment slice" functionality we discussed, I think a function to perform this would be a useful addition to the API (either of Alignment or of the appropriate utility class). Thanks, Ed -- View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5170318 Sent from the BioJava forum at Nabble.com. From mark.schreiber at novartis.com Wed Jul 5 01:00:36 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 5 Jul 2006 09:00:36 +0800 Subject: [Biojava-l] Getting a Slice of an Alignment Message-ID: The method would be useful but Alignment is an interface so you can't add it there. Typically in biojava we use a Tools class that contains static methods to do common things. For example DNATools, DistributionTools, RichSequence.IOTools. As you can see the last case is an inner class of the RichSequence interface. This is probably a tidier approach. - Mark Dexter Riley Sent by: biojava-l-bounces at lists.open-bio.org 07/05/2006 12:46 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] Getting a Slice of an Alignment I will give this a try. If this provides the "alignment slice" functionality we discussed, I think a function to perform this would be a useful addition to the API (either of Alignment or of the appropriate utility class). Thanks, Ed -- View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5170318 Sent from the BioJava forum at Nabble.com. _______________________________________________ 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 Thu Jul 6 18:44:42 2006 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 6 Jul 2006 19:44:42 +0100 Subject: [Biojava-l] biojava wiki and Jmol Message-ID: Hi! I will commit some new protein structure functionality to CVS soon (structure alignments). For this it would be nice if I could show some examples in 3D with the Jmol applet in the BioJava Wiki pages. Could somebody with admin rights install the Jmol-wiki extension for MediaWiki? - not sure who to contact about that... instructions would be here: http://wiki.jmol.org/index.php/MediaWiki#Installation Thanks! :-) Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From arareko at campus.iztacala.unam.mx Thu Jul 6 21:45:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 06 Jul 2006 16:45:34 -0500 Subject: [Biojava-l] biojava wiki and Jmol In-Reply-To: References: Message-ID: <44AD847E.9030306@campus.iztacala.unam.mx> Hi Andreas, I have admin privileges for the open-bio.org webserver. Unless Mark Schreiber (who appears to be the website admin for BioJava) has other opinion, I can help you with this and get the extension installed and configured for the wiki. Regards, Mauricio. Andreas Prlic wrote: > Hi! > > I will commit some new protein structure functionality to CVS soon > (structure alignments). > For this it would be nice if I could show some examples in 3D with the > Jmol applet in > the BioJava Wiki pages. > > Could somebody with admin rights install the Jmol-wiki extension for > MediaWiki? - not sure who to contact about that... > instructions would be here: > http://wiki.jmol.org/index.php/MediaWiki#Installation > > Thanks! :-) > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From mark.schreiber at novartis.com Fri Jul 7 00:56:04 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 7 Jul 2006 08:56:04 +0800 Subject: [Biojava-l] biojava wiki and Jmol Message-ID: Be my guest!! Mauricio Herrera Cuadra Sent by: biojava-l-bounces at lists.open-bio.org 07/07/2006 05:45 AM To: Andreas Prlic cc: biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] biojava wiki and Jmol Hi Andreas, I have admin privileges for the open-bio.org webserver. Unless Mark Schreiber (who appears to be the website admin for BioJava) has other opinion, I can help you with this and get the extension installed and configured for the wiki. Regards, Mauricio. Andreas Prlic wrote: > Hi! > > I will commit some new protein structure functionality to CVS soon > (structure alignments). > For this it would be nice if I could show some examples in 3D with the > Jmol applet in > the BioJava Wiki pages. > > Could somebody with admin rights install the Jmol-wiki extension for > MediaWiki? - not sure who to contact about that... > instructions would be here: > http://wiki.jmol.org/index.php/MediaWiki#Installation > > Thanks! :-) > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Fri Jul 7 02:29:57 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 7 Jul 2006 10:29:57 +0800 Subject: [Biojava-l] submission of bug reports and requests for enhancement Message-ID: Hello all - Biojava now has a working bug reporting and tracking system based on bugzilla. You can submit and track bugs or requests for enhancement at http://bugzilla.open-bio.org/ (I will add this link to the biojava wiki). >From now on this should be the prefered way to report a bug in biojava. This is so we don't forget about the bugs that we haven't dealt with and the new features people want that we should add. By default bugs will be 'assigned' to biojava-dev but from time to time I may reassign really bad ones to the appropriate person to clear them more quickly. Please make use of this so we can make biojava better. Thanks, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From arareko at campus.iztacala.unam.mx Fri Jul 7 14:23:05 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 07 Jul 2006 09:23:05 -0500 Subject: [Biojava-l] biojava wiki and Jmol In-Reply-To: References: Message-ID: <44AE6E49.9030107@campus.iztacala.unam.mx> Mark and Andreas, The Jmol extension is installed now and should be working. I configured it with all the steps from the installation page. For the moment, I've only added *.cml files to the allowed extensions to upload. If you want to upload other types of files, please let me know and I'll perform the necessary steps. Andreas - please try to upload some files and play with the Jmol wiki tags to see if everything works as it should. Regards, Mauricio. PS. I'm Cc'ing this to some BioPerl friends to see if someone gets interested in having this for our wiki also ;) mark.schreiber at novartis.com wrote: > Be my guest!! > > > Mauricio Herrera Cuadra > Sent by: biojava-l-bounces at lists.open-bio.org > 07/07/2006 05:45 AM > > > To: Andreas Prlic > cc: biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark > Schreiber/GP/Novartis) > Subject: Re: [Biojava-l] biojava wiki and Jmol > > > Hi Andreas, > > I have admin privileges for the open-bio.org webserver. Unless Mark > Schreiber (who appears to be the website admin for BioJava) has other > opinion, I can help you with this and get the extension installed and > configured for the wiki. > > Regards, > Mauricio. > > Andreas Prlic wrote: >> Hi! >> >> I will commit some new protein structure functionality to CVS soon >> (structure alignments). >> For this it would be nice if I could show some examples in 3D with the >> Jmol applet in >> the BioJava Wiki pages. >> >> Could somebody with admin rights install the Jmol-wiki extension for >> MediaWiki? - not sure who to contact about that... >> instructions would be here: >> http://wiki.jmol.org/index.php/MediaWiki#Installation >> >> Thanks! :-) >> Andreas >> >> ----------------------------------------------------------------------- >> >> Andreas Prlic Wellcome Trust Sanger Institute >> Hinxton, Cambridge CB10 1SA, UK >> +44 (0) 1223 49 6891 >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From michael.tran at acpfg.com.au Wed Jul 5 01:21:56 2006 From: michael.tran at acpfg.com.au (Michael Tran) Date: Wed, 5 Jul 2006 10:51:56 +0930 Subject: [Biojava-l] API for global alignments References: Message-ID: Hi Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file. The BioJava API 1.4 doesn't seem to have this. org.biojava.bio.alignment Interfaces AlignmentElement ARAlignment EditableAlignment QualitativeAlignment UnequalLengthAlignment Classes AbstractULAlignment FlexibleAlignment SimpleAlignmentElement Exceptions IllegalAlignmentEditException Any help appreciated. Cheers, MT -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4762 bytes Desc: not available URL: From chen_li3 at yahoo.com Sun Jul 9 17:42:30 2006 From: chen_li3 at yahoo.com (chen li) Date: Sun, 9 Jul 2006 10:42:30 -0700 (PDT) Subject: [Biojava-l] some source code In-Reply-To: Message-ID: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> Hi all, It sounds like stupid but I just wonder if it is possible to read some source codes for a specific method from a class, for instance, the source code for reverse method in DNAtools. