From andrew.craig at cambridgebluegnome.com Mon Sep 3 04:20:27 2007 From: andrew.craig at cambridgebluegnome.com (Andrew Craig) Date: Mon, 3 Sep 2007 09:20:27 +0100 Subject: [Biojava-l] BioJava 1.5 in Matlab and DNATools Class In-Reply-To: <93b45ca50708311846g2257389fqefdd0198481b88b6@mail.gmail.com> Message-ID: <002e01c7ee03$498d5460$1001a8c0@FRANKLIN> Dear Mark, Thanks for your suggestion. I have checked my Matlab install directories and there are no biojava jar files. I am using Matlab without any additional Mathworks toolboxes but perhaps what you say applies to the Mathworks Bioinformatics toolbox? In any case I don't think that is causing my problem here. Does anyone else have another suggestion? Best wishes, Andrew Craig -----Original Message----- From: Mark Schreiber [mailto:markjschreiber at gmail.com] Sent: 01 September 2007 02:47 To: Andrew Craig Cc: biojava-l at lists.open-bio.org Subject: Re: [Biojava-l] BioJava 1.5 in Matlab and DNATools Class Hi - I know that some parts of matlab use biojava. Probably version 1.4 or 1.3. It may be that it is using this jar file instead of the one you want it not. I'm not a matlab expert so I don't know how you can resolve this. - Mark On 9/1/07, Andrew Craig wrote: > Dear List, > > I am trying to use BioJava-1.5 from Matlab (7.2), in order to retrieve the > raw chromatogram data from some .AB1 files. > > I have added biojava-1.5.jar to the Matlab java class path. I then import > the following classes. > import java.io.*; > import java.util.*; > import org.biojava.bio.*; > import org.biojava.bio.chromatogram.*; > import org.biojava.bio.program.abi.*; > import org.biojava.bio.seq.*; > import org.biojava.bio.seq.impl.*; > import org.biojava.bio.seq.io.*; > import org.biojava.bio.symbol.*; > > Next I read the raw chromatogram file with > > myTrace = ChromatogramFactory.create(myFile); > > Then I try to retrieve the raw data for the a base using > > raw_a = myTrace.getTrace(DNATools.a()); > > This works fine for a, t and g bases. My problem is when I call DNATools.c() > it returns the following error > > ??? No method 'c' with matching signature found for class > 'org.biojava.bio.seq.DNATools' > > Can anyone diagnose what is wrong and why only the .c method is giving an > error? I can get around this by using DNATools.complement(G) but I would > prefer to understand what is going on and get things working properly. > > Best regards, > > Andrew Craig > > ____________________________________________________________________ > > This email is confidential and privileged.If you are not the > intended recipient pleaseaccept our apologies; please do not > disclose, copy, or distribute information in this email nor take any > action in reliance on its contents: to do so is strictly prohibited > and may be unlawful. > > Please inform us that this message has gone astray before deleting > it. > > Thank you for your co-operation. > > Andrew Craig andrew.craig at cambridgebluegnome.com > BlueGnome Limited http://www.cambridgebluegnome.com > > Breaks House > Mill Court > Great Shelford > Cambridge > CB2 5LD > > Tel: 01223 844441 Fax: 01223 844445 > US: 1 800 418 9656 > ____________________________________________________________________ > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From abhi232 at cc.gatech.edu Tue Sep 4 03:02:04 2007 From: abhi232 at cc.gatech.edu (abhinav) Date: Tue, 04 Sep 2007 02:02:04 -0500 Subject: [Biojava-l] Problem running applet Message-ID: <46DD02EC.5080702@cc.gatech.edu> Hi all, I am having trouble running an applet with sequencepanel in it. the error that I am getting is Java Plug-in 1.6.0 Using JRE version 1.6.0 Java HotSpot(TM) Client VM User home directory = C:\Documents and Settings\Abhi ---------------------------------------------------- c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message l: dump classloader list m: print memory usage o: trigger logging p: reload proxy configuration q: hide console r: reload policy configuration s: dump system and deployment properties t: dump thread list v: dump thread stack x: clear classloader cache 0-5: set trace level to ---------------------------------------------------- java.lang.NoClassDefFoundError: org/biojava/bio/gui/sequence/SequenceRenderer at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Unknown Source) at java.lang.Class.getConstructor0(Unknown Source) at java.lang.Class.newInstance0(Unknown Source) at java.lang.Class.newInstance(Unknown Source) at sun.applet.AppletPanel.createApplet(Unknown Source) at sun.plugin.AppletViewer.createApplet(Unknown Source) at sun.applet.AppletPanel.runLoader(Unknown Source) at sun.applet.AppletPanel.run(Unknown Source) at java.lang.Thread.run(Unknown Source) ... What shld be done abt this? Thanks in advance From bertrand.beckert at gmail.com Tue Sep 4 05:09:56 2007 From: bertrand.beckert at gmail.com (bertrand beckert) Date: Tue, 4 Sep 2007 11:09:56 +0200 Subject: [Biojava-l] How to launch a blast on ncbi server via biojava? Message-ID: <500217090709040209w5155402bl48617504cc6e8ed4@mail.gmail.com> Hi, Sorry for this silly question, but I would like to know if it is possible to launch some blast via biojava on the ncbi server for an example and also to retrieve the result as it is possible in in the bioperl project. I found some information in the biojava cookbook as how to parse some blast file result but I didn't find any information/example for launch blast on the ncbi server.... Could you help me please Thanks Bertrand From bertrand.beckert at gmail.com Tue Sep 4 09:03:21 2007 From: bertrand.beckert at gmail.com (bertrand beckert) Date: Tue, 4 Sep 2007 15:03:21 +0200 Subject: [Biojava-l] How to launch a blast on ncbi server via biojava? In-Reply-To: <20070904114718.133078F5A2@mail2.pmf.sc.gov.br> References: <500217090709040209w5155402bl48617504cc6e8ed4@mail.gmail.com> <20070904114718.133078F5A2@mail2.pmf.sc.gov.br> Message-ID: <500217090709040603u55c596aatf063bb798acc88c6@mail.gmail.com> Thanks for this code... but this piece is good if you want to retrieve a specific sequence with a particular ID... What I want to do, is to submit a blast and then retrieve the result and then parse the result in oder to know what are the ID.... I already found in the NCBI site ( http://users.encs.concordia.ca/~f_kohant/ncbiblast/) a java interface but the documentation is not so nice....and the link with biojava is quit obscure for me.... could you help me please thanks for all Bertrand 2007/9/4, Dickson Guedes : > > Hi Bertrand, > > > You may use a code like this: > > > try { > NCBISequenceDB impSequence = new NCBISequenceDB(); > > Sequence mySequence = impSequence.getSequence("156447465"); > > System.out.print( > mySequence.getAnnotation() > .getProperty("description") > .toString() > ); > } catch (BioException e) { > System.out.println(e.getMessage()); > } > > > []s > Guedes > > -----Mensagem original----- > De: biojava-l-bounces at lists.open-bio.org > [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de bertrand beckert > Enviada em: ter?a-feira, 4 de setembro de 2007 06:10 > Para: biojava-l at lists.open-bio.org > Assunto: [Biojava-l] How to launch a blast on ncbi server via biojava? > > Hi, > > Sorry for this silly question, but I would like to know if it is possible > to > launch some blast via biojava on the ncbi server for an example and also > to > retrieve the result as it is possible in in the bioperl project. > I found some information in the biojava cookbook as how to parse some > blast > file result but I didn't find any information/example for launch blast on > the ncbi server.... > Could you help me please > > Thanks > > Bertrand > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > -- > Esta mensagem foi verificada pelo sistema de antiv?rus e > acredita-se estar livre de perigo. > > Prefeitura Municipal de Florianopolis - PMF > PMF.SC.GOV.BR > -- > > -- Bertrand BECKERT PhD student IBMC - UPR 9002 du CNRS - ARN 15, rue Rene Descartes F-67084 STRASBOURG Cedex b.beckert at ibmc.u-strasbg.fr bertrand.beckert at gmail.com From jwang at biohealthbase.org Tue Sep 4 09:09:54 2007 From: jwang at biohealthbase.org (Jianjun Wang) Date: Tue, 04 Sep 2007 09:09:54 -0400 Subject: [Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB Message-ID: <20070904130954.6faf638e@biohealthbase.org> Hi Colleagues, I used the Blast parsing example from the Biojava tutorial and ran into this problem: ###################### Failed to build SeqSimilaritySearchResult: org.biojava.bio.BioException: Running BlastLikeSearchBuilder with null query SequenceDB at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSearchResult(BlastLikeSearchBuilder.java:239) at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.endSearch(BlastLikeSearchBuilder.java:319) at org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.endElement(SeqSimilarityStAXAdapter.java:119) at org.biojava.utils.stax.SAX2StAXAdaptor.endElement(SAX2StAXAdaptor.java:153) at org.biojava.bio.program.ssbind.SeqSimilarityAdapter.endElement(SeqSimilarityAdapter.java:136) at org.biojava.bio.program.sax.AbstractNativeAppSAXParser.endElement(AbstractNativeAppSAXParser.java:300) at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:181) at org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311) at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274) at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) ########################### I experimented with both supported Blast versions such as 2.2.3 and later ones, such as 2.2.13, and with the lazymode both on and off, and concluded that this problem is independent of Blast version and the lazymode. My debugging didn't yield much fruit, except that the obvious cause of the exception was BlastLikeSearchBuilder.querySeqHolder being null. Can someone shed some light on this? Here is the relevant section of my code: try { StringReader sr = new StringReader(in); BlastLikeSAXParser parser = new BlastLikeSAXParser(); //works for 2.2.13? //parser.setModeLazy(); //make the SAX event adapter that will pass events to a Handler. SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); //set the parsers SAX event adapter parser.setContentHandler(adapter); //The list to hold the SeqSimilaritySearchResults //List results = new ArrayList(); //create the SearchContentHandler that will build SeqSimilaritySearchResults //in the results List SearchContentHandler builder = new BlastLikeSearchBuilder(results); //register builder with adapter adapter.setSearchContentHandler(builder); //parse the file, after this the result List will be populated with SeqSimilaritySearchResults parser.parse(new InputSource(sr)); //output some blast details - expect 1 result only ...... Thanks, Jianjun From markjschreiber at gmail.com Tue Sep 4 10:05:46 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 4 Sep 2007 22:05:46 +0800 Subject: [Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB In-Reply-To: <20070904130954.6faf638e@biohealthbase.org> References: <20070904130954.6faf638e@biohealthbase.org> Message-ID: <93b45ca50709040705n62a9b8cbwc96d31e1a550aa72@mail.gmail.com> Hello - Just out of interest what type of blast were you running. Some of the more exotic forms like PSIBlast probably don't work well. - Mark On 9/4/07, Jianjun Wang wrote: > Hi Colleagues, > > I used the Blast parsing example from the Biojava tutorial and ran into this problem: > ###################### > Failed to build SeqSimilaritySearchResult: > org.biojava.bio.BioException: Running BlastLikeSearchBuilder with null query SequenceDB > at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSearchResult(BlastLikeSearchBuilder.java:239) > at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.endSearch(BlastLikeSearchBuilder.java:319) > at org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.endElement(SeqSimilarityStAXAdapter.java:119) > at org.biojava.utils.stax.SAX2StAXAdaptor.endElement(SAX2StAXAdaptor.java:153) > at org.biojava.bio.program.ssbind.SeqSimilarityAdapter.endElement(SeqSimilarityAdapter.java:136) > at org.biojava.bio.program.sax.AbstractNativeAppSAXParser.endElement(AbstractNativeAppSAXParser.java:300) > at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:181) > at org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311) > at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274) > at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) > > ########################### > > I experimented with both supported Blast versions such as 2.2.3 and later ones, such as 2.2.13, and with the lazymode both on and off, and concluded that this problem is independent of Blast version and the lazymode. My debugging didn't yield much fruit, except that the obvious cause of the exception was BlastLikeSearchBuilder.querySeqHolder being