From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:03:39 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:03:39 -0400 Subject: [Biojava-dev] [Bug 2306] New: build.xml is in an unusable state Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2306 Summary: build.xml is in an unusable state Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at build.xml of the current biojava1.5-beta2 "complete download" has an incorrect classpath setting. Compiling is not possible. Unified Diff attached... -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:04:08 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:04:08 -0400 Subject: [Biojava-dev] [Bug 2306] build.xml is in an unusable state In-Reply-To: Message-ID: <200706061404.l56E48jC016660@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2306 ------- Comment #1 from brunner at imp.ac.at 2007-06-06 10:04 EST ------- Created an attachment (id=664) --> (http://bugzilla.open-bio.org/attachment.cgi?id=664&action=view) Unified diff -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:06:25 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:06:25 -0400 Subject: [Biojava-dev] [Bug 2307] New: biojava "complete download" redundant Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2307 Summary: biojava "complete download" redundant Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at The biojava 1.5-beta2 "complete download" contains a package of itself. This leads to longer download times. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:11:42 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:11:42 -0400 Subject: [Biojava-dev] [Bug 2308] New: More exact values for amino acid masses Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2308 Summary: More exact values for amino acid masses Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: symbol AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at With state-of-the-art high-resolution mass spectrometers, the current amino acid masses contain not enough digits. What about using the values from http://www.ionsource.com/Card/aatable/aatable_print.htm If nobody else wants to do this, I will attach an updated XML file for these symbols. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:18:05 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:18:05 -0400 Subject: [Biojava-dev] [Bug 2309] New: Digest.addDigestFeatures() does not work Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2309 Summary: Digest.addDigestFeatures() does not work Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: major Priority: P2 Component: bio AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at org.biojava.bio.proteomics.Digest not functional: Digesting protein sequences yields only one fragment (Feature). The problem seems to be in the Feature.compare() function. Individual peptides are not distinguished by the compare() function, leaving only one fragment in the features TreeMap. I will provide a patch in the next the if I can make it work. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:22:00 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:22:00 -0400 Subject: [Biojava-dev] [Bug 2307] biojava "complete download" redundant In-Reply-To: Message-ID: <200706061422.l56EM0kM017790@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2307 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |mark.schreiber at novartis.com ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:21 EST ------- Again for you Mark I think? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:22:05 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:22:05 -0400 Subject: [Biojava-dev] [Bug 2306] build.xml is in an unusable state In-Reply-To: Message-ID: <200706061422.l56EM5ml017827@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2306 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |mark.schreiber at novartis.com ------- Comment #2 from holland at ebi.ac.uk 2007-06-06 10:22 EST ------- Mark can you fix this? I assume you made the change? Looks like a relative path problem - it shouldn't need the lib/ prefixes in the classpath line. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:23:01 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:23:01 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706061423.l56EN1Z5017908@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:23 EST ------- If you could attach an updated XML file to this bug report then I will make the changes on your behalf. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 10:24:20 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:24:20 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061424.l56EOKYU018003@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:24 EST ------- Great stuff - looking forward to seeing the patch. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 11:28:34 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 11:28:34 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061528.l56FSYkL021929@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 ------- Comment #2 from brunner at imp.ac.at 2007-06-06 11:28 EST ------- Created an attachment (id=665) --> (http://bugzilla.open-bio.org/attachment.cgi?id=665&action=view) Proposed fix As I am quite new to biojava (only have downloaded it this week) I do not know whether the fix fits into the concept. But IMO features can also differ in respect to their location to qualify them as a distinct entity. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 12:05:40 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 12:05:40 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061605.l56G5eLu024438@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #3 from holland at ebi.ac.uk 2007-06-06 12:05 EST ------- OK, I found the problem - SimpleRichFeature by default sets a rank of 0. By setting it to have unique ranks instead, the location check suggested becomes unnecessary (it is feasible for two otherwise identical features to have different locations, when really only one of them should be present). Now all features are unique by default by virtue of having different ranks, Digest will produce correct results. Fixed in CVS (head). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From felipe.albrecht at gmail.com Thu Jun 7 00:01:13 2007 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Thu, 7 Jun 2007 01:01:13 -0300 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? Message-ID: Hello, im trying to convert a protein multiple alignment in fasta format to phylip format. The source is: BufferedReader br = new BufferedReader(new FileReader(args[0])); PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); RichSequenceIterator richSequenceIterator = IOTools.readFastaProtein(br, null); List l = new LinkedList(); Sequence seq = null; while (richSequenceIterator.hasNext()) { l.add(richSequenceIterator.nextSequence()); } builder.startFile(); builder.setSequenceCount(l.size()); builder.setSitesCount(seq.seqString().length()); for (Sequence sequence : l) { builder.setCurrentSequenceName(sequence.getName()); builder.receiveSequence(sequence.seqString()); } builder.endFile(); As I said, my input data is a protein multiple alignment. Running this source, this trace is showed: Exception in thread "main" org.biojava.bio.BioError: Something has gone badly wrong with DNA at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) at FastaParser.main(FastaParser.java:54) Caused by: org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: 'Q' at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) ... 