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From mark.schreiber at novartis.com Mon Jul 10 01:40:46 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 10 Jul 2006 09:40:46 +0800 Subject: [Biojava-l] some source code Message-ID: You can get the source code from here. http://biojava.org/wiki/BioJava:Download chen li Sent by: biojava-l-bounces at lists.open-bio.org 07/10/2006 01:42 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] some source code Hi all, It sounds like stupid but I just wonder if it is possible to read some source codes for a specific method from a class, for instance, the source code for reverse method in DNAtools. Thanks, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From debesis at gmail.com Tue Jul 11 12:06:25 2006 From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=) Date: Tue, 11 Jul 2006 15:06:25 +0300 Subject: [Biojava-l] blast parser Message-ID: Hi, i'm trying to parse blast output text with BlastLikeSaxParser and I get an exception: Exception in thread "main" org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.14 is not supported by the biojava blast-like parsing framework Do you know any working parser for the newest version of blast? Thanks in advance, Valdemaras Rep?ys ** From online1 at dewkid.com Tue Jul 11 19:24:28 2006 From: online1 at dewkid.com (Dewkid) Date: Tue, 11 Jul 2006 12:24:28 -0700 (PDT) Subject: [Biojava-l] blast parser In-Reply-To: References: Message-ID: <5276129.post@talk.nabble.com> I'm new to this list, but I also ran into this problem. The easy solution, is to call the setModeLazy method in your BlastLikeSaxParser object, and it will ignore the version. Near as I can tell, the parser works just fine this way. Still, I'm anxious to see this parser updated to support the newer blast versions! -- View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 Sent from the BioJava forum at Nabble.com. From k_stellar at msn.com Tue Jul 11 21:43:30 2006 From: k_stellar at msn.com (Kikia Carter) Date: Tue, 11 Jul 2006 17:43:30 -0400 Subject: [Biojava-l] SCF Chromatogram Read Error Message-ID: I am having the following problem when trying to create a chromatogram from an SCF file: java.lang.IndexOutOfBoundsException at java.io.FileInputStream.readBytes(Native Method) at java.io.FileInputStream.read(FileInputStream.java:194) at java.io.DataInputStream.read(DataInputStream.java:224) at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) at org.biojava.bio.program.scf.SCF.load(SCF.java:122) at org.biojava.bio.program.scf.SCF.load(SCF.java:117) at org.biojava.bio.program.scf.SCF.create(SCF.java:104) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) Can anyone offer advice on this problem? Thanks in advance! _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar ? get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ From mark.schreiber at novartis.com Wed Jul 12 02:32:00 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 12 Jul 2006 10:32:00 +0800 Subject: [Biojava-l] blast parser Message-ID: Hi - Essentially someone needs to do some testing with the new versions of blast. If the parser seems to produce the correct results then we can add version 2.x.x to the 'certified' list. As always we need volunteers. Also if people notice it doesn't work then perhaps submit a bug report detailing the version etc. Thanks, - Mark Dewkid Sent by: biojava-l-bounces at lists.open-bio.org 07/12/2006 03:24 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] blast parser I'm new to this list, but I also ran into this problem. The easy solution, is to call the setModeLazy method in your BlastLikeSaxParser object, and it will ignore the version. Near as I can tell, the parser works just fine this way. Still, I'm anxious to see this parser updated to support the newer blast versions! -- View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Wed Jul 12 02:36:06 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 12 Jul 2006 10:36:06 +0800 Subject: [Biojava-l] SCF Chromatogram Read Error Message-ID: Hi Kikia - This might be a bug. To be sure we need more details. Please submit a bug report to http://bugzilla.open-bio.org/ (under biojava) with as much detail as possible. Try and include some sample code so we can recreate the error. Best regards, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 "Kikia Carter" Sent by: biojava-l-bounces at lists.open-bio.org 07/12/2006 05:43 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] SCF Chromatogram Read Error I am having the following problem when trying to create a chromatogram from an SCF file: java.lang.IndexOutOfBoundsException at java.io.FileInputStream.readBytes(Native Method) at java.io.FileInputStream.read(FileInputStream.java:194) at java.io.DataInputStream.read(DataInputStream.java:224) at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) at org.biojava.bio.program.scf.SCF.load(SCF.java:122) at org.biojava.bio.program.scf.SCF.load(SCF.java:117) at org.biojava.bio.program.scf.SCF.create(SCF.java:104) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) Can anyone offer advice on this problem? Thanks in advance! _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar ? get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From debesis at gmail.com Wed Jul 12 07:39:12 2006 From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=) Date: Wed, 12 Jul 2006 10:39:12 +0300 Subject: [Biojava-l] blast parser In-Reply-To: References: Message-ID: Thanks for the help. It really works fine with lazy mode on when parsing blastpgp output (i tried versions 2.2.14 & 2.2.10). The thing is I need a psiblast-on-the-web parser, the text output from the web and command line differs slightly and web output does not parse. I think I have no choise but to write my own parser.. Valdemaras Rep?ys On 7/12/06, mark.schreiber at novartis.com wrote: > > Hi - > > Essentially someone needs to do some testing with the new versions of > blast. If the parser seems to produce the correct results then we can add > version 2.x.x to the 'certified' list. > > As always we need volunteers. Also if people notice it doesn't work then > perhaps submit a bug report detailing the version etc. > > Thanks, > > - Mark > > > > > > Dewkid > Sent by: biojava-l-bounces at lists.open-bio.org > 07/12/2006 03:24 AM > > > To: biojava-l at lists.open-bio.org > cc: (bcc: Mark Schreiber/GP/Novartis) > Subject: Re: [Biojava-l] blast parser > > > > I'm new to this list, but I also ran into this problem. The easy > solution, > is to call the setModeLazy method in your BlastLikeSaxParser object, and > it > will ignore the version. Near as I can tell, the parser works just fine > this way. > > Still, I'm anxious to see this parser updated to support the newer blast > versions! > -- > View this message in context: http://www.nabble.com/blast-parser-tf1924149.html#a5276129 > > Sent from the BioJava forum at Nabble.com. > > _______________________________________________ > 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 richard.holland at ebi.ac.uk Wed Jul 12 11:02:58 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 12 Jul 2006 12:02:58 +0100 Subject: [Biojava-l] API for global alignments In-Reply-To: References: Message-ID: <1152702178.3943.9.camel@texas.ebi.ac.uk> 1.4 doesn't have anything for this, but 1.5 will do (the code is already in the head branch of CVS). Needleman-Wunsch and Smith-Waterman implementations are both in the org.biojava.bio.alignment package. cheers, Richard On Wed, 2006-07-05 at 10:51 +0930, Michael Tran wrote: > Hi > > Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file. > > The BioJava API 1.4 doesn't seem to have this. > > org.biojava.bio.alignment > Interfaces > AlignmentElement > ARAlignment > EditableAlignment > QualitativeAlignment > UnequalLengthAlignment > Classes > AbstractULAlignment > FlexibleAlignment > SimpleAlignmentElement > Exceptions > IllegalAlignmentEditException > > Any help appreciated. > > Cheers, > > MT > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From richard.holland at ebi.ac.uk Wed Jul 12 10:59:21 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Wed, 12 Jul 2006 11:59:21 +0100 Subject: [Biojava-l] some source code In-Reply-To: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> References: <20060709174230.5743.qmail@web36801.mail.mud.yahoo.com> Message-ID: <1152701961.3943.4.camel@texas.ebi.ac.uk> Check out the source from CVS, then find the source file for the class you are looking for in the 'src' folder. (in this instance, DNATools.java). The methods are inside the source for the class. cheers, Richard On Sun, 2006-07-09 at 10:42 -0700, chen li wrote: > Hi all, > > It sounds like stupid but I just wonder if it is > possible to read some source codes for a specific > method from a class, for instance, the source code for > reverse method in DNAtools. > > > Thanks, > > Li > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From ady at sanger.ac.uk Wed Jul 12 12:45:25 2006 From: ady at sanger.ac.uk (Andy Yates) Date: Wed, 12 Jul 2006 13:45:25 +0100 Subject: [Biojava-l] SCF Chromatogram Read Error In-Reply-To: References: Message-ID: <44B4EEE5.6020009@sanger.ac.uk> Hi Kikia, Have you tried the latest version of the chromatogram parser code from CVS. It didn't make it into the 1.4 release of biojava which is why you may be having a problem. If not then I guess it is a proper bug. The src can be accessed @ http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/program/scf/SCF.java?cvsroot=biojava Cheers, Andy Yates Kikia Carter wrote: > I am having the following problem when trying to create a chromatogram > from an SCF file: > java.lang.IndexOutOfBoundsException > at java.io.FileInputStream.readBytes(Native Method) > at java.io.FileInputStream.read(FileInputStream.java:194) > at java.io.DataInputStream.read(DataInputStream.java:224) > at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:348) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:313) > at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:176) > at