null. Can someone shed some light on this? > > Here is the relevant section of my code: > > try { > StringReader sr = new StringReader(in); > BlastLikeSAXParser parser = new BlastLikeSAXParser(); > //works for 2.2.13? > //parser.setModeLazy(); > > //make the SAX event adapter that will pass events to a Handler. > SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); > > //set the parsers SAX event adapter > parser.setContentHandler(adapter); > > //The list to hold the SeqSimilaritySearchResults > //List results = new ArrayList(); > > //create the SearchContentHandler that will build SeqSimilaritySearchResults > //in the results List > SearchContentHandler builder = new BlastLikeSearchBuilder(results); > > //register builder with adapter > adapter.setSearchContentHandler(builder); > > //parse the file, after this the result List will be populated with SeqSimilaritySearchResults > parser.parse(new InputSource(sr)); > > //output some blast details - expect 1 result only > ...... > > Thanks, > Jianjun > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From markjschreiber at gmail.com Tue Sep 4 10:15:56 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 4 Sep 2007 22:15:56 +0800 Subject: [Biojava-l] How to launch a blast on ncbi server via biojava? In-Reply-To: <500217090709040603u55c596aatf063bb798acc88c6@mail.gmail.com> References: <500217090709040209w5155402bl48617504cc6e8ed4@mail.gmail.com> <20070904114718.133078F5A2@mail2.pmf.sc.gov.br> <500217090709040603u55c596aatf063bb798acc88c6@mail.gmail.com> Message-ID: <93b45ca50709040715r76037e86o990925c8838c3ec5@mail.gmail.com> Hi - BioJava doesn't have a mechanism to do this however EBI does expose a webservice for NCBI BLAST. The details can be found at http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast They have a java client with source code you could reuse. You can then use biojava to parse the results. If the results are in XML you can use biojava's BLAST XML parser or you could just use XPath to get the bits you want. If you build a solution that makes use of biojava it would be great if you can add it to the cookbook section of the biojava wiki. - Mark On 9/4/07, bertrand beckert wrote: > Thanks for this code... > but this piece is good if you want to retrieve a specific sequence with a > particular ID... > What I want to do, is to submit a blast and then retrieve the result and > then parse the result in oder to know what are the ID.... > I already found in the NCBI site ( > http://users.encs.concordia.ca/~f_kohant/ncbiblast/) a java interface but > the documentation is not so nice....and the link with biojava is quit > obscure for me.... > > could you help me please > > thanks for all > > Bertrand > > > > > > > 2007/9/4, Dickson Guedes : > > > > Hi Bertrand, > > > > > > You may use a code like this: > > > > > > try { > > NCBISequenceDB impSequence = new NCBISequenceDB(); > > > > Sequence mySequence = impSequence.getSequence("156447465"); > > > > System.out.print( > > mySequence.getAnnotation() > > .getProperty("description") > > .toString() > > ); > > } catch (BioException e) { > > System.out.println(e.getMessage()); > > } > > > > > > []s > > Guedes > > > > -----Mensagem original----- > > De: biojava-l-bounces at lists.open-bio.org > > [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de bertrand beckert > > Enviada em: ter?a-feira, 4 de setembro de 2007 06:10 > > Para: biojava-l at lists.open-bio.org > > Assunto: [Biojava-l] How to launch a blast on ncbi server via biojava? > > > > Hi, > > > > Sorry for this silly question, but I would like to know if it is possible > > to > > launch some blast via biojava on the ncbi server for an example and also > > to > > retrieve the result as it is possible in in the bioperl project. > > I found some information in the biojava cookbook as how to parse some > > blast > > file result but I didn't find any information/example for launch blast on > > the ncbi server.... > > Could you help me please > > > > Thanks > > > > Bertrand > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > -- > > Esta mensagem foi verificada pelo sistema de antiv?rus e > > acredita-se estar livre de perigo. > > > > Prefeitura Municipal de Florianopolis - PMF > > PMF.SC.GOV.BR > > -- > > > > > > > -- > Bertrand BECKERT > PhD student > IBMC - UPR 9002 du CNRS - ARN > 15, rue Rene Descartes > F-67084 STRASBOURG Cedex > > b.beckert at ibmc.u-strasbg.fr > bertrand.beckert at gmail.com > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From jwang at biohealthbase.org Tue Sep 4 10:17:02 2007 From: jwang at biohealthbase.org (Jianjun Wang) Date: Tue, 04 Sep 2007 10:17:02 -0400 Subject: [Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB In-Reply-To: 93b45ca50709040705n62a9b8cbwc96d31e1a550aa72@mail.gmail.com Message-ID: <20070904141702.84f565f4@biohealthbase.org> Oh, no, not PsiBlast. I'm using ncbi blastn. Thx. _____ From: Mark Schreiber [mailto:markjschreiber at gmail.com] To: Jianjun Wang [mailto:jwang at biohealthbase.org] Cc: biojava-l at lists.open-bio.org Sent: Tue, 04 Sep 2007 10:05:46 -0400 Subject: Re: [Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB Hello - Just out of interest what type of blast were you running. Some of the more exotic forms like PSIBlast probably don't work well. - Mark On 9/4/07, Jianjun Wang wrote: > Hi Colleagues, > > I used the Blast parsing example from the Biojava tutorial and ran into this problem: > ###################### > Failed to build SeqSimilaritySearchResult: > org.biojava.bio.BioException: Running BlastLikeSearchBuilder with null query SequenceDB > at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSearchResult(BlastLikeSearchBuilder.java:239) > at org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.endSearch(BlastLikeSearchBuilder.java:319) > at org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.endElement(SeqSimilarityStAXAdapter.java:119) > at org.biojava.utils.stax.SAX2StAXAdaptor.endElement(SAX2StAXAdaptor.java:153) > at org.biojava.bio.program.ssbind.SeqSimilarityAdapter.endElement(SeqSimilarityAdapter.java:136) > at org.biojava.bio.program.sax.AbstractNativeAppSAXParser.endElement(AbstractNativeAppSAXParser.java:300) > at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:181) > at org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311) > at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274) > at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) > > ########################### > > I experimented with both supported Blast versions such as 2.2.3 and later ones, such as 2.2.13, and with the lazymode both on and off, and concluded that this problem is independent of Blast version and the lazymode. My debugging didn't yield much fruit, except that the obvious cause of the exception was BlastLikeSearchBuilder.querySeqHolder being null. Can someone shed some light on this? > > Here is the relevant section of my code: > > try { > StringReader sr = new StringReader(in); > BlastLikeSAXParser parser = new BlastLikeSAXParser(); > //works for 2.2.13? > //parser.setModeLazy(); > > //make the SAX event adapter that will pass events to a Handler. > SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); > > //set the parsers SAX event adapter > parser.setContentHandler(adapter); > > //The list to hold the SeqSimilaritySearchResults > //List results = new ArrayList(); > > //create the SearchContentHandler that will build SeqSimilaritySearchResults > //in the results List > SearchContentHandler builder = new BlastLikeSearchBuilder(results); > > //register builder with adapter > adapter.setSearchContentHandler(builder); > > //parse the file, after this the result List will be populated with SeqSimilaritySearchResults > parser.parse(new InputSource(sr)); > > //output some blast details - expect 1 result only > ...... > > Thanks, > Jianjun > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From PhilipHeller at comcast.net Tue Sep 4 10:49:18 2007 From: PhilipHeller at comcast.net (PhilipHeller at comcast.net) Date: Tue, 04 Sep 2007 14:49:18 +0000 Subject: [Biojava-l] Mutable Symbol Lists Message-ID: <090420071449.18472.46DD706E000BCCCD0000482822073007939D0A04040AB89F07040708AF@comcast.net> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.open-bio.org/pipermail/biojava-l/attachments/20070904/32ddf107/attachment.pl From markjschreiber at gmail.com Tue Sep 4 22:06:04 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 5 Sep 2007 10:06:04 +0800 Subject: [Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB In-Reply-To: <20070904141702.84f565f4@biohealthbase.org> References: <20070904141702.84f565f4@biohealthbase.org> Message-ID: <93b45ca50709041906p12965d6av28b44e3793400f2c@mail.gmail.com> Hi - Can you post the BLAST output that caused the problem? - Mark On 9/4/07, Jianjun Wang wrote: > > Oh, no, not PsiBlast. I'm using ncbi blastn. Thx. > ________________________________ > From: Mark Schreiber [mailto:markjschreiber at gmail.com] > To: Jianjun Wang [mailto:jwang at biohealthbase.org] > Cc: biojava-l at lists.open-bio.org > Sent: Tue, 04 Sep 2007 10:05:46 -0400 > Subject: Re: [Biojava-l] Exception on Running BlastLikeSearchBuilder with > null query SequenceDB > > > Hello - > > Just out of interest what type of blast were you running. Some of the > more exotic forms like PSIBlast probably don't work well. > > - Mark > > On 9/4/07, Jianjun Wang wrote: > > Hi Colleagues, > > > > I used the Blast parsing example from the Biojava tutorial and ran into > this problem: > > ###################### > > Failed to build SeqSimilaritySearchResult: > > org.biojava.bio.BioException: Running BlastLikeSearchBuilder with null > query SequenceDB > > at > org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSearchResult(BlastLikeSearchBuilder.java:239) > > at > org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.endSearch(BlastLikeSearchBuilder.java:319) > > at > org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.endElement(SeqSimilarityStAXAdapter.java:119) > > at > org.biojava.utils.stax.SAX2StAXAdaptor.endElement(SAX2StAXAdaptor.java:153) > > at > org.biojava.bio.program.ssbind.SeqSimilarityAdapter.endElement(SeqSimilarityAdapter.java:136) > > at > org.biojava.bio.program.sax.AbstractNativeAppSAXParser.endElement(AbstractNativeAppSAXParser.java:300) > > at > org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:181) > > at > org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311) > > at > org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274) > > at > org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) > > > > ########################### > > > > I experimented with both supported Blast versions such as 2.2.3 and later > ones, such as 2.2.13, and with the lazymode both on and off, and concluded > that this problem is independent of Blast version and the lazymode. My > debugging didn't yield much fruit, except that the obvious cause of the > exception was BlastLikeSearchBuilder.querySeqHolder being > null. Can someone shed some light on this? > > > > Here is the relevant section of my code: > > > > try { > > StringReader sr = new StringReader(in); > > BlastLikeSAXParser parser = new BlastLikeSAXParser(); > > //works for 2.2.13? > > //parser.setModeLazy(); > > > > //make the SAX event adapter that will pass events to a Handler. > > SeqSimilarityAdapter adapter = new SeqSimilarityAdapter(); > > > > //set the parsers SAX event adapter > > parser.setContentHandler(adapter); > > > > //The list to hold the SeqSimilaritySearchResults > > //List results = new ArrayList(); > > > > //create the SearchContentHandler that will build > SeqSimilaritySearchResults > > //in the results List > > SearchContentHandler builder = new > BlastLikeSearchBuilder(results); > > > > //register builder with adapter > > adapter.setSearchContentHandler(builder); > > > > //parse the file, after this the result List will be populated with > SeqSimilaritySearchResults > > parser.parse(new InputSource(sr)); > > > > //output some blast details - expect 1 result only > > ...... > > > > Thanks, > > Jianjun > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > From markjschreiber at gmail.com Tue Sep 4 22:11:55 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 5 Sep 2007 10:11:55 +0800 Subject: [Biojava-l] Mutable Symbol Lists In-Reply-To: <090420071449.18472.46DD706E000BCCCD0000482822073007939D0A04040AB89F07040708AF@comcast.net> References: <090420071449.18472.46DD706E000BCCCD0000482822073007939D0A04040AB89F07040708AF@comcast.net> Message-ID: <93b45ca50709041911p366ada20te79bd7a41d1bc048@mail.gmail.com> Hi Philip - SymbolLists are not mutable in the bean sense of the word but that can be modified by using the Edit object. An example is here: http://biojava.org/wiki/BioJava:Cookbook:Sequence:Edit