From j.gao at usip.edu Tue Jun 5 16:42:35 2007 From: j.gao at usip.edu (Jun Gao) Date: Tue, 5 Jun 2007 16:42:35 -0400 Subject: [Biojava-l] question about pdb x-ray information Message-ID: Hi all, I am trying to get X-ray information from PDB file using BioJava, But I only get the information that if it is X-ray Structure, How can I get Resolution information? thanks! Jun From ap3 at sanger.ac.uk Tue Jun 5 18:39:10 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 5 Jun 2007 23:39:10 +0100 (BST) Subject: [Biojava-l] question about pdb x-ray information In-Reply-To: References: Message-ID: Hi Jun, The resolution is available only for protein structures that have been obtained using X-ray. You can't get it for those where NMR has been used. Andreas -------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK On Tue, 5 Jun 2007, Jun Gao wrote: > > Hi all, > > I am trying to get X-ray information from PDB file using BioJava, But I only get the information that if it is X-ray Structure, How can I get Resolution information? > > thanks! > > Jun > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- 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 ap3 at sanger.ac.uk Wed Jun 6 10:39:20 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 6 Jun 2007 15:39:20 +0100 Subject: [Biojava-l] question about pdb x-ray information In-Reply-To: References: Message-ID: <535ce4ea28c4cf96ee0744e7d6b96122@sanger.ac.uk> Hi Jun, I put an example for how to access the PDB - header information at http://biojava.org/wiki/BioJava:CookBook:PDB:header Andreas On 6 Jun 2007, at 13:47, Jun Gao wrote: > Hi Andreas, > > If it is X-ray Structure,how can I get it? > > Thanks > > Jun > > > -----Original Message----- > From: Andreas Prlic [mailto:ap3 at sanger.ac.uk] > Sent: Tue 6/5/2007 6:39 PM > To: Jun Gao > Cc: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] question about pdb x-ray information > > Hi Jun, > > The resolution is available only for protein structures > that have been obtained using X-ray. You can't > get it for those where NMR has been used. > > Andreas > > > > > -------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > > > > On Tue, 5 Jun 2007, Jun Gao wrote: > >> >> Hi all, >> >> I am trying to get X-ray information from PDB file using BioJava, But >> I only get the information that if it is X-ray Structure, How can I >> get Resolution information? >> >> thanks! >> >> Jun >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > -- > 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. > > > > > ----------------------------------------------------------------------- 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 orest.kozyar at gmail.com Wed Jun 6 15:14:51 2007 From: orest.kozyar at gmail.com (Orest Kozyar) Date: Wed, 6 Jun 2007 15:14:51 -0400 Subject: [Biojava-l] Extracting information from Genbank Message-ID: I've been trying to figure out how to use Biojava to extract information from Genbank. It seems that the following code would work according to the API docs: GenbankRichSequenceDB db = new GenbankRichSequenceDB(); RichSequence rs = db.getRichSequence("'NM_177408"); I've also tried variations on the ID (such as gi:NNNNNN) with and without the gi: annotation where the number corresponds to the record of interest, but no luck so far. I keep getting the following error: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException at org.biojava.bio.seq.FeatureFilter$OnlyChildren.(FeatureFilter.java:1270) at org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813) at org.biojava.bio.seq.SimpleFeatureHolder.(SimpleFeatureHolder.java:54) at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167) at org.biojavax.bio.seq.io.RichSeqIOAdapter.(RichSeqIOAdapter.java:61) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.(SimpleRichSequenceBuilder.java:100) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:70) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:154) at Test.main(Test.java:58) Java Result: 1 Perhaps I am just not formatting the string properly? Any guidance you can provide will greatly be appreciated! Thanks, Orest From orest.kozyar at gmail.com Wed Jun 6 15:30:04 2007 From: orest.kozyar at gmail.com (Orest Kozyar) Date: Wed, 6 Jun 2007 15:30:04 -0400 Subject: [Biojava-l] Extracting information from Genbank In-Reply-To: References: Message-ID: I should also add that for some reason, the bytecode folder is not present in my BioJava 1.5b2 package. Orest On 6/6/07, Orest Kozyar wrote: > I've been trying to figure out how to use Biojava to extract > information from Genbank. It seems that the following code would work > according to the API docs: > > GenbankRichSequenceDB db = new GenbankRichSequenceDB(); > RichSequence rs = db.getRichSequence("'NM_177408"); > > I've also tried variations on the ID (such as gi:NNNNNN) with and > without the gi: annotation where the number corresponds to the record > of interest, but no luck so far. I keep getting the following error: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org/biojava/utils/bytecode/CodeException > at org.biojava.bio.seq.FeatureFilter$OnlyChildren.(FeatureFilter.java:1270) > at org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813) > at org.biojava.bio.seq.SimpleFeatureHolder.(SimpleFeatureHolder.java:54) > at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167) > at org.biojavax.bio.seq.io.RichSeqIOAdapter.(RichSeqIOAdapter.java:61) > at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.(SimpleRichSequenceBuilder.java:100) > at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:70) > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:154) > at Test.main(Test.java:58) > Java Result: 1 > > Perhaps I am just not formatting the string properly? Any guidance > you can provide will greatly be appreciated! > Thanks, > Orest > From j.gao at usip.edu Thu Jun 7 17:27:53 2007 From: j.gao at usip.edu (Jun Gao) Date: Thu, 7 Jun 2007 17:27:53 -0400 Subject: [Biojava-l] question about pdb reader Message-ID: Hi all, when I use PDBFileReader to open pdbfile(PDB ID 1rei),I always get these exception: java.lang.NumberFormatException: For input string: "OMS A" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224) at java.lang.Float.parseFloat(Float.java:394) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFileParser.java:334) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileParser.java:349) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:845) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:764) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:189) java.lang.NumberFormatException: For input string: "OMS W" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224) at java.lang.Float.parseFloat(Float.java:394) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFileParser.java:334) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileParser.java:349) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:845) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:764) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:189) Is this a bug of PDBFileReader? thanks! Jun From markjschreiber at gmail.com Fri Jun 8 02:49:25 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 8 Jun 2007 14:49:25 +0800 Subject: [Biojava-l] Biojava 1.5 beta3 Released Message-ID: <93b45ca50706072349p3b2e4ec3mb6748a61e6c30a40@mail.gmail.com> Hi - I have prepared a final beta release before we make the final biojava 1.5. It is available for download at (http://biojava.org/wiki/BioJava:Download) Pleasingly this will be one of the most stable releases with more tests, docs and bugfixes than ever before. Thanks to the huge number of people who have contributed, pointed out bugs and helped to fix them! I am aiming for a biojava 1.5 official release shortly although I don't expect too many changes. Enjoy! - Mark Schreiber From ap3 at sanger.ac.uk Fri Jun 8 11:25:16 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 8 Jun 2007 16:25:16 +0100 Subject: [Biojava-l] question about pdb reader In-Reply-To: <4669637C.4060300@ebi.ac.uk> References: <4669275F.2080704@ebi.ac.uk> <4669637C.4060300@ebi.ac.uk> Message-ID: <33308ab01e77cf668dcc54055fe528b9@sanger.ac.uk> Hi ! To me this looks like output from an old version of the parser. The one that is available in the current version of BioJava version prints some warnings and shows the lines that can not be parsed, but it can read the rest of the file fine. Jun: can you make sure you are on the latest version of BioJava? The problems with both files is that the REMARK 2 line is not according to the PDB file spec. - This is unfortunately something that happens in several of the PDB files, but the parser can deal with this. Andreas On 8 Jun 2007, at 15:11, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi there. > > The bug I mentioned was to do with more informative error messages, > which indeed were implemented in the most recent code. However, it > seems > your file either has a bad REMARK 2 block, or our parser is incorrectly > treating REMARK 20-29 and REMARK 200-299 blocks as REMARK 2 blocks. > > ANDREAS - can you check to see that the code wouldn't accidentally pick > up REMARK 20-29/200-299 blocks whilst looking for REMARK 2 blocks? If > it > does, can you fix it? > > JUN GAO - can you open up your file in a text editor and locate all the > REMARK 2 blocks to see if they conform to the pattern "REMARK 2 > RESOLUTION ANGSTROMS"? If they don't, can you post one to > this list that doesn't conform? > > cheers, > Richard > > > Jun Gao wrote: >> another one: >> >> 1mcr >> java.lang.NumberFormatException: For input string: "E BEA" >> at >> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >> 1224) >> at java.lang.Float.parseFloat(Float.java:394) >> at >> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFil >> eParser.java:334) >> at >> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileP >> arser.java:349) >> at >> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. >> java:845) >> at >> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. >> java:764) >> at >> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileRea >> der.java:189) >> >> >> -----Original Message----- >> From: Richard Holland [mailto:holland at ebi.ac.uk] >> Sent: Fri 6/8/2007 5:54 AM >> To: Jun Gao >> Cc: biojava-l at lists.open-bio.org >> Subject: Re: [Biojava-l] question about pdb reader >> >> Hi there. >> >> This bug has already been fixed in the most recent beta releases of >> BioJava 1.5 >> >> cheers, >> Richard >> >> >> Jun Gao wrote: >>>> Hi all, >>>> >>>> when I use PDBFileReader to open pdbfile(PDB ID 1rei),I always get >>>> these exception: >>>> >>>> java.lang.NumberFormatException: For input string: "OMS A" >>>> at >>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >>>> 1224) >>>> at java.lang.Float.parseFloat(Float.java:394) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF >>>> ileParser.java:334) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil >>>> eParser.java:349) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:845) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:764) >>>> at >>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR >>>> eader.java:189) >>>> java.lang.NumberFormatException: For input string: "OMS W" >>>> at >>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >>>> 