5 more IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method createSequence , where is done: try { DNATools.createGappedDNASequence(sequence, name); } catch (IllegalSymbolException e) { isDNA = false; } Where is execpeted that DNATools.CreateGappedDNASequence throws a IllegalSymbolException , but seeking this method, in the file DNAToos.java line 198: } catch (BioException se) { throw new BioError("Something has gone badly wrong with DNA", se); } Being the IllegalSymbolException subclass of the BioError, they is "catched" and a new exception is created and in NATools.createSequences they arent catched. I solved this problem adding: } catch (IllegalSymbolException ie) { throw ie; } in createDNASequence, but it's a workaround for the exception be catched. A better solution, is check the type of the sequence. Exist a method for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses it, also the exceptions must be used when occurs an exception and dont for flow control. PS: Im using the biojava source code downloaded today from http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz Thanks and Im waiting opinions. Felipe Albrecht From felipe.albrecht at gmail.com Thu Jun 7 00:02:55 2007 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Thu, 7 Jun 2007 01:02:55 -0300 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? In-Reply-To: References: Message-ID: Sorry, from my example file, substitute the line builder.setSitesCount(seq.seqString().length()); to builder.setSitesCount(l.get(l.size()-1).seqString().length()); Thanks Felipe Albrecht On 6/7/07, Felipe Albrecht wrote: > Hello, im trying to convert a protein multiple alignment in fasta > format to phylip format. > > The source is: > > BufferedReader br = new BufferedReader(new FileReader(args[0])); > PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); > RichSequenceIterator richSequenceIterator = > IOTools.readFastaProtein(br, null); > List l = new LinkedList(); > Sequence seq = null; > while (richSequenceIterator.hasNext()) { > l.add(richSequenceIterator.nextSequence()); > } > builder.startFile(); > builder.setSequenceCount(l.size()); > builder.setSitesCount(seq.seqString().length()); > for (Sequence sequence : l) { > builder.setCurrentSequenceName(sequence.getName()); > builder.receiveSequence(sequence.seqString()); > } > builder.endFile(); > > As I said, my input data is a protein multiple alignment. > > Running this source, this trace is showed: > > Exception in thread "main" org.biojava.bio.BioError: Something has > gone badly wrong with DNA > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) > at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) > at FastaParser.main(FastaParser.java:54) > Caused by: org.biojava.bio.symbol.IllegalSymbolException: This > tokenization doesn't contain character: 'Q' > at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) > at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) > at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) > at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) > ... 5 more > > IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method > createSequence , where is done: > try { > DNATools.createGappedDNASequence(sequence, name); > } catch (IllegalSymbolException e) { > isDNA = false; > } > > Where is execpeted that DNATools.CreateGappedDNASequence throws a > IllegalSymbolException , but seeking this method, in the file > DNAToos.java line 198: > } catch (BioException se) { > throw new BioError("Something has gone badly wrong with DNA", se); > } > Being the IllegalSymbolException subclass of the BioError, they is > "catched" and a new exception is created and in > NATools.createSequences they arent catched. > > > I solved this problem adding: > } catch (IllegalSymbolException ie) { > throw ie; > } > > in createDNASequence, but it's a workaround for the exception be catched. > > A better solution, is check the type of the sequence. Exist a method > for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses > it, also the exceptions must be used when occurs an exception and dont > for flow control. > > PS: Im using the biojava source code downloaded today from > http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz > > Thanks and Im waiting opinions. > > Felipe Albrecht > From bugzilla-daemon at portal.open-bio.org Thu Jun 7 00:07:47 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 00:07:47 -0400 Subject: [Biojava-dev] [Bug 2311] New: Bug in PHYLIPFileBuilder with protein sequences Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2311 Summary: Bug in PHYLIPFileBuilder with protein sequences Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: minor Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: felipe.albrecht at gmail.com Hello, im trying to convert a protein multiple alignment in fasta format to phylip format. The source is: BufferedReader br = new BufferedReader(new FileReader(args[0])); PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); RichSequenceIterator richSequenceIterator = IOTools.readFastaProtein(br, null); List l = new LinkedList(); Sequence seq = null; while (richSequenceIterator.hasNext()) { l.add(richSequenceIterator.nextSequence()); } builder.startFile(); builder.setSequenceCount(l.size()); builder.setSitesCount(seq.seqString().length()); for (Sequence sequence : l) { builder.setCurrentSequenceName(sequence.getName()); builder.receiveSequence(sequence.seqString()); } builder.endFile(); As I said, my input data is a protein multiple alignment. Running this source, this trace is showed: Exception in thread "main" org.biojava.bio.BioError: Something has gone badly wrong with DNA at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) at FastaParser.main(FastaParser.java:54) Caused by: org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: 'Q' at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) ... 5 more IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method createSequence , where is done: try { DNATools.createGappedDNASequence(sequence, name); } catch (IllegalSymbolException e) { isDNA = false; } Where is execpeted that DNATools.CreateGappedDNASequence throws a IllegalSymbolException , but seeking this method, in the file DNAToos.java line 198: } catch (BioException se) { throw new BioError("Something has gone badly wrong with DNA", se); } Being the IllegalSymbolException subclass of the BioError, they is "catched" and a new exception is created and in NATools.createSequences they arent catched. I solved this problem adding: } catch (IllegalSymbolException ie) { throw ie; } in createDNASequence, but it's a workaround for the exception be catched. A better solution, is check the type of the sequence. Exist a method for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses it, also the exceptions must be used when occurs an exception and dont for flow control. PS: Im using the biojava source code downloaded today from http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 7 00:08:37 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 00:08:37 -0400 Subject: [Biojava-dev] [Bug 2311] Bug in PHYLIPFileBuilder with protein sequences In-Reply-To: Message-ID: <200706070408.l5748b2u027260@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2311 ------- Comment #1 from felipe.albrecht at gmail.com 2007-06-07 00:08 EST ------- Created an attachment (id=666) --> (http://bugzilla.open-bio.org/attachment.cgi?id=666&action=view) Source that reproduce the error -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 7 03:51:35 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 03:51:35 -0400 Subject: [Biojava-dev] [Bug 2311] Bug in PHYLIPFileBuilder with protein sequences In-Reply-To: Message-ID: <200706070751.l577pZZO004077@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2311 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from holland at ebi.ac.uk 2007-06-07 03:51 EST ------- This was a silly bug in DNATools - the createDNASequence() method said it threw IllegalSymybolException, but in fact it was catching all occurrences of this and converting them to BioException which is uncatchable. The fix for this was to stop the unnecessary conversion and therefore make the code behave exactly as its signature and JavaDocs say it will. Fixed in CVS (head). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From holland at ebi.ac.uk Thu Jun 7 04:22:15 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 07 Jun 2007 09:22:15 +0100 Subject: [Biojava-dev] http://bugzilla.open-bio.org/show_bug.cgi?id=2311 In-Reply-To: References: Message-ID: <4667C037.7070703@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The PHYLIPFileFormat code already does that. The problem was that the exception it catches to determine non-DNA-ness was not happening because DNATools was not throwing it. There is no easy way to determine a sequence file's type short of reading the whole file in and scanning through it in advance to spot symbol combinations that are unique to a particular alphabet, then repeating the read of the file to do the actual parsing. As BioJava uses mostly stream-based parsers which don't expect to be able to repeatedly read the same data, they have to rely on other methods. They make good guesses wherever they can but obviously they don't always get that guess right. Wherever the API allows it is always a good idea to specify the type of sequence in advance. PHYLIPFileFormat is not an API that allows this though, although there's nothing saying it couldn't be modified to do so by some willing volunteer! :) cheers, Richard Felipe Albrecht wrote: > Hello, > > about http://bugzilla.open-bio.org/show_bug.cgi?id=2311 > > isnt better check the sequence before create the DNA/RNA/Protein sequence? > That is: dont wait for an exception, but view what is the type. > > Felipe Albrecht -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGZ8A24C5LeMEKA/QRAginAJ40bL5YJl4pUgmRb1yBf9jDXz72bQCbBssO k24Us468mhs8wCx/f/gnU68= =4xYe -----END PGP SIGNATURE----- From markjschreiber at gmail.com Thu Jun 7 06:46:47 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 7 Jun 2007 18:46:47 +0800 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? In-Reply-To: References: Message-ID: <93b45ca50706070346o5a52c1d8t68cb95217e835f37@mail.gmail.com> Hi - BioJava's phylogenetics support is very experimental right now. However, this would be something that our Google SOC student might want to take a look at. - Mark On 6/7/07, Felipe Albrecht wrote: > Sorry, > from my example file, substitute the line > builder.setSitesCount(seq.seqString().length()); > to > builder.setSitesCount(l.get(l.size()-1).seqString().length()); > > Thanks > > Felipe Albrecht > > > On 6/7/07, Felipe Albrecht wrote: > > Hello, im trying to convert a protein multiple alignment in fasta > > format to phylip format. > > > > The source is: > > > > BufferedReader br = new BufferedReader(new FileReader(args[0])); > > PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); > > RichSequenceIterator richSequenceIterator = > > IOTools.readFastaProtein(br, null); > > List l = new LinkedList(); > > Sequence seq = null; > > while (richSequenceIterator.hasNext()) { > > l.add(richSequenceIterator.nextSequence()); > > } > > builder.startFile(); > > builder.setSequenceCount(l.size()); > > builder.setSitesCount(seq.seqString().length()); > > for (Sequence sequence : l) { > > builder.setCurrentSequenceName(sequence.getName()); > > builder.receiveSequence(sequence.seqString()); > > } > > builder.endFile(); > > > > As I said, my input data is a protein multiple alignment. > > > > Running this source, this trace is showed: > > > > Exception in thread "main" org.biojava.bio.BioError: Something has > > gone badly wrong with DNA > > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) > > at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) > > at FastaParser.main(FastaParser.java:54) > > Caused by: org.biojava.bio.symbol.IllegalSymbolException: This > > tokenization doesn't contain character: 'Q' > > at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) > > at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) > > at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) > > at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) > > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) > > ... 5 more > > > > IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method > > createSequence , where is done: > > try { > > DNATools.createGappedDNASequence(sequence, name); > > } catch (IllegalSymbolException e) { > > isDNA = false; > > } > > > > Where is execpeted that DNATools.CreateGappedDNASequence throws a > > IllegalSymbolException , but seeking this method, in the file > > DNAToos.java line 198: > > } catch (BioException se) { > > throw new BioError("Something has gone badly wrong with DNA", se); > > } > > Being the IllegalSymbolException subclass of the BioError, they is > > "catched" and a new exception is created and in > > NATools.createSequences they arent catched. > > > > > > I solved this problem adding: > > } catch (IllegalSymbolException ie) { > > throw ie; > > } > > > > in createDNASequence, but it's a workaround for the exception be catched. > > > > A better solution, is check the type of the sequence. Exist a method > > for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses > > it, also the exceptions must be used when occurs an exception and dont > > for flow control. > > > > PS: Im using the biojava source code downloaded today from > > http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz > > > > Thanks and Im waiting opinions. > > > > Felipe Albrecht > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > 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-dev] 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 bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:00:02 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:00:02 -0400 Subject: [Biojava-dev] [Bug 2315] New: UniProtFormat fail on long protein sequence. Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2315 Summary: UniProtFormat fail on long protein sequence. Product: BioJava Version: live (CVS source) Platform: PC OS/Version: All Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: miyabe at port4.info It seems some errors in the renewal of the symbol buffer of org.biojava.bio.seq.io.ChunkedSymbolListFactory. Here is a stacktrace. -- Exception in thread "main" org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at jp.co.maze.intact.RestructMain.exec(RestructMain.java:90) at jp.co.maze.intact.RestructMain.main(RestructMain.java:42) Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.UniProtFormat Accession=Q8WXI7 Id= Comments= Parse_block=SQ MLKPSGLPGS SSPTRSLMTG SRSTKATPEM DSGLTGATLS PKTSTGAIVV TEHTLPFTSP DKTLASPTSS VVGRTTQSLG VMSSALPEST SRGMTHSEQR TSPSLSPQVN GTPSRNYPAT SMVSGLSSPR TRTSSTEGNF TKEASTYTLT VETTSGPVTE KYTVPTETST TEGDSTETPW DTRYIPVKIT SPMKTFADST ASKENAPVSM TPAETTVTDS HTPGRTNPSF GTLYSSFLDL SPKGTPNSRG ETSLELILST TGYPFSSPEP GSAGHSRIST SAPLSSSASV LDNKISETSI FSGQSLTSPL SPGVPEARAS TMPNSAIPFS MTLSNAETSA ERVRSTISSL GTPSISTKQT AETILTFHAF AETMDIPSTH IAKTLASEWL GSPGTLGGTS TSALTTTSPS TTLVSEETNT HHSTSGKETE GTLNTSMTPL ETSAPGEESE MTATLVPTLG FTTLDSKIRS PSQVSSSHPT RELRTTGSTS GRQSSSTAAH GSSDILRATT SSTSKASSWT SESTAQQFSE PQHTQWVETS PSMKTERPPA STSVAAPITT SVPSVVSGFT TLKTSSTKGI WLEETSADTL IGESTAGPTT HQFAVPTGIS MTGGSSTRGS QGTTHLLTRA TASSETSADL TLATNGVPVS VSPAVSKTAA GSSPPGGTKP SYTMVSSVIP ETSSLQSSAF REGTSLGLTP LNTRHPFSSP EPDSAGHTKI STSIPLLSSA SVLEDKVSAT STFSHHKATS SITTGTPEIS TKTKPSSAVL SSMTLSNAAT SPERVRNATS PLTHPSPSGE ETAGSVLTLS TSAETTDSPN IHPTGTLTSE SSESPSTLSL PSVSGVKTTF SSSTPSTHLF TSGEETEETS NPSVSQPETS VSRVRTTLAS TSVPTPVFPT MDTWPTRSAQ FSSSHLVSEL RATSSTSVTN STGSALPKIS HLTGTATMSQ TNRDTFNDSA APQSTTWPET SPRFKTGLPS ATTTVSTSAT SLSATVMVSK FTSPATSSME ATSIREPSTT ILTTETTNGP GSMAVASTNI PIGKGYITEG RLDTSHLPIG TTASSETSMD FTMAKESVSM SVSPSQSMDA AGSSTPGRTS QFVDTFSDDV YHLTSREITI PRDGTSSALT PQMTATHPPS PDPGSARSTW LGILSSSPSS PTPKVTMSST FSTQRVTTSM IMDTVETSRW NMPNLPSTTS LTPSNIPTSG AIGKSTLVPL DTPSPATSLE ASEGGLPTLS TYPESTNTPS IHLGAHASSE SPSTIKLTMA SVVKPGSYTP LTFPSIETHI HVSTARMAYS SGSSPEMTAP GETNTGSTWD PTTYITTTDP KDTSSAQVST PHSVRTLRTT ENHPKTESAT PAAYSGSPKI SSSPNLTSPA TKAWTITDTT EHSTQLHYTK LAEKSSGFET QSAPGPVSVV IPTSPTIGSS TLELTSDVPG EPLVLAPSEQ TTITLPMATW LSTSLTEEMA STDLDISSPS SPMSTFAIFP PMSTPSHELS KSEADTSAIR NTDSTTLDQH LGIRSLGRTG DLTTVPITPL TTTWTSVIEH STQAQDTLSA TMSPTHVTQS LKDQTSIPAS ASPSHLTEVY PELGTQGRSS SEATTFWKPS TDTLSREIET GPTNIQSTPP MDNTTTGSSS SGVTLGIAHL PIGTSSPAET STNMALERRS STATVSMAGT MGLLVTSAPG RSISQSLGRV SSVLSESTTE GVTDSSKGSS PRLNTQGNTA LSSSLEPSYA EGSQMSTSIP LTSSPTTPDV EFIGGSTFWT KEVTTVMTSD ISKSSARTES SSATLMSTAL GSTENTGKEK LRTASMDLPS PTPSMEVTPW ISLTLSNAPN TTDSLDLSHG VHTSSAGTLA TDRSLNTGVT RASRLENGSD TSSKSLSMGN STHTSMTDTE KSEVSSSIHP RPETSAPGAE TTLTSTPGNR AISLTLPFSS IPVEEVISTG ITSGPDINSA PMTHSPITPP TIVWTSTGTI EQSTQPLHAV SSEKVSVQTQ STPYVNSVAV SASPTHENSV SSGSSTSSPY SSASLESLDS TISRRNAITS WLWDLTTSLP TTTWPSTSLS EALSSGHSGV SNPSSTTTEF PLFSAASTSA AKQRNPETET HGPQNTAAST LNTDASSVTG LSETPVGASI SSEVPLPMAI TSRSDVSGLT SESTANPSLG TASSAGTKLT RTISLPTSES LVSFRMNKDP WTVSIPLGSH PTTNTETSIP VNSAGPPGLS TVASDVIDTP SDGAESIPTV SFSPSPDTEV TTISHFPEKT THSFRTISSL THELTSRVTP IPGDWMSSAM STKPTGASPS ITLGERRTIT SAAPTTSPIV LTASFTETST VSLDNETTVK TSDILDARKT NELPSDSSSS SDLINTSIAS STMDVTKTAS ISPTSISGMT ASSSPSLFSS DRPQVPTSTT ETNTATSPSV SSNTYSLDGG SNVGGTPSTL PPFTITHPVE TSSALLAWSR PVRTFSTMVS TDTASGENPT SSNSVVTSVP APGTWASVGS TTDLPAMGFL KTSPAGEAHS LLASTIEPAT AFTPHLSAAV VTGSSATSEA SLLTTSESKA IHSSPQTPTT PTSGANWETS ATPESLLVVT ETSDTTLTSK ILVTDTILFS TVSTPPSKFP STGTLSGASF PTLLPDTPAI PLTATEPTSS LATSFDSTPL VTIASDSLGT VPETTLTMSE TSNGDALVLK