Your ideas on a MutableSymbolList would be of interest though. Especially if you could implement it as a Bean. - Mark On 9/4/07, PhilipHeller at comcast.net wrote: > Dear BioJava Community - > > I'm an experienced Java programmer/author and brand-new bioinformatics grad student. > > For one of my courses, I'm required to contribute to an open-source project. I'd like to contribute to BioJava. The tutorial mentions a future MutableSymbolList interface that would support modifying the underlying sequence data. I'd like to develop such an interface, plus an implementing class. > > Of course, I want my contribution to be useful. If anyone has suggestions, requests, strong feelings, or burning desires, I'd be grateful for any guidance you can provide. > > Regards, > Phil Heller > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From heuermh at acm.org Tue Sep 4 22:30:36 2007 From: heuermh at acm.org (Michael Heuer) Date: Tue, 4 Sep 2007 22:30:36 -0400 (EDT) Subject: [Biojava-l] Mutable Symbol Lists In-Reply-To: <93b45ca50709041911p366ada20te79bd7a41d1bc048@mail.gmail.com> Message-ID: Hello Philip, If I remember correctly, the rub is that SymbolLists are mutable by default (Changeable) but use ChangeListener.ALWAYS_VETO to provide a sort of immutabilty. It might be more efficient to have the implementation be truly immutable by default and add mutabily in a separate implementation. If you take a look at the number of classes that implement Changeable, you might get a feel for how significant a design change this would be. michael On Wed, 5 Sep 2007, Mark Schreiber wrote: > Hi Philip - > > SymbolLists are not mutable in the bean sense of the word but that can > be modified by using the Edit object. > > An example is here: http://biojava.org/wiki/BioJava:Cookbook:Sequence:Edit > > Your ideas on a MutableSymbolList would be of interest though. > Especially if you could implement it as a Bean. > > - Mark > > On 9/4/07, PhilipHeller at comcast.net wrote: > > Dear BioJava Community - > > > > I'm an experienced Java programmer/author and brand-new bioinformatics grad student. > > > > For one of my courses, I'm required to contribute to an open-source project. I'd like to contribute to BioJava. The tutorial mentions a future MutableSymbolList interface that would support modifying the underlying sequence data. I'd like to develop such an interface, plus an implementing class. > > > > Of course, I want my contribution to be useful. If anyone has suggestions, requests, strong feelings, or burning desires, I'd be grateful for any guidance you can provide. > > > > Regards, > > Phil Heller > > _______________________________________________ > > 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 gtg477y at mail.gatech.edu Wed Sep 5 12:41:14 2007 From: gtg477y at mail.gatech.edu (gtg477y at mail.gatech.edu) Date: Wed, 05 Sep 2007 12:41:14 -0400 Subject: [Biojava-l] Help with Chromatogram applet Message-ID: <1189010474.46dedc2a32aa6@webmail.mail.gatech.edu> Hi all, It seems I might not be the first person to ask about this, but I am working on a chromatogram applet. I am trying to open chromatogram files using ChromatogramFactory. I first tried it in a stand alone app, and it worked fine, but when I try to use the ChromatogramFactory.create method in an applet, it gives me the following message: Exception in thread "AWT-EventQueue-1" java.security.AccessControlException: access denied (java.io.FilePermission 3422_A01.ab1 read) at java.security.AccessControlContext.checkPermission(AccessControlContext.java:264) at java.security.AccessController.checkPermission(AccessController.java:427) at java.lang.SecurityManager.checkPermission(SecurityManager.java:532) at java.lang.SecurityManager.checkRead(SecurityManager.java:871) at java.io.FileInputStream.(FileInputStream.java:100) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:69) at ChromatogramApplet.paint(ChromatogramApplet.java:19) at sun.awt.RepaintArea.paintComponent(RepaintArea.java:248) at sun.awt.RepaintArea.paint(RepaintArea.java:224) at sun.awt.windows.WComponentPeer.handleEvent(WComponentPeer.java:254) at java.awt.Component.dispatchEventImpl(Component.java:4060) at java.awt.Container.dispatchEventImpl(Container.java:2024) at java.awt.Component.dispatchEvent(Component.java:3819) at java.awt.EventQueue.dispatchEvent(EventQueue.java:463) at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149) at java.awt.EventDispatchThread.run(EventDispatchThread.java:110) I'm pretty new to Java, so I don't know what a lot of it means, but I assume that for some reason I don't have permission to access the file from an applet. Is that pretty much correct? Is there any way to get around this? Or should I perhaps use a different class to open the files? -- From markjschreiber at gmail.com Wed Sep 5 22:48:15 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 6 Sep 2007 10:48:15 +0800 Subject: [Biojava-l] Help with Chromatogram applet In-Reply-To: <1189010474.46dedc2a32aa6@webmail.mail.gatech.edu> References: <1189010474.46dedc2a32aa6@webmail.mail.gatech.edu> Message-ID: <93b45ca50709051948r1e665b6an1ef6957ee4df1d92@mail.gmail.com> Hi - You need to sign the jar (and possibly the applet) to give it access outside the 'sandbox'. To do this get a recent copy of the biojava source code and jar from http://www.spice-3d.org/cruise/ To sign biojava.jar using a self signed certificate do: ant sign to verify that a biojava.jar has a valid signature do: jarsigner -verify biojava.jar For more info, google something like applet security, signing jars or java sandbox. - Mark On 9/6/07, gtg477y at mail.gatech.edu wrote: > Hi all, > > It seems I might not be the first person to ask about this, but I am working on > a chromatogram applet. I am trying to open chromatogram files using > ChromatogramFactory. I first tried it in a stand alone app, and it worked fine, > but when I try to use the ChromatogramFactory.create method in an applet, it > gives me the following message: > > Exception in thread "AWT-EventQueue-1" java.security.AccessControlException: > access denied (java.io.FilePermission 3422_A01.ab1 read) > > at > java.security.AccessControlContext.checkPermission(AccessControlContext.java:264) > at java.security.AccessController.checkPermission(AccessController.java:427) > at java.lang.SecurityManager.checkPermission(SecurityManager.java:532) > at java.lang.SecurityManager.checkRead(SecurityManager.java:871) > at java.io.FileInputStream.(FileInputStream.java:100) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:69) > at ChromatogramApplet.paint(ChromatogramApplet.java:19) > at sun.awt.RepaintArea.paintComponent(RepaintArea.java:248) > at sun.awt.RepaintArea.paint(RepaintArea.java:224) > at sun.awt.windows.WComponentPeer.handleEvent(WComponentPeer.java:254) > at java.awt.Component.dispatchEventImpl(Component.java:4060) > at java.awt.Container.dispatchEventImpl(Container.java:2024) > at java.awt.Component.dispatchEvent(Component.java:3819) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:463) > at > java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163) > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157) > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149) > at java.awt.EventDispatchThread.run(EventDispatchThread.java:110) > > > I'm pretty new to Java, so I don't know what a lot of it means, but I assume > that for some reason I don't have permission to access the file from an applet. > Is that pretty much correct? Is there any way to get around this? Or should I > perhaps use a different class to open the files? > > -- > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From daniel.rohrbach at web.de Thu Sep 6 06:43:27 2007 From: daniel.rohrbach at web.de (Daniel Rohrbach) Date: Thu, 06 Sep 2007 12:43:27 +0200 Subject: [Biojava-l] Problems loading SingleDP object via serialization Message-ID: <1742885970@web.de> Hi all, I have problems loading a SingleDP object via serialization. The Exception is java.io.InvalidClassException: org.biojava.bio.dp.onehead.SingleDP; no valid constructor I hope that I don't misunderstand something. The reason for the exception may is that SingleDP which implements serializable inherits from DP which isn't serializable. In such a case I think the super class (DP) must offer a no-arg constructor. If this is the reason the same exception should also occur for the PairwiseDP. has someone any idea? Many greetings and thanks in advance _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 From markjschreiber at gmail.com Thu Sep 6 09:19:04 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 6 Sep 2007 21:19:04 +0800 Subject: [Biojava-l] Problems loading SingleDP object via serialization In-Reply-To: <1742885970@web.de> References: <1742885970@web.de> Message-ID: <93b45ca50709060619m159eaa88pb43709063099135c@mail.gmail.com> Hi - Please post a bug report to the biojava bugzilla page (follow the link on biojava.org) and include the biojava version the stack trace and some example code that replicates the bug. That way we can track the bug and make sure it gets fixed. - Mark On 9/6/07, Daniel Rohrbach wrote: > > Hi all, > > I have problems loading a SingleDP object via serialization. > > The Exception is > java.io.InvalidClassException: org.biojava.bio.dp.onehead.SingleDP; no valid constructor > > I hope that I don't misunderstand something. The reason for the exception may is that SingleDP which implements serializable inherits from DP which isn't serializable. In such a case I think the super class (DP) must offer a no-arg constructor. > > If this is the reason the same exception should also occur for the PairwiseDP. > > has someone any idea? > > Many greetings and thanks in advance > > > _____________________________________________________________________ > Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! > http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From bertrand.beckert at gmail.com Thu Sep 6 09:20:56 2007 From: bertrand.beckert at gmail.com (bertrand beckert) Date: Thu, 6 Sep 2007 15:20:56 +0200 Subject: [Biojava-l] How to launch a blast on ncbi server via biojava? In-Reply-To: <93b45ca50709040715r76037e86o990925c8838c3ec5@mail.gmail.com> References: <500217090709040209w5155402bl48617504cc6e8ed4@mail.gmail.com> <20070904114718.133078F5A2@mail2.pmf.sc.gov.br> <500217090709040603u55c596aatf063bb798acc88c6@mail.gmail.com> <93b45ca50709040715r76037e86o990925c8838c3ec5@mail.gmail.com> Message-ID: <500217090709060620t5a46858mfd9f048aa6a36549@mail.gmail.com> Thanks for all those answers So first I tried the NCBI blast interface which you can found at: http://users.encs.concordia.ca/~f_kohant/ncbiblast/ which work, but the result are in xhtml format.... then I test the EBI webservice for NCBI blast which also work and teh result are in xml format. I use the biojava Blast XML parser, but always some exception occurs: org.xml.sax.SAXException: Could not recognise the format of this file as one supported by the framework at org.biojava.bio.program.sax.BlastLikeSAXParser.parse( BlastLikeSAXParser.java:182).... I also tried to put the parsing in the lazy mode but it doesn't change anything. Remark: the BlastLikeSAXParser seem to be able to parse the NCBI Blast version: 2.0.11 , 2.2.2 , 2.2.3 and the blast version received is : program name="NCBI-blastn" version=" 2.2.15 ".... Bertrand 2007/9/4, Mark Schreiber : > > Hi - > > BioJava doesn't have a mechanism to do this however EBI does expose a > webservice for NCBI BLAST. The details can be found at > http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast > > They have a java client with source code you could reuse. > > You can then use biojava to parse the results. If the results are in > XML you can use biojava's BLAST XML parser or you could just use XPath > to get the bits you want. > > If you build a solution that makes use of biojava it would be great if > you can add it to the cookbook section of the biojava wiki. > > - Mark > > On 9/4/07, bertrand beckert wrote: > > Thanks for this code... > > but this piece is good if you want to retrieve a specific sequence with > a > > particular ID... > > What I want to do, is to submit a blast and then retrieve the result and > > then parse the result in oder to know what are the ID.... > > I already found in the NCBI site ( > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/) a java interface > but > > the documentation is not so nice....and the link with biojava is quit > > obscure for me.... > > > > could you help me please > > > > thanks for all > > > > Bertrand > > > > > > > > > > > > > > 2007/9/4, Dickson Guedes : > > > > > > Hi Bertrand, > > > > > > > > > You may use a code like this: > > > > > > > > > try { > > > NCBISequenceDB impSequence = new