1224) >>>> at java.lang.Float.parseFloat(Float.java:394) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF >>>> ileParser.java:334) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil >>>> eParser.java:349) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:845) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:764) >>>> at >>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR >>>> eader.java:189) >>>> >>>> Is this a bug of PDBFileReader? >>>> >>>> thanks! >>>> >>>> Jun >>>> >>>> _______________________________________________ >>>> 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 > > iD8DBQFGaWN74C5LeMEKA/QRAkLGAJwMfzWeX2T+5r7T+Stj9rLzT+BVPACePQF0 > 9JvRE8/4LZZf+lcxnhJugKY= > =GK7T > -----END PGP SIGNATURE----- > > ----------------------------------------------------------------------- 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 susy at ysbl.york.ac.uk Mon Jun 11 08:15:42 2007 From: susy at ysbl.york.ac.uk (Susy Griffiths) Date: Mon, 11 Jun 2007 13:15:42 +0100 Subject: [Biojava-l] Blast parser Message-ID: <466D3CEE.9090400@ysbl.york.ac.uk> Hi, I am trying to modify the BioJava cookbook example 'BlastParser' to process output from a Blast search. I get the following exception when I run this with the output I have from the EBI web services NCBIBlast tool. org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not supported by the biojava blast-like parsing framework at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret (BlastLikeSaxParser.java:241) at org.biojava.bio.program.sax.BlastLikeSaxParser.parse (BlastLikeSaxParser.java:160) Also, are there BioJava tools to process the xml output rather than the raw Blast output? many thanks, Susy -- ********************************************************* Dr S.L. Griffiths YSBL Department of Chemistry University of York Heslington York YO10 5YW UK http://www.pims-lims.org/ email: susy at ysbl.york.ac.uk Tel. +44 (0)1904 328270 Fax +44 (0)1904 328266 ********************************************************* From mark.schreiber at novartis.com Mon Jun 11 21:34:31 2007 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 12 Jun 2007 09:34:31 +0800 Subject: [Biojava-l] Blast parser Message-ID: Hi - If you call parser.setModeLazy(); you will avoid the parser attempting to check the version of blast. I think lazy should be the default. I might submit a fix for this. To parse XML into biojava objects you can use BlastXMLParser and BlastXMLParserFacade. If you do this could you submit a recipe to the cookbook as we don't have one for BlastXML yet. Alternatively if you just want a single value from the BlastXML you could probably just use an XPath compliant parser (XPath is supported in JDK1.5) and get it that way. - Mark Susy Griffiths Sent by: biojava-l-bounces at lists.open-bio.org 06/11/2007 08:15 PM Please respond to susy To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Blast parser Hi, I am trying to modify the BioJava cookbook example 'BlastParser' to process output from a Blast search. I get the following exception when I run this with the output I have from the EBI web services NCBIBlast tool. org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not supported by the biojava blast-like parsing framework at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret (BlastLikeSaxParser.java:241) at org.biojava.bio.program.sax.BlastLikeSaxParser.parse (BlastLikeSaxParser.java:160) Also, are there BioJava tools to process the xml output rather than the raw Blast output? many thanks, Susy -- ********************************************************* Dr S.L. Griffiths YSBL Department of Chemistry University of York Heslington York YO10 5YW UK http://www.pims-lims.org/ email: susy at ysbl.york.ac.uk Tel. +44 (0)1904 328270 Fax +44 (0)1904 328266 ********************************************************* _______________________________________________ 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 Jun 13 11:31:30 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 16:31:30 +0100 Subject: [Biojava-l] BioJava 1.5 Released Message-ID: <46700DD2.7040400@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all. BioJava 1.5 has been released and is available for download from our website at http://biojava.org/ Thanks to everyone who has made contributions, and in particular to those who have spent many hours testing our new file parsers with every combination of scenarios under the sun. In addition to numerous bugfixes and enhancements, the highlights of this release are brand new parsers for the most common file formats (GenBank, Fasta, etc.), and a brand new BioSQL persistence layer that uses Hibernate to interact with sequence databases. There is also a new set of classes for creating genetic algorithms. These are all part of the new org.biojavax package which represents extensions to BioJava that would not fit easily into the existing package structure. The classes in org.biojavax mostly extend and improve on existing classes which could not be removed or replaced in order to maintain compatibility with older code. As usual if anyone finds any bugs in this release, please do report them to us using the BugZilla tool at http://bugzilla.open-bio.org/ Please also note that this will be the last release of BioJava that will be able to compile and run on Java 1.4. The next release (1.6) will move at least to Java 5 or maybe straight to Java 6 (decision not yet made). cheers, Richard -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcA3S4C5LeMEKA/QRAkKtAJwObiJa6cUpWAlS91z7T66MrEMW3gCeNBvr ei4DldeopmvwE5HzsPN/iR4= =VGAl -----END PGP SIGNATURE----- From koeberle at mpiib-berlin.mpg.de Fri Jun 15 06:06:05 2007 From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-15?Q?Christian_K=F6berle?=) Date: Fri, 15 Jun 2007 12:06:05 +0200 Subject: [Biojava-l] NCBISequenceDB getSequence failed Message-ID: <4672648D.6010601@mpiib-berlin.mpg.de> Hi, I try to download Sequences via NCBISequenceDB, but is dos not work. I get an Error: org.biojava.bio.BioException: Could not read sequence I try also with the 1.5 BIO-JAVA but it also not work. I found that the BIO-JAVA start a request with on with this URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=NM_000530&dopt=FASTA the result is a XML, but BIO-JAVA expect a FASTA fil [at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)]. It looks like that NCBI has changed the API. Christian -- Christian K?berle Max Planck Institute for Infection Biology Department of Immunology Campus Charit? Mitte Charit?platz 1 10117 Berlin Tel: +49 30 28 460 562 From koeberle at mpiib-berlin.mpg.de Fri Jun 15 09:35:43 2007 From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-15?Q?Christian_K=F6berle?=) Date: Fri, 15 Jun 2007 15:35:43 +0200 Subject: [Biojava-l] get Sequence by GeneID Message-ID: <467295AF.6080807@mpiib-berlin.mpg.de> Hi, is it possible to get a Sequence from NCBI by a GeneID. Or get the GeneID with a Accessionnumber? I can not find the GeneID in a RichSequence-Object that I have from GenbankRichSequenceDB .getSequence() Christian -- Christian K?berle Max Planck Institute for Infection Biology Department of Immunology Campus Charit? Mitte Charit?platz 1 10117 Berlin Tel: +49 30 28 460 562 From holland at ebi.ac.uk Fri Jun 15 10:42:41 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 15 Jun 2007 15:42:41 +0100 Subject: [Biojava-l] get Sequence by GeneID In-Reply-To: <467295AF.6080807@mpiib-berlin.mpg.de> References: <467295AF.6080807@mpiib-berlin.mpg.de> Message-ID: <4672A561.6040506@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The getSequence() method interrogates NCBI via the eUtils Java tool (part of Entrez) and downloads Genbank-format files which it then parses into RichSequence objects. It can only search by primary ID using EFetch (see eUtils documentation here: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#PrimaryIDs ), but the GI is returned for all records as part of the result. The GI tag (from the VERSION field) is retrieved by calling getIdentifier() - it is returned without the GI: prefix. cheers, Richard Christian K?berle wrote: > Hi, > > is it possible to get a Sequence from NCBI by a GeneID. Or get the > GeneID with a Accessionnumber? > I can not find the GeneID in a RichSequence-Object that I have from > GenbankRichSequenceDB .getSequence() > > Christian > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcqVh4C5LeMEKA/QRAsfFAJ47vGtpBJSSQmlgDtJLsUAQl135EQCfdtjK lF3bx2KiPHZoxx7+w+HfEHo= =2MQz -----END PGP SIGNATURE----- From holland at ebi.ac.uk Fri Jun 15 10:44:32 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 15 Jun 2007 15:44:32 +0100 Subject: [Biojava-l] NCBISequenceDB getSequence failed In-Reply-To: <4672648D.6010601@mpiib-berlin.mpg.de> References: <4672648D.6010601@mpiib-berlin.mpg.de> Message-ID: <4672A5D0.7050302@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 NCBISequenceDB is deprecated since 1.5 and no longer supported. Use Gen{bank,pept}SequenceDB instead in the org.biojavax.bio.db.ncbi package. cheers, Richard Christian K?berle wrote: > Hi, > > I try to download Sequences via NCBISequenceDB, but is dos not work. I > get an Error: org.biojava.bio.BioException: Could not read sequence > I try also with the 1.5 BIO-JAVA but it also not work. I found that the > BIO-JAVA start a request with on with this URL: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=NM_000530&dopt=FASTA > the result is a XML, but BIO-JAVA expect a FASTA fil [at > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)]. > It looks like that NCBI has changed the API. > > Christian > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcqXP4C5LeMEKA/QRAunHAJ4qL/lUct9oFhLbFKT5blohmcQkhACfYsE8 T26+k7vzgTNirt7Caof0ChQ= =w1IH -----END PGP SIGNATURE----- From Jerome.Lane at igh.cnrs.fr Mon Jun 25 14:15:52 2007 From: Jerome.Lane at igh.cnrs.fr (Jerome LANE) Date: Mon, 25 Jun 2007 20:15:52 +0200 Subject: [Biojava-l] Pattern Message-ID: <46800658.8060507@igh.cnrs.fr> Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome From Jerome.Lane at igh.cnrs.fr Mon Jun 25 14:24:10 2007 From: Jerome.Lane at igh.cnrs.fr (Jerome LANE) Date: Mon, 25 Jun 2007 20:24:10 +0200 Subject: [Biojava-l] Pattern matching Message-ID: <4680084A.8000706@igh.cnrs.fr> Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome From mark.schreiber at novartis.com Mon Jun 25 21:33:02 2007 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 26 Jun 2007 09:33:02 +0800 Subject: [Biojava-l] Pattern matching Message-ID: Hi - I think this has come up before on the list. Matcher.find() by default will begin a new search at the end of the old search. To make it begin it's search at any other place use the other form of the Matcher.find(int start) method. - Mark Jerome LANE Sent by: biojava-l-bounces at lists.open-bio.org 06/26/2007 02:24 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Pattern matching Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From kavita_mbi at yahoo.com Thu Jun 28 03:02:38 2007 From: kavita_mbi at yahoo.com (Kavita Agarwal) Date: Thu, 28 Jun 2007 00:02:38 -0700 (PDT) Subject: [Biojava-l] problem in initialising DNATools Message-ID: <470881.55081.qm@web39714.mail.mud.yahoo.com> Hi! I am using biojava1.5 in jdk1.5.0. In my applet when I use