TVSNPDRSIP GITIQGVTES PLHPSSTSPS KIVAPRNTTY EGSITVALST LPAGTTGSLV FSQSSENSET TALVDSSAGL ERASVMPLTT GSQGMASSGG IRSGSTHSTG TKTFSSLPLT MNPGEVTAMS EITTNRLTAT QSTAPKGIPV KPTSAESGLL TPVSASSSPS KAFASLTTAP PSTWGIPQST LTFEFSEVPS LDTKSASLPT PGQSLNTIPD SDASTASSSL SKSPEKNPRA RMMTSTKAIS ASSFQSTGFT ETPEGSASPS MAGHEPRVPT SGTGDPRYAS ESMSYPDPSK ASSAMTSTSL ASKLTTLFST GQAARSGSSS SPISLSTEKE TSFLSPTAST SRKTSLFLGP SMARQPNILV HLQTSALTLS PTSTLNMSQE EPPELTSSQT IAEEEGTTAE TQTLTFTPSE TPTSLLPVSS PTEPTARRKS SPETWASSIS VPAKTSLVET TDGTLVTTIK MSSQAAQGNS TWPAPAEETG TSPAGTSPGS PEVSTTLKIM SSKEPSISPE IRSTVRNSPW KTPETTVPME TTVEPVTLQS TALGSGSTSI SHLPTGTTSP TKSPTENMLA TERVSLSPSP PEAWTNLYSG TPGGTRQSLA TMSSVSLESP TARSITGTGQ QSSPELVSKT TGMEFSMWHG STGGTTGDTH VSLSTSSNIL EDPVTSPNSV SSLTDKSKHK TETWVSTTAI PSTVLNNKIM AAEQQTSRSV DEAYSSTSSW SDQTSGSDIT LGASPDVTNT LYITSTAQTT SLVSLPSGDQ GITSLTNPSG GKTSSASSVT SPSIGLETLR ANVSAVKSDI APTAGHLSQT SSPAEVSILD VTTAPTPGIS TTITTMGTNS ISTTTPNPEV GMSTMDSTPA TERRTTSTEH PSTWSSTAAS DSWTVTDMTS NLKVARSPGT ISTMHTTSFL ASSTELDSMS TPHGRITVIG TSLVTPSSDA SAVKTETSTS ERTLSPSDTT ASTPISTFSR VQRMSISVPD ILSTSWTPSS TEAEDVPVSM VSTDHASTKT DPNTPLSTFL FDSLSTLDWD TGRSLSSATA TTSAPQGATT PQELTLETMI SPATSQLPFS IGHITSAVTP AAMARSSGVT FSRPDPTSKK AEQTSTQLPT TTSAHPGQVP RSAATTLDVI PHTAKTPDAT FQRQGQTALT TEARATSDSW NEKEKSTPSA PWITEMMNSV SEDTIKEVTS SSSVLKDPEY AGHKLGIWDD FIPKFGKAAH MRELPLLSPP QDKEAIHPST NTVETTGWVT SSEHASHSTI PAHSASSKLT SPVVTTSTRE QAIVSMSTTT WPESTRARTE PNSFLTIELR DVSPYMDTSS TTQTSIISSP GSTAITKGPR TEITSSKRIS SSFLAQSMRS SDSPSEAITR LSNFPAMTES GGMILAMQTS PPGATSLSAP TLDTSATASW TGTPLATTQR FTYSEKTTLF SKGPEDTSQP SPPSVEETSS SSSLVPIHAT TSPSNILLTS QGHSPSSTPP VTSVFLSETS GLGKTTDMSR ISLEPGTSLP PNLSSTAGEA LSTYEASRDT KAIHHSADTA VTNMEATSSE YSPIPGHTKP SKATSPLVTS HIMGDITSST SVFGSSETTE IETVSSVNQG LQERSTSQVA SSATETSTVI THVSSGDATT HVTKTQATFS SGTSISSPHQ FITSTNTFTD VSTNPSTSLI MTESSGVTIT TQTGPTGAAT QGPYLLDTST MPYLTETPLA VTPDFMQSEK TTLISKGPKD VTWTSPPSVA ETSYPSSLTP FLVTTIPPAT STLQGQHTSS PVSATSVLTS GLVKTTDMLN TSMEPVTNSP QNLNNPSNEI LATLAATTDI ETIHPSINKA VTNMGTASSA HVLHSTLPVS SEPSTATSPM VPASSMGDAL ASISIPGSET TDIEGEPTSS LTAGRKENST LQEMNSTTES NIILSNVSVG AITEATKMEV PSFDATFIPT PAQSTKFPDI FSVASSRLSN SPPMTISTHM TTTQTGSSGA TSKIPLALDT STLETSAGTP SVVTEGFAHS KITTAMNNDV KDVSQTNPPF QDEASSPSSQ APVLVTTLPS SVAFTPQWHS TSSPVSMSSV LTSSLVKTAG KVDTSLETVT SSPQSMSNTL DDISVTSAAT TDIETTHPSI NTVVTNVGTT GSAFESHSTV SAYPEPSKVT SPNVTTSTME DTTISRSIPK SSKTTRTETE TTSSLTPKLR ETSISQEITS STETSTVPYK ELTGATTEVS RTDVTSSSST SFPGPDQSTV SLDISTETNT RLSTSPIMTE SAEITITTQT GPHGATSQDT FTMDPSNTTP QAGIHSAMTH GFSQLDVTTL MSRIPQDVSW TSPPSVDKTS SPSSFLSSPA MTTPSLISST LPEDKLSSPM TSLLTSGLVK ITDILRTRLE PVTSSLPNFS STSDKILATS KDSKDTKEIF PSINTEETNV KANNSGHESH SPALADSETP KATTQMVITT TVGDPAPSTS MPVHGSSETT NIKREPTYFL TPRLRETSTS QESSFPTDTS FLLSKVPTGT ITEVSSTGVN SSSKISTPDH DKSTVPPDTF TGEIPRVFTS SIKTKSAEMT ITTQASPPES ASHSTLPLDT STTLSQGGTH STVTQGFPYS EVTTLMGMGP GNVSWMTTPP VEETSSVSSL MSSPAMTSPS PVSSTSPQSI PSSPLPVTAL PTSVLVTTTD VLGTTSPESV TSSPPNLSSI THERPATYKD TAHTEAAMHH STNTAVTNVG TSGSGHKSQS SVLADSETSK ATPLMSTTST LGDTSVSTST PNISQTNQIQ TEPTASLSPR LRESSTSEKT SSTTETNTAF SYVPTGAITQ ASRTEISSSR TSISDLDRPT IAPDISTGMI TRLFTSPIMT KSAEMTVTTQ TTTPGATSQG ILPWDTSTTL FQGGTHSTVS QGFPHSEITT LRSRTPGDVS WMTTPPVEET SSGFSLMSPS MTSPSPVSST SPESIPSSPL PVTALLTSVL VTTTNVLGTT SPETVTSSPP NLSSPTQERL TTYKDTAHTE AMHASMHTNT AVANVGTSIS GHESQSSVPA DSHTSKATSP MGITFAMGDT SVSTSTPAFF ETRIQTESTS SLIPGLRDTR TSEEINTVTE TSTVLSEVPT TTTTEVSRTE VITSSRTTIS GPDHSKMSPY ISTETITRLS TFPFVTGSTE MAITNQTGPI GTISQATLTL DTSSTASWEG THSPVTQRFP HSEETTTMSR STKGVSWQSP PSVEETSSPS SPVPLPAITS HSSLYSAVSG SSPTSALPVT SLLTSGRRKT IDMLDTHSEL VTSSLPSASS FSGEILTSEA STNTETIHFS ENTAETNMGT TNSMHKLHSS VSIHSQPSGH TPPKVTGSMM EDAIVSTSTP GSPETKNVDR DSTSPLTPEL KEDSTALVMN STTESNTVFS SVSLDAATEV SRAEVTYYDP TFMPASAQST KSPDISPEAS SSHSNSPPLT ISTHKTIATQ TGPSGVTSLG QLTLDTSTIA TSAGTPSART QDFVDSETTS VMNNDLNDVL KTSPFSAEEA NSLSSQAPLL VTTSPSPVTS TLQEHSTSSL VSVTSVPTPT LAKITDMDTN LEPVTRSPQN LRNTLATSEA TTDTHTMHPS INTAMANVGT TSSPNEFYFT VSPDSDPYKA TSAVVITSTS GDSIVSTSMP RSSAMKKIES ETTFSLIFRL RETSTSQKIG SSSDTSTVFD KAFTAATTEV SRTELTSSSR TSIQGTEKPT MSPDTSTRSV TMLSTFAGLT KSEERTIATQ TGPHRATSQG TLTWDTSITT SQAGTHSAMT HGFSQLDLST LTSRVPEYIS GTSPPSVEKT SSSSSLLSLP AITSPSPVPT TLPESRPSSP VHLTSLPTSG LVKTTDMLAS VASLPPNLGS TSHKIPTTSE DIKDTEKMYP STNIAVTNVG TTTSEKESYS SVPAYSEPPK VTSPMVTSFN IRDTIVSTSM PGSSEITRIE MESTFSVAHG LKGTSTSQDP IVSTEKSAVL HKLTTGATET SRTEVASSRR TSIPGPDHST ESPDISTEVI PSLPISLGIT ESSNMTIITR TGPPLGSTSQ GTFTLDTPTT SSRAGTHSMA TQEFPHSEMT TVMNKDPEIL SWTIPPSIEK TSFSSSLMPS PAMTSPPVSS TLPKTIHTTP SPMTSLLTPS LVMTTDTLGT SPEPTTSSPP NLSSTSHVIL TTDEDTTAIE AMHPSTSTAA TNVETTCSGH GSQSSVLTDS EKTKATAPMD TTSTMGHTTV STSMSVSSET TKIKRESTYS LTPGLRETSI SQNASFSTDT SIVLSEVPTG TTAEVSRTEV TSSGRTSIPG PSQSTVLPEI STRTMTRLFA SPTMTESAEM TIPTQTGPSG STSQDTLTLD TSTTKSQAKT HSTLTQRFPH SEMTTLMSRG PGDMSWQSSP SLENPSSLPS LLSLPATTSP PPISSTLPVT ISSSPLPVTS LLTSSPVTTT DMLHTSPELV TSSPPKLSHT SDERLTTGKD TTNTEAVHPS TNTAASNVEI PSFGHESPSS ALADSETSKA TSPMFITSTQ EDTTVAISTP HFLETSRIQK ESISSLSPKL RETGSSVETS SAIETSAVLS EVSIGATTEI SRTEVTSSSR TSISGSAEST MLPEISTTRK IIKFPTSPIL AESSEMTIKT QTSPPGSTSE STFTLDTSTT PSLVITHSTM TQRLPHSEIT TLVSRGAGDV PRPSSLPVEE TSPPSSQLSL SAMISPSPVS STLPASSHSS SASVTSPLTP GQVKTTEVLD ASAEPETSSP PSLSSTSVEI LATSEVTTDT EKIHPFPNTA VTKVGTSSSG HESPSSVLPD SETTKATSAM GTISIMGDTS VSTLTPALSN TRKIQSEPAS SLTTRLRETS TSEETSLATE ANTVLSKVST GATTEVSRTE AISFSRTSMS GPEQSTMSQD ISIGTIPRIS ASSVLTESAK MTITTQTGPS ESTLESTLNL NTATTPSWVE THSIVIQGFP HPEMTTSMGR GPGGVSWPSP PFVKETSPPS SPLSLPAVTS PHPVSTTFLA HIPPSPLPVT SLLTSGPATT TDILGTSTEP GTSSSSSLST TSHERLTTYK DTAHTEAVHP STNTGGTNVA TTSSGYKSQS SVLADSSPMC TTSTMGDTSV LTSTPAFLET RRIQTELASS LTPGLRESSG SEGTSSGTKM STVLSKVPTG ATTEISKEDV TSIPGPAQST ISPDISTRTV SWFSTSPVMT ESAEITMNTH TSPLGATTQG TSTLATSSTT SLTMTHSTIS QGFSHSQMST LMRRGPEDVS WMSPPLLEKT RPSFSLMSSP ATTSPSPVSS TLPESISSSP LPVTSLLTSG LAKTTDMLHK SSEPVTNSPA NLSSTSVEIL ATSEVTTDTE KTHPSSNRTV TDVGTSSSGH ESTSFVLADS QTSKVTSPMV ITSTMEDTSV STSTPGFFET SRIQTEPTSS LTLGLRKTSS SEGTSLATEM STVLSGVPTG ATAEVSRTEV TSSSRTSISG FAQLTVSPET STETITRLPT SSIMTESAEM MIKTQTDPPG STPESTHTVD ISTTPNWVET HSTVTQRFSH SEMTTLVSRS PGDMLWPSQS SVEETSSASS LLSLPATTSP SPVSSTLVED FPSASLPVTS LLTPGLVITT DRMGISREPG TSSTSNLSST SHERLTTLED TVDTEDMQPS THTAVTNVRT SISGHESQSS VLSDSETPKA TSPMGTTYTM GETSVSISTS DFFETSRIQI EPTSSLTSGL RETSSSERIS SATEGSTVLS EVPSGATTEV SRTEVISSRG TSMSGPDQFT ISPDISTEAI TRLSTSPIMT ESAESAITIE TGSPGATSEG TLTLDTSTTT FWSGTHSTAS PGFSHSEMTT LMSRTPGDVP WPSLPSVEEA SSVSSSLSSP AMTSTSFFSA LPESISSSPH PVTALLTLGP VKTTDMLRTS SEPETSSPPN LSSTSAEILA TSEVTKDREK IHPSSNTPVV NVGTVIYKHL SPSSVLADLV TTKPTSPMAT TSTLGNTSVS TSTPAFPETM MTQPTSSLTS GLREISTSQE TSSATERSAS LSGMPTGATT KVSRTEALSL GRTSTPGPAQ STISPEISTE TITRISTPLT TTGSAEMTIT PKTGHSGASS QGTFTLDTSS RASWPGTHSA ATHRSPHSGM TTPMSRGPED VSWPSRPSVE KTSPPSSLVS LSAVTSPSPL YSTPSESSHS SPLRVTSLFT PVMMKTTDML DTSLEPVTTS PPSMNITSDE SLATSKATME TEAIQLSENT AVTQMGTISA RQEFYSSYPG LPEPSKVTSP VVTSSTIKDI VSTTIPASSE ITRIEMESTS TLTPTPRETS TSQEIHSATK PSTVPYKALT SATIEDSMTQ VMSSSRGPSP DQSTMSQDIS SEVITRLSTS PIKAESTEMT ITTQTGSPGA TSRGTLTLDT STTFMSGTHS TASQGFSHSQ MTALMSRTPG DVPWLSHPSV EEASSASFSL SSPVMTSSSP VSSTLPDSIH SSSLPVTSLL TSGLVKTTEL LGTSSEPETS SPPNLSSTSA EILATTEVTT DTEKLEMTNV VTSGYTHESP SSVLADSVTT KATSSMGITY PTGDTNVLTS TPAFSDTSRI QTKSKLSLTP GLMETSISEE TSSATEKSTV LSSVPTGATT EVSRTEAISS SRTSIPGPAQ STMSSDTSME TITRISTPLT RKESTDMAIT PKTGPSGATS QGTFTLDSSS TASWPGTHSA TTQRFPQSVV TTPMSRGPED VSWPSPLSVE KNSPPSSLVS SSSVTSPSPL YSTPSGSSHS SPVPVTSLFT SIMMKATDML DASLEPETTS APNMNITSDE SLATSKATTE TEAIHVFENT AASHVETTSA TEELYSSSPG FSEPTKVISP VVTSSSIRDN MVSTTMPGSS GITRIEIESM SSLTPGLRET RTSQDITSST ETSTVLYKMS SGATPEVSRT EVMPSSRTSI PGPAQSTMSL DISDEVVTRL STSPIMTESA EITITTQTGY SLATSQVTLP LGTSMTFLSG THSTMSQGLS HSEMTNLMSR GPESLSWTSP RFVETTRSSS SLTSLPLTTS LSPVSSTLLD SSPSSPLPVT SLILPGLVKT TEVLDTSSEP KTSSSPNLSS TSVEIPATSE IMTDTEKIHP SSNTAVAKVR TSSSVHESHS SVLADSETTI TIPSMGITSA VDDTTVFTSN PAFSETRRIP TEPTFSLTPG FRETSTSEET TSITETSAVL YGVPTSATTE VSMTEIMSSN RTHIPDSDQS TMSPDIITEV ITRLSSSSMM SESTQMTITT QKSSPGATAQ STLTLATTTA PLARTHSTVP PRFLHSEMTT LMSRSPENPS WKSSPFVEKT SSSSSLLSLP VTTSPSVSST LPQSIPSSSF SVTSLLTPGM VKTTDTSTEP GTSLSPNLSG TSVEILAASE VTTDTEKIHP SSSMAVTNVG TTSSGHELYS SVSIHSEPSK ATYPVGTPSS MAETSISTSM PANFETTGFE AEPFSHLTSG FRKTNMSLDT SSVTPTNTPS SPGSTHLLQS SKTDFTSSAK TSSPDWPPAS QYTEIPVDII TPFNASPSIT ESTGITSFPE SRFTMSVTES THHLSTDLLP SAETISTGTV MPSLSEAMTS FATTGVPRAI SGSGSPFSRT ESGPGDATLS TIAESLPSST PVPFSSSTFT TTDSSTIPAL HEITSSSATP YRVDTSLGTE