org.biojava.bio.program.scf.SCF.load(SCF.java:122) > at org.biojava.bio.program.scf.SCF.load(SCF.java:117) > at org.biojava.bio.program.scf.SCF.create(SCF.java:104) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) > > > Can anyone offer advice on this problem? Thanks in advance! > > _________________________________________________________________ > FREE pop-up blocking with the new MSN Toolbar ? get it now! > http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From dreher at mpiib-berlin.mpg.de Thu Jul 13 18:46:00 2006 From: dreher at mpiib-berlin.mpg.de (Felix Dreher) Date: Thu, 13 Jul 2006 20:46:00 +0200 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI Message-ID: <44B694E8.9060207@mpiib-berlin.mpg.de> Hello, I have a problem with the parsing of Genbank-Sequences from NCBI. The probably most important line of the log (see below) is the following: Error while trying to call new class org.biojavax.SimpleDocRef(class java.util.ArrayList,class java.lang.String,class java.lang.String) This exception is thrown when I run the following code (with the latest CVS version): GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); RichSequence rs = ncbi.getRichSequence("110002612"); If I use the CVS version of March 2006, a different exception is thrown. This is said to be fixed (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI ASN.1 daily update files Richard Holland Fri, 02 Jun 2006 02:16:07 -0700) Any help would be highly appreciated! Best regards, Felix current exception: 2006-07-13 20:28:04,446 ERROR [main] Error: org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) at rnaiserver.calculation.TestRun.main(TestRun.java:40) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) ... 2 more Caused by: java.lang.RuntimeException: Error while trying to call new class org.biojavax.SimpleDocRef(class java.util.ArrayList,class java.lang.String,class java.lang.String) at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) ... 3 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) ... 6 more Caused by: org.hibernate.exception.GenericJDBCException: could not execute query at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2148) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) at org.hibernate.loader.Loader.list(Loader.java:2024) at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) at org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) ... 11 more Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) at org.hibernate.loader.Loader.doQuery(Loader.java:662) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) at org.hibernate.loader.Loader.doList(Loader.java:2145) ... 19 more 'old' exception with Biojava-live from March 2006: 2006-07-13 20:22:08,425 ERROR [main] Error: org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) at rnaiserver.calculation.TestRun.main(TestRun.java:40) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) ... 2 more Caused by: java.lang.IllegalArgumentException: Authors string cannot be null at org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) ... 3 more From richard.holland at ebi.ac.uk Fri Jul 14 08:56:11 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Fri, 14 Jul 2006 09:56:11 +0100 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <44B694E8.9060207@mpiib-berlin.mpg.de> References: <44B694E8.9060207@mpiib-berlin.mpg.de> Message-ID: <1152867372.3943.66.camel@texas.ebi.ac.uk> This exception happens whenever the Genbank record has a reference that either does not have any author or consortium tags, or has no location. Are you sure you're using the latest version from CVS? The code I've got here works just fine and it's the same as what's in CVS. cheers, Richard On Thu, 2006-07-13 at 20:46 +0200, Felix Dreher wrote: > Hello, > > I have a problem with the parsing of Genbank-Sequences from NCBI. > > The probably most important line of the log (see below) is the following: > Error while trying to call new class org.biojavax.SimpleDocRef(class > java.util.ArrayList,class java.lang.String,class java.lang.String) > > This exception is thrown when I run the following code (with the latest > CVS version): > > GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); > ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); > RichSequence rs = ncbi.getRichSequence("110002612"); > > > If I use the CVS version of March 2006, a different exception is thrown. > This is said to be fixed > (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI > ASN.1 daily update files > Richard Holland > Fri, 02 Jun 2006 02:16:07 -0700) > > > > Any help would be highly appreciated! > Best regards, > Felix > > > > current exception: > > 2006-07-13 20:28:04,446 ERROR [main] > Error: > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) > at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) > at rnaiserver.calculation.TestRun.main(TestRun.java:40) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) > ... 2 more > Caused by: java.lang.RuntimeException: Error while trying to call new > class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,class java.lang.String) > at > org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > ... 3 more > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:585) > at > org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) > ... 6 more > Caused by: org.hibernate.exception.GenericJDBCException: could not > execute query > at > org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > at org.hibernate.loader.Loader.doList(Loader.java:2148) > at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) > at org.hibernate.loader.Loader.list(Loader.java:2024) > at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) > at > org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) > at > org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) > at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) > at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) > at > org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) > ... 11 more > Caused by: org.postgresql.util.PSQLException: ERROR: current transaction > is aborted, commands ignored until end of transaction block > at > org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) > at > org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) > at > org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) > at > org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) > at > org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) > at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) > at org.hibernate.loader.Loader.doQuery(Loader.java:662) > at > org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) > at org.hibernate.loader.Loader.doList(Loader.java:2145) > ... 19 more > > > > > > > 'old' exception with Biojava-live from March 2006: > > 2006-07-13 20:22:08,425 ERROR [main] > Error: > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) > at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) > at rnaiserver.calculation.TestRun.main(TestRun.java:40) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) > ... 2 more > Caused by: java.lang.IllegalArgumentException: Authors string cannot be null > at > org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) > ... 3 more > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From dreher at mpiib-berlin.mpg.de Fri Jul 14 16:45:54 2006 From: dreher at mpiib-berlin.mpg.de (Felix Dreher) Date: Fri, 14 Jul 2006 18:45:54 +0200 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <1152867372.3943.66.camel@texas.ebi.ac.uk> References: <44B694E8.9060207@mpiib-berlin.mpg.de> <1152867372.3943.66.camel@texas.ebi.ac.uk> Message-ID: <44B7CA42.90700@mpiib-berlin.mpg.de> Hello, as I found out in the mean-time, the download from NCBI was not the original problem. By changing the IDE (from Studio Creator to Netbeans), I got a more informative error message... :-) It seems to have to do with specific Genbank sequence characteristics and trying to change the feature set of the sequences. So the problem is not really critical, but anyway maybe someone knows what's going wrong?! The code I use is shown below. What I do is create a GI-number list with efetch (outside of Java), download the respective sequences from NCBI, filter them by CDS, and store them in a local BioSQL-database. So all features and annotations that have nothing to do with the CDS get discarded. After the successful filtering of one sequence, the following exception was thrown (in addition to the stack-trace in my last post). This was the case for quite a number of GI-numbers (unfortunately right now I can't tell exactly which numbers, because our in-house server is down for backup-purposes and I can't verify the GI-numbers. But I could do that next week). When the filtering was commented out, the download of sequences was functioning without errors. Regards, Felix java.sql.BatchUpdateException: *Batch entry 0 update reference set title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences, *authors=Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., Marra,M.A. and Mammalian Gene Collection Program Team (consortium), location=Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002), crc=ffffffffc6201355fae78655, dbxref_id=11 where reference_id=61 was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2497) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1298) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:347) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2559) at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:58) at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:195) ... 