createDNA function to convert sequence retrived from textbox into dna ,I get the error:- >Unable to initialise DNATools and also.. >Couldn,t locate AlphabetManager.xml >This pribably means that your biojava file is corrupt or incorrectly built. I have unzipped the biojava1.5 and found AlphabetManager.xml in or->bio>symbol. What should I do to remove this error. --------------------------------- Be a PS3 game guru. Get your game face on with the latest PS3 news and previews at Yahoo! Games. From holland at ebi.ac.uk Thu Jun 28 03:53:44 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 08:53:44 +0100 Subject: [Biojava-l] problem in initialising DNATools In-Reply-To: <470881.55081.qm@web39714.mail.mud.yahoo.com> References: <470881.55081.qm@web39714.mail.mud.yahoo.com> Message-ID: <46836908.4020809@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. If you downloaded a binary version make sure it's the latest one from biojava.org and the download was completed OK. If you are compiling BioJava from source, make sure you have compiled BioJava correctly using the supplied ant file. The command is 'ant' (no task name required). In both cases, you should check that all the JAR files in biojava/lib are in your program's classpath, including the biojava.jar file. (It won't work if you only include the source tree in the classpath, it must have the JAR file.) cheers, Richard Kavita Agarwal wrote: > Hi! > > I am using biojava1.5 in jdk1.5.0. > > In my applet when I use createDNA function to convert sequence retrived from textbox into dna ,I get the error:- > > >Unable to initialise DNATools > > and also.. > > >Couldn,t locate AlphabetManager.xml > >This pribably means that your biojava file is corrupt or incorrectly built. > > I have unzipped the biojava1.5 and found AlphabetManager.xml in or->bio>symbol. > > What should I do to remove this error. > > > > --------------------------------- > Be a PS3 game guru. > Get your game face on with the latest PS3 news and previews at Yahoo! Games. > _______________________________________________ > 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 iD8DBQFGg2kI4C5LeMEKA/QRAtEWAJ9P1prwQTkjBHWPCAYePCxc/uxrOgCdH9QA rR9XgSEKgWYKkdo3BRnb8oA= =SKLw -----END PGP SIGNATURE----- From kavita_mbi at yahoo.com Thu Jun 28 04:39:53 2007 From: kavita_mbi at yahoo.com (Kavita Agarwal) Date: Thu, 28 Jun 2007 01:39:53 -0700 (PDT) Subject: [Biojava-l] biojava error Message-ID: <523009.28275.qm@web39710.mail.mud.yahoo.com> hi! I have downloaded the latest version of biojava and i have included all the jar files in the (java home)/jre/lib/ext folder. Problem is that my code runs fine when I run it in an application but it is not working in the applet. One thing which I have noticed is that functions defined in DNATools are static and I am calling a static function from a non-static one , is this any bug? Thanks a lot for ur reply. --------------------------------- Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. From holland at ebi.ac.uk Thu Jun 28 05:48:18 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 10:48:18 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <523009.28275.qm@web39710.mail.mud.yahoo.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> Message-ID: <468383E2.2020709@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This is a security issue. BioJava attempts to load the Alphabet.xml file from inside the JAR file. The applet security model disallows this. See: http://java.sun.com/sfaq/ Does someone else on this list know how to modify BioJava to load files from within a JAR file in a way that keeps the applet security model happy? cheers, Richard Kavita Agarwal wrote: > hi! > > I have downloaded the latest version of biojava and i have included all > the jar files in the > > (java home)/jre/lib/ext folder. Problem is that my code runs fine when > I run it in an application but it is not working in the applet. > > One thing which I have noticed is that functions defined in DNATools are > static and I am calling a static function from a non-static one , is > this any bug? > > Thanks a lot for ur reply. > > ------------------------------------------------------------------------ > Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > to > see what's on, when. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh 6hY3O3WqoZT85IqqdBBhsXI= =3NlO -----END PGP SIGNATURE----- From ap3 at sanger.ac.uk Thu Jun 28 06:21:14 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 28 Jun 2007 11:21:14 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <468383E2.2020709@ebi.ac.uk> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> Message-ID: Did you try signing your applet using jarsigner? e.g. see http://www.raditha.com/java/sandbox/index.php Andreas > Kavita Agarwal wrote: >> hi! >> >> I have downloaded the latest version of biojava and i have included >> all >> the jar files in the >> >> (java home)/jre/lib/ext folder. Problem is that my code runs fine >> when >> I run it in an application but it is not working in the applet. >> >> One thing which I have noticed is that functions defined in DNATools >> are >> static and I am calling a static function from a non-static one , is >> this any bug? >> >> Thanks a lot for ur reply. >> >> ---------------------------------------------------------------------- >> -- >> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> > 222>to >> see what's on, when. > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > 6hY3O3WqoZT85IqqdBBhsXI= > =3NlO > -----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 markjschreiber at gmail.com Fri Jun 29 02:35:58 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 29 Jun 2007 14:35:58 +0800 Subject: [Biojava-l] biojava error In-Reply-To: References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> Message-ID: <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> Hi - Is there any reason why we shouldn't digitally sign the biojava.jar as part of our distribution? It would save other people doing it. I think we would just use a self generated certificate as a third party one is expensive and doesn't really proove anything anyway. Just a thought, - Mark On 6/28/07, Andreas Prlic wrote: > Did you try signing your applet using jarsigner? > > e.g. see > http://www.raditha.com/java/sandbox/index.php > > Andreas > > > > Kavita Agarwal wrote: > >> hi! > >> > >> I have downloaded the latest version of biojava and i have included > >> all > >> the jar files in the > >> > >> (java home)/jre/lib/ext folder. Problem is that my code runs fine > >> when > >> I run it in an application but it is not working in the applet. > >> > >> One thing which I have noticed is that functions defined in DNATools > >> are > >> static and I am calling a static function from a non-static one , is > >> this any bug? > >> > >> Thanks a lot for ur reply. > >> > >> ---------------------------------------------------------------------- > >> -- > >> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > >> >> 222>to > >> see what's on, when. > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.4.2.2 (GNU/Linux) > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > > > iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > > 6hY3O3WqoZT85IqqdBBhsXI= > > =3NlO > > -----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. > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ayates at ebi.ac.uk Fri Jun 29 04:40:10 2007 From: ayates at ebi.ac.uk (Andy Yates) Date: Fri, 29 Jun 2007 09:40:10 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> Message-ID: <4684C56A.8050700@ebi.ac.uk> Hey, Normally digitally signing a jar can cause problems for people who want to uncompress our jar & re-compress into a distribution for themselves (a one shot executable jar scenario). Applets are very strange as I'm sure it's possible to load resources from the server and applet is created from (I did it ages ago for an applet which worked with blast output). So it's a bit of a shock that the applet sandbox doesn't allow us to call a getResourceAsStream() method (well I say surprise ... it doesn't really). It's probably not a bad thing to offer a digitally signed version of the JAR for people wanting to use it in applets but if the main distribution could continue with unsigned JARs I think that would be the best. Andy Mark Schreiber wrote: > Hi - > > Is there any reason why we shouldn't digitally sign the biojava.jar as > part of our distribution? It would save other people doing it. > > I think we would just use a self generated certificate as a third > party one is expensive and doesn't really proove anything anyway. > > Just a thought, > > - Mark > > On 6/28/07, Andreas Prlic wrote: >> Did you try signing your applet using jarsigner? >> >> e.g. see >> http://www.raditha.com/java/sandbox/index.php >> >> Andreas >> >> >>> Kavita Agarwal wrote: >>>> hi! >>>> >>>> I have downloaded the latest version of biojava and i have included >>>> all >>>> the jar files in the >>>> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs fine >>>> when >>>> I run it in an application but it is not working in the applet. >>>> >>>> One thing which I have noticed is that functions defined in DNATools >>>> are >>>> static and I am calling a static function from a non-static one , is >>>> this any bug? >>>> >>>> Thanks a lot for ur reply. >>>> >>>> ---------------------------------------------------------------------- >>>> -- >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >>>> >>> 222>to >>>> see what's on, when. >>> -----BEGIN PGP SIGNATURE----- >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >>> >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >>> 6hY3O3WqoZT85IqqdBBhsXI= >>> =3NlO >>> -----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. >> _______________________________________________ >> 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 markjschreiber at gmail.com Fri Jun 29 04:49:24 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 29 Jun 2007 16:49:24 +0800 Subject: [Biojava-l] biojava error In-Reply-To: <4684C56A.8050700@ebi.ac.uk> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> Message-ID: <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> In this case then maybe the best solution is to provide a "How to sign your biojava.jar" page on the wiki. Possibly it could go into a "How to make a BioJava empowered Applet" recipe for the cookbook. Does anyone feel motivated to provide a trivial (or even not so trivial) example? - Mark On 6/29/07, Andy Yates wrote: > Hey, > > Normally digitally signing a jar can cause problems for people who want > to uncompress our jar & re-compress into a distribution for themselves > (a one shot executable jar scenario). Applets are very strange as I'm > sure it's possible to load resources from the server and applet is > created from (I did it ages ago for an applet which worked with blast > output). So it's a bit of a shock that the applet sandbox doesn't allow > us to call a getResourceAsStream() method (well I say surprise ... it > doesn't really). > > It's probably not a bad thing to offer a digitally signed version of the > JAR for people wanting to use it in applets but if the main distribution > could continue with unsigned JARs I think that would be the best. > > Andy > > Mark Schreiber wrote: > > Hi - > > > > Is there any reason why we shouldn't digitally sign the biojava.jar as > > part of our distribution? It would save other people doing it. > > > > I think we would just use a self generated certificate as a third > > party one is expensive and doesn't really proove anything anyway. > > > > Just a thought, > > > > - Mark > > > > On 6/28/07, Andreas Prlic wrote: > >> Did you try signing your applet using jarsigner? > >> > >> e.g. see > >> http://www.raditha.com/java/sandbox/index.php > >> > >> Andreas > >> > >> > >>> Kavita Agarwal wrote: > >>>> hi! > >>>> > >>>> I have downloaded the latest version of biojava and i have included > >>>> all > >>>> the jar files in the > >>>> > >>>> (java home)/jre/lib/ext folder. Problem is that my code runs fine > >>>> when > >>>> I run it in an application but it is not working in the applet. > >>>> > >>>> One thing which I have noticed is that functions defined in DNATools > >>>> are > >>>> static and I am calling a static function from a non-static one , is > >>>> this any bug? > >>>> > >>>> Thanks a lot for ur reply. > >>>> > >>>> ---------------------------------------------------------------------- > >>>> -- > >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > >>>> >>>> 222>to > >>>> see what's on, when. > >>> -----BEGIN PGP SIGNATURE----- > >>> Version: GnuPG v1.4.2.2 (GNU/Linux) > >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > >>> > >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > >>> 6hY3O3WqoZT85IqqdBBhsXI= > >>> =3NlO > >>> -----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. > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ap3 at sanger.ac.uk Fri Jun 29 04:57:31 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 29 Jun 2007 09:57:31 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> Message-ID: <63c181b1fc4b070de2bc6ef8f7ef2185@sanger.ac.uk> we could provide an ant task that would sign it and the default would be not to have it signed. Andreas On 29 Jun 2007, at 09:49, Mark Schreiber wrote: > In this case then maybe the best solution is to provide a "How to sign > your biojava.jar" page on the wiki. > > Possibly it could go into a "How to make a BioJava empowered Applet" > recipe for the cookbook. Does anyone feel motivated to provide a > trivial (or even not so trivial) example? > > - Mark > > On 6/29/07, Andy Yates wrote: >> Hey, >> >> Normally digitally signing a jar can cause problems for people who >> want >> to uncompress our jar & re-compress into a distribution for themselves >> (a one shot executable jar scenario). Applets are very strange as I'm >> sure it's possible to load resources from the server and applet is >> created from (I did it ages ago for an applet which worked with blast >> output). So it's a bit of a shock that the applet sandbox doesn't >> allow >> us to call a getResourceAsStream() method (well I say surprise ... it >> doesn't really). >> >> It's probably not a bad thing to offer a digitally signed version of >> the >> JAR for people wanting to use it in applets but if the main >> distribution >> could continue with unsigned JARs I think that would be the best. >> >> Andy >> >> Mark Schreiber wrote: >> > Hi - >> > >> > Is there any reason why we shouldn't digitally sign the biojava.jar >> as >> > part of our distribution? It would save other people doing it. >> > >> > I think we would just use a self generated certificate as a third >> > party one is expensive and doesn't really proove anything anyway. >> > >> > Just a thought, >> > >> > - Mark >> > >> > On 6/28/07, Andreas Prlic wrote: >> >> Did you try signing your applet using jarsigner? >> >> >> >> e.g. see >> >> http://www.raditha.com/java/sandbox/index.php >> >> >> >> Andreas >> >> >> >> >> >>> Kavita Agarwal wrote: >> >>>> hi! >> >>>> >> >>>> I have downloaded the latest version of biojava and i have >> included >> >>>> all >> >>>> the jar files in the >> >>>> >> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs >> fine >> >>>> when >> >>>> I run it in an application but it is not working in the applet. >> >>>> >> >>>> One thing which I have noticed is that functions defined in >> DNATools >> >>>> are >> >>>> static and I am calling a static function from a non-static one >> , is >> >>>> this any bug? >> >>>> >> >>>> Thanks a lot for ur reply. >> >>>> >> >>>> >> ---------------------------------------------------------------------- >> >>>> -- >> >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> >>>> >> > >>>> 222>to >> >>>> see what's on, when. >> >>> -----BEGIN PGP SIGNATURE----- >> >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >>> >> >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >> >>> 6hY3O3WqoZT85IqqdBBhsXI= >> >>> =3NlO >> >>> -----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. >> >> _______________________________________________ >> >> 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 >> > > ----------------------------------------------------------------------- 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 ap3 at sanger.ac.uk Fri Jun 29 09:18:35 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 29 Jun 2007 14:18:35 +0100 Subject: [Biojava-l] biojava digital signature In-Reply-To: <93b45ca50706290450i21ff232cl6c7627ecebfed8c6@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> <63c181b1fc4b070de2bc6ef8f7ef2185@sanger.ac.uk> <93b45ca50706290450i21ff232cl6c7627ecebfed8c6@mail.gmail.com> Message-ID: The latest checkout from BioJava CVS can now be digitally signed. This is optional. try the following: ant clean; ant sign; jarsigner -verify ant-build/biojava.jar Andreas On 29 Jun 2007, at 12:50, Mark Schreiber wrote: > By we, do you mean you? > > : ) > > On 6/29/07, Andreas Prlic wrote: >> we could provide an ant task that would sign it and the default would >> be not to have it signed. >> >> Andreas >> >> >> On 29 Jun 2007, at 09:49, Mark Schreiber wrote: >> >> > In this case then maybe the best solution is to provide a "How to >> sign >> > your biojava.jar" page on the wiki. >> > >> > Possibly it could go into a "How to make a BioJava empowered Applet" >> > recipe for the cookbook. Does anyone feel motivated to provide a >> > trivial (or even not so trivial) example? >> > >> > - Mark >> > >> > On 6/29/07, Andy Yates wrote: >> >> Hey, >> >> >> >> Normally digitally signing a jar can cause problems for people who >> >> want >> >> to uncompress our jar & re-compress into a distribution for >> themselves >> >> (a one shot executable jar scenario). Applets are very strange as >> I'm >> >> sure it's possible to load resources from the server and applet is >> >> created from (I did it ages ago for an applet which worked with >> blast >> >> output). So it's a bit of a shock that the applet sandbox doesn't >> >> allow >> >> us to call a getResourceAsStream() method (well I say surprise ... >> it >> >> doesn't really). >> >> >> >> It's probably not a bad thing to offer a digitally signed version >> of >> >> the >> >> JAR for people wanting to use it in applets but if the main >> >> distribution >> >> could continue with unsigned JARs I think that would be the best. >> >> >> >> Andy >> >> >> >> Mark Schreiber wrote: >> >> > Hi - >> >> > >> >> > Is there any reason why we shouldn't digitally sign the >> biojava.jar >> >> as >> >> > part of our distribution? It would save other people doing it. >> >> > >> >> > I think we would just use a self generated certificate as a third >> >> > party one is expensive and doesn't really proove anything anyway. >> >> > >> >> > Just a thought, >> >> > >> >> > - Mark >> >> > >> >> > On 6/28/07, Andreas Prlic wrote: >> >> >> Did you try signing your applet using jarsigner? >> >> >> >> >> >> e.g. see >> >> >> http://www.raditha.com/java/sandbox/index.php >> >> >> >> >> >> Andreas >> >> >> >> >> >> >> >> >>> Kavita Agarwal wrote: >> >> >>>> hi! >> >> >>>> >> >> >>>> I have downloaded the latest version of biojava and i have >> >> included >> >> >>>> all >> >> >>>> the jar files in the >> >> >>>> >> >> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs >> >> fine >> >> >>>> when >> >> >>>> I run it in an application but it is not working in the >> applet. >> >> >>>> >> >> >>>> One thing which I have noticed is that functions defined in >> >> DNATools >> >> >>>> are >> >> >>>> static and I am calling a static function from a non-static >> one >> >> , is >> >> >>>> this any bug? >> >> >>>> >> >> >>>> Thanks a lot for ur reply. >> >> >>>> >> >> >>>> >> >> >> ---------------------------------------------------------------------- >> >> >>>> -- >> >> >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> >> >>>> >> >> > >> >>>> 222>to >> >> >>>> see what's on, when. >> >> >>> -----BEGIN PGP SIGNATURE----- >> >> >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >> >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >> >>> >> >> >>> >> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >> >> >>> 6hY3O3WqoZT85IqqdBBhsXI= >> >> >>> =3NlO >> >> >>> -----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. >> >> >> _______________________________________________ >> >> >> 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 >> >> >> > >> > >> ---------------------------------------------------------------------- >> - >> >> 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. >> > > ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Thu Jun 28 05:51:20 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 09:51:20 -0000 Subject: [Biojava-l] [Fwd: Re: The Java sandbox and BioJava] Message-ID: <46838472.6030203@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Kavita - having just sent you an email about your problem with Alphabet.xml, I searched the lists and found someone already solved it. Here is the solution which was posted to the list this time last year. (Forwarded below). cheers, Richard -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGg4Rw4C5LeMEKA/QRAmQ8AJoC2DgK3uXr1CQizo0dHA01aOFuYACeN1Ar MwkAP2HJeOhp0ultkmadM0A= =m7hv -----END PGP SIGNATURE----- -------------- next part -------------- An embedded message was scrubbed... From: Andrew Walsh Subject: Re: [Biojava-l] The Java sandbox and BioJava Date: Wed, 21 Jun 2006 13:38:42 -0400 Size: 5274 Url: http://lists.open-bio.org/pipermail/biojava-l/attachments/20070628/d90e57b1/attachment.mht From j.gao at usip.edu Tue Jun 5 20:42:35 2007 From: j.gao at usip.edu (Jun Gao) Date: Tue, 5 Jun 2007 16:42:35 -0400 Subject: [Biojava-l] question about pdb x-ray information Message-ID: Hi all, I am trying to get X-ray information from PDB file using BioJava, But I only get the information that if it is X-ray Structure, How can I get Resolution information? thanks! Jun From ap3 at sanger.ac.uk Tue Jun 5 22:39:10 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 5 Jun 2007 23:39:10 +0100 (BST) Subject: [Biojava-l] question about pdb x-ray information In-Reply-To: References: Message-ID: Hi Jun, The resolution is available only for protein structures that have been obtained using X-ray. You can't get it for those where NMR has been used. Andreas -------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK On Tue, 5 Jun 2007, Jun Gao wrote: > > Hi all, > > I am trying to get X-ray information from PDB file using BioJava, But I only get the information that