SSTTEGRLVM VSTLDTSSQP GRTSSTPILD TRMTESVELG TVTSAYQVPS LSTRLTRTDG IMEHITKIPN EAAHRGTIRP VKGPQTSTSP ASPKGLHTGG TKRMETTTTA LKTTTTALKT TSRATLTTSV YTPTLGTLTP LNASRQMAST ILTEMMITTP YVFPDVPETT SSLATSLGAE TSTALPRTTP SVLNRESETT ASLVSRSGAE RSPVIQTLDV SSSEPDTTAS WVIHPAETIP TVSKTTPNFF HSELDTVSST ATSHGADVSS AIPTNISPSE LDALTPLVTI SGTDTSTTFP TLTKSPHETE TRTTWLTHPA ETSSTIPRTI PNFSHHESDA TPSIATSPGA ETSSAIPIMT VSPGAEDLVT SQVTSSGTDR NMTIPTLTLS PGEPKTIASL VTHPEAQTSS AIPTSTISPA VSRLVTSMVT SLAAKTSTTN RALTNSPGEP ATTVSLVTHP AQTSPTVPWT TSIFFHSKSD TTPSMTTSHG AESSSAVPTP TVSTEVPGVV TPLVTSSRAV ISTTIPILTL SPGEPETTPS MATSHGEEAS SAIPTPTVSP GVPGVVTSLV TSSRAVTSTT IPILTFSLGE PETTPSMATS HGTEAGSAVP TVLPEVPGMV TSLVASSRAV TSTTLPTLTL SPGEPETTPS MATSHGAEAS STVPTVSPEV PGVVTSLVTS SSGVNSTSIP TLILSPGELE TTPSMATSHG AEASSAVPTP TVSPGVSGVV TPLVTSSRAV TSTTIPILTL SSSEPETTPS MATSHGVEAS SAVLTVSPEV PGMVTSLVTS SRAVTSTTIP TLTISSDEPE TTTSLVTHSE AKMISAIPTL AVSPTVQGLV TSLVTSSGSE TSAFSNLTVA SSQPETIDSW VAHPGTEASS VVPTLTVSTG EPFTNISLVT HPAESSSTLP RTTSRFSHSE LDTMPSTVTS PEAESSSAIS TTISPGIPGV LTSLVTSSGR DISATFPTVP ESPHESEATA SWVTHPAVTS TTVPRTTPNY SHSEPDTTPS IATSPGAEAT SDFPTITVSP DVPDMVTSQV TSSGTDTSIT IPTLTLSSGE PETTTSFITY SETHTSSAIP TLPVSPGASK MLTSLVISSG TDSTTTFPTL TETPYEPETT AIQLIHPAET NTMVPKTTPK FSHSKSDTTL PVAITSPGPE ASSAVSTTTI SPDMSDLVTS LVPSSGTDTS TTFPTLSETP YEPETTVTWL THPAETSTTV SGTIPNFSHR GSDTAPSMVT SPGVDTRSGV PTTTIPPSIP GVVTSQVTSS ATDTSTAIPT LTPSPGEPET TASSATHPGT QTGFTVPIRT VPSSEPDTMA SWVTHPPQTS TPVSRTTSSF SHSSPDATPV MATSPRTEAS SAVLTTISPG APEMVTSQIT SSGAATSTTV PTLTHSPGMP ETTALLSTHP RTGTSKTFPA STVFPQVSET TASLTIRPGA ETSTALPTQT TSSLFTLLVT GTSRVDLSPT ASPGVSAKTA PLSTHPGTET STMIPTSTLS LGLLETTGLL ATSSSAETST STLTLTVSPA VSGLSSASIT TDKPQTVTSW NTETSPSVTS VGPPEFSRTV TGTTMTLIPS EMPTPPKTSH GEGVSPTTIL RTTMVEATNL ATTGSSPTVA KTTTTFNTLA GSLFTPLTTP GMSTLASESV TSRTSYNHRS WISTTSSYNR RYWTPATSTP VTSTFSPGIS TSSIPSSTAA TVPFMVPFTL NFTITNLQYE EDMRHPGSRK FNATERELQG LLKPLFRNSS LEYLYSGCRL ASLRPEKDSS AMAVDAICTH RPDPEDLGLD RERLYWELSN LTNGIQELGP YTLDRNSLYV NGFTHRSSMP TTSTPGTSTV DVGTSGTPSS SPSPTAAGPL LMPFTLNFTI TNLQYEEDMR RTGSRKFNTM ESVLQGLLKP LFKNTSVGPL YSGCRLTLLR PEKDGAATGV DAICTHRLDP KSPGLNREQL YWELSKLTND IEELGPYTLD RNSLYVNGFT HQSSVSTTST PGTSTVDLRT SGTPSSLSSP TIMAAGPLLV PFTLNFTITN LQYGEDMGHP GSRKFNTTER VLQGLLGPIF KNTSVGPLYS GCRLTSLRSE KDGAATGVDA ICIHHLDPKS PGLNRERLYW ELSQLTNGIK ELGPYTLDRN SLYVNGFTHR TSVPTTSTPG TSTVDLGTSG TPFSLPSPAT AGPLLVLFTL NFTITNLKYE EDMHRPGSRK FNTTERVLQT LLGPMFKNTS VGLLYSGCRL TLLRSEKDGA ATGVDAICTH RLDPKSPGLD REQLYWELSQ LTNGIKELGP YTLDRNSLYV NGFTHWIPVP TSSTPGTSTV DLGSGTPSSL PSPTAAGPLL VPFTLNFTIT NLQYEEDMHH PGSRKFNTTE RVLQGLLGPM FKNTSVGLLY SGCRLTLLRS EKDGAATGVD AICTHRLDPK SPGVDREQLY WELSQLTNGI KELGPYTLDR NSLYVNGFTH QTSAPNTSTP GTSTVDLGTS GTPSSLPSPT SAGPLLVPFT LNFTITNLQY EEDMRHPGSR KFNTTERVLQ GLLKPLFKST SVGPLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGV DREQLYWELS QLTNGIKELG PYTLDRNSLY VNGFTHQTSA PNTSTPGTST VDLGTSGTPS SLPSPTSAGP LLVPFTLNFT ITNLQYEEDM HHPGSRKFNT TERVLQGLLG PMFKNTSVGL LYSGCRLTLL RPEKNGAATG MDAICSHRLD PKSPGLNREQ LYWELSQLTH GIKELGPYTL DRNSLYVNGF THRSSVAPTS TPGTSTVDLG TSGTPSSLPS PTTAVPLLVP FTLNFTITNL QYGEDMRHPG SRKFNTTERV LQGLLGPLFK NSSVGPLYSG CRLISLRSEK DGAATGVDAI CTHHLNPQSP GLDREQLYWQ LSQMTNGIKE LGPYTLDRNS LYVNGFTHRS SGLTTSTPWT STVDLGTSGT PSPVPSPTTA GPLLVPFTLN FTITNLQYEE DMHRPGSRKF NTTERVLQGL LSPIFKNSSV GPLYSGCRLT SLRPEKDGAA TGMDAVCLYH PNPKRPGLDR EQLYWELSQL THNITELGPY SLDRDSLYVN GFTHQNSVPT TSTPGTSTVY WATTGTPSSF PGHTEPGPLL IPFTFNFTIT NLHYEENMQH PGSRKFNTTE RVLQGLLKPL FKNTSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY WELSQLTHNI TELGPYSLDR DSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT EPGPLLIPFT FNFTITNLHY EENMQHPGSR KFNTTERVLQ GLLKPLFKNT SVGPLYSGCR LTLLRPEKHE AATGVDTICT HRVDPIGPGL DRERLYWELS QLTNSITELG PYTLDRDSLY VNGFNPRSSV PTTSTPGTST VHLATSGTPS SLPGHTAPVP LLIPFTLNFT ITNLHYEENM QHPGSRKFNT TERVLQGLLK PLFKNTSVGP LYSGCRLTLL RPEKHEAATG VDTICTHRVD PIGPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTSAGPLLVP FTLNFTITNL QYEEDMHHPG SRKFNTTERV LQGLLGPMFK NTSVGLLYSG CRLTLLRPEK NGAATGMDAI CSHRLDPKSP GLDREQLYWE LSQLTHGIKE LGPYTLDRNS LYVNGFTHRS SVAPTSTPGT STVDLGTSGT PSSLPSPTTA VPLLVPFTLN FTITNLQYGE DMRHPGSRKF NTTERVLQGL LGPLFKNSSV GPLYSGCRLI SLRSEKDGAA TGVDAICTHH LNPQSPGLDR EQLYWQLSQM TNGIKELGPY TLDRNSLYVN GFTHRSSGLT TSTPWTSTVD LGTSGTPSPV PSPTTAGPLL VPFTLNFTIT NLQYEEDMHR PGSRKFNATE RVLQGLLSPI FKNSSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY WELSQLTHNI TELGPYSLDR DSLYVNGFTH QSSMTTTRTP DTSTMHLATS RTPASLSGPT TASPLLVLFT INCTITNLQY EEDMRRTGSR KFNTMESVLQ GLLKPLFKNT SVGPLYSGCR LTLLRPKKDG AATGVDAICT HRLDPKSPGL NREQLYWELS KLTNDIEELG PYTLDRNSLY VNGFTHQSSV STTSTPGTST VDLRTSGTPS SLSSPTIMXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTERVLQGL LRPLFKNTSV SSLYSGCRLT LLRPEKDGAA TRVDAACTYR PDPKSPGLDR EQLYWELSQL THSITELGPY TLDRVSLYVN GFNPRSSVPT TSTPGTSTVH LATSGTPSSL PGHTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE RVLQGLLKPL FRNSSLEYLY SGCRLASLRP EKDSSAMAVD AICTHRPDPE DLGLDRERLY WELSNLTNGI QELGPYTLDR NSLYVNGFTH RSSGLTTSTP WTSTVDLGTS GTPSPVPSPT TAGPLLVPFT LNFTITNLQY EEDMHRPGSR RFNTTERVLQ GLLTPLFKNT SVGPLYSGCR LTLLRPEKQE AATGVDTICT HRVDPIGPGL DRERLYWELS QLTNSITELG PYTLDRDSLY VNGFNPWSSV PTTSTPGTST VHLATSGTPS SLPGHTAPVP LLIPFTLNFT ITDLHYEENM QHPGSRKFNT TERVLQGLLK PLFKSTSVGP LYSGCRLTLL RPEKHGAATG VDAICTLRLD PTGPGLDRER LYWELSQLTN SVTELGPYTL DRDSLYVNGF THRSSVPTTS IPGTSAVHLE TSGTPASLPG HTAPGPLLVP FTLNFTITNL QYEEDMRHPG SRKFSTTERV LQGLLKPLFK NTSVSSLYSG CRLTLLRPEK DGAATRVDAV CTHRPDPKSP GLDRERLYWK LSQLTHGITE LGPYTLDRHS LYVNGFTHQS SMTTTRTPDT STMHLATSRT PASLSGPTTA SPLLVLFTIN FTITNLRYEE NMHHPGSRKF NTTERVLQGL LRPVFKNTSV GPLYSGCRLT TLRPKKDGAA TKVDAICTYR PDPKSPGLDR EQLYWELSQL THSITELGPY TQDRDSLYVN GFTHRSSVPT TSIPGTSAVH LETSGTPASL PGHTAPGPLL VPFTLNFTIT NLQYEEDMRH PGSRKFNTTE RVLQGLLKPL FKSTSVGPLY SGCRLTLLRP EKRGAATGVD TICTHRLDPL NPGLDREQLY WELSKLTRGI IELGPYLLDR GSLYVNGFTH RTSVPTTSTP GTSTVDLGTS GTPFSLPSPA XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTERVLQ TLLGPMFKNT SVGLLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGV DREQLYWELS QLTNGIKELG PYTLDRNSLY VNGFTHWIPV PTSSTPGTST VDLGSGTPSS LPSPTTAGPL LVPFTLNFTI TNLKYEEDMH CPGSRKFNTT ERVLQSLLGP MFKNTSVGPL YSGCRLTLLR SEKDGAATGV DAICTHRLDP KSPGVDREQL YWELSQLTNG IKELGPYTLD RNSLYVNGFT HQTSAPNTST PGTSTVDLGT SGTPSSLPSP TXXXPLLXPF TXNXTITNLX XXXXMXXPGS RKFNTTEXVL QGLLXPXFKN XSVGXLYSGC RLTXLRXEKX GAATGXDAIC XHXXXPKXPG LXXEXLYWEL SXLTXXIXEL GPYTLDRXSL YVNGFTHWIP VPTSSTPGTS TVDLGSGTPS SLPSPTTAGP LLVPFTLNFT ITNLKYEEDM HCPGSRKFNT TERVLQSLLG PMFKNTSVGP LYSGCRLTSL RSEKDGAATG VDAICTHRVD PKSPGVDREQ LYWELSQLTN GIKELGPYTL DRNSLYVNGF THQTSAPNTS TPGTSTVXXG TSGTPSSXPX XTSAGPLLVP FTLNFTITNL QYEEDMHHPG SRKFNTTERV LQGLLGPMFK NTSVGLLYSG CRLTLLRPEK NGATTGMDAI CTHRLDPKSP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHXX SXPTTSTPGT STVXXGTSGT PSSXPXXTXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTERVLQGL LKPLFRNSSL EYLYSGCRLA SLRPEKDSSA MAVDAICTHR PDPEDLGLDR ERLYWELSNL TNGIQELGPY TLDRNSLYVN GFTHRSSMPT TSTPGTSTVD VGTSGTPSSS PSPTTAGPLL IPFTLNFTIT NLQYGEDMGH PGSRKFNTTE RVLQGLLGPI FKNTSVGPLY SGCRLTSLRS EKDGAATGVD AICIHHLDPK SPGLNRERLY WELSQLTNGI KELGPYTLDR NSLYVNGFTH RTSVPTTSTP GTSTVDLGTS GTPFSLPSPA TAGPLLVLFT LNFTITNLKY EEDMHRPGSR KFNTTERVLQ TLLGPMFKNT SVGLLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHXXSX PTTSTPGTST VXXGTSGTPS SXPXXTXXXP LLXPFTXNXT ITNLXXXXXM XXPGSRKFNT TERVLQGLLR PVFKNTSVGP LYSGCRLTLL RPKKDGAATK VDAICTYRPD PKSPGLDREQ LYWELSQLTH SITELGPYTQ DRDSLYVNGF THRSSVPTTS IPGTSAVHLE TTGTPSSFPG HTEPGPLLIP FTFNFTITNL RYEENMQHPG SRKFNTTERV LQGLLTPLFK NTSVGPLYSG CRLTLLRPEK QEAATGVDTI CTHRVDPIGP GLDRERLYWE LSQLTNSITE LGPYTLDRDS LYVDGFNPWS SVPTTSTPGT STVHLATSGT PSPLPGHTAP VPLLIPFTLN FTITDLHYEE NMQHPGSRKF NTTERVLQGL LKPLFKSTSV GPLYSGCRLT LLRPEKHGAA TGVDAICTLR LDPTGPGLDR ERLYWELSQL TNSITELGPY TLDRDSLYVN GFNPWSSVPT TSTPGTSTVH LATSGTPSSL PGHTTAGPLL VPFTLNFTIT NLKYEEDMHC PGSRKFNTTE RVLQSLHGPM FKNTSVGPLY SGCRLTLLRS EKDGAATGVD AICTHRLDPK SPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH XXSXPTTSTP GTSTVXXGTS GTPSSXPXXT XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTEXVLQ GLLXPXFKNX SVGXLYSGCR LTXLRXEKXG AATGXDAICX HXXXPKXPGL XXEXLYWELS XLTNSITELG PYTLDRDSLY VNGFTHRSSM PTTSIPGTSA VHLETSGTPA SLPGHTAPGP LLVPFTLNFT ITNLQYEEDM RHPGSRKFNT TERVLQGLLK PLFKSTSVGP LYSGCRLTLL RPEKRGAATG VDTICTHRLD PLNPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTXXXPLLXP FTXNXTITNL XXXXXMXXPG SRKFNTTEXV LQGLLXPXFK NXSVGXLYSG CRLTXLRXEK XGAATGXDAI CXHXXXPKXP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFHPRS SVPTTSTPGT STVHLATSGT PSSLPGHTAP VPLLIPFTLN FTITNLHYEE NMQHPGSRKF NTTERVLQGL LGPMFKNTSV GLLYSGCRLT LLRPEKNGAA TGMDAICSHR LDPKSPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHXXSXPT TSTPGTSTVX XGTSGTPSSX PXXTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE XVLQGLLXPX FKNXSVGXLY SGCRLTXLRX EKXGAATGXD AICXHXXXPK XPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT EPGPLLIPFT FNFTITNLHY EENMQHPGSR KFNTTERVLQ GLLTPLFKNT SVGPLYSGCR LTLLRPEKQE AATGVDTICT HRVDPIGPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHXXSX PTTSTPGTST VXXGTSGTPS SXPXXTXXXP LLXPFTXNXT ITNLXXXXXM XXPGSRKFNT TEXVLQGLLX PXFKNXSVGX LYSGCRLTXL RXEKXGAATG XDAICXHXXX PKXPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THRSSVPTTS SPGTSTVHLA TSGTPSSLPG HTAPVPLLIP FTLNFTITNL HYEENMQHPG SRKFNTTERV LQGLLKPLFK STSVGPLYSG CRLTLLRPEK HGAATGVDAI CTLRLDPTGP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHXX SXPTTSTPGT STVXXGTSGT PSSXPXXTXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTEXVLQGL LXPXFKNXSV GXLYSGCRLT XLRXEKXGAA TGXDAICXHX XXPKXPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHRTSVPT TSTPGTSTVH LATSGTPSSL PGHTAPVPLL IPFTLNFTIT NLQYEEDMHR PGSRKFNTTE RVLQGLLSPI FKNSSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY CELSQLTHNI TELGPYSLDR DSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTEXVLQ GLLXPXFKNX SVGXLYSGCR LTXLRXEKXG AATGXDAICX HXXXPKXPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHWSSG LTTSTPWTST VDLGTSGTPS PVPSPTTAGP LLVPFTLNFT ITNLQYEEDM HRPGSRKFNA TERVLQGLLS PIFKNTSVGP LYSGCRLTLL RPEKQEAATG VDTICTHRVD PIGPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTXXXPLLXP FTXNXTITNL XXXXXMXXPG SRKFNTTEXV LQGLLXPXFK NXSVGXLYSG CRLTXLRXEK XGAATGXDAI CXHXXXPKXP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHRS FGLTTSTPWT STVDLGTSGT PSPVPSPTTA GPLLVPFTLN FTITNLQYEE DMHRPGSRKF NTTERVLQGL LTPLFRNTSV SSLYSGCRLT LLRPEKDGAA TRVDAVCTHR PDPKSPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHXXSXPT TSTPGTSTVX XGTSGTPSSX PXXTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE XVLQGLLXPX FKNXSVGXLY SGCRLTXLRX EKXGAATGXD AICXHXXXPK XPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH WIPVPTSSTP GTSTVDLGSG TPSSLPSPTT AGPLLVPFTL NFTITNLQYG EDMGHPGSRK FNTTERVLQG LLGPIFKNTS VGPLYSGCRL TSLRSEKDGA ATGVDAICIH HLDPKSPGLX XEXLYWELSX LTXXIXELGP YTLDRXSLYV NGFTHXXSXP TTSTPGTSTV XXGTSGTPSS XPXXTXXXPL LXPFTXNXTI TNLXXXXXMX XPGSRKFNTT EXVLQGLLXP XFKNXSVGXL YSGCRLTXLR XEKXGAATGX DAICXHXXXP KXPGLXXEXL YWELSXLTXX IXELGPYTLD RXSLYVNGFT HQTFAPNTST PGTSTVDLGT SGTPSSLPSP TSAGPLLVPF TLNFTITNLQ YEEDMHHPGS RKFNTTERVL QGLLGPMFKN TSVGLLYSGC RLTLLRPEKN GAATRVDAVC THRPDPKSPG LXXEXLYWEL SXLTXXIXEL GPYTLDRXSL YVNGFTHXXS XPTTSTPGTS TVXXGTSGTP SSXPXXTAPV PLLIPFTLNF TITNLHYEEN MQHPGSRKFN TTERVLQGLL KPLFKSTSVG PLYSGCRLTL LRPEKHGAAT GVDAICTLRL DPTGPGLDRE RLYWELSQLT NSVTELGPYT LDRDSLYVNG FTQRSSVPTT SIPGTSAVHL ETSGTPASLP GHTAPGPLLV PFTLNFTITN LQYEVDMRHP GSRKFNTTER VLQGLLKPLF KSTSVGPLYS GCRLTLLRPE KRGAATGVDT ICTHRLDPLN PGLDREQLYW ELSKLTRGII ELGPYLLDRG SLYVNGFTHR NFVPITSTPG TSTVHLGTSE TPSSLPRPIV PGPLLVPFTL NFTITNLQYE EAMRHPGSRK FNTTERVLQG LLRPLFKNTS IGPLYSSCRL TLLRPEKDKA ATRVDAICTH HPDPQSPGLN REQLYWELSQ LTHGITELGP YTLDRDSLYV DGFTHWSPIP TTSTPGTSIV NLGTSGIPPS LPETTXXXPL LXPFTXNXTI TNLXXXXXMX XPGSRKFNTT ERVLQGLLKP LFKSTSVGPL YSGCRLTLLR PEKDGVATRV DAICTHRPDP KIPGLDRQQL YWELSQLTHS ITELGPYTLD RDSLYVNGFT QRSSVPTTST PGTFTVQPET SETPSSLPGP TATGPVLLPF TLNFTITNLQ YEEDMHRPGS RKFNTTERVL QGLLMPLFKN TSVSSLYSGC RLTLLRPEKD GAATRVDAVC THRPDPKSPG LDRERLYWKL SQLTHGITEL GPYTLDRHSL YVNGFTHQSS MTTTRTPDTS TMHLATSRTP ASLSGPTTAS PLLVLFTINF TITNLRYEEN MHHPGSRKFN TTERVLQGLL RPVFKNTSVG PLYSGCRLTL LRPKKDGAAT KVDAICTYRP DPKSPGLDRE QLYWELSQLT HSITELGPYT LDRDSLYVNG FTQRSSVPTT SIPGTPTVDL GTSGTPVSKP GPSAASPLLV LFTLNFTITN LRYEENMQHP GSRKFNTTER VLQGLLRSLF KSTSVGPLYS GCRLTLLRPE KDGTATGVDA ICTHHPDPKS PRLDREQLYW ELSQLTHNIT ELGHYALDND SLFVNGFTHR SSVSTTSTPG TPTVYLGASK TPASIFGPSA ASHLLILFTL NFTITNLRYE ENMWPGSRKF NTTERVLQGL LRPLFKNTSV GPLYSGSRLT LLRPEKDGEA TGVDAICTHR PDPTGPGLDR EQLYLELSQL THSITELGPY TLDRDSLYVN GFTHRSSVPT TSTGVVSEEP FTLNFTINNL RYMADMGQPG SLKFNITDNV MKHLLSPLFQ RSSLGARYTG CRVIALRSVK NGAETRVDLL CTYLQPLSGP GLPIKQVFHE LSQQTHGITR LGPYSLDKDS LYLNGYNEPG LDEPPTTPKP ATTFLPPLSE ATTAMGYHLK TLTLNFTISN LQYSPDMGKG SATFNSTEGV LQHLLRPLFQ KSSMGPFYLG CQLISLRPEK DGAATGVDTT CTYHPDPVGP GLDIQQLYWE LSQLTHGVTQ LGFYVLDRDS LFINGYAPQN LSIRGEYQIN FHIVNWNLSN PDPTSSEYIT LLRDIQDKVT TLYKGSQLHD TFRFCLVTNL TMDSVLVTVK ALFSSNLDPS LVEQVFLDKT LNASFHWLGS TYQLVDIHVT EMESSVYQPT SSSSTQHFYL NFTITNLPYS QDKAQPGTTN YQRNKRNIED ALNQLFRNSS IKSYFSDCQV STFRSVPNRH HTGVDSLCNF SPLARRVDRV AIYEEFLRMT RNGTQLQNFT LDRSSVLVDG YSPNRNEPLT GNSDLPFWAV ILIGLAGLLG LITCLICGVL VTTRRRKKEG EYNVQQQCPG YYQSHLDLED LQ Stack trace follows .... at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:609) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: org.biojava.bio.symbol.IllegalAlphabetException: Can't handle this in the general case: PROTEIN-TERM at org.biojava.bio.symbol.PackingFactory.getPacking(PackingFactory.java:75) at org.biojava.bio.symbol.PackedSymbolListFactory.makeSymbolList(PackedSymbolListFactory.java:88) at org.biojava.bio.seq.io.ChunkedSymbolListFactory.addSymbols(ChunkedSymbolListFactory.java:220) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.addSymbols(SimpleRichSequenceBuilder.java:256) at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:604) ... 3 more -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:14:03 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:14:03 -0400 Subject: [Biojava-dev] [Bug 2316] New: UniProtFormat fail on read RX record. Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2316 Summary: UniProtFormat fail on read RX record. Product: BioJava Version: live (CVS source) Platform: PC OS/Version: All Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: miyabe at port4.info Isn't the delimiter not ";" but "; "? I changed row #481 of UniProtFormat to below and it works. String[] refs = val.split("; "); -- Exception in thread "main" org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at jp.co.maze.intact.RestructMain.exec(RestructMain.java:90) at jp.co.maze.intact.RestructMain.main(RestructMain.java:42) Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.UniProtFormat Accession=Q13362 Id= Comments= Parse_block=RN [6]RP IDENTIFICATION AS A RENAL CANCER ANTIGEN.RC TISSUE=Renal cell carcinoma;RX MEDLINE=99438124; PubMed=10508479; DOI=10.1002/(SICI)1097-0215(19991112)83:4<456::AID-IJC4>3.0.CO;2-5;RA Scanlan M.J., Gordan J.D., Williamson B., Stockert E., Bander N.H., Jongeneel C.V., Gure A.O., Jaeger D., Jaeger E., Knuth A., Chen Y.-T., Old L.J.;RT "Antigens recognized by autologous antibody in patients with renal- cell carcinoma.";RL Int. J. Cancer 83:456-464(1999). Stack trace follows .... at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:615) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 1 at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:486) ... 3 more -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:28:35 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:28:35 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706110928.l5B9SZGD031197@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 ------- Comment #2 from brunner at imp.ac.at 2007-06-11 05:28 EST ------- Created an attachment (id=673) --> (http://bugzilla.open-bio.org/attachment.cgi?id=673&action=view) More exact values for some AA masses -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:32:52 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:32:52 -0400 Subject: [Biojava-dev] [Bug 2315] UniProtFormat fail on long protein sequence. In-Reply-To: Message-ID: <200706110932.l5B9WqZJ032294@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2315 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:33:00 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:00 -0400 Subject: [Biojava-dev] [Bug 2316] UniProtFormat fail on read RX record. In-Reply-To: Message-ID: <200706110933.l5B9X0IB032352@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2316 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:33:26 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:26 -0400 Subject: [Biojava-dev] [Bug 2315] UniProtFormat fail on long protein sequence. In-Reply-To: Message-ID: <200706110933.l5B9XQdu032525@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2315 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |holland