18 more Source code: static private int[] numbers = {109732075, 109732055, 109731929, 109731809, 109731807, 109731805}; //and so on static private GenbankRichSequenceDB gbDb= new GenbankRichSequenceDB(); static private FeatureFilter ffCDS = new FeatureFilter.ByType("CDS"); public static void main(String[] args) { for(int i=0; i This exception happens whenever the Genbank record has a reference that > either does not have any author or consortium tags, or has no location. > > Are you sure you're using the latest version from CVS? The code I've got > here works just fine and it's the same as what's in CVS. > > cheers, > Richard > > On Thu, 2006-07-13 at 20:46 +0200, Felix Dreher wrote: > >> Hello, >> >> I have a problem with the parsing of Genbank-Sequences from NCBI. >> >> The probably most important line of the log (see below) is the following: >> Error while trying to call new class org.biojavax.SimpleDocRef(class >> java.util.ArrayList,class java.lang.String,class java.lang.String) >> >> This exception is thrown when I run the following code (with the latest >> CVS version): >> >> GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); >> ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace()); >> RichSequence rs = ncbi.getRichSequence("110002612"); >> >> >> If I use the CVS version of March 2006, a different exception is thrown. >> This is said to be fixed >> (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI >> ASN.1 daily update files >> Richard Holland >> Fri, 02 Jun 2006 02:16:07 -0700) >> >> >> >> Any help would be highly appreciated! >> Best regards, >> Felix >> >> >> >> current exception: >> >> 2006-07-13 20:28:04,446 ERROR [main] >> Error: >> org.biojava.bio.BioException: Failed to read Genbank sequence >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157) >> at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) >> at rnaiserver.calculation.TestRun.main(TestRun.java:40) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153) >> ... 2 more >> Caused by: java.lang.RuntimeException: Error while trying to call new >> class org.biojavax.SimpleDocRef(class java.util.ArrayList,class >> java.lang.String,class java.lang.String) >> at >> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156) >> at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104) >> at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385) >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) >> ... 3 more >> Caused by: java.lang.reflect.InvocationTargetException >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> at java.lang.reflect.Method.invoke(Method.java:585) >> at >> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123) >> ... 6 more >> Caused by: org.hibernate.exception.GenericJDBCException: could not >> execute query >> at >> org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91) >> at >> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79) >> at >> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) >> at org.hibernate.loader.Loader.doList(Loader.java:2148) >> at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029) >> at org.hibernate.loader.Loader.list(Loader.java:2024) >> at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375) >> at >> org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308) >> at >> org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153) >> at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129) >> at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79) >> at >> org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749) >> ... 11 more >> Caused by: org.postgresql.util.PSQLException: ERROR: current transaction >> is aborted, commands ignored until end of transaction block >> at >> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) >> at >> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297) >> at >> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) >> at >> org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) >> at >> org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139) >> at org.hibernate.loader.Loader.getResultSet(Loader.java:1669) >> at org.hibernate.loader.Loader.doQuery(Loader.java:662) >> at >> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) >> at org.hibernate.loader.Loader.doList(Loader.java:2145) >> ... 19 more >> >> >> >> >> >> >> 'old' exception with Biojava-live from March 2006: >> >> 2006-07-13 20:22:08,425 ERROR [main] >> Error: >> org.biojava.bio.BioException: Failed to read Genbank sequence >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156) >> at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237) >> at rnaiserver.calculation.TestRun.main(TestRun.java:40) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111) >> at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152) >> ... 2 more >> Caused by: java.lang.IllegalArgumentException: Authors string cannot be null >> at >> org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75) >> at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323) >> at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108) >> ... 3 more >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> From heatkent at gmail.com Fri Jul 14 21:41:37 2006 From: heatkent at gmail.com (Heather Kent) Date: Fri, 14 Jul 2006 16:41:37 -0500 Subject: [Biojava-l] SCF and ABI chromatogram read error Message-ID: Hi! im also having a problem creating a chromatogram object from abi or scf files. The abi files i have are sequences that have been processed for heterozygotes so there are symbols for incompletely specified bases in the sequence (for instance r or y). The ABI and SCF parsers in biojava apear to only parse the DNA atomic symbols or a gap symbol. Right now im in the middle of trying to override the decodeDNAToken method in the ABIFParser.java class. I'll create my own finite alphabet with the other symbols i need the parser to recognize. Am i heading in the right direction here or is there an easier way?? The SCF parser is set up the same way so i'll have to override it too.... any help would be appreciated!! thanx heather From chen_li3 at yahoo.com Sat Jul 15 19:04:08 2006 From: chen_li3 at yahoo.com (chen li) Date: Sat, 15 Jul 2006 12:04:08 -0700 (PDT) Subject: [Biojava-l] how to avoid duplicate codes Message-ID: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> Hi guys, I am a newie in java and biojava. I just write a small program for my study java purpose. What bother me is that method do_revSeq() and do_revComSeq () look like duplicate. I have problems to chain method do_revSeq() and do_comSeq to get the revComSeq. Any ideas on how to improve/correct it? Thanks, Li public class SeqReader { private String my_seq; private String my_revSeq; private String my_comSeq; private String my_reComSeq; public SeqReader() { my_seq="aatT ccGG"; } private String do_seq() { return my_seq.replace(" ", "");//sequence clean up } public String do_revSeq() { my_revSeq=new StringBuilder(do_seq()).reverse().toString().toUpperCase(); return my_revSeq; } public String do_comSeq() { my_comSeq=do_seq().toLowerCase().replace('a', 'T').replace('t', 'A').replace('c', 'G').replace('g', 'C'); return my_comSeq; } public String do_revComSeq () { my_reComSeq=new StringBuilder(do_comSeq()).reverse().toString().toUpperCase(); return my_reComSeq; } public void print_results() { System.out.println(do_seq()); System.out.println(do_revSeq()); System.out.println( do_comSeq()); System.out.println(do_revComSeq ()); } } __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From richard.holland at ebi.ac.uk Mon Jul 17 08:30:24 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 17 Jul 2006 09:30:24 +0100 Subject: [Biojava-l] how to avoid duplicate codes In-Reply-To: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> References: <20060715190408.34962.qmail@web36814.mail.mud.yahoo.com> Message-ID: <1153125024.3957.1.camel@texas.ebi.ac.uk> There is nothing wrong with the way you are approaching the bioinformatics part of the problem - the solution you have already is just fine. However, there are a few technical issues with the Java code you have written, but that is for your Java tutor to solve, not us! :) Good luck. cheers, Richard On Sat, 2006-07-15 at 12:04 -0700, chen li wrote: > Hi guys, > > I am a newie in java and biojava. I just write a small > program for my study java purpose. What bother me > is that method do_revSeq() and do_revComSeq () look > like duplicate. I have problems to chain method > do_revSeq() and do_comSeq to get the revComSeq. Any > ideas on how to improve/correct it? > > Thanks, > > Li > > public class SeqReader > { > private String my_seq; > private String my_revSeq; > private String my_comSeq; > private String my_reComSeq; > > public SeqReader() > { > my_seq="aatT ccGG"; > } > > private String do_seq() > { > return my_seq.replace(" ", "");//sequence > clean up > } > > public String do_revSeq() > { > my_revSeq=new > StringBuilder(do_seq()).reverse().toString().toUpperCase(); > return my_revSeq; > } > > public String do_comSeq() > { > > my_comSeq=do_seq().toLowerCase().replace('a', > 'T').replace('t', 'A').replace('c', 'G').replace('g', > 'C'); > return my_comSeq; > > } > > public String do_revComSeq () > { > my_reComSeq=new > StringBuilder(do_comSeq()).reverse().toString().toUpperCase(); > return my_reComSeq; > } > > public void print_results() > { > System.out.println(do_seq()); > System.out.println(do_revSeq()); > System.out.println( do_comSeq()); > System.out.println(do_revComSeq ()); > } > } > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From richard.holland at ebi.ac.uk Mon Jul 17 08:51:17 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 17 Jul 2006 09:51:17 +0100 Subject: [Biojava-l] Parsing Genbank-sequences from NCBI In-Reply-To: <44B7CA42.90700@mpiib-berlin.mpg.de> References: <44B694E8.9060207@mpiib-berlin.mpg.de> <1152867372.3943.66.camel@texas.ebi.ac.uk> <44B7CA42.90700@mpiib-berlin.mpg.de> Message-ID: <1153126277.3957.8.camel@texas.ebi.ac.uk> There is a hint in the exception stack trace you sent: > Call getNextException to see the cause. Posting the results from that call might help explain it a bit better. Also, you didn't include in your example code any of the calls you make to persist the sequence to BioSQL - including establishing the connection to BioSQL, etc. Judging from the stacktrace, this is a problem at the BJX/BioSQL level, so I need to see the entire example, not just the bits that are doing the filtering. cheers, Richard -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From heatkent at gmail.com Wed Jul 19 13:50:47 2006 From: heatkent at gmail.com (Heather Kent) Date: Wed, 19 Jul 2006 08:50:47 -0500 Subject: [Biojava-l] SCF and ABI chromatogram read error Message-ID: I have a parser that will read abi files with ambiguity symbols now, heather From ramyaraghukumar at gmail.com Sun Jul 23 22:02:02 2006 From: ramyaraghukumar at gmail.com (Ramya Raghukumar) Date: Sun, 23 Jul 2006 17:02:02 -0500 Subject: [Biojava-l] Help needed for a GUI Message-ID: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> Hello, I am new to BioJava and am exploring its features. I am planning to build a simple editor for alignments(something like a wordpad, but to handle alignments).Does Biojava support this? Could someone please show me some pointers for this? I did search in "Google Scholar" for hints, but could not find any. Also I tried to display an alignment on a GUI, but did not succeed. Any suggestions would be of help. Thanks for the time, ramya From richard.holland at ebi.ac.uk Mon Jul 24 08:27:58 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 24 Jul 2006 09:27:58 +0100 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> References: <9b9b3f860607231502r4f1518a3y96dc14284dd95b49@mail.gmail.com> Message-ID: <1153729678.4138.9.camel@localhost.localdomain> Google Scholar won't be much help with any programming problems as it only catalogs published papers, of which there are not many which discuss Biojava, and even less which include sample code. You're better off searching vanilla-Google, which gives lots of hits if you search for "biojava alignment viewer". Most of the hits Google returns will be to the BioJava mailing list archive. Here is a thread from that archive that discusses exactly what you ask: http://lists.open-bio.org/pipermail/biojava-l/2003-May/003800.html cheers, Richard On Sun, 2006-07-23 at 17:02 -0500, Ramya Raghukumar wrote: > Hello, > > I am new to BioJava and am exploring its features. I am planning to build a > simple editor for alignments(something like a wordpad, but to handle > alignments).Does Biojava support this? Could someone please show me some > pointers for this? > > I did search in "Google Scholar" for hints, but could not find any. Also I > tried to display an alignment on a GUI, but did not succeed. > > Any suggestions would be of help. > > Thanks for the time, > ramya > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From Russell.Smithies at agresearch.co.nz Mon Jul 24 21:14:51 2006 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 25 Jul 2006 09:14:51 +1200 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <1153729678.4138.9.camel@localhost.localdomain> Message-ID: Give Krugle a go too http://www.krugle.com It's still in beta but very good as it searches source code. Russell > -----Original Message----- > From: biojava-l-bounces at lists.open-bio.org > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of > Richard Holland > Sent: Monday, 24 July 2006 8:28 p.m. > To: Ramya Raghukumar > Cc: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] Help needed for a GUI > > Google Scholar won't be much help with any programming > problems as it only catalogs published papers, of which there > are not many which discuss Biojava, and even less which > include sample code. You're better off searching > vanilla-Google, which gives lots of hits if you search for > "biojava alignment viewer". > > Most of the hits Google returns will be to the BioJava > mailing list archive. Here is a thread from that archive that > discusses exactly what you ask: > > http://lists.open-bio.org/pipermail/biojava-l/2003-May/003800.html > > cheers, > Richard > > On Sun, 2006-07-23 at 17:02 -0500, Ramya Raghukumar wrote: > > Hello, > > > > I am new to BioJava and am exploring its features. I am planning to > > build a simple editor for alignments(something like a > wordpad, but to > > handle alignments).Does Biojava support this? Could someone please > > show me some pointers for this? > > > > I did search in "Google Scholar" for hints, but could not find any. > > Also I tried to display an alignment on a GUI, but did not succeed. > > > > Any suggestions would be of help. > > > > Thanks for the time, > > ramya > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- > Richard Holland (BioMart Team) > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > UNITED KINGDOM > Tel: +44-(0)1223-494416 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From christoph.gille at charite.de Mon Jul 24 21:16:20 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 24 Jul 2006 23:16:20 +0200 (CEST) Subject: [Biojava-l] Help needed for a GUI Message-ID: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> >I am new to BioJava and am exploring its features. I am planning to build a >simple editor for alignments(something like a wordpad, but to handle >alignments).Does Biojava support this? Could someone please show me some >pointers for this? Using the classes /interfaces - MultiLineRenderer - FeatureRenderer - SequenceRenderer - SequencePanel - FeatureBlockSequenceRenderer one can easily display a gapped sequence with annotations. Perhaps one could place several SequencePanels over each other and put everything in one scroll-panel? Will this wordpad-like program be part of a larger application? From russ at kepler-eng.com Mon Jul 24 21:38:20 2006 From: russ at kepler-eng.com (Russ Kepler) Date: Mon, 24 Jul 2006 15:38:20 -0600 Subject: [Biojava-l] Help needed for a GUI In-Reply-To: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> References: <61097.84.190.8.113.1153775780.squirrel@webmail.charite.de> Message-ID: <200607241538.20730.russ@kepler-eng.com> On Monday 24 July 2006 03:16 pm, Dr. Christoph Gille wrote: > >I am new to BioJava and am exploring its features. I am planning to build > > a simple editor for alignments(something like a wordpad, but to handle > > alignments).Does Biojava support this? Could someone please show me some > > pointers for this? > > Using the classes /interfaces > - MultiLineRenderer > - FeatureRenderer > - SequenceRenderer > - SequencePanel > - FeatureBlockSequenceRenderer > one can easily display a gapped sequence with annotations. > Perhaps one could place several SequencePanels over each other and put > everything in one scroll-panel? Better to put the alignment into a TranslatedSequencePanel, and populate the panel with AlignmentRenderers, one per aligned sequence. The AlignmentRenderer accepts a label that it uses to extract the "current" sequence from the alignment that the TranslatedSequencePanel has. Below the AlignmentRenderer are the MultiLineRenderers, etc. From mark.schreiber at novartis.com Tue Jul 25 01:26:20 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 25 Jul 2006 09:26:20 +0800 Subject: [Biojava-l] Help needed for a GUI Message-ID: General Plea - Could someone add some examples of these to the biojava cook book in the wiki. I'm not really familiar with the GUI classes so I wouldn't be the best person to put up demo code. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Russ Kepler Sent by: biojava-l-bounces at lists.open-bio.org 07/25/2006 05:38 AM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] Help needed for a GUI On Monday 24 July 2006 03:16 pm, Dr. Christoph Gille wrote: > >I am new to BioJava and am exploring its features. I am planning to build > > a simple editor for alignments(something like a wordpad, but to handle > > alignments).Does Biojava support this? Could someone please show me some > > pointers for this? > > Using the classes /interfaces > - MultiLineRenderer > - FeatureRenderer > - SequenceRenderer > - SequencePanel > - FeatureBlockSequenceRenderer > one can easily display a gapped sequence with annotations. > Perhaps one could place several SequencePanels over each other and put > everything in one scroll-panel? Better to put the alignment into a TranslatedSequencePanel, and populate the panel with AlignmentRenderers, one per aligned sequence. The AlignmentRenderer accepts a label that it uses to extract the "current" sequence from the alignment that the TranslatedSequencePanel has. Below the AlignmentRenderer are the MultiLineRenderers, etc. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From bornmand at BATTELLE.ORG Tue Jul 25 20:16:55 2006 From: bornmand at BATTELLE.ORG (Bornman, Daniel M) Date: Tue, 25 Jul 2006 16:16:55 -0400 Subject: [Biojava-l] Setup problems on Linux Message-ID: Dear Listers, I am having problems getting my biojava-1.4 set up on my linux machine. I have java2-sdk-1.4.2 working just fine. I also have a working install of biojava on my windows machine so I'm surprised to have ran into such a problem. I put all the .jar files in a directory '/usr/local/biojava' and set the permissions to each of the .jar files to 755. I am using a bash shell so I inluded a command in my bash_profile to inlcude the jar files in the CLASSPATH variable. (i.e. export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah blah blah...) Also, mozilla browser forced the jar files to be saved with a .zip extension. So I downloaded a .zip version and a .jar version of each of the jar files and tried each of these extensions set in the bash_profile with no luck. Argh! Does someone have an idea of what I can try next??? Thank You, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 From mark.schreiber at novartis.com Wed Jul 26 03:33:33 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 26 Jul 2006 11:33:33 +0800 Subject: [Biojava-l] Setup problems on Linux Message-ID: What is the specific problem? I assume you are getting some sort of ClassNotFound exception but it's hard to know what is going wrong without an example. To make sure your CLASSPATH variable is actually being set you could try echo $CLASSPATH What comes back should be what you set it to. If you get a blank line for some reason it is not set. Note that you also need to set the classpath to include the classes or jar of any program you compiled yourself. Hence if you compiled a program called Main.class from a package called examples and it is in /usr/home/me/myprogram/classes/examples you need to append /usr/home/me/myprogram/classes to your classpath. There are lots of ways to do this. One of my favourites is to make a script to setup the classpath and execute the program all in one go. something like #! /bin/bash #basic biojava export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah #classes for my program export CLASSPATH=$CLASSPATH:/usr/home/me/myprogram/classes/ #run the program java examples.Main Make this shell script executable and run it. You may find that as you get more java experience you will end up with some projects having huge numbers of jar dependencies and possibly projects that require different versions of jars, for example some programs might be fine with biojava1.4 some may need biojava-live. By setting your classpath in the script you keep everything seperate and don't end up with a mammoth environment variable with possible naming collisions. Another way to do it is to put commonly used CLASSPATHs in your .bashrc with different names. eg #default export CLASSPATH=/usr/jars/default.jar export CLASSPATH_BIOJAVA=/usr/biojava/biojava.jar:/usr/biojava/blah export CLASSPATH_MYAPP=/usr/home/me/app/build/myapp.jar:/usr/jar/someotherstuff.jar #extends CLASSPATH_BIOJAVA export CLASSPATH_BIOJAVA_DEMOS=$CLASSPATH_BIOJAVA:/usr/biojava/demos/classes and then from the java command line you can do this neat trick java myproject.Main (runs Main.class from the myproject package with the default classpath) java -cp $CLASSPATH_MYAPP myapp.MainApp (runs MainApp.class from the myapp package with the MYAPP classpath) java -cp $CLASSPATH_BIOJAVA_DEMOS demo.Demo1 (runs Demo1.class from the demo package with the BIOJAVA_DEMO classpath) Hope this helps, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 "Bornman, Daniel M" Sent by: biojava-l-bounces at lists.open-bio.org 07/26/2006 04:16 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Setup problems on Linux Dear Listers, I am having problems getting my biojava-1.4 set up on my linux machine. I have java2-sdk-1.4.2 working just fine. I also have a working install of biojava on my windows machine so I'm surprised to have ran into such a problem. I put all the .jar files in a directory '/usr/local/biojava' and set the permissions to each of the .jar files to 755. I am using a bash shell so I inluded a command in my bash_profile to inlcude the jar files in the CLASSPATH variable. (i.e. export CLASSPATH=/usr/local/biojava/biojava-1.4.jar:/usr/local/biojava/blah blah blah...) Also, mozilla browser forced the jar files to be saved with a .zip extension. So I downloaded a .zip version and a .jar version of each of the jar files and tried each of these extensions set in the bash_profile with no luck. Argh! Does someone have an idea of what I can try next??? Thank You, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Wed Jul 26 07:02:25 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 26 Jul 2006 15:02:25 +0800 Subject: [Biojava-l] [Off Topic] Research Investigator position at NITD in Singapore Message-ID: Dear All - Apologies for the off topic post... A bioinformatics position has become available at NITD in Singapore (Details below). If you wish to apply, please use the URL Listed below. DO NOT reply to this email, all applications must be via the website. Research Investigator Bioinformatics Job ID 18053BR The successful candidate will provide general bioinformatics support to the research institute (malaria project), using both remote and locally available research tools and databases. Requirements: * PhD in Biology plus post graduate qualification in Bioinformatics, Statistics, Computer Science or Information Science, with at least 2 years' relevant postdoc or industry experience. * Demonstrable experience in systems biology or integrative bioinformatics is essential * Must have programming skills in one or more of Java, Perl, Python or C/C++, and proficiency in working with a Linux/Unix operating system. * Knowledge of malarial biology will be an advantage. * Experience in in-silico drug target identification and validation, and in use and management of databases. * Able to work effectively with multidisciplinary and remote teams and possess excellent communication skills. Successful candidate will be offered up to 5-year contract and relocation assistance to work in Singapore. For more details and to apply, please visit our careers website www.novartis.com/careers quoting the appropriate Job ID or selecting country (Singapore) to view all job postings in Singapore. Regards, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From czaleski at albany.edu Wed Jul 26 16:59:48 2006 From: czaleski at albany.edu (czaleski) Date: Wed, 26 Jul 2006 09:59:48 -0700 (PDT) Subject: [Biojava-l] Am I misunderstanding? Message-ID: <5507066.post@talk.nabble.com> I'm worried I may be misunderstanding the intended usage of BioJava. What made me question this was a simple example... I followed the tutorial, and examples in the cookbook. I make a Sequence via the DNATools.createDNASequence(str, str) method. This returns a Sequence object. Sequence is an Interface, so there must be an implementation I don't see... however by following the examples, it shouldn't be necessary to worry about it. According to the tutorial there are 2 global pieces of annotation that have their own accessors - name and URN. The name gets set when I called createDNASequence, but how do I set the URN? There is no method declared on Sequence, or anything it inherits to be able to set the URN. This seems weird. So I start to dig through the source code. I find that createDNASequence(str, str) eventually ends up returning a SimpleSequence impl object, and sure enough, SimpleSequence implements setURN(str); So... in my code... if I want to set the URN, I need to create SimpleSequence objects explicitly instead of referencing them as Sequence objects. Like this: SimpleSequence simpSeq = (SimpleSequence)DNATools.createDNASequence(seq, name); This seems like an unintentional use of the package, and I only even came to this possibility by having to search through the source sode. If this is true and you are you not supposed to use the .impl classes directly, then how would I perform the simple task of setting the URN? Am I misunderstanding? Thanks much. -- View this message in context: http://www.nabble.com/Am-I-misunderstanding--tf2004940.html#a5507066 Sent from the BioJava forum at Nabble.com. From bornmand at BATTELLE.ORG Wed Jul 26 17:26:42 2006 From: bornmand at BATTELLE.ORG (Bornman, Daniel M) Date: Wed, 26 Jul 2006 13:26:42 -0400 Subject: [Biojava-l] MultiAlignClustalW tutorial