if it is X-ray Structure, How can I get Resolution information? > > thanks! > > Jun > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- 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 ap3 at sanger.ac.uk Wed Jun 6 14:39:20 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 6 Jun 2007 15:39:20 +0100 Subject: [Biojava-l] question about pdb x-ray information In-Reply-To: References: Message-ID: <535ce4ea28c4cf96ee0744e7d6b96122@sanger.ac.uk> Hi Jun, I put an example for how to access the PDB - header information at http://biojava.org/wiki/BioJava:CookBook:PDB:header Andreas On 6 Jun 2007, at 13:47, Jun Gao wrote: > Hi Andreas, > > If it is X-ray Structure,how can I get it? > > Thanks > > Jun > > > -----Original Message----- > From: Andreas Prlic [mailto:ap3 at sanger.ac.uk] > Sent: Tue 6/5/2007 6:39 PM > To: Jun Gao > Cc: biojava-l at lists.open-bio.org > Subject: Re: [Biojava-l] question about pdb x-ray information > > Hi Jun, > > The resolution is available only for protein structures > that have been obtained using X-ray. You can't > get it for those where NMR has been used. > > Andreas > > > > > -------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > > > > On Tue, 5 Jun 2007, Jun Gao wrote: > >> >> Hi all, >> >> I am trying to get X-ray information from PDB file using BioJava, But >> I only get the information that if it is X-ray Structure, How can I >> get Resolution information? >> >> thanks! >> >> Jun >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > -- > 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. > > > > > ----------------------------------------------------------------------- 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 orest.kozyar at gmail.com Wed Jun 6 19:14:51 2007 From: orest.kozyar at gmail.com (Orest Kozyar) Date: Wed, 6 Jun 2007 15:14:51 -0400 Subject: [Biojava-l] Extracting information from Genbank Message-ID: I've been trying to figure out how to use Biojava to extract information from Genbank. It seems that the following code would work according to the API docs: GenbankRichSequenceDB db = new GenbankRichSequenceDB(); RichSequence rs = db.getRichSequence("'NM_177408"); I've also tried variations on the ID (such as gi:NNNNNN) with and without the gi: annotation where the number corresponds to the record of interest, but no luck so far. I keep getting the following error: Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException at org.biojava.bio.seq.FeatureFilter$OnlyChildren.(FeatureFilter.java:1270) at org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813) at org.biojava.bio.seq.SimpleFeatureHolder.(SimpleFeatureHolder.java:54) at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167) at org.biojavax.bio.seq.io.RichSeqIOAdapter.(RichSeqIOAdapter.java:61) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.(SimpleRichSequenceBuilder.java:100) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:70) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:154) at Test.main(Test.java:58) Java Result: 1 Perhaps I am just not formatting the string properly? Any guidance you can provide will greatly be appreciated! Thanks, Orest From orest.kozyar at gmail.com Wed Jun 6 19:30:04 2007 From: orest.kozyar at gmail.com (Orest Kozyar) Date: Wed, 6 Jun 2007 15:30:04 -0400 Subject: [Biojava-l] Extracting information from Genbank In-Reply-To: References: Message-ID: I should also add that for some reason, the bytecode folder is not present in my BioJava 1.5b2 package. Orest On 6/6/07, Orest Kozyar wrote: > I've been trying to figure out how to use Biojava to extract > information from Genbank. It seems that the following code would work > according to the API docs: > > GenbankRichSequenceDB db = new GenbankRichSequenceDB(); > RichSequence rs = db.getRichSequence("'NM_177408"); > > I've also tried variations on the ID (such as gi:NNNNNN) with and > without the gi: annotation where the number corresponds to the record > of interest, but no luck so far. I keep getting the following error: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org/biojava/utils/bytecode/CodeException > at org.biojava.bio.seq.FeatureFilter$OnlyChildren.(FeatureFilter.java:1270) > at org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813) > at org.biojava.bio.seq.SimpleFeatureHolder.(SimpleFeatureHolder.java:54) > at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167) > at org.biojavax.bio.seq.io.RichSeqIOAdapter.(RichSeqIOAdapter.java:61) > at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.(SimpleRichSequenceBuilder.java:100) > at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:70) > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:154) > at Test.main(Test.java:58) > Java Result: 1 > > Perhaps I am just not formatting the string properly? Any guidance > you can provide will greatly be appreciated! > Thanks, > Orest > From j.gao at usip.edu Thu Jun 7 21:27:53 2007 From: j.gao at usip.edu (Jun Gao) Date: Thu, 7 Jun 2007 17:27:53 -0400 Subject: [Biojava-l] question about pdb reader Message-ID: Hi all, when I use PDBFileReader to open pdbfile(PDB ID 1rei),I always get these exception: java.lang.NumberFormatException: For input string: "OMS A" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224) at java.lang.Float.parseFloat(Float.java:394) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFileParser.java:334) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileParser.java:349) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:845) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:764) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:189) java.lang.NumberFormatException: For input string: "OMS W" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224) at java.lang.Float.parseFloat(Float.java:394) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFileParser.java:334) at org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileParser.java:349) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:845) at org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:764) at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:189) Is this a bug of PDBFileReader? thanks! Jun From markjschreiber at gmail.com Fri Jun 8 06:49:25 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 8 Jun 2007 14:49:25 +0800 Subject: [Biojava-l] Biojava 1.5 beta3 Released Message-ID: <93b45ca50706072349p3b2e4ec3mb6748a61e6c30a40@mail.gmail.com> Hi - I have prepared a final beta release before we make the final biojava 1.5. It is available for download at (http://biojava.org/wiki/BioJava:Download) Pleasingly this will be one of the most stable releases with more tests, docs and bugfixes than ever before. Thanks to the huge number of people who have contributed, pointed out bugs and helped to fix them! I am aiming for a biojava 1.5 official release shortly although I don't expect too many changes. Enjoy! - Mark Schreiber From ap3 at sanger.ac.uk Fri Jun 8 15:25:16 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 8 Jun 2007 16:25:16 +0100 Subject: [Biojava-l] question about pdb reader In-Reply-To: <4669637C.4060300@ebi.ac.uk> References: <4669275F.2080704@ebi.ac.uk> <4669637C.4060300@ebi.ac.uk> Message-ID: <33308ab01e77cf668dcc54055fe528b9@sanger.ac.uk> Hi ! To me this looks like output from an old version of the parser. The one that is available in the current version of BioJava version prints some warnings and shows the lines that can not be parsed, but it can read the rest of the file fine. Jun: can you make sure you are on the latest version of BioJava? The problems with both files is that the REMARK 2 line is not according to the PDB file spec. - This is unfortunately something that happens in several of the PDB files, but the parser can deal with this. Andreas On 8 Jun 2007, at 15:11, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi there. > > The bug I mentioned was to do with more informative error messages, > which indeed were implemented in the most recent code. However, it > seems > your file either has a bad REMARK 2 block, or our parser is incorrectly > treating REMARK 20-29 and REMARK 200-299 blocks as REMARK 2 blocks. > > ANDREAS - can you check to see that the code wouldn't accidentally pick > up REMARK 20-29/200-299 blocks whilst looking for REMARK 2 blocks? If > it > does, can you fix it? > > JUN GAO - can you open up your file in a text editor and locate all the > REMARK 2 blocks to see if they conform to the pattern "REMARK 2 > RESOLUTION ANGSTROMS"? If they don't, can you post one to > this list that doesn't conform? > > cheers, > Richard > > > Jun Gao wrote: >> another one: >> >> 1mcr >> java.lang.NumberFormatException: For input string: "E BEA" >> at >> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >> 1224) >> at java.lang.Float.parseFloat(Float.java:394) >> at >> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFil >> eParser.java:334) >> at >> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileP >> arser.java:349) >> at >> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. >> java:845) >> at >> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. >> java:764) >> at >> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileRea >> der.java:189) >> >> >> -----Original Message----- >> From: Richard Holland [mailto:holland at ebi.ac.uk] >> Sent: Fri 6/8/2007 5:54 AM >> To: Jun Gao >> Cc: biojava-l at lists.open-bio.org >> Subject: Re: [Biojava-l] question about pdb reader >> >> Hi there. >> >> This bug has already been fixed in the most recent beta releases of >> BioJava 1.5 >> >> cheers, >> Richard >> >> >> Jun Gao wrote: >>>> Hi all, >>>> >>>> when I use PDBFileReader to open pdbfile(PDB ID 1rei),I always get >>>> these exception: >>>> >>>> java.lang.NumberFormatException: For input string: "OMS A" >>>> at >>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >>>> 1224) >>>> at java.lang.Float.parseFloat(Float.java:394) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF >>>> ileParser.java:334) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil >>>> eParser.java:349) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:845) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:764) >>>> at >>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR >>>> eader.java:189) >>>> java.lang.NumberFormatException: For input string: "OMS W" >>>> at >>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: >>>> 1224) >>>> at java.lang.Float.parseFloat(Float.java:394) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF >>>> ileParser.java:334) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil >>>> eParser.java:349) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:845) >>>> at >>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse >>>> r.java:764) >>>> at >>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR >>>> eader.java:189) >>>> >>>> Is this a bug of PDBFileReader? >>>> >>>> thanks! >>>> >>>> Jun >>>> >>>> _______________________________________________ >>>> 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 > > iD8DBQFGaWN74C5LeMEKA/QRAkLGAJwMfzWeX2T+5r7T+Stj9rLzT+BVPACePQF0 > 9JvRE8/4LZZf+lcxnhJugKY= > =GK7T > -----END PGP SIGNATURE----- > > ----------------------------------------------------------------------- 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 susy at ysbl.york.ac.uk Mon