at ebi.ac.uk Status|ASSIGNED |NEW -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 05:33:34 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:34 -0400 Subject: [Biojava-dev] [Bug 2316] UniProtFormat fail on read RX record. In-Reply-To: Message-ID: <200706110933.l5B9XYFi032578@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2316 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |holland at ebi.ac.uk Status|ASSIGNED |NEW -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 10:47:30 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 10:47:30 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706111447.l5BElUwF016411@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |NEW ------- Comment #3 from holland at ebi.ac.uk 2007-06-11 10:47 EST ------- Done on head of CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 10:47:41 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 10:47:41 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706111447.l5BElfdT016435@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from holland at ebi.ac.uk 2007-06-11 10:47 EST ------- Done on head of CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 13 04:28:49 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 13 Jun 2007 04:28:49 -0400 Subject: [Biojava-dev] [Bug 2301] Initialization error of org.biojava.bio.alignment.NeedlemanWunsch when considering affine gap penalty In-Reply-To: Message-ID: <200706130828.l5D8SnSD032089@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2301 mark.schreiber at novartis.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from mark.schreiber at novartis.com 2007-06-13 04:28 EST ------- fixed in CVS -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From markjschreiber at gmail.com Wed Jun 13 04:43:57 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 13 Jun 2007 16:43:57 +0800 Subject: [Biojava-dev] Problem with Phylo Code in CVS Message-ID: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Hi = CVS is currently unbuildable because of recent commits of phylo code. There are two problems. 1) The code has a reliance on JGraphT. This needs to be commited in the appropriate place and added to the classpath etc in the ant build file. 2) The code contains java 1.5 reliant code (generics) that won't compile with the biojava standard JDK (1.4.2). This is not really an issue as I am about to do a final BioJava 1.5 build after which we switch to JDK1.5 (or maybe even 1.6). Can someone checkin JGraphT and make the appropriate changes to the build XML? Please also ensure the licenses are acceptable and properly replicated. - Mark From holland at ebi.ac.uk Wed Jun 13 05:01:45 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 10:01:45 +0100 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Message-ID: <466FB279.5090506@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 JGraphT is LGPL. I have added the current JGraphT JAR file (Java 1.5) and modified build.xml. Can you temporarily omit JGraphT and the phylo packages from the 1.5 build process? cheers, Richard Mark Schreiber wrote: > Hi = > > CVS is currently unbuildable because of recent commits of phylo code. > There are two problems. > > 1) The code has a reliance on JGraphT. This needs to be commited in > the appropriate place and added to the classpath etc in the ant build > file. > > 2) The code contains java 1.5 reliant code (generics) that won't > compile with the biojava standard JDK (1.4.2). This is not really an > issue as I am about to do a final BioJava 1.5 build after which we > switch to JDK1.5 (or maybe even 1.6). > > Can someone checkin JGraphT and make the appropriate changes to the > build XML? Please also ensure the licenses are acceptable and properly > replicated. > > - Mark > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGb7J54C5LeMEKA/QRAofUAJ9fhc2CffT63qasVhmoy8hHz9j4+wCbB1eg JWLke1WXeYDxq4ijBDDVDLY= =zWib -----END PGP SIGNATURE----- From markjschreiber at gmail.com Wed Jun 13 05:15:54 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 13 Jun 2007 17:15:54 +0800 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <466FB279.5090506@ebi.ac.uk> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> <466FB279.5090506@ebi.ac.uk> Message-ID: <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> Yes, I will omit the phylo package as it is not stable (or finished). Also noticed that the MassCalcTest fails after the update of the new Mass values. Does no-one attempt to run tests before commiting?? I will commit a patch to the test today. - Mark On 6/13/07, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > JGraphT is LGPL. > > I have added the current JGraphT JAR file (Java 1.5) and modified build.xml. > > Can you temporarily omit JGraphT and the phylo packages from the 1.5 > build process? > > cheers, > Richard > > Mark Schreiber wrote: > > Hi = > > > > CVS is currently unbuildable because of recent commits of phylo code. > > There are two problems. > > > > 1) The code has a reliance on JGraphT. This needs to be commited in > > the appropriate place and added to the classpath etc in the ant build > > file. > > > > 2) The code contains java 1.5 reliant code (generics) that won't > > compile with the biojava standard JDK (1.4.2). This is not really an > > issue as I am about to do a final BioJava 1.5 build after which we > > switch to JDK1.5 (or maybe even 1.6). > > > > Can someone checkin JGraphT and make the appropriate changes to the > > build XML? Please also ensure the licenses are acceptable and properly > > replicated. > > > > - Mark > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGb7J54C5LeMEKA/QRAofUAJ9fhc2CffT63qasVhmoy8hHz9j4+wCbB1eg > JWLke1WXeYDxq4ijBDDVDLY= > =zWib > -----END PGP SIGNATURE----- > From ap3 at sanger.ac.uk Wed Jun 13 05:41:06 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 13 Jun 2007 10:41:06 +0100 Subject: [Biojava-dev] after this release In-Reply-To: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Message-ID: <17b17e8f8f538b2068d81eafaff69ac8@sanger.ac.uk> Hi Mark, > This is not really an > issue as I am about to do a final BioJava 1.5 build after which we > switch to JDK1.5 (or maybe even 1.6). Thanks for all your work in getting this release out. A while ago we also were discussing to move to Subversion after this release. Is this still on? Greetings, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Wed Jun 13 08:16:43 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 13:16:43 +0100 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> <466FB279.5090506@ebi.ac.uk> <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> Message-ID: <466FE02B.7080006@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I did notice it failed but wasn't sure what to do about it. What is the fix? cheers, Richard Mark Schreiber wrote: > Yes, I will omit the phylo package as it is not stable (or finished). > > Also noticed that the MassCalcTest fails after the update of the new > Mass values. Does no-one attempt to run tests before commiting?? I > will commit a patch to the test today. > > - Mark > > On 6/13/07, Richard Holland wrote: > JGraphT is LGPL. > > I have added the current JGraphT JAR file (Java 1.5) and modified > build.xml. > > Can you temporarily omit JGraphT and the phylo packages from the 1.5 > build process? > > cheers, > Richard > > Mark Schreiber wrote: >> Hi = > >> CVS is currently unbuildable because of recent commits of phylo code. >> There are two problems. > >> 1) The code has a reliance on JGraphT. This needs to be commited in >> the appropriate place and added to the classpath etc in the ant build >> file. > >> 2) The code contains java 1.5 reliant code (generics) that won't >> compile with the biojava standard JDK (1.4.2). This is not really an >> issue as I am about to do a final BioJava 1.5 build after which we >> switch to JDK1.5 (or maybe even 1.6). > >> Can someone checkin JGraphT and make the appropriate changes to the >> build XML? Please also ensure the licenses are acceptable and properly >> replicated. > >> - Mark >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGb+Ar4C5LeMEKA/QRAlwHAJ41XTBBd5PvLRoTRg2rZB34fmT3LACfc6FL QOWkjIVahdkoBjMoNBHJjxk= =ywTL -----END PGP SIGNATURE----- From holland at ebi.ac.uk Wed Jun 13 11:15:48 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 16:15:48 +0100 Subject: [Biojava-dev] BioJava 1.5 Released Message-ID: <46700A24.4040305@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 iD4DBQFGcAoj4C5LeMEKA/QRAvZiAJjhHGWvq5nrj8aanmUtCpA8U8dpAJ0bsxzy tv5LVdSEtAuA7gp12nLMCA== =/Wbu -----END PGP SIGNATURE----- From bugzilla-daemon at portal.open-bio.org Wed Jun 13 11:52:20 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 13 Jun 2007 11:52:20 -0400 Subject: [Biojava-dev] [Bug 2318] New: NPE in org.biojavax.bio.seq.io.EMBLxmlFormat Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2318 Summary: NPE in org.biojavax.bio.seq.io.EMBLxmlFormat Product: BioJava Version: unspecified Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: dmitry.repchevski at bsc.es Hi! Using RichSequence.IOTools.readStream() I got a Null Pointer Exception in EMBLxmlFormat when the sequence is not an xml and less than 2 lines: Here is a stack: ***************************************** SEVERE: java.lang.NullPointerException at java.util.regex.Matcher.getTextLength(Unknown Source) at java.util.regex.Matcher.reset(Unknown Source) at java.util.regex.Matcher.