NCBISequenceDB(); > > > > > > Sequence mySequence = impSequence.getSequence("156447465"); > > > > > > System.out.print( > > > mySequence.getAnnotation() > > > .getProperty("description") > > > .toString() > > > ); > > > } catch (BioException e) { > > > System.out.println(e.getMessage()); > > > } > > > > > > > > > []s > > > Guedes > > > > > > -----Mensagem original----- > > > De: biojava-l-bounces at lists.open-bio.org > > > [mailto:biojava-l-bounces at lists.open-bio.org] Em nome de bertrand > beckert > > > Enviada em: ter?a-feira, 4 de setembro de 2007 06:10 > > > Para: biojava-l at lists.open-bio.org > > > Assunto: [Biojava-l] How to launch a blast on ncbi server via biojava? > > > > > > Hi, > > > > > > Sorry for this silly question, but I would like to know if it is > possible > > > to > > > launch some blast via biojava on the ncbi server for an example and > also > > > to > > > retrieve the result as it is possible in in the bioperl project. > > > I found some information in the biojava cookbook as how to parse some > > > blast > > > file result but I didn't find any information/example for launch blast > on > > > the ncbi server.... > > > Could you help me please > > > > > > Thanks > > > > > > Bertrand > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > -- > > > Esta mensagem foi verificada pelo sistema de antiv?rus e > > > acredita-se estar livre de perigo. > > > > > > Prefeitura Municipal de Florianopolis - PMF > > > PMF.SC.GOV.BR > > > -- > > > > > > > > > > > > -- > > Bertrand BECKERT > > PhD student > > IBMC - UPR 9002 du CNRS - ARN > > 15, rue Rene Descartes > > F-67084 STRASBOURG Cedex > > > > b.beckert at ibmc.u-strasbg.fr > > bertrand.beckert at gmail.com > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > From bertrand.beckert at gmail.com Fri Sep 7 07:23:13 2007 From: bertrand.beckert at gmail.com (bertrand beckert) Date: Fri, 7 Sep 2007 13:23:13 +0200 Subject: [Biojava-l] How to launch a blast on ncbi server via biojava? In-Reply-To: <006701c7f0bb$e38f2bf0$0801230a@ssssgggg> References: <500217090709060620t5a46858mfd9f048aa6a36549@mail.gmail.com> <006701c7f0bb$e38f2bf0$0801230a@ssssgggg> Message-ID: <500217090709070423pd89a07eg5dd04c05139bb738@mail.gmail.com> Yes it could be nice... For the moment, as I said before the biojava blast parser seem to doesn't work I made my own EBI result parser by using XMLBeans and the XML schema of the EBI XML result. thanks for your help Bertrand 2007/9/6, Stefan Goetz : > > Hi Bertrand, > Blast2GO uses the NCBI Qblast to run, retrieve and parse blasts since > several years and is completly implemted in Java and works stable. Maybe > you would like to have a look at the aplication first and if you think > that would suit you or be helpfull we can see if I can "cut out" some > code. > Try http://www.blast2go.org/. > Best regards, > Stefan > > > > -----Original Message----- > > From: biojava-l-bounces at lists.open-bio.org > > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of > > bertrand beckert > > Sent: Thursday, September 06, 2007 3:21 PM > > To: Mark Schreiber > > Cc: biojava-l at lists.open-bio.org; Dickson Guedes > > Subject: Re: [Biojava-l] How to launch a blast on ncbi server > > via biojava? > > > > > > Thanks for all those answers > > > > So first I tried the NCBI blast interface which you can found at: > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/ > > which work, but the result are in xhtml format.... > > then I test the EBI webservice for NCBI blast which also work > > and teh result > > are in xml format. > > I use the biojava Blast XML parser, but always some exception occurs: > > org.xml.sax.SAXException : Could not recognise the format of > > this file as one > > supported by the framework > > at org.biojava.bio.program.sax.BlastLikeSAXParser.parse( > > BlastLikeSAXParser.java:182).... > > I also tried to put the parsing in the lazy mode but it doesn't change > > anything. > > > > Remark: > > the BlastLikeSAXParser seem to be able to parse the NCBI > > Blast version: > > 2.0.11 , 2.2.2 , 2.2.3 > > and the blast version received is : program > > name="NCBI-blastn" version=" > > 2.2.15 ".... > > > > Bertrand > > > > > > 2007/9/4, Mark Schreiber : > > > > > > Hi - > > > > > > BioJava doesn't have a mechanism to do this however EBI > > does expose a > > > webservice for NCBI BLAST. The details can be found at > > > http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast > > > > > > They have a java client with source code you could reuse. > > > > > > You can then use biojava to parse the results. If the results are in > > > XML you can use biojava's BLAST XML parser or you could > > just use XPath > > > to get the bits you want. > > > > > > If you build a solution that makes use of biojava it would > > be great if > > > you can add it to the cookbook section of the biojava wiki. > > > > > > - Mark > > > > > > On 9/4/07, bertrand beckert wrote: > > > > Thanks for this code... > > > > but this piece is good if you want to retrieve a specific > > sequence with > > > a > > > > particular ID... > > > > What I want to do, is to submit a blast and then retrieve > > the result and > > > > then parse the result in oder to know what are the ID.... > > > > I already found in the NCBI site ( > > > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/) > a > > java interface > > > but > > > > the documentation is not so nice....and the link with > > biojava is quit > > > > obscure for me.... > > > > > > > > could you help me please > > > > > > > > thanks for all > > > > > > > > Bertrand > > > > > > > > > > > > > > > > > > > > > > > > > > > > 2007/9/4, Dickson Guedes < guedes at pmf.sc.gov.br>: > > > > > > > > > > Hi Bertrand, > > > > > > > > > > > > > > > You may use a code like this: > > > > > > > > > > > > > > > try { > > > > > NCBISequenceDB impSequence = new NCBISequenceDB(); > > > > > > > > > > Sequence mySequence = > > impSequence.getSequence("156447465"); > > > > > > > > > > System.out.print( > > > > > mySequence.getAnnotation() > > > > > .getProperty("description") > > > > > .toString() > > > > > ); > > > > > } catch (BioException e) { > > > > > System.out.println(e.getMessage()); > > > > > } > > > > > > > > > > > > > > > []s > > > > > Guedes > > > > > > > > > > -----Mensagem original----- > > > > > De: biojava-l-bounces at lists.open-bio.org > > > > > [mailto:biojava-l-bounces at lists.open-bio.org] Em nome > > de bertrand > > > beckert > > > > > Enviada em: ter?a-feira, 4 de setembro de 2007 06:10 > > > > > Para: biojava-l at lists.open-bio.org > > > > > Assunto: [Biojava-l] How to launch a blast on ncbi > > server via biojava? > > > > > > > > > > Hi, > > > > > > > > > > Sorry for this silly question, but I would like to know if it is > > > possible > > > > > to > > > > > launch some blast via biojava on the ncbi server for an > > example and > > > also > > > > > to > > > > > retrieve the result as it is possible in in the bioperl project. > > > > > I found some information in the biojava cookbook as > > how to parse some > > > > > blast > > > > > file result but I didn't find any information/example > > for launch blast > > > on > > > > > the ncbi server.... > > > > > Could you help me please > > > > > > > > > > Thanks > > > > > > > > > > Bertrand > > > > > _______________________________________________ > > > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > > > > -- > > > > > Esta mensagem foi verificada pelo sistema de antiv?rus e > > > > > acredita-se estar livre de perigo. > > > > > > > > > > Prefeitura Municipal de Florianopolis - PMF > > > > > PMF.SC.GOV.BR > > > > > -- > > > > > > > > > > > > > > > > > > > > > > -- > > > > Bertrand BECKERT > > > > PhD student > > > > IBMC - UPR 9002 du CNRS - ARN > > > > 15, rue Rene Descartes > > > > F-67084 STRASBOURG Cedex > > > > > > > > b.beckert at ibmc.u-strasbg.fr > > > > bertrand.beckert at gmail.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 davidfeitosa at gmail.com Sat Sep 8 19:37:47 2007 From: davidfeitosa at gmail.com (David Barbosa Feitosa) Date: Sat, 8 Sep 2007 20:37:47 -0300 Subject: [Biojava-l] Project Message-ID: <93dd9ad00709081637l38eff1fdq24b526163ed11562@mail.gmail.com> Hello guys! It?s my first time here. I am studying in Brazil. My teacher asked me if I would like to work with BioJava for the mastering project. Some of you know if the BioJava project has some module in development or some set of algorithms that needs improvement that I can contribute and use in my mastering thesys? Thanks for the attention and excuse any english mistake :-), David. From abhi232 at cc.gatech.edu Mon Sep 10 02:57:44 2007 From: abhi232 at cc.gatech.edu (abhinav) Date: Mon, 10 Sep 2007 01:57:44 -0500 Subject: [Biojava-l] Problem with reversecomplement Message-ID: <46E4EAE8.2090401@cc.gatech.edu> hello all, I am using the biojava library to get the reversecomplement of a sequence.The problem is I am not getting the required reverse complement. I am converting an ab1 file into a trace and from that I am generating the sequence for the particular file. Then I am applying the subsequence() method to get the subsequence and am applying the reversecomplement ()function on the particular subsequence so that the two sequences that I am getting using the blast shouls match up.But I am not getting the correct Reverse Complement. Is there anything wrong with this approach? Another thing is I am not able to set the ruler in the sequence panel to go from max to min.i.e from say 550 to 0.How do I go about it? Thanks a lot in advance. From holland at ebi.ac.uk Mon Sep 10 04:36:36 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 10 Sep 2007 09:36:36 +0100 Subject: [Biojava-l] Problem running applet In-Reply-To: <46DD02EC.5080702@cc.gatech.edu> References: <46DD02EC.5080702@cc.gatech.edu> Message-ID: <46E50214.3020700@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Sounds like you haven't got the BioJava jar on the applet's classpath. cheers, Richard abhinav wrote: > Hi all, > I am having trouble running an applet with sequencepanel in it. > > the error that I am getting is > Java Plug-in 1.6.0 > Using JRE version 1.6.0 Java HotSpot(TM) Client VM > User home directory = C:\Documents and Settings\Abhi > > > ---------------------------------------------------- > c: clear console window > f: finalize objects on finalization queue > g: garbage collect > h: display this help message > l: dump classloader list > m: print memory usage > o: trigger logging > p: reload proxy configuration > q: hide console > r: reload policy configuration > s: dump system and deployment properties > t: dump thread list > v: dump thread stack > x: clear classloader cache > 0-5: set trace level to > ---------------------------------------------------- > > java.lang.NoClassDefFoundError: > org/biojava/bio/gui/sequence/SequenceRenderer > at java.lang.Class.getDeclaredConstructors0(Native Method) > at java.lang.Class.privateGetDeclaredConstructors(Unknown Source) > at java.lang.Class.getConstructor0(Unknown Source) > at java.lang.Class.newInstance0(Unknown Source) > at java.lang.Class.newInstance(Unknown Source) > at sun.applet.AppletPanel.createApplet(Unknown Source) > at sun.plugin.AppletViewer.createApplet(Unknown Source) > at sun.applet.AppletPanel.runLoader(Unknown Source) > at sun.applet.AppletPanel.