Jun 11 12:15:42 2007 From: susy at ysbl.york.ac.uk (Susy Griffiths) Date: Mon, 11 Jun 2007 13:15:42 +0100 Subject: [Biojava-l] Blast parser Message-ID: <466D3CEE.9090400@ysbl.york.ac.uk> Hi, I am trying to modify the BioJava cookbook example 'BlastParser' to process output from a Blast search. I get the following exception when I run this with the output I have from the EBI web services NCBIBlast tool. org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not supported by the biojava blast-like parsing framework at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret (BlastLikeSaxParser.java:241) at org.biojava.bio.program.sax.BlastLikeSaxParser.parse (BlastLikeSaxParser.java:160) Also, are there BioJava tools to process the xml output rather than the raw Blast output? many thanks, Susy -- ********************************************************* Dr S.L. Griffiths YSBL Department of Chemistry University of York Heslington York YO10 5YW UK http://www.pims-lims.org/ email: susy at ysbl.york.ac.uk Tel. +44 (0)1904 328270 Fax +44 (0)1904 328266 ********************************************************* From mark.schreiber at novartis.com Tue Jun 12 01:34:31 2007 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 12 Jun 2007 09:34:31 +0800 Subject: [Biojava-l] Blast parser Message-ID: Hi - If you call parser.setModeLazy(); you will avoid the parser attempting to check the version of blast. I think lazy should be the default. I might submit a fix for this. To parse XML into biojava objects you can use BlastXMLParser and BlastXMLParserFacade. If you do this could you submit a recipe to the cookbook as we don't have one for BlastXML yet. Alternatively if you just want a single value from the BlastXML you could probably just use an XPath compliant parser (XPath is supported in JDK1.5) and get it that way. - Mark Susy Griffiths Sent by: biojava-l-bounces at lists.open-bio.org 06/11/2007 08:15 PM Please respond to susy To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Blast parser Hi, I am trying to modify the BioJava cookbook example 'BlastParser' to process output from a Blast search. I get the following exception when I run this with the output I have from the EBI web services NCBIBlast tool. org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not supported by the biojava blast-like parsing framework at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret (BlastLikeSaxParser.java:241) at org.biojava.bio.program.sax.BlastLikeSaxParser.parse (BlastLikeSaxParser.java:160) Also, are there BioJava tools to process the xml output rather than the raw Blast output? many thanks, Susy -- ********************************************************* Dr S.L. Griffiths YSBL Department of Chemistry University of York Heslington York YO10 5YW UK http://www.pims-lims.org/ email: susy at ysbl.york.ac.uk Tel. +44 (0)1904 328270 Fax +44 (0)1904 328266 ********************************************************* _______________________________________________ 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 Jun 13 15:31:30 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 16:31:30 +0100 Subject: [Biojava-l] BioJava 1.5 Released Message-ID: <46700DD2.7040400@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all. BioJava 1.5 has been released and is available for download from our website at http://biojava.org/ Thanks to everyone who has made contributions, and in particular to those who have spent many hours testing our new file parsers with every combination of scenarios under the sun. In addition to numerous bugfixes and enhancements, the highlights of this release are brand new parsers for the most common file formats (GenBank, Fasta, etc.), and a brand new BioSQL persistence layer that uses Hibernate to interact with sequence databases. There is also a new set of classes for creating genetic algorithms. These are all part of the new org.biojavax package which represents extensions to BioJava that would not fit easily into the existing package structure. The classes in org.biojavax mostly extend and improve on existing classes which could not be removed or replaced in order to maintain compatibility with older code. As usual if anyone finds any bugs in this release, please do report them to us using the BugZilla tool at http://bugzilla.open-bio.org/ Please also note that this will be the last release of BioJava that will be able to compile and run on Java 1.4. The next release (1.6) will move at least to Java 5 or maybe straight to Java 6 (decision not yet made). cheers, Richard -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcA3S4C5LeMEKA/QRAkKtAJwObiJa6cUpWAlS91z7T66MrEMW3gCeNBvr ei4DldeopmvwE5HzsPN/iR4= =VGAl -----END PGP SIGNATURE----- From koeberle at mpiib-berlin.mpg.de Fri Jun 15 10:06:05 2007 From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-15?Q?Christian_K=F6berle?=) Date: Fri, 15 Jun 2007 12:06:05 +0200 Subject: [Biojava-l] NCBISequenceDB getSequence failed Message-ID: <4672648D.6010601@mpiib-berlin.mpg.de> Hi, I try to download Sequences via NCBISequenceDB, but is dos not work. I get an Error: org.biojava.bio.BioException: Could not read sequence I try also with the 1.5 BIO-JAVA but it also not work. I found that the BIO-JAVA start a request with on with this URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=NM_000530&dopt=FASTA the result is a XML, but BIO-JAVA expect a FASTA fil [at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)]. It looks like that NCBI has changed the API. Christian -- Christian K?berle Max Planck Institute for Infection Biology Department of Immunology Campus Charit? Mitte Charit?platz 1 10117 Berlin Tel: +49 30 28 460 562 From koeberle at mpiib-berlin.mpg.de Fri Jun 15 13:35:43 2007 From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-15?Q?Christian_K=F6berle?=) Date: Fri, 15 Jun 2007 15:35:43 +0200 Subject: [Biojava-l] get Sequence by GeneID Message-ID: <467295AF.6080807@mpiib-berlin.mpg.de> Hi, is it possible to get a Sequence from NCBI by a GeneID. Or get the GeneID with a Accessionnumber? I can not find the GeneID in a RichSequence-Object that I have from GenbankRichSequenceDB .getSequence() Christian -- Christian K?berle Max Planck Institute for Infection Biology Department of Immunology Campus Charit? Mitte Charit?platz 1 10117 Berlin Tel: +49 30 28 460 562 From holland at ebi.ac.uk Fri Jun 15 14:42:41 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 15 Jun 2007 15:42:41 +0100 Subject: [Biojava-l] get Sequence by GeneID In-Reply-To: <467295AF.6080807@mpiib-berlin.mpg.de> References: <467295AF.6080807@mpiib-berlin.mpg.de> Message-ID: <4672A561.6040506@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The getSequence() method interrogates NCBI via the eUtils Java tool (part of Entrez) and downloads Genbank-format files which it then parses into RichSequence objects. It can only search by primary ID using EFetch (see eUtils documentation here: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#PrimaryIDs ), but the GI is returned for all records as part of the result. The GI tag (from the VERSION field) is retrieved by calling getIdentifier() - it is returned without the GI: prefix. cheers, Richard Christian K?berle wrote: > Hi, > > is it possible to get a Sequence from NCBI by a GeneID. Or get the > GeneID with a Accessionnumber? > I can not find the GeneID in a RichSequence-Object that I have from > GenbankRichSequenceDB .getSequence() > > Christian > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcqVh4C5LeMEKA/QRAsfFAJ47vGtpBJSSQmlgDtJLsUAQl135EQCfdtjK lF3bx2KiPHZoxx7+w+HfEHo= =2MQz -----END PGP SIGNATURE----- From holland at ebi.ac.uk Fri Jun 15 14:44:32 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Fri, 15 Jun 2007 15:44:32 +0100 Subject: [Biojava-l] NCBISequenceDB getSequence failed In-Reply-To: <4672648D.6010601@mpiib-berlin.mpg.de> References: <4672648D.6010601@mpiib-berlin.mpg.de> Message-ID: <4672A5D0.7050302@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 NCBISequenceDB is deprecated since 1.5 and no longer supported. Use Gen{bank,pept}SequenceDB instead in the org.biojavax.bio.db.ncbi package. cheers, Richard Christian K?berle wrote: > Hi, > > I try to download Sequences via NCBISequenceDB, but is dos not work. I > get an Error: org.biojava.bio.BioException: Could not read sequence > I try also with the 1.5 BIO-JAVA but it also not work. I found that the > BIO-JAVA start a request with on with this URL: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=NM_000530&dopt=FASTA > the result is a XML, but BIO-JAVA expect a FASTA fil [at > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)]. > It looks like that NCBI has changed the API. > > Christian > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGcqXP4C5LeMEKA/QRAunHAJ4qL/lUct9oFhLbFKT5blohmcQkhACfYsE8 T26+k7vzgTNirt7Caof0ChQ= =w1IH -----END PGP SIGNATURE----- From Jerome.Lane at igh.cnrs.fr Mon Jun 25 18:15:52 2007 From: Jerome.Lane at igh.cnrs.fr (Jerome LANE) Date: Mon, 25 Jun 2007 20:15:52 +0200 Subject: [Biojava-l] Pattern Message-ID: <46800658.8060507@igh.cnrs.fr> Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome From Jerome.Lane at igh.cnrs.fr Mon Jun 25 18:24:10 2007 From: Jerome.Lane at igh.cnrs.fr (Jerome LANE) Date: Mon, 25 Jun 2007 20:24:10 +0200 Subject: [Biojava-l] Pattern matching Message-ID: <4680084A.8000706@igh.cnrs.fr> Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome From mark.schreiber at novartis.com Tue Jun 26 01:33:02 2007 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Tue, 26 Jun 2007 09:33:02 +0800 Subject: [Biojava-l] Pattern matching Message-ID: Hi - I think this has come up before on the list. Matcher.find() by default will begin a new search at the end of the old search. To make it begin it's search at any other place use the other form of the Matcher.find(int start) method. - Mark Jerome LANE Sent by: biojava-l-bounces at lists.open-bio.org 06/26/2007 02:24 AM To: biojava-l at lists.open-bio.