(Unknown Source) at java.util.regex.Pattern.matcher(Unknown Source) at org.biojavax.bio.seq.io.EMBLxmlFormat.canRead(EMBLxmlFormat.java:238) at org.biojavax.bio.seq.RichSequence$IOTools.readStream(RichSequence.java:683) at org.biojavax.bio.seq.RichSequence$IOTools.readStream(RichSequence.java:705) ... ***************************************** Looking into the code I can see ***************************************** public boolean canRead(BufferedInputStream stream) throws IOException { stream.mark(2000); // some streams may not support this BufferedReader br = new BufferedReader(new InputStreamReader(stream)); br.readLine(); // skip first line boolean readable = xmlSchema.matcher(br.readLine()).matches(); // check on second line ... ***************************************** that there is no br.readLine() == null check. the same with [public boolean canRead(File file)] method. the method supposed to check if the stream is an EMBL XML format... thank you in advance. Dmitry -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 14 05:00:15 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 14 Jun 2007 05:00:15 -0400 Subject: [Biojava-dev] [Bug 2318] NPE in org.biojavax.bio.seq.io.EMBLxmlFormat In-Reply-To: Message-ID: <200706140900.l5E90FoJ006653@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2318 ------- Comment #1 from dmitry.repchevski at bsc.es 2007-06-14 05:00 EST ------- The same with UniProtXMLFormat -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 15 10:52:09 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 15 Jun 2007 10:52:09 -0400 Subject: [Biojava-dev] [Bug 2318] NPE in org.biojavax.bio.seq.io.EMBLxmlFormat In-Reply-To: Message-ID: <200706151452.l5FEq9cN001674@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2318 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from holland at ebi.ac.uk 2007-06-15 10:52 EST ------- Fixed in head on CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From blee34 at mail.gatech.edu Tue Jun 19 13:50:23 2007 From: blee34 at mail.gatech.edu (blee34 at mail.gatech.edu) Date: Tue, 19 Jun 2007 13:50:23 -0400 Subject: [Biojava-dev] Helps needed for NexusParser Message-ID: <1182275423.4678175fe5775@webmail.mail.gatech.edu> Dear group, Hi, I'm a GSOC student Bohyun participating in BioJava project (as a part of NESCent phyloinformatics work) for this summer! I need some helps using (Nexus) TAXA Block Parser (which were included in BioJava1.5-beta2). Can anyone give me a sample code for Parsing a TAXA Block? What I am trying to do now is to parse a TAXA block and construct a phylo tree by using methods like UPGMA, Neighbor-Joining. (http://biojava.org/wiki/BioJava:PhyloSOC07) Also, I'd appreciate if there's anyone who can tell me where to find javadoc pages for biojavax.phylo package. (It was there on the wiki with Biojava1.5-beta2 release. I heard that It's been temporarily omitted for the BioJava1.5 version, but I'd like to get those files for the reference.) Thank you very much for your help. Best regards, Bohyun From markjschreiber at gmail.com Tue Jun 19 21:11:26 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 20 Jun 2007 09:11:26 +0800 Subject: [Biojava-dev] Helps needed for NexusParser In-Reply-To: <1182275423.4678175fe5775@webmail.mail.gatech.edu> References: <1182275423.4678175fe5775@webmail.mail.gatech.edu> Message-ID: <93b45ca50706191811y4ff9dc72k49f9b5139ade3932@mail.gmail.com> Hi - The phylo package was omitted from the biojava1.5 build but it is still accessible form the biojava-live distribution on CVS. If you have CVS access you should be able to get it. Additionally you can build any docs using JavaDoc or better yet build the entire package with Ant using the build.xml file. - Mark On 6/20/07, blee34 at mail.gatech.edu wrote: > > Dear group, > > Hi, I'm a GSOC student Bohyun participating in BioJava project (as a part of > NESCent phyloinformatics work) for this summer! > > I need some helps using (Nexus) TAXA Block Parser (which were included in > BioJava1.5-beta2). Can anyone give me a sample code for Parsing a TAXA Block? > > What I am trying to do now is to parse a TAXA block and construct a phylo tree > by > using methods like UPGMA, Neighbor-Joining. > (http://biojava.org/wiki/BioJava:PhyloSOC07) > > Also, I'd appreciate if there's anyone who can tell me where to find javadoc > pages for biojavax.phylo package. (It was there on the wiki with > Biojava1.5-beta2 release. I heard that It's been temporarily omitted for the > BioJava1.5 version, but I'd like to get those files for the reference.) > > Thank you very much for your help. > > Best regards, > Bohyun > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From bugzilla-daemon at portal.open-bio.org Mon Jun 25 08:35:10 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 25 Jun 2007 08:35:10 -0400 Subject: [Biojava-dev] [Bug 2260] Bug in UkkonenSuffixTree In-Reply-To: Message-ID: <200706251235.l5PCZAZM026974@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2260 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from holland at ebi.ac.uk 2007-06-25 08:35 EST ------- Fixed now in CVS on the head. Problem was quite simple - the loop that iterated over portions of a multiple string was identifying the end of each portion but lumping in the whole of the preceding portions with each one. Net effect was this: Input: aaa$bbb$ccc Sequences: aaa, aaa$bbb, aaa$bbb$ccc The corrected behaviour is this: Input: aaa$bbb$ccc Sequences: aaa, bbb, ccc -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From kannanbimatics at yahoo.com Mon Jun 25 05:15:10 2007 From: kannanbimatics at yahoo.com (kannan kannan) Date: Mon, 25 Jun 2007 09:15:10 -0000 Subject: [Biojava-dev] Requesting for project Message-ID: <322810.71032.qm@web57415.mail.re1.yahoo.com> Respected SIR / MADAM, I very much pleased to introduce myself as V.S Kannan, pursuing II M.Sc.bioinformatics, at kongunadu arts & science College, Coimbatore, Tamilnadu. I have completed my graduation in Biochemistry from Periyar University. As part of my curriculum, I have to do a project for a period of 4-6 months during December 2007-April 2008. I am very much interested in computational biology and have developed bioinformatics tools PERL,BIOJAVA and C. I have also completed two projects on Development of database for Signal peptide Database and Restriction site tracer using Oracle and Visual Basic. From the website I came to know about the projects done at your Institution and I am very much interested to do my project under your guidance. I kindly request you to consider my application and I assure you to put in my best efforts during the project. I have enclosed a copy of my resume for your kind perusal. Anticipating a favourable reply. Thanking you Regards, kannan --------------------------------- Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. -------------- next part -------------- A non-text attachment was scrubbed... Name: kannan cv.doc Type: application/msword Size: 45568 bytes Desc: 1964471048-kannan cv.doc Url : http://lists.open-bio.org/pipermail/biojava-dev/attachments/20070625/b12a45f5/attachment.doc From mark.schreiber at novartis.com Fri Jun 1 01:32:32 2007 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 1 Jun 2007 09:32:32 +0800 Subject: [Biojava-dev] fixed and streamlined SmithWaterman.java Message-ID: Hi - Could the person who maintains the SW code (Andreas Drager??) take