example Message-ID: All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 From guedes at unisul.br Wed Jul 26 19:37:06 2006 From: guedes at unisul.br (Dickson S. Guedes) Date: Wed, 26 Jul 2006 16:37:06 -0300 Subject: [Biojava-l] RES: MultiAlignClustalW tutorial example In-Reply-To: Message-ID: <200607261936.k6QJaqA7004999@relay.unisul.br> Hi Daniel, The algorithm for MultAlignTest is: - Instantiate a ClustalWAlign class with some name; - Add the sequences to be aligned to this class; - Call the "doMultAlign()" method who make multi-align; To see the results, you may get a Iterator with the aligned sequences like this session code: SequenceIterator it = alSequences.getIterator(); while (it.hasNext()) { Sequence seq = it.nextSequence(); System.out.println(seq.getName() + ": " + seq.seqString()); } System.out.print("GUIDE TREE:" + alSequences.getGuideTree()); You sad "cannot get any output from this external process.". Well, In ClustalWAlign.java there are a session code: Process proc = rt.exec(strComando); InputStream stdin = proc.getInputStream(); BufferedReader br = new BufferedReader(new InputStreamReader(stdin)); while ( (br.readLine()) != null) { // do nothing only read "stdout" from ClustalW // you can put a System.out.print here to prints // the output from ClustalW to console. } exitVal = proc.waitFor(); The loop while hide the output of process but files will be created at path in the "clustalwPath" constant. The String "strComando" is an array with the arguments to run ClustalW by command-line, and contains the follow structure: String [] strComando = { clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align" }; The First Element is: clustalwPath+"ClustalW.EXE" clustalwPath is a constant point to Clustal Executable directory and "ClustalW.EXE" is a String with the name of executable, this value must be changed in other platforms, sorry but I've used this code in Windows. :( Well, another change that must be made is at the end of array if you need more than default multi-alignment (in Windows I can see a list of arguments by type at command line "ClustalW /help"): ... "/align" }; You can add more command-line arguments to something like this: ... "/align", "/tossgaps", "/another_clustal_argument1", "/another_clustal_argument2" . . . }; Yes, the class ClustalWAlign.java need little changes to be portable, and I will make it, or apologize who can do. ;) Have you any other questions about? If yes, send me a e-mail and I'll try to help you. Thanks, Dickson S. Guedes - ATI - Assessoria de Tecnologia da Informa??o UNISUL - Universidade do Sul de Santa Catarina +55 (0xx48) 3621-3200 - http://www.unisul.br -----Mensagem original----- De: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de Bornman, Daniel M Enviada em: quarta-feira, 26 de julho de 2006 14:27 Para: biojava-l at lists.open-bio.org Assunto: [Biojava-l] MultiAlignClustalW tutorial example All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From guedes at unisul.br Wed Jul 26 18:42:21 2006 From: guedes at unisul.br (Dickson S. Guedes) Date: Wed, 26 Jul 2006 15:42:21 -0300 Subject: [Biojava-l] RES: MultiAlignClustalW tutorial example In-Reply-To: Message-ID: <200607261842.k6QIg7A7072533@relay.unisul.br> Hi Daniel, I've developed this code to my environment, but I can help you to do something like it. Please wait a few minutes, because I?m at lunch now and will send another e-mail with more explanation about. []?s Dickson S. Guedes - ATI - Assessoria de Tecnologia da Informa??o UNISUL - Universidade do Sul de Santa Catarina +55 (0xx48) 3621-3200 - http://www.unisul.br -----Mensagem original----- De: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de Bornman, Daniel M Enviada em: quarta-feira, 26 de julho de 2006 14:27 Para: biojava-l at lists.open-bio.org Assunto: [Biojava-l] MultiAlignClustalW tutorial example All, I am currently trying to work through the MultiAlignClustalW example on the wiki but I am having some problems getting output. After changing the necessary variable to work on my Linux machine and choosing to use the ClustalWAlign(BufferedReader,String) construtor from my test class, I cannot get any output from this external process. I am using the latest version of ClustalW and I have noticed that when running it from the command line directly, I am prompted for many inputs. Does the java example take these into account? It seems like it attempts to in this section of code: String [] strComando = {clustalwPath+"ClustalW.EXE", "/infile=" + clustalwPath + fileName + ".input", "/outfile=" + clustalwPath + fileName + ".output", "/output=" + fileFormat, "/align"}; ...but I don't quite understand what all elements of this array are intending to do or how if fits into the series of prompts when running clustalw from the command line? Thank You for any insight, Daniel Bornman Researcher Battelle Memorial Institute 505 King Ave Columbus, OH 43201 614.424.3229 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Thu Jul 27 00:58:36 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Thu, 27 Jul 2006 08:58:36 +0800 Subject: [Biojava-l] Am I misunderstanding? Message-ID: Hi - You are correct that when a method says it returns a Sequence it returns an instance of Sequence. It can infact return any instance of Sequence so it is not entirely safe to cast it to SimpleSequence although in this case you are ok. In previous versions of BioJava SimpleSequence was not in an impl package. I think the whole thing came up as a debate surrounding how modifiable sequences should be. As a preference we prefer people build sequences through one of the Tools methods you used or through a SequenceBuilder. There are good reasons why you may want to modify a SimpleSequence and you should regardless of it being in an impl package if you need to. Retrospectively this is probably not the best design. Also when RichSequences become available (in biojava 1.5 or now if you download from CVS) we have deprecated the URN for 3 reasons. 1. Its not clear what should go in there. Possibly an LSID but no-one can agree. 2. BioSQL doesn't store it (not directly anyway). 3. The presence of the BioEntry interface somewhat removes the need for it. Hope this helps, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 czaleski Sent by: biojava-l-bounces at lists.open-bio.org 07/27/2006 12:59 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Am I misunderstanding? I'm worried I may be misunderstanding the intended usage of BioJava. What made me question this was a simple example... I followed the tutorial, and examples in the cookbook. I make a Sequence via the DNATools.createDNASequence(str, str) method. This returns a Sequence object. Sequence is an Interface, so there must be an implementation I don't see... however by following the examples, it shouldn't be necessary to worry about it. According to the tutorial there are 2 global pieces of annotation that have their own accessors - name and URN. The name gets set when I called createDNASequence, but how do I set the URN? There is no method declared on Sequence, or anything it inherits to be able to set the URN. This seems weird. So I start to dig through the source code. I find that createDNASequence(str, str) eventually ends up returning a SimpleSequence impl object, and sure enough, SimpleSequence implements setURN(str); So... in my code... if I want to set the URN, I need to create SimpleSequence objects explicitly instead of referencing them as Sequence objects. Like this: SimpleSequence simpSeq = (SimpleSequence)DNATools.createDNASequence(seq, name); This seems like an unintentional use of the package, and I only even came to this possibility by having to search through the source sode. If this is true and you are you not supposed to use the .impl classes directly, then how would I perform the simple task of setting the URN? Am I misunderstanding? Thanks much. -- View this message in context: http://www.nabble.com/Am-I-misunderstanding--tf2004940.html#a5507066 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From t.juettemann at sms.ed.ac.uk Thu Jul 27 16:49:49 2006 From: t.juettemann at sms.ed.ac.uk (=?ISO-8859-1?Q?Thomas_J=FCttemann?=) Date: Thu, 27 Jul 2006 17:49:49 +0100 Subject: [Biojava-l] installation - java newbie Message-ID: <44C8EEAD.9040306@sms.ed.ac.uk> Hi all! I recently started using Java, today I tried to install BioJava 1.4. As suggested in the "Getting Started" section I put the jar-file into the "ext" directory (D:\Program Files\Java\jre1.5.0_07\lib\ext). When then trying to import org.biojava.bio.*; Eclipse tells me that it can't resolve it. I also tried to use set CLASSPATH, but didn't work. I'm trying this on a windows machine, but have to say I am not that experienced with Windows administration. I tried: set CLASSPATH D:\biojava-1.4\biojava.jar; but when I do: echo %CLASSPATH% the result is: .;C:\Program Files\QuickTime\QTSystem\QTJava.zip The "biojava.jar" is in 2 directories at the moment, one in D:\biojava-1.4 and one in D:\Program Files\Java\jre1.5.0_07\lib\ext Any hints? Apologies if I am blinded by the obvious! Cheers, Thomas From mheusel at gmail.com Thu Jul 27 18:48:22 2006 From: mheusel at gmail.com (Martin Heusel) Date: Thu, 27 Jul 2006 20:48:22 +0200 Subject: [Biojava-l] installation - java newbie In-Reply-To: <44C8EEAD.9040306@sms.ed.ac.uk> References: <44C8EEAD.9040306@sms.ed.ac.uk> Message-ID: <6127fc200607271148p22a69813p1571cb8cb196ca48@mail.gmail.com> On 27/07/06, Thomas J?ttemann wrote: > import org.biojava.bio.