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Pattern matching Hi, I have used biojava Pattern class to match DNA sequence. But I can't find all matches for my sequence. For example here a bit of code that I have implemented to search for "aa" pattern in "aaaa" DNA sequence : ----------------------------------- try { // Variables needed... org.biojava.utils.regex.Matcher occurences ; FiniteAlphabet IUPAC = DNATools.getDNA(); SymbolList WorkingSequence = DNATools.createDNA("aaaa"); // Create pattern using pattern factory. org.biojava.utils.regex.Pattern pattern; PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC); try{ pattern = FACTORY.compile("aa"); } catch(Exception e) {e.printStackTrace(); return;} System.out.println("Searching for: "+pattern.patternAsString( ) ); // Obtain iterator of matches. try { occurences = pattern.matcher( WorkingSequence ); } catch(Exception e) {e.printStackTrace(); return;} // Foreach match while( occurences.find( ) ) { System.out.println("Match: " +"\t"+ WorkingSequence +"\n"+ occurences.start() +"\t"+ occurences.group().seqString()); } } catch (Exception ex) { ex.printStackTrace(); System.exit(1); } ---------------------------- And this is the output : ---------------------------- Searching for: aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 1 aa Match: org.biojava.bio.symbol.SimpleSymbolList at ea82ff69 length: 4 3 aa -------------------------------- But for the input sequence "aaaa" I should have 3 matchs at postion 1, 2 and 3. Is there any parameter to provide for it ? Best regards Jerome _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From kavita_mbi at yahoo.com Thu Jun 28 07:02:38 2007 From: kavita_mbi at yahoo.com (Kavita Agarwal) Date: Thu, 28 Jun 2007 00:02:38 -0700 (PDT) Subject: [Biojava-l] problem in initialising DNATools Message-ID: <470881.55081.qm@web39714.mail.mud.yahoo.com> Hi! I am using biojava1.5 in jdk1.5.0. In my applet when I use createDNA function to convert sequence retrived from textbox into dna ,I get the error:- >Unable to initialise DNATools and also.. >Couldn,t locate AlphabetManager.xml >This pribably means that your biojava file is corrupt or incorrectly built. I have unzipped the biojava1.5 and found AlphabetManager.xml in or->bio>symbol. What should I do to remove this error. --------------------------------- Be a PS3 game guru. Get your game face on with the latest PS3 news and previews at Yahoo! Games. From holland at ebi.ac.uk Thu Jun 28 07:53:44 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 08:53:44 +0100 Subject: [Biojava-l] problem in initialising DNATools In-Reply-To: <470881.55081.qm@web39714.mail.mud.yahoo.com> References: <470881.55081.qm@web39714.mail.mud.yahoo.com> Message-ID: <46836908.4020809@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. If you downloaded a binary version make sure it's the latest one from biojava.org and the download was completed OK. If you are compiling BioJava from source, make sure you have compiled BioJava correctly using the supplied ant file. The command is 'ant' (no task name required). In both cases, you should check that all the JAR files in biojava/lib are in your program's classpath, including the biojava.jar file. (It won't work if you only include the source tree in the classpath, it must have the JAR file.) cheers, Richard Kavita Agarwal wrote: > Hi! > > I am using biojava1.5 in jdk1.5.0. > > In my applet when I use createDNA function to convert sequence retrived from textbox into dna ,I get the error:- > > >Unable to initialise DNATools > > and also.. > > >Couldn,t locate AlphabetManager.xml > >This pribably means that your biojava file is corrupt or incorrectly built. > > I have unzipped the biojava1.5 and found AlphabetManager.xml in or->bio>symbol. > > What should I do to remove this error. > > > > --------------------------------- > Be a PS3 game guru. > Get your game face on with the latest PS3 news and previews at Yahoo! Games. > _______________________________________________ > 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 iD8DBQFGg2kI4C5LeMEKA/QRAtEWAJ9P1prwQTkjBHWPCAYePCxc/uxrOgCdH9QA rR9XgSEKgWYKkdo3BRnb8oA= =SKLw -----END PGP SIGNATURE----- From kavita_mbi at yahoo.com Thu Jun 28 08:39:53 2007 From: kavita_mbi at yahoo.com (Kavita Agarwal) Date: Thu, 28 Jun 2007 01:39:53 -0700 (PDT) Subject: [Biojava-l] biojava error Message-ID: <523009.28275.qm@web39710.mail.mud.yahoo.com> hi! I have downloaded the latest version of biojava and i have included all the jar files in the (java home)/jre/lib/ext folder. Problem is that my code runs fine when I run it in an application but it is not working in the applet. One thing which I have noticed is that functions defined in DNATools are static and I am calling a static function from a non-static one , is this any bug? Thanks a lot for ur reply. --------------------------------- Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. From holland at ebi.ac.uk Thu Jun 28 09:48:18 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 10:48:18 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <523009.28275.qm@web39710.mail.mud.yahoo.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> Message-ID: <468383E2.2020709@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This is a security issue. BioJava attempts to load the Alphabet.xml file from inside the JAR file. The applet security model disallows this. See: http://java.sun.com/sfaq/ Does someone else on this list know how to modify BioJava to load files from within a JAR file in a way that keeps the applet security model happy? cheers, Richard Kavita Agarwal wrote: > hi! > > I have downloaded the latest version of biojava and i have included all > the jar files in the > > (java home)/jre/lib/ext folder. Problem is that my code runs fine when > I run it in an application but it is not working in the applet. > > One thing which I have noticed is that functions defined in DNATools are > static and I am calling a static function from a non-static one , is > this any bug? > > Thanks a lot for ur reply. > > ------------------------------------------------------------------------ > Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > to > see what's on, when. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh 6hY3O3WqoZT85IqqdBBhsXI= =3NlO -----END PGP SIGNATURE----- From ap3 at sanger.ac.uk Thu Jun 28 10:21:14 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 28 Jun 2007 11:21:14 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <468383E2.2020709@ebi.ac.uk> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> Message-ID: Did you try signing your applet using jarsigner? e.g. see http://www.raditha.com/java/sandbox/index.php Andreas > Kavita Agarwal wrote: >> hi! >> >> I have downloaded the latest version of biojava and i have included >> all >> the jar files in the >> >> (java home)/jre/lib/ext folder. Problem is that my code runs fine >> when >> I run it in an application but it is not working in the applet. >> >> One thing which I have noticed is that functions defined in DNATools >> are >> static and I am calling a static function from a non-static one , is >> this any bug? >> >> Thanks a lot for ur reply. >> >> ---------------------------------------------------------------------- >> -- >> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> > 222>to >> see what's on, when. > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > 6hY3O3WqoZT85IqqdBBhsXI= > =3NlO > -----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 markjschreiber at gmail.com Fri Jun 29 06:35:58 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 29 Jun 2007 14:35:58 +0800 Subject: [Biojava-l] biojava error In-Reply-To: References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> Message-ID: <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> Hi - Is there any reason why we shouldn't digitally sign the biojava.jar as part of our distribution? It would save other people doing it. I think we would just use a self generated certificate as a third party one is expensive and doesn't really proove anything anyway. Just a thought, - Mark On 6/28/07, Andreas Prlic wrote: > Did you try signing your applet using jarsigner? > > e.g. see > http://www.raditha.com/java/sandbox/index.php > > Andreas > > > > Kavita Agarwal wrote: > >> hi! > >> > >> I have downloaded the latest version of biojava and i have included > >> all > >> the jar files in the > >> > >> (java home)/jre/lib/ext folder. Problem is that my code runs fine > >> when > >> I run it in an application but it is not working in the applet. > >> > >> One thing which I have noticed is that functions defined in DNATools > >> are > >> static and I am calling a static function from a non-static one , is > >> this any bug? > >> > >> Thanks a lot for ur reply. > >> > >> ---------------------------------------------------------------------- > >> -- > >> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > >> >> 222>to > >> see what's on, when. > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.4.2.2 (GNU/Linux) > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > > > iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > > 6hY3O3WqoZT85IqqdBBhsXI= > > =3NlO > > -----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. > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ayates at ebi.ac.uk Fri Jun 29 08:40:10 2007 From: ayates at ebi.ac.uk (Andy Yates) Date: Fri, 29 Jun 2007 09:40:10 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> Message-ID: <4684C56A.8050700@ebi.ac.uk> Hey, Normally digitally signing a jar can cause problems for people who want to uncompress our jar & re-compress into a distribution for themselves (a one shot executable jar scenario). Applets are very strange as I'm sure it's possible to load resources from the server and applet is created from (I did it ages ago for an applet which worked with blast output). So it's a bit of a shock that the applet sandbox doesn't allow us to call a getResourceAsStream() method (well I say surprise ... it doesn't really). It's probably not a bad thing to offer a digitally signed version of the JAR for people wanting to use it in applets but if the main distribution could continue with unsigned JARs I think that would be the best. Andy Mark Schreiber wrote: > Hi - > > Is there any reason why we shouldn't digitally sign the biojava.jar as > part of our distribution? It would save other people doing it. > > I think we would just use a self generated certificate as a third > party one is expensive and doesn't really proove anything anyway. > > Just a thought, > > - Mark > > On 6/28/07, Andreas Prlic wrote: >> Did you try signing your applet using jarsigner? >> >> e.g. see >> http://www.raditha.com/java/sandbox/index.php >> >> Andreas >> >> >>> Kavita Agarwal wrote: >>>> hi! >>>> >>>> I have downloaded the latest version of biojava and i have included >>>> all >>>> the jar files in the >>>> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs fine >>>> when >>>> I run it in an application but it is not working in the applet. >>>> >>>> One thing which I have noticed is that functions defined in DNATools >>>> are >>>> static and I am calling a static function from a non-static one , is >>>> this any bug? >>>> >>>> Thanks a lot for ur reply. >>>> >>>> ---------------------------------------------------------------------- >>>> -- >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >>>> >>> 222>to >>>> see what's on, when. >>> -----BEGIN PGP SIGNATURE----- >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >>> >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >>> 6hY3O3WqoZT85IqqdBBhsXI= >>> =3NlO >>> -----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. >> _______________________________________________ >> 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 markjschreiber at gmail.com Fri Jun 29 08:49:24 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 29 Jun 2007 16:49:24 +0800 Subject: [Biojava-l] biojava error In-Reply-To: <4684C56A.8050700@ebi.ac.uk> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> Message-ID: <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> In this case then maybe the best solution is to provide a "How to sign your biojava.jar" page on the wiki. Possibly it could go into a "How to make a BioJava empowered Applet" recipe for the cookbook. Does anyone feel motivated to provide a trivial (or even not so trivial) example? - Mark On 6/29/07, Andy Yates wrote: > Hey, > > Normally digitally signing a jar can cause problems for people who want > to uncompress our jar & re-compress into a distribution