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > ... > > What shld be done abt this? > Thanks in advance > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG5QIU4C5LeMEKA/QRArIiAKCKA1r/Iey5EdkXtKk/aeIN7wqicwCbBDni sXokQd5Jhx+Si6t4/JEnFDs= =czok -----END PGP SIGNATURE----- From holland at ebi.ac.uk Mon Sep 10 04:39:49 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 10 Sep 2007 09:39:49 +0100 Subject: [Biojava-l] Problem with reversecomplement In-Reply-To: <46E4EAE8.2090401@cc.gatech.edu> References: <46E4EAE8.2090401@cc.gatech.edu> Message-ID: <46E502D5.4000903@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Could you provide the sequences you are working with, including the sequence you are expecting and the actual sequence you are getting? It's hard to tell what is wrong without seeing the actual sequences involved. Also I'm not sure what you mean in your second question about the sequence panel. What class are you working with? Is there a method you have tried but doesn't work, or is it that you cannot find the method to do what you want to do? cheers, Richard abhinav wrote: > hello all, > I am using the biojava library to get the reversecomplement of a > sequence.The problem is I am not getting the required reverse complement. > I am converting an ab1 file into a trace and from that I am generating > the sequence for the particular file. > Then I am applying the subsequence() method to get the subsequence and > am applying the reversecomplement ()function on the particular > subsequence so that the two sequences that I am getting using the blast > shouls match up.But I am not getting the correct Reverse Complement. > Is there anything wrong with this approach? > Another thing is I am not able to set the ruler in the sequence panel to > go from max to min.i.e from say 550 to 0.How do I go about it? > Thanks a lot in advance. > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG5QLV4C5LeMEKA/QRAqPsAKClU4HAU3NrTiPFxxiQAuBdjKUJvACeKQe1 7+XezbnqoxBsX95ojtma6so= =0jVq -----END PGP SIGNATURE----- From abhi232 at cc.gatech.edu Fri Sep 14 02:45:47 2007 From: abhi232 at cc.gatech.edu (abhinav) Date: Fri, 14 Sep 2007 01:45:47 -0500 Subject: [Biojava-l] How to get Sequence from a file other than ABI or SCF? Message-ID: <46EA2E1B.70201@cc.gatech.edu> Hello all, I need some help once again. My situation is that I have already generated the following files from phred: .scf, .qual, .seq. The goal is to create a Trace object for an applet. Now I want to get a Sequence file as my final output for displaying it onto a SequencePanel. I want to use the files generated from the phred tool to create a Sequence. I have explored much of biojava but i could not find any suitable classes that could be used to encapsulate the data obtained from the phred output. The approach that I want to use is somehow get a SymbolList from the data that I have.After that I want to Run the PhredSequence . After that I want to run the PhredTools.create() method to generate the Sequence... ************************************************* File ft = new File("C:/Documents and Settings/Abhi/apptest/src/3422_A01.ab1"); // I am currently using the ab1 file but I want to use the .phd or the .seq file here. SymbolList seq_sym = trace.getSequence(); PhredSequence temp = new PhredSequence(seq_sem , " " ," ", Annotation.EMPTY_ANNOTATION); SymbolList seq_qual = temp.getQuality(); Sequence final_seq = PhredTools.create(seq_sym,seq_qual); *************************************************** When I run this particular code I get the exception that PhredSequence cannot DNA symbolList as input. So that basically is the problem. I wanted to make sure if the method that I am following is the correct one and if not then what approach can be taken so that my Final output is a sequence that can be rendered. From matthew.pocock at ncl.ac.uk Mon Sep 17 05:34:56 2007 From: matthew.pocock at ncl.ac.uk (Matthew Pocock) Date: Mon, 17 Sep 2007 10:34:56 +0100 Subject: [Biojava-l] BioJava 2 status In-Reply-To: References: <200707312126.44821.matthew.pocock@ncl.ac.uk> Message-ID: <200709171034.56548.matthew.pocock@ncl.ac.uk> Somebody asked me: > I was wondering whether BioJava provides standard scoring matrices > (e.g. BLOSUM62, etc.) as "constants" anywhere for doing alignments. I > couldn't seem to find this anywhere in the code but, admittedly, have > not looked very closely yet. And rather embarasingly, I don't know the answer. Does someone here? Matthew From markjschreiber at gmail.com Mon Sep 17 06:06:48 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Mon, 17 Sep 2007 18:06:48 +0800 Subject: [Biojava-l] BioJava 2 status In-Reply-To: <200709171034.56548.matthew.pocock@ncl.ac.uk> References: <200707312126.44821.matthew.pocock@ncl.ac.uk> <200709171034.56548.matthew.pocock@ncl.ac.uk> Message-ID: <93b45ca50709170306t65c0627dg85da2ed50057a83b@mail.gmail.com> Hello - Recent versions of biojava contain NW and SW algorithm implementations in org.biojava.bio.alignment. There is aslo a SubstitutionMatrix object that can hold the information found in the BLOSUM etc matrix files that one can download from NCBI. Hope this helps, - Mark On 9/17/07, Matthew Pocock wrote: > Somebody asked me: > > > I was wondering whether BioJava provides standard scoring matrices > > (e.g. BLOSUM62, etc.) as "constants" anywhere for doing alignments. I > > couldn't seem to find this anywhere in the code but, admittedly, have > > not looked very closely yet. > > And rather embarasingly, I don't know the answer. Does someone here? > > Matthew > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From holland at ebi.ac.uk Mon Sep 17 06:09:58 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 17 Sep 2007 11:09:58 +0100 Subject: [Biojava-l] BioJava 2 status In-Reply-To: <200709171034.56548.matthew.pocock@ncl.ac.uk> References: <200707312126.44821.matthew.pocock@ncl.ac.uk> <200709171034.56548.matthew.pocock@ncl.ac.uk> Message-ID: <46EE5276.9040803@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 @see org.biojava.bio.align.SubstitutionMatrix Basically it doesn't include any matrices, but the above class will load matrix definition files the user has downloaded from the NCBI FTP site, so you can obtain standard matrices that way. Matthew Pocock wrote: > Somebody asked me: > >> I was wondering whether BioJava provides standard scoring matrices >> (e.g. BLOSUM62, etc.) as "constants" anywhere for doing alignments. I >> couldn't seem to find this anywhere in the code but, admittedly, have >> not looked very closely yet. > > And rather embarasingly, I don't know the answer. Does someone here? > > Matthew > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG7lJ14C5LeMEKA/QRAhzZAJ0bcGko6nLMFXcRsvk092Iz2WBJJgCeJBm9 62Vv3F3jp6Mv2Zcoyx4yln0= =bAYC -----END PGP SIGNATURE----- From ap3 at sanger.ac.uk Wed Sep 19 06:21:08 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 19 Sep 2007 11:21:08 +0100 Subject: [Biojava-l] BioJava 2 status In-Reply-To: <46EE5276.9040803@ebi.ac.uk> References: <200707312126.44821.matthew.pocock@ncl.ac.uk> <200709171034.56548.matthew.pocock@ncl.ac.uk> <46EE5276.9040803@ebi.ac.uk> Message-ID: <83DA3A1D-33F9-46D2-AA09-D0EEDE3E0F5E@sanger.ac.uk> For an example that uses the blosum 62 matrix see the junit test org.biojava.bio.align.SubstitutionMatrixTest Andreas On 17 Sep 2007, at 11:09, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > @see org.biojava.bio.align.SubstitutionMatrix > > Basically it doesn't include any matrices, but the above class will > load > matrix definition files the user has downloaded from the NCBI FTP > site, > so you can obtain standard matrices that way. > > > Matthew Pocock wrote: >> Somebody asked me: >> >>> I was wondering whether BioJava provides standard scoring matrices >>> (e.g. BLOSUM62, etc.) as "constants" anywhere for doing >>> alignments. I >>> couldn't seem to find this anywhere in the code but, admittedly, >>> have >>> not looked very closely yet. >> >> And rather embarasingly, I don't know the answer. Does someone here? >> >> Matthew >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFG7lJ14C5LeMEKA/QRAhzZAJ0bcGko6nLMFXcRsvk092Iz2WBJJgCeJBm9 > 62Vv3F3jp6Mv2Zcoyx4yln0= > =bAYC > -----END PGP SIGNATURE----- > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From rsvancara at wsu.edu Fri Sep 21 12:08:44 2007 From: rsvancara at wsu.edu (Svancara, Randall) Date: Fri, 21 Sep 2007 09:08:44 -0700 Subject: [Biojava-l] Reflection Errors reading FASTA file using Biojava. Message-ID: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> Hi, I am new to biojava. I am trying to read a fasta file using the following code: 1. public Fasta(File fastafile) throws Exception{ 2. this.fastafile = fastafile; 3. BufferedReader br = new BufferedReader(new FileReader(fastafile)); 4. FastaFormat fastaformat = new FastaFormat(); 5. if(fastaformat.canRead(fastafile)){ 6. SymbolTokenization cTok = fastaformat.guessSymbolTokenization(fastafile); 7. RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok, RichObjectFactory.getDefaultNamespace()); 8. while(it.hasNext()){ 9. Sequence seq = it.nextRichSequence(); 10. } 11. } 13. } My problem is that I want to be able to read a fasta file and figure out first if it is a protein or DNA sequence file, and next parse out the sequences. However, when I run this code i receive the following errors. I have only included part of the exception stack. However, you can see that there are reflection errors being thrown. I am using biojava in a struts2 environment running on apache tomcat 6.0.12 with JDK 1.6 release 2. javax.servlet.ServletException: java.lang.reflect.InvocationTargetException org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515) org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419) root cause java.lang.reflect.InvocationTargetException sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) java.lang.reflect.Method.invoke(Method.java:597) com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404) com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229) com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) Thanks, -- Randall Svancara System Administrator From holland at ebi.ac.uk Fri Sep 21 13:59:19 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 21 Sep 2007 18:59:19 +0100 (BST) Subject: [Biojava-l] Reflection Errors reading FASTA file using Biojava. In-Reply-To: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> References: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> Message-ID: <32970.80.42.55.181.1190397559.squirrel@webmail.ebi.ac.uk> The exception stack shows that the error is being thrown by some part of the software package called com.opensymphony.xwork2. This is not part of BioJava. If you try running your code outside of the Tomcat/Struts environment, I think you'll find it works fine (it does for me, anyhow!). I suspect that you have some kind of profiling tool active which is interfering with the process. Try disabling profiling and try again. If this persists, you should attempt to contact the manufacturers of your profiling tool (which I guess is OpenSymphony, based on the classnames involved) to see if they can tell you what would cause their software to throw such exceptions. If they can trace it to a particular fault in BioJava then we would be glad to hear of it, but we are unable to do this tracing ourselves as the exception is not being thrown from within BioJava. cheers, Richard On Fri, September 21, 2007 5:08 pm, Svancara, Randall wrote: > Hi, I am new to biojava. I am trying to read a fasta file using the > following code: > > 1. public Fasta(File fastafile) throws Exception{ > 2. this.fastafile = fastafile; > 3. BufferedReader br = new BufferedReader(new FileReader(fastafile)); > > 4. FastaFormat fastaformat = new FastaFormat(); > 5. if(fastaformat.canRead(fastafile)){ > 6. SymbolTokenization cTok = > fastaformat.guessSymbolTokenization(fastafile); > > 7. RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok, > RichObjectFactory.getDefaultNamespace()); > > 8. while(it.hasNext()){ > 9. Sequence seq = it.nextRichSequence(); > 10. } > 11. } > 13. } > > My problem is that I want to be able to read a fasta file and figure out > first if it is a protein or DNA sequence file, and next parse out the > sequences. However, when I run this code i receive the following > errors. I have only included part of the exception stack. However, you > can see that there are reflection errors being thrown. I am using > biojava in a struts2 environment running on apache tomcat 6.0.12 with > JDK 1.6 release 2. > > javax.servlet.ServletException: > java.lang.reflect.InvocationTargetException > org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515) > org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419) > > root cause > > java.lang.reflect.InvocationTargetException > sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > java.lang.reflect.Method.invoke(Method.java:597) > com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404) > com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267) > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229) > com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167) > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121) > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > Thanks, > > -- > Randall Svancara > System Administrator > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK From rsvancara at wsu.edu Fri Sep 21 16:05:39 2007 From: rsvancara at wsu.edu (Randall Svancara) Date: Fri, 21 Sep 2007 13:05:39 -0700 Subject: [Biojava-l] Reflection Errors reading FASTA file using Biojava. In-Reply-To: <32970.80.42.55.181.1190397559.squirrel@webmail.ebi.ac.uk> References: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> <32970.80.42.55.181.1190397559.squirrel@webmail.ebi.ac.uk> Message-ID: <1190405139.22343.54.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> I have created a stand alone class that calls this same code as described below and and it executes just fine by itself. However using Struts 2.0 that uses classes from WebWork MVC framework, this same code fails. If i comment out lines 8,9,10, there are no errors. So does the iterator use reflection to obtain at run-time the correct sequence object to load? Randall On Fri, 2007-09-21 at 18:59 +0100, Richard Holland wrote: > The exception stack shows that the error is being thrown by some part of > the software package called com.opensymphony.xwork2. > > This is not part of BioJava. > > If you try running your code outside of the Tomcat/Struts environment, I > think you'll find it works fine (it does for me, anyhow!). > > I suspect that you have some kind of profiling tool active which is > interfering with the process. Try disabling profiling and try again. > > If this persists, you should attempt to contact the manufacturers of your > profiling tool (which I guess is OpenSymphony, based on the classnames > involved) to see if they can tell you what would cause their software to > throw such exceptions. If they can trace it to a particular fault in > BioJava then we would be glad to hear of it, but we are unable to do this > tracing ourselves as the exception is not being thrown from within > BioJava. > > cheers, > Richard > > On Fri, September 21, 2007 5:08 pm, Svancara, Randall wrote: > > Hi, I am new to biojava. I am trying to read a fasta file using the > > following code: > > > > 1. public Fasta(File fastafile) throws Exception{ > > 2. this.fastafile = fastafile; > > 3. BufferedReader br = new BufferedReader(new FileReader(fastafile)); > > > > 4. FastaFormat fastaformat = new FastaFormat(); > > 5. if(fastaformat.canRead(fastafile)){ > > 6. SymbolTokenization cTok = > > fastaformat.guessSymbolTokenization(fastafile); > > > > 7. RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok, > > RichObjectFactory.getDefaultNamespace()); > > > > 8. while(it.hasNext()){ > > 9. Sequence seq = it.nextRichSequence(); > > 10. } > > 11. } > > 13. } > > > > My problem is that I want to be able to read a fasta file and figure out > > first if it is a protein or DNA sequence file, and next parse out the > > sequences. However, when I run this code i receive the following > > errors. I have only included part of the exception stack. However, you > > can see that there are reflection errors being thrown. I am using > > biojava in a struts2 environment running on apache tomcat 6.0.12 with > > JDK 1.6 release 2. > > > > javax.servlet.ServletException: > > java.lang.reflect.InvocationTargetException > > org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515) > > org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419) > > > > root cause > > > > java.lang.reflect.InvocationTargetException > > sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > java.lang.reflect.Method.invoke(Method.java:597) > > com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404) > > com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267) > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229) > > com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167) > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121) > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > > > Thanks, > > > > -- > > Randall Svancara > > System Administrator > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > -- Randall Svancara System Administrator Horticulture and Landscape Architecture 509-335-7093 From markjschreiber at gmail.com Sat Sep 22 07:07:56 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Sat, 22 Sep 2007 19:07:56 +0800 Subject: [Biojava-l] Reflection Errors reading FASTA file using Biojava. In-Reply-To: <1190405139.22343.54.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> References: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> <32970.80.42.55.181.1190397559.squirrel@webmail.ebi.ac.uk> <1190405139.22343.54.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> Message-ID: <93b45ca50709220407o1613c996l7ff43e7cd5ed233a@mail.gmail.com> >From a quick look at the stack trace it seems it is Struts 2.0 that is doing the reflection (and failing). I don't see any indication that this is a biojava problem. From the trace it doesn't look like any biojava methods have been called. - Mark On 9/22/07, Randall Svancara wrote: > I have created a stand alone class that calls this same code as > described below and and it executes just fine by itself. However using > Struts 2.0 that uses classes from WebWork MVC framework, this same code > fails. If i comment out lines 8,9,10, there are no errors. So does the > iterator use reflection to obtain at run-time the correct sequence > object to load? > > Randall > > On Fri, 2007-09-21 at 18:59 +0100, Richard Holland wrote: > > The exception stack shows that the error is being thrown by some part of > > the software package called com.opensymphony.xwork2. > > > > This is not part of BioJava. > > > > If you try running your code outside of the Tomcat/Struts environment, I > > think you'll find it works fine (it does for me, anyhow!). > > > > I suspect that you have some kind of profiling tool active which is > > interfering with the process. Try disabling profiling and try again. > > > > If this persists, you should attempt to contact the manufacturers of your > > profiling tool (which I guess is OpenSymphony, based on the classnames > > involved) to see if they can tell you what would cause their software to > > throw such exceptions. If they can trace it to a particular fault in > > BioJava then we would be glad to hear of it, but we are unable to do this > > tracing ourselves as the exception is not being thrown from within > > BioJava. > > > > cheers, > > Richard > > > > On Fri, September 21, 2007 5:08 pm, Svancara, Randall wrote: > > > Hi, I am new to biojava. I am trying to read a fasta file using the > > > following code: > > > > > > 1. public Fasta(File fastafile) throws Exception{ > > > 2. this.fastafile = fastafile; > > > 3. BufferedReader br = new BufferedReader(new FileReader(fastafile)); > > > > > > 4. FastaFormat fastaformat = new FastaFormat(); > > > 5. if(fastaformat.canRead(fastafile)){ > > > 6. SymbolTokenization cTok = > > > fastaformat.guessSymbolTokenization(fastafile); > > > > > > 7. RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok, > > > RichObjectFactory.getDefaultNamespace()); > > > > > > 8. while(it.hasNext()){ > > > 9. Sequence seq = it.nextRichSequence(); > > > 10. } > > > 11. } > > > 13. } > > > > > > My problem is that I want to be able to read a fasta file and figure out > > > first if it is a protein or DNA sequence file, and next parse out the > > > sequences. However, when I run this code i receive the following > > > errors. I have only included part of the exception stack. However, you > > > can see that there are reflection errors being thrown. I am using > > > biojava in a struts2 environment running on apache tomcat 6.0.12 with > > > JDK 1.6 release 2. > > > > > > javax.servlet.ServletException: > > > java.lang.reflect.InvocationTargetException > > > org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515) > > > org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419) > > > > > > root cause > > > > > > java.lang.reflect.InvocationTargetException > > > sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > > > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > > java.lang.reflect.Method.invoke(Method.java:597) > > > com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404) > > > com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267) > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229) > > > com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167) > > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121) > > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > > > > > > Thanks, > > > > > > -- > > > Randall Svancara > > > System Administrator > > > > > > > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > -- > Randall Svancara > System Administrator > Horticulture and Landscape Architecture > 509-335-7093 > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From rsvancara at wsu.edu Sat Sep 22 14:18:16 2007 From: rsvancara at wsu.edu (Randall Svancara) Date: Sat, 22 Sep 2007 11:18:16 -0700 Subject: [Biojava-l] Reflection Errors reading FASTA file using Biojava. In-Reply-To: <93b45ca50709220407o1613c996l7ff43e7cd5ed233a@mail.gmail.com> References: <1190390924.22343.22.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> <32970.80.42.55.181.1190397559.squirrel@webmail.ebi.ac.uk> <1190405139.22343.54.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> <93b45ca50709220407o1613c996l7ff43e7cd5ed233a@mail.gmail.com> Message-ID: <1190485096.7817.6.camel@mainlabcp1.mainlabcp1.cahe.wsu.edu> I figured out the problem and it was rather simple. I forgot to put bytecode.jar into my class path. I am guessing there is a problem with the Struts 2.0 error handling. Digging into the catalina.out logs for tomcat revealed that their was a No Class Definition Exception being thrown. Once I found that, it was just a matter of finding the right jar to include in the classpath. Otherwise, BioJava works great. I am going to be incorporating it into a lot of projects we are working on including a web based blast tool that will integrate with Sun Grid Engine. I needed BioJava for parsing Fasta formated files and I may use it to convert other formats to Fasta, if I can. Thanks for your help Mark and thanks for responding on this list so quickly. Randall Svancara On Sat, 2007-09-22 at 19:07 +0800, Mark Schreiber wrote: > From a quick look at the stack trace it seems it is Struts 2.0 that is > doing the reflection (and failing). > > I don't see any indication that this is a biojava problem. From the > trace it doesn't look like any biojava methods have been called. > > - Mark > > On 9/22/07, Randall Svancara wrote: > > I have created a stand alone class that calls this same code as > > described below and and it executes just fine by itself. However using > > Struts 2.0 that uses classes from WebWork MVC framework, this same code > > fails. If i comment out lines 8,9,10, there are no errors. So does the > > iterator use reflection to obtain at run-time the correct sequence > > object to load? > > > > Randall > > > > On Fri, 2007-09-21 at 18:59 +0100, Richard Holland wrote: > > > The exception stack shows that the error is being thrown by some part of > > > the software package called com.opensymphony.xwork2. > > > > > > This is not part of BioJava. > > > > > > If you try running your code outside of the Tomcat/Struts environment, I > > > think you'll find it works fine (it does for me, anyhow!). > > > > > > I suspect that you have some kind of profiling tool active which is > > > interfering with the process. Try disabling profiling and try again. > > > > > > If this persists, you should attempt to contact the manufacturers of your > > > profiling tool (which I guess is OpenSymphony, based on the classnames > > > involved) to see if they can tell you what would cause their software to > > > throw such exceptions. If they can trace it to a particular fault in > > > BioJava then we would be glad to hear of it, but we are unable to do this > > > tracing ourselves as the exception is not being thrown from within > > > BioJava. > > > > > > cheers, > > > Richard > > > > > > On Fri, September 21, 2007 5:08 pm, Svancara, Randall wrote: > > > > Hi, I am new to biojava. I am trying to read a fasta file using the > > > > following code: > > > > > > > > 1. public Fasta(File fastafile) throws Exception{ > > > > 2. this.fastafile = fastafile; > > > > 3. BufferedReader br = new BufferedReader(new FileReader(fastafile)); > > > > > > > > 4. FastaFormat fastaformat = new FastaFormat(); > > > > 5. if(fastaformat.canRead(fastafile)){ > > > > 6. SymbolTokenization cTok = > > > > fastaformat.guessSymbolTokenization(fastafile); > > > > > > > > 7. RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok, > > > > RichObjectFactory.getDefaultNamespace()); > > > > > > > > 8. while(it.hasNext()){ > > > > 9. Sequence seq = it.nextRichSequence(); > > > > 10. } > > > > 11. } > > > > 13. } > > > > > > > > My problem is that I want to be able to read a fasta file and figure out > > > > first if it is a protein or DNA sequence file, and next parse out the > > > > sequences. However, when I run this code i receive the following > > > > errors. I have only included part of the exception stack. However, you > > > > can see that there are reflection errors being thrown. I am using > > > > biojava in a struts2 environment running on apache tomcat 6.0.12 with > > > > JDK 1.6 release 2. > > > > > > > > javax.servlet.ServletException: > > > > java.lang.reflect.InvocationTargetException > > > > org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515) > > > > org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419) > > > > > > > > root cause > > > > > > > > java.lang.reflect.InvocationTargetException > > > > sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > > > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > > > > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > > > java.lang.reflect.Method.invoke(Method.java:597) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229) > > > > com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > > com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167) > > > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > > org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > > com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121) > > > > com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455) > > > > com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221) > > > > org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224) > > > > com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223) > > > > > > > > > > > > Thanks, > > > > > > > > -- > > > > Randall Svancara > > > > System Administrator > > > > > > > > > > > > _______________________________________________ > > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > -- > > Randall Svancara > > System Administrator > > Horticulture and Landscape Architecture > > 509-335-7093 > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- Randall Svancara System Administrator Horticulture and Landscape Architecture 509-335-7093 From abhishekalwar at rediffmail.com Sun Sep 23 05:16:31 2007 From: abhishekalwar at rediffmail.com (abhishek saini) Date: 23 Sep 2007 09:16:31 -0000 Subject: [Biojava-l] (no subject) Message-ID: <20070923091631.7827.qmail@f5mail15.rediffmail.com> ? i wnt to install biojava ################################################## From hkaya at iontek.com.tr Sun Sep 23 06:56:08 2007 From: hkaya at iontek.com.tr (hkaya) Date: Sun, 23 Sep 2007 13:56:08 +0300 Subject: [Biojava-l] ChromatogramFactory fails on Windows and Mac Message-ID: <20070923105314.M78327@iontek.com.tr> Hello The following small code perfectly runs on Linux but it fails on Windows and Mac. I'm using biojava 1.5. Could anybody tell me where i am doing something wrong? Thanks Huseyin Kaya 1. TraceTest.java import java.io.File; import org.biojava.bio.chromatogram.Chromatogram; import org.biojava.bio.chromatogram.ChromatogramFactory; public class TraceTest { public static void main(String[] args) { try { Chromatogram trace = ChromatogramFactory.create(new File("test.scf")); System.out.println("Success!"); } catch (Exception e){ System.out.println("Failed!"); e.printStackTrace(); } } } 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf 3. Exception thrown in Windows XP/Vista: Desktop> java -classpath biojava-1.5.jar;. TraceTest Exception in thread "main" org.biojava.bio.BioError: Unable to initialize DNATools at org.biojava.bio.seq.DNATools.(DNATools.java:117) at org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) at org.biojava.bio.program.scf.SCF.load(SCF.java:149) at org.biojava.bio.program.scf.SCF.load(SCF.java:141) at org.biojava.bio.program.scf.SCF.create(SCF.java:126) at org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) at TraceTest.main(TraceTest.java:8) Caused by: org.biojava.bio.BioError: Unable to initialize RNATools at org.biojava.bio.seq.RNATools.(RNATools.java:126) at org.biojava.bio.seq.DNATools.(DNATools.java:110) ... 8 more Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) at org.biojava.bio.seq.RNATools.(RNATools.java:124) ... 9 more Caused by: org.biojava.bio.symbol.IllegalSymbolException: Token `his' does not appear as a named symbol in alphabet `PROTEIN-TERM' at org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) ... 10 more From holland at ebi.ac.uk Sun Sep 23 07:16:43 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Sun, 23 Sep 2007 12:16:43 +0100 (BST) Subject: [Biojava-l] (no subject) In-Reply-To: <20070923091631.7827.qmail@f5mail15.rediffmail.com> References: <20070923091631.7827.qmail@f5mail15.rediffmail.com> Message-ID: <51846.80.42.55.181.1190546203.squirrel@webmail.ebi.ac.uk> What specifically do you want us to help with? cheers, Richard On Sun, September 23, 2007 10:16 am, abhishek saini wrote: > > i wnt to install biojava > > ################################################## > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK From markjschreiber at gmail.com Sun Sep 23 08:19:09 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Sun, 23 Sep 2007 20:19:09 +0800 Subject: [Biojava-l] ChromatogramFactory fails on Windows and Mac In-Reply-To: <20070923105314.M78327@iontek.com.tr> References: <20070923105314.M78327@iontek.com.tr> Message-ID: <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> The stack trace indicates that the resources in you biojava.jar file are missing or corrupt. Where did you get it from? If you copy the jar from you linux machine to windows do you still get the same error? - Mark On 9/23/07, hkaya wrote: > Hello > > The following small code perfectly runs on Linux but > it fails on Windows and Mac. I'm using biojava 1.5. > Could anybody tell me where i am doing something wrong? > > Thanks > Huseyin Kaya > > > 1. TraceTest.java > > import java.io.File; > import org.biojava.bio.chromatogram.Chromatogram; > import org.biojava.bio.chromatogram.ChromatogramFactory; > > public class TraceTest { > public static void main(String[] args) { > try { > Chromatogram trace = ChromatogramFactory.create(new File("test.scf")); > System.out.println("Success!"); > } catch (Exception e){ > System.out.println("Failed!"); > e.printStackTrace(); > } > } > } > > 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf > > 3. Exception thrown in Windows XP/Vista: > > Desktop> java -classpath biojava-1.5.jar;. TraceTest > Exception in thread "main" org.biojava.bio.BioError: Unable to initialize > DNATools > at org.biojava.bio.seq.DNATools.(DNATools.java:117) > at org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) > at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > at org.biojava.bio.program.scf.SCF.load(SCF.java:141) > at org.biojava.bio.program.scf.SCF.create(SCF.java:126) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) > at TraceTest.main(TraceTest.java:8) > Caused by: org.biojava.bio.BioError: Unable to initialize RNATools > at org.biojava.bio.seq.RNATools.(RNATools.java:126) > at org.biojava.bio.seq.DNATools.(DNATools.java:110) > ... 8 more > Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml > at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) > at org.biojava.bio.seq.RNATools.(RNATools.java:124) > ... 9 more > Caused by: org.biojava.bio.symbol.IllegalSymbolException: > Token `his' does not appear as a named symbol in alphabet `PROTEIN-TERM' > at > org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) > at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) > ... 10 more > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From hkaya at iontek.com.tr Sun Sep 23 10:52:21 2007 From: hkaya at iontek.com.tr (hkaya) Date: Sun, 23 Sep 2007 17:52:21 +0300 Subject: [Biojava-l] ChromatogramFactory fails on Windows and Mac In-Reply-To: <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> References: <20070923105314.M78327@iontek.com.tr> <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> Message-ID: <20070923145142.M91232@iontek.com.tr> On windows machine, I downloaded http://www.biojava.org/download/bj15/bin/BioJava1.5-bin.tar.gz with Internet Explorer and extract jar files. I also tried downloading the same file on linux and copy the jar files to windows with samba. On both case the same error occurs. After your message I delete and downloaded the same file again, but the situation is same. Huseyin On Sun, 23 Sep 2007 20:19:09 +0800, Mark Schreiber wrote > The stack trace indicates that the resources in you biojava.jar file > are missing or corrupt. Where did you get it from? > > If you copy the jar from you linux machine to windows do you still > get the same error? > > - Mark > > On 9/23/07, hkaya wrote: > > Hello > > > > The following small code perfectly runs on Linux but > > it fails on Windows and Mac. I'm using biojava 1.5. > > Could anybody tell me where i am doing something wrong? > > > > Thanks > > Huseyin Kaya > > > > > > 1. TraceTest.java > > > > import java.io.File; > > import org.biojava.bio.chromatogram.Chromatogram; > > import org.biojava.bio.chromatogram.ChromatogramFactory; > > > > public class TraceTest { > > public static void main(String[] args) { > > try { > > Chromatogram trace = ChromatogramFactory.create(new File("test.scf")); > > System.out.println("Success!"); > > } catch (Exception e){ > > System.out.println("Failed!"); > > e.printStackTrace(); > > } > > } > > } > > > > 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf > > > > 3. Exception thrown in Windows XP/Vista: > > > > Desktop> java -classpath biojava-1.5.jar;. TraceTest > > Exception in thread "main" org.biojava.bio.BioError: Unable to initialize > > DNATools > > at org.biojava.bio.seq.DNATools.(DNATools.java:117) > > at org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) > > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) > > at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > > at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > > at org.biojava.bio.program.scf.SCF.load(SCF.java:141) > > at org.biojava.bio.program.scf.SCF.create(SCF.java:126) > > at > > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) > > at TraceTest.main(TraceTest.java:8) > > Caused by: org.biojava.bio.BioError: Unable to initialize RNATools > > at org.biojava.bio.seq.RNATools.(RNATools.java:126) > > at org.biojava.bio.seq.DNATools.(DNATools.java:110) > > ... 8 more > > Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml > > at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) > > at org.biojava.bio.seq.RNATools.(RNATools.java:124) > > ... 9 more > > Caused by: org.biojava.bio.symbol.IllegalSymbolException: > > Token `his' does not appear as a named symbol in alphabet `PROTEIN-TERM' > > at > > org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) > > at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) > > ... 10 more > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > Huseyin From holland at ebi.ac.uk Mon Sep 24 03:59:20 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 24 Sep 2007 08:59:20 +0100 Subject: [Biojava-l] ChromatogramFactory fails on Windows and Mac In-Reply-To: <20070923145142.M91232@iontek.com.tr> References: <20070923105314.M78327@iontek.com.tr> <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> <20070923145142.M91232@iontek.com.tr> Message-ID: <46F76E58.7020905@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Could this be an encoding problem with the XML file in the JAR? i.e. Linux and Windows generally use different text encodings and so may misinterpret some of the characters in the XML file, generating the errors you see. I suppose this could be an issue if the Windows environment is running internationalisation under a non-Western-European character set, whereas the Linux box is running with an English character set. Unfortunately I do not have access to a Windows machine to test this on. Do any other BJ developers out there have access to a Windows machine that they can investigate this with? cheers, Richard hkaya wrote: > On windows machine, I downloaded > http://www.biojava.org/download/bj15/bin/BioJava1.5-bin.tar.gz with Internet > Explorer and extract jar files. I also tried downloading the same file on > linux and > copy the jar files to windows with samba. On both case the same error occurs. > After your message I delete and downloaded the same file again, but > the situation is same. > > Huseyin > > On Sun, 23 Sep 2007 20:19:09 +0800, Mark Schreiber wrote >> The stack trace indicates that the resources in you biojava.jar file >> are missing or corrupt. Where did you get it from? >> >> If you copy the jar from you linux machine to windows do you still >> get the same error? >> >> - Mark >> >> On 9/23/07, hkaya wrote: >>> Hello >>> >>> The following small code perfectly runs on Linux but >>> it fails on Windows and Mac. I'm using biojava 1.5. >>> Could anybody tell me where i am doing something wrong? >>> >>> Thanks >>> Huseyin Kaya >>> >>> >>> 1. TraceTest.java >>> >>> import java.io.File; >>> import org.biojava.bio.chromatogram.Chromatogram; >>> import org.biojava.bio.chromatogram.ChromatogramFactory; >>> >>> public class TraceTest { >>> public static void main(String[] args) { >>> try { >>> Chromatogram trace = > ChromatogramFactory.create(new File("test.scf")); >>> System.out.println("Success!"); >>> } catch (Exception e){ >>> System.out.println("Failed!"); >>> e.printStackTrace(); >>> } >>> } >>> } >>> >>> 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf >>> >>> 3. Exception thrown in Windows XP/Vista: >>> >>> Desktop> java -classpath biojava-1.5.jar;. TraceTest >>> Exception in thread "main" org.biojava.bio.BioError: Unable to initialize >>> DNATools >>> at org.biojava.bio.seq.DNATools.(DNATools.java:117) >>> at org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) >>> at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) >>> at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:149) >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:141) >>> at org.biojava.bio.program.scf.SCF.create(SCF.java:126) >>> at >>> > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) >>> at TraceTest.main(TraceTest.java:8) >>> Caused by: org.biojava.bio.BioError: Unable to initialize RNATools >>> at org.biojava.bio.seq.RNATools.(RNATools.java:126) >>> at org.biojava.bio.seq.DNATools.(DNATools.java:110) >>> ... 8 more >>> Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) >>> at org.biojava.bio.seq.RNATools.(RNATools.java:124) >>> ... 9 more >>> Caused by: org.biojava.bio.symbol.IllegalSymbolException: >>> Token `his' does not appear as a named symbol in alphabet > `PROTEIN-TERM' >>> at >>> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) >>> ... 10 more >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > > Huseyin > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG925X4C5LeMEKA/QRAhP0AKCM42VcwZmwPFBRvwK3NtNdmZJwJQCdF3EO GNJ0p5xNdQeQ1oNYwrdSmMg= =Hu8w -----END PGP SIGNATURE----- From hkaya at iontek.com.tr Tue Sep 25 10:32:19 2007 From: hkaya at iontek.com.tr (hkaya) Date: Tue, 25 Sep 2007 17:32:19 +0300 Subject: [Biojava-l] ChromatogramFactory fails on Windows and Mac In-Reply-To: <46F76E58.7020905@ebi.ac.uk> References: <20070923105314.M78327@iontek.com.tr> <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> <20070923145142.M91232@iontek.com.tr> <46F76E58.7020905@ebi.ac.uk> Message-ID: <20070925141259.M94082@iontek.com.tr> You are right. When I do the following replacements "his" -> "HIS" and "ile" -> "ILE" in the org/biojava/bio/seq/TranslationTables.xml my code and a TraceViewer demo in biojava package perfectly worked on Windows and Linux. I think the problem is related with lower/upper case conversions. In turkish uppercase of 'i' is not 'I' but 'I' with a dot. Also lower case of 'I' is not 'i' but lower case dotless i (?). Current locale settings affects the behaivour of toLower(), toUpper(). http://java.sun.com/j2se/1.4.2/docs/api/java/lang/String.html#toUpperCase(java.util.Locale) I made the code run by modifying XML file in biojava.jar but i know it is not a nice solution. Thank you Huseyin Kaya On Mon, 24 Sep 2007 08:59:20 +0100, Richard Holland wrote > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Could this be an encoding problem with the XML file in the JAR? i.e. > Linux and Windows generally use different text encodings and so may > misinterpret some of the characters in the XML file, generating the > errors you see. I suppose this could be an issue if the Windows > environment is running internationalisation under a non-Western-European > character set, whereas the Linux box is running with an English > character set. > > Unfortunately I do not have access to a Windows machine to test this > on. > > Do any other BJ developers out there have access to a Windows machine > that they can investigate this with? > > cheers, > Richard > > hkaya wrote: > > On windows machine, I downloaded > > http://www.biojava.org/download/bj15/bin/BioJava1.5-bin.tar.gz with Internet > > Explorer and extract jar files. I also tried downloading the same file on > > linux and > > copy the jar files to windows with samba. On both case the same error occurs. > > After your message I delete and downloaded the same file again, but > > the situation is same. > > > > Huseyin > > > > On Sun, 23 Sep 2007 20:19:09 +0800, Mark Schreiber wrote > >> The stack trace indicates that the resources in you biojava.jar file > >> are missing or corrupt. Where did you get it from? > >> > >> If you copy the jar from you linux machine to windows do you still > >> get the same error? > >> > >> - Mark > >> > >> On 9/23/07, hkaya wrote: > >>> Hello > >>> > >>> The following small code perfectly runs on Linux but > >>> it fails on Windows and Mac. I'm using biojava 1.5. > >>> Could anybody tell me where i am doing something wrong? > >>> > >>> Thanks > >>> Huseyin Kaya > >>> > >>> > >>> 1. TraceTest.java > >>> > >>> import java.io.File; > >>> import org.biojava.bio.chromatogram.Chromatogram; > >>> import org.biojava.bio.chromatogram.ChromatogramFactory; > >>> > >>> public class TraceTest { > >>> public static void main(String[] args) { > >>> try { > >>> Chromatogram trace = > > ChromatogramFactory.create(new File("test.scf")); > >>> System.out.println("Success!"); > >>> } catch (Exception e){ > >>> System.out.println("Failed!"); > >>> e.printStackTrace(); > >>> } > >>> } > >>> } > >>> > >>> 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf > >>> > >>> 3. Exception thrown in Windows XP/Vista: > >>> > >>> Desktop> java -classpath biojava-1.5.jar;. TraceTest > >>> Exception in thread "main" org.biojava.bio.BioError: Unable to initialize > >>> DNATools > >>> at org.biojava.bio.seq.DNATools.(DNATools.java:117) > >>> at org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) > >>> at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) > >>> at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:141) > >>> at org.biojava.bio.program.scf.SCF.create(SCF.java:126) > >>> at > >>> > > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) > >>> at TraceTest.main(TraceTest.java:8) > >>> Caused by: org.biojava.bio.BioError: Unable to initialize RNATools > >>> at org.biojava.bio.seq.RNATools.(RNATools.java:126) > >>> at org.biojava.bio.seq.DNATools.(DNATools.java:110) > >>> ... 8 more > >>> Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml > >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) > >>> at org.biojava.bio.seq.RNATools.(RNATools.java:124) > >>> ... 9 more > >>> Caused by: org.biojava.bio.symbol.IllegalSymbolException: > >>> Token `his' does not appear as a named symbol in alphabet > > `PROTEIN-TERM' > >>> at > >>> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) > >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) > >>> ... 10 more > >>> > >>> > >>> _______________________________________________ > >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/biojava-l > >>> > > > > > > Huseyin > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFG925X4C5LeMEKA/QRAhP0AKCM42VcwZmwPFBRvwK3NtNdmZJwJQCdF3EO > GNJ0p5xNdQeQ1oNYwrdSmMg= > =Hu8w > -----END PGP SIGNATURE----- Huseyin From abhi232 at cc.gatech.edu Wed Sep 26 13:24:34 2007 From: abhi232 at cc.gatech.edu (abhi232 at cc.gatech.edu) Date: Wed, 26 Sep 2007 13:24:34 -0400 (EDT) Subject: [Biojava-l] Problem Running program on command line In-Reply-To: <20070925141259.M94082@iontek.com.tr> References: <20070923105314.M78327@iontek.com.tr> <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> <20070923145142.M91232@iontek.com.tr> <46F76E58.7020905@ebi.ac.uk> <20070925141259.M94082@iontek.com.tr> Message-ID: <4688.130.207.66.142.1190827474.squirrel@webmail.cc.gatech.edu> Hello all, I am trying a simple command line program in which i take a abi file as input and then print the sequence out. This is my source code: import java.io.File; import java.io.IOException; import org.biojava.bio.program.abi.ABITrace; import org.biojava.bio.seq.*; import org.biojava.bio.Annotation; import org.biojava.bio.seq.SequenceTools; import org.biojava.bio.seq.DNATools; /* * Command.java */ public class Command { /** Creates a new instance of Command */ public Command() { } public static void main(String args[]) { String arg; int len = args.length; arg = args[0]; System.out.println("The input argument path is:"+arg); //String path = "C:/applicationfolder/"; File ft = new File(arg); System.out.println("File object created successfully"); try { System.out.println("here1"); ABITrace trace = new ABITrace(ft); Sequence new_seq = SequenceTools.createSequence(trace.getSequence(),ft.toString(),ft.toString(),Annotation.EMPTY_ANNOTATION); String sequence = new_seq.seqString(); System.out.println("The sequence is:"+sequence); } catch (IOException ex) { ex.printStackTrace(); } } } I have set the classpath with all the jar files the biojava library has.But I am getting the following error. Exception in thread "main" org.biojava.bio.BioError: Unable to initialize DNATools at org.biojava.bio.seq.DNATools.() (Unknown Source) at java.lang.Class.initializeClass() (/usr/lib64/libgcj.so.5.0.0) at _Jv_ResolvePoolEntry(java.lang.Class, int) (/usr/lib64/libgcj.so.5.0.0) at org.biojava.bio.program.abi.ABITrace.getSequence() (Unknown Source) at Command.main(java.lang.String[]) (Unknown Source) Caused by: java.lang.IncompatibleClassChangeError: field org.biojava.bio.seq.io.CharacterTokenization.CHARACTER was not found. at _Jv_ResolvePoolEntry(java.lang.Class, int) (/usr/lib64/libgcj.so.5.0.0) at org.biojava.bio.seq.io.CharacterTokenization.getTokenType() (Unknown Source) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.getTokenType() (Unknown Source) at org.biojava.bio.symbol.SimpleSymbolList.SimpleSymbolList(org.biojava.bio.seq.io.SymbolTokenization, java.lang.String) (Unknown Source) at org.biojava.bio.seq.DNATools.() (Unknown Source) Can somebody please guide me on this? Thanks in advance. _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > > From holland at ebi.ac.uk Wed Sep 26 14:25:16 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 26 Sep 2007 19:25:16 +0100 (BST) Subject: [Biojava-l] Problem Running program on command line In-Reply-To: <4688.130.207.66.142.1190827474.squirrel@webmail.cc.gatech.edu> References: <20070923105314.M78327@iontek.com.tr> <93b45ca50709230519l73efe0bbk5c9a392bfc4de618@mail.gmail.com> <20070923145142.M91232@iontek.com.tr> <46F76E58.7020905@ebi.ac.uk> <20070925141259.M94082@iontek.com.tr> <4688.130.207.66.142.1190827474.squirrel@webmail.cc.gatech.edu> Message-ID: <60595.80.42.107.115.1190831116.squirrel@webmail.ebi.ac.uk> That's a very odd stack trace. It looks like you're running this through a java-to-native-code compiler - gcj, jikes, etc.? The exception appears to be thrown by libgcj, not any part of biojava. Could you try running it with a more traditional JRE such as the ones supplied by Sun. If it works, then the problem lies with gcj or whatever it is you are using to run this at present. If it doesn't, please report the new stack trace to us and we will investigate further. cheers, Richard On Wed, September 26, 2007 6:24 pm, abhi232 at cc.gatech.edu wrote: > > Hello all, > I am trying a simple command line program in which i take a abi file as > input and then print the sequence out. > > This is my source code: > import java.io.File; > import java.io.IOException; > import org.biojava.bio.program.abi.ABITrace; > import org.biojava.bio.seq.*; > import org.biojava.bio.Annotation; > import org.biojava.bio.seq.SequenceTools; > import org.biojava.bio.seq.DNATools; > /* > * Command.java > > */ > > > public class Command { > > /** Creates a new instance of Command */ > public Command() { > } > > public static void main(String args[]) > { > String arg; > int len = args.length; > arg = args[0]; > System.out.println("The input argument path is:"+arg); > //String path = "C:/applicationfolder/"; > File ft = new File(arg); > > System.out.println("File object created successfully"); > > > try { > System.out.println("here1"); > ABITrace trace = new ABITrace(ft); > Sequence new_seq = > SequenceTools.createSequence(trace.getSequence(),ft.toString(),ft.toString(),Annotation.EMPTY_ANNOTATION); > String sequence = new_seq.seqString(); > System.out.println("The sequence is:"+sequence); > > } catch (IOException ex) { > ex.printStackTrace(); > } > } > > } > > I have set the classpath with all the jar files the biojava library > has.But I am getting the following error. > > Exception in thread "main" org.biojava.bio.BioError: Unable to initialize > DNATools > at org.biojava.bio.seq.DNATools.() (Unknown Source) > at java.lang.Class.initializeClass() (/usr/lib64/libgcj.so.5.0.0) > at _Jv_ResolvePoolEntry(java.lang.Class, int) > (/usr/lib64/libgcj.so.5.0.0) > at org.biojava.bio.program.abi.ABITrace.getSequence() (Unknown Source) > at Command.main(java.lang.String[]) (Unknown Source) > Caused by: java.lang.IncompatibleClassChangeError: field > org.biojava.bio.seq.io.CharacterTokenization.CHARACTER was not found. > at _Jv_ResolvePoolEntry(java.lang.Class, int) > (/usr/lib64/libgcj.so.5.0.0) > at org.biojava.bio.seq.io.CharacterTokenization.getTokenType() (Unknown > Source) > at > org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.getTokenType() > (Unknown Source) > at > org.biojava.bio