*; > > Eclipse tells me that it can't resolve it. Hi Thomas, you can set the classpath/add Jars in Eclipse by right-clicking on the project root and then Properties->Java Build Path->Libraries->Add External Jars.. hth bye Martin -- + In theory, there is no difference between theory and practice. + But, in practice, there is. ~ Jan L. A. van de Snepscheut From clarelz2003 at yahoo.com Sun Jul 30 03:00:57 2006 From: clarelz2003 at yahoo.com (clare) Date: Sat, 29 Jul 2006 20:00:57 -0700 (PDT) Subject: [Biojava-l] the biojava error message Message-ID: <5560299.post@talk.nabble.com> Hi,i'm a newman for bioJava. when i run bioJava , it always show me the biojava error message: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/db/SequenceDB I do not know what's that. Is there anybody could help me to deal with this problem? thank you! -- View this message in context: http://www.nabble.com/the-biojava-error-message-tf2022250.html#a5560299 Sent from the BioJava forum at Nabble.com. From mark.schreiber at novartis.com Mon Jul 31 01:25:34 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Mon, 31 Jul 2006 09:25:34 +0800 Subject: [Biojava-l] the biojava error message Message-ID: This is a problem with biojava not being on your classpath.. Take a look at http://biojava.org/wiki/BioJava:GetStarted - Mark clare Sent by: biojava-l-bounces at lists.open-bio.org 07/30/2006 11:00 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] the biojava error message Hi,i'm a newman for bioJava. when i run bioJava , it always show me the biojava error message: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/db/SequenceDB I do not know what's that. Is there anybody could help me to deal with this problem? thank you! -- View this message in context: http://www.nabble.com/the-biojava-error-message-tf2022250.html#a5560299 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From andreas.draeger at uni-tuebingen.de Mon Jul 31 13:08:29 2006 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Mon, 31 Jul 2006 15:08:29 +0200 Subject: [Biojava-l] Citation Message-ID: <44CE00CD.3020107@uni-tuebingen.de> Hello, I think it would be great to have a BibTeX entry on the BioJava Wiki and I would like to suggest to write such an entry. That would make citations of the BioJava project much easier. Is there anybody who could write this? Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From richard.holland at ebi.ac.uk Mon Jul 31 15:31:57 2006 From: richard.holland at ebi.ac.uk (Richard Holland) Date: Mon, 31 Jul 2006 16:31:57 +0100 Subject: [Biojava-l] Citation In-Reply-To: <44CE00CD.3020107@uni-tuebingen.de> References: <44CE00CD.3020107@uni-tuebingen.de> Message-ID: <1154359918.4151.19.camel@localhost.localdomain> Sounds like a good idea, but I have no idea how to do it. Sorry I can't be more help! On Mon, 2006-07-31 at 15:08 +0200, Andreas Dr?ger wrote: > Hello, > > I think it would be great to have a BibTeX entry on the BioJava Wiki and > I would like to suggest to write such an entry. That would make > citations of the BioJava project much easier. Is there anybody who could > write this? > > Cheers > Andreas > -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 From fpepin at cs.mcgill.ca Mon Jul 31 17:52:58 2006 From: fpepin at cs.mcgill.ca (Francois Pepin) Date: Mon, 31 Jul 2006 13:52:58 -0400 Subject: [Biojava-l] Citation In-Reply-To: <44CE00CD.3020107@uni-tuebingen.de> References: <44CE00CD.3020107@uni-tuebingen.de> Message-ID: <1154368378.29618.11.camel@elm.mcb.mcgill.ca> Hi Andreas, Are you asking about getting a specific citation for it, or just to format it in bibtex? Bibtex formatting is easy (jabref is an excellent program for it), and I'd be happy to form one up if there is a specific citation to use. For the 2000 article in ACM SIGBIO (they have a bibtex citation off their website): @article{biojava, author = {Matthew Pocock and Thomas Down and Tim Hubbard}, title = {BioJava: open source components for bioinformatics}, journal = {SIGBIO Newsl.}, volume = {20}, number = {2}, year = {2000}, issn = {0163-5697}, pages = {10--12}, doi = {http://doi.acm.org/10.1145/360262.360266}, publisher = {ACM Press}, address = {New York, NY, USA}, } Another article from pubmed (generated by jabref using the pubmed it): @ARTICLE{Mangalam2002, author = {Harry Mangalam}, title = {The Bio* toolkits--a brief overview.}, journal = {Brief Bioinform}, year = {2002}, volume = {3}, pages = {296--302}, number = {3}, month = {Sep}, abstract = {Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.}, keywords = {Computational Biology; Computer Systems; Humans; Internet; Programming Languages; Software; User-Computer Interface}, pmid = {12230038} } Is there another article that is the current biojava citation? Francois On Mon, 2006-07-31 at 15:08 +0200, Andreas Dr?ger wrote: > Hello, > > I think it would be great to have a BibTeX entry on the BioJava Wiki and > I would like to suggest to write such an entry. That would make > citations of the BioJava project much easier. Is there anybody who could > write this? > > Cheers > Andreas > From mjoss at bio.mq.edu.au Mon Jul 31 21:50:47 2006 From: mjoss at bio.mq.edu.au (Michael Joss) Date: Tue, 01 Aug 2006 07:50:47 +1000 Subject: [Biojava-l] Problem Inserting Genbank File Message-ID: <44CF07D70200004E00003B08@gwc2cn06.its.mq.edu.au> Hi all, I am pretty new to this whole BioJava/BioJavaX thing. I thought I would start with something reasonably basic. At least what I thought would be. I wanted to open a Genbank file and save it into a BioSQL DB. I have got the BioSQL Database all running and BioJava and BioJavaX seem to be working ok ( I might have messed up some stuff along the way but it does appear to be working). I can open the file and can convert it to fasta etc .. all the code was found in various examples. When I use session.saveOrUpdate: BufferedReader br = new BufferedReader(new FileReader("C:/CODE/AY928791.GBANK")); // a namespace to override that in the file Namespace ns = RichObjectFactory.getDefaultNamespace(); // we are reading DNA sequences RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(br,ns); while (seqs.hasNext()) { RichSequence rs = seqs.nextRichSequence(); session.saveOrUpdate("Sequence",rs); } I get an error saying it can't insert a taxon, the taxon and taxon_name tables seem to be populated correctly and I am not sure how to work out why its attempting to insert a taxon that is already there? I just don't know enough about .. well anything.. but hibernate in particular. Any ideas? If you need anything else please let me know? The file is simply a single genbank record with locus the same name as the file. I tried a few others and got the same result. I am using the latest CVS of BioJavaX and BioJava 1.4 and Hibernate 3.1. Cheers Joss 6860 [main] DEBUG org.hibernate.engine.Cascade - processing cascade ACTION_SAVE_UPDATE for: Sequence 6860 [main] DEBUG org.hibernate.engine.CascadingAction - cascading to saveOrUpdate: Taxon 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - transient instance of: Taxon 6860 [main] DEBUG org.hibernate.event.def.DefaultSaveOrUpdateEventListener - saving transient instance 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - saving [Taxon#] 6860 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener - executing insertions 6860 [main] DEBUG org.hibernate.event.def.WrapVisitor - Wrapped collection in role: Taxon.nameSet 6875 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Inserting entity: Taxon (native id) 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - about to open PreparedStatement (open PreparedStatements: 0, globally: 0) 6875 [main] DEBUG org.hibernate.SQL - insert into taxon (ncbi_taxon_id, node_rank, genetic_code, mito_genetic_code, left_value, right_value, parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?) 6875 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - preparing statement 6891 [main] DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Dehydrating entity: [Taxon#] 6891 [main] DEBUG org.hibernate.type.IntegerType - binding '36865' to parameter: 1 6891 [main] DEBUG org.hibernate.type.StringType - binding null to parameter: 2 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 3 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 4 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 5 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 6 6891 [main] DEBUG org.hibernate.type.IntegerType - binding null to parameter: 7 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - about to close PreparedStatement (open PreparedStatements: 1, globally: 1) 6953 [main] DEBUG org.hibernate.jdbc.AbstractBatcher - closing statement 6953 [main] DEBUG org.hibernate.util.JDBCExceptionReporter - could not insert: [Taxon] [insert into taxon (ncbi_taxon_id, node_rank, genetic_code, mito_genetic_code, left_value, right_value, parent_taxon_id) values (?, ?, ?, ?, ?, ?, ?)] java.sql.SQLException: Duplicate entry '36865' for key 2