for themselves > (a one shot executable jar scenario). Applets are very strange as I'm > sure it's possible to load resources from the server and applet is > created from (I did it ages ago for an applet which worked with blast > output). So it's a bit of a shock that the applet sandbox doesn't allow > us to call a getResourceAsStream() method (well I say surprise ... it > doesn't really). > > It's probably not a bad thing to offer a digitally signed version of the > JAR for people wanting to use it in applets but if the main distribution > could continue with unsigned JARs I think that would be the best. > > Andy > > Mark Schreiber wrote: > > Hi - > > > > Is there any reason why we shouldn't digitally sign the biojava.jar as > > part of our distribution? It would save other people doing it. > > > > I think we would just use a self generated certificate as a third > > party one is expensive and doesn't really proove anything anyway. > > > > Just a thought, > > > > - Mark > > > > On 6/28/07, Andreas Prlic wrote: > >> Did you try signing your applet using jarsigner? > >> > >> e.g. see > >> http://www.raditha.com/java/sandbox/index.php > >> > >> Andreas > >> > >> > >>> Kavita Agarwal wrote: > >>>> hi! > >>>> > >>>> I have downloaded the latest version of biojava and i have included > >>>> all > >>>> the jar files in the > >>>> > >>>> (java home)/jre/lib/ext folder. Problem is that my code runs fine > >>>> when > >>>> I run it in an application but it is not working in the applet. > >>>> > >>>> One thing which I have noticed is that functions defined in DNATools > >>>> are > >>>> static and I am calling a static function from a non-static one , is > >>>> this any bug? > >>>> > >>>> Thanks a lot for ur reply. > >>>> > >>>> ---------------------------------------------------------------------- > >>>> -- > >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge > >>>> >>>> 222>to > >>>> see what's on, when. > >>> -----BEGIN PGP SIGNATURE----- > >>> Version: GnuPG v1.4.2.2 (GNU/Linux) > >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > >>> > >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh > >>> 6hY3O3WqoZT85IqqdBBhsXI= > >>> =3NlO > >>> -----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. > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > _______________________________________________ > > Biojava-l mailing list - Biojava-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ap3 at sanger.ac.uk Fri Jun 29 08:57:31 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 29 Jun 2007 09:57:31 +0100 Subject: [Biojava-l] biojava error In-Reply-To: <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> Message-ID: <63c181b1fc4b070de2bc6ef8f7ef2185@sanger.ac.uk> we could provide an ant task that would sign it and the default would be not to have it signed. Andreas On 29 Jun 2007, at 09:49, Mark Schreiber wrote: > In this case then maybe the best solution is to provide a "How to sign > your biojava.jar" page on the wiki. > > Possibly it could go into a "How to make a BioJava empowered Applet" > recipe for the cookbook. Does anyone feel motivated to provide a > trivial (or even not so trivial) example? > > - Mark > > On 6/29/07, Andy Yates wrote: >> Hey, >> >> Normally digitally signing a jar can cause problems for people who >> want >> to uncompress our jar & re-compress into a distribution for themselves >> (a one shot executable jar scenario). Applets are very strange as I'm >> sure it's possible to load resources from the server and applet is >> created from (I did it ages ago for an applet which worked with blast >> output). So it's a bit of a shock that the applet sandbox doesn't >> allow >> us to call a getResourceAsStream() method (well I say surprise ... it >> doesn't really). >> >> It's probably not a bad thing to offer a digitally signed version of >> the >> JAR for people wanting to use it in applets but if the main >> distribution >> could continue with unsigned JARs I think that would be the best. >> >> Andy >> >> Mark Schreiber wrote: >> > Hi - >> > >> > Is there any reason why we shouldn't digitally sign the biojava.jar >> as >> > part of our distribution? It would save other people doing it. >> > >> > I think we would just use a self generated certificate as a third >> > party one is expensive and doesn't really proove anything anyway. >> > >> > Just a thought, >> > >> > - Mark >> > >> > On 6/28/07, Andreas Prlic wrote: >> >> Did you try signing your applet using jarsigner? >> >> >> >> e.g. see >> >> http://www.raditha.com/java/sandbox/index.php >> >> >> >> Andreas >> >> >> >> >> >>> Kavita Agarwal wrote: >> >>>> hi! >> >>>> >> >>>> I have downloaded the latest version of biojava and i have >> included >> >>>> all >> >>>> the jar files in the >> >>>> >> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs >> fine >> >>>> when >> >>>> I run it in an application but it is not working in the applet. >> >>>> >> >>>> One thing which I have noticed is that functions defined in >> DNATools >> >>>> are >> >>>> static and I am calling a static function from a non-static one >> , is >> >>>> this any bug? >> >>>> >> >>>> Thanks a lot for ur reply. >> >>>> >> >>>> >> ---------------------------------------------------------------------- >> >>>> -- >> >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> >>>> >> > >>>> 222>to >> >>>> see what's on, when. >> >>> -----BEGIN PGP SIGNATURE----- >> >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >>> >> >>> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >> >>> 6hY3O3WqoZT85IqqdBBhsXI= >> >>> =3NlO >> >>> -----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. >> >> _______________________________________________ >> >> 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 >> > > ----------------------------------------------------------------------- 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 ap3 at sanger.ac.uk Fri Jun 29 13:18:35 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Fri, 29 Jun 2007 14:18:35 +0100 Subject: [Biojava-l] biojava digital signature In-Reply-To: <93b45ca50706290450i21ff232cl6c7627ecebfed8c6@mail.gmail.com> References: <523009.28275.qm@web39710.mail.mud.yahoo.com> <468383E2.2020709@ebi.ac.uk> <93b45ca50706282335k7e44b289nffc9d06d4cc463b2@mail.gmail.com> <4684C56A.8050700@ebi.ac.uk> <93b45ca50706290149p210c58b9tb4df6bfb0cbfd47f@mail.gmail.com> <63c181b1fc4b070de2bc6ef8f7ef2185@sanger.ac.uk> <93b45ca50706290450i21ff232cl6c7627ecebfed8c6@mail.gmail.com> Message-ID: The latest checkout from BioJava CVS can now be digitally signed. This is optional. try the following: ant clean; ant sign; jarsigner -verify ant-build/biojava.jar Andreas On 29 Jun 2007, at 12:50, Mark Schreiber wrote: > By we, do you mean you? > > : ) > > On 6/29/07, Andreas Prlic wrote: >> we could provide an ant task that would sign it and the default would >> be not to have it signed. >> >> Andreas >> >> >> On 29 Jun 2007, at 09:49, Mark Schreiber wrote: >> >> > In this case then maybe the best solution is to provide a "How to >> sign >> > your biojava.jar" page on the wiki. >> > >> > Possibly it could go into a "How to make a BioJava empowered Applet" >> > recipe for the cookbook. Does anyone feel motivated to provide a >> > trivial (or even not so trivial) example? >> > >> > - Mark >> > >> > On 6/29/07, Andy Yates wrote: >> >> Hey, >> >> >> >> Normally digitally signing a jar can cause problems for people who >> >> want >> >> to uncompress our jar & re-compress into a distribution for >> themselves >> >> (a one shot executable jar scenario). Applets are very strange as >> I'm >> >> sure it's possible to load resources from the server and applet is >> >> created from (I did it ages ago for an applet which worked with >> blast >> >> output). So it's a bit of a shock that the applet sandbox doesn't >> >> allow >> >> us to call a getResourceAsStream() method (well I say surprise ... >> it >> >> doesn't really). >> >> >> >> It's probably not a bad thing to offer a digitally signed version >> of >> >> the >> >> JAR for people wanting to use it in applets but if the main >> >> distribution >> >> could continue with unsigned JARs I think that would be the best. >> >> >> >> Andy >> >> >> >> Mark Schreiber wrote: >> >> > Hi - >> >> > >> >> > Is there any reason why we shouldn't digitally sign the >> biojava.jar >> >> as >> >> > part of our distribution? It would save other people doing it. >> >> > >> >> > I think we would just use a self generated certificate as a third >> >> > party one is expensive and doesn't really proove anything anyway. >> >> > >> >> > Just a thought, >> >> > >> >> > - Mark >> >> > >> >> > On 6/28/07, Andreas Prlic wrote: >> >> >> Did you try signing your applet using jarsigner? >> >> >> >> >> >> e.g. see >> >> >> http://www.raditha.com/java/sandbox/index.php >> >> >> >> >> >> Andreas >> >> >> >> >> >> >> >> >>> Kavita Agarwal wrote: >> >> >>>> hi! >> >> >>>> >> >> >>>> I have downloaded the latest version of biojava and i have >> >> included >> >> >>>> all >> >> >>>> the jar files in the >> >> >>>> >> >> >>>> (java home)/jre/lib/ext folder. Problem is that my code runs >> >> fine >> >> >>>> when >> >> >>>> I run it in an application but it is not working in the >> applet. >> >> >>>> >> >> >>>> One thing which I have noticed is that functions defined in >> >> DNATools >> >> >>>> are >> >> >>>> static and I am calling a static function from a non-static >> one >> >> , is >> >> >>>> this any bug? >> >> >>>> >> >> >>>> Thanks a lot for ur reply. >> >> >>>> >> >> >>>> >> >> >> ---------------------------------------------------------------------- >> >> >>>> -- >> >> >>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge >> >> >>>> >> >> > >> >>>> 222>to >> >> >>>> see what's on, when. >> >> >>> -----BEGIN PGP SIGNATURE----- >> >> >>> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >> >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >> >>> >> >> >>> >> iD8DBQFGg4Pi4C5LeMEKA/QRArpHAJ91uzlAlJ0qeTMiRMtWahdT5TCYVACeKpVh >> >> >>> 6hY3O3WqoZT85IqqdBBhsXI= >> >> >>> =3NlO >> >> >>> -----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. >> >> >> _______________________________________________ >> >> >> 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 >> >> >> > >> > >> ---------------------------------------------------------------------- >> - >> >> 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. >> > > ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Thu Jun 28 09:51:20 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 28 Jun 2007 09:51:20 -0000 Subject: [Biojava-l] [Fwd: Re: The Java sandbox and BioJava] Message-ID: <46838472.6030203@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Kavita - having just sent you an email about your problem with Alphabet.xml, I searched the lists and found someone already solved it. Here is the solution which was posted to the list this time last year. (Forwarded below). cheers, Richard -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGg4Rw4C5LeMEKA/QRAmQ8AJoC2DgK3uXr1CQizo0dHA01aOFuYACeN1Ar MwkAP2HJeOhp0ultkmadM0A= =m7hv -----END PGP SIGNATURE----- -------------- next part -------------- An embedded message was scrubbed... From: Andrew Walsh Subject: Re: [Biojava-l] The Java sandbox and BioJava Date: Wed, 21 Jun 2006 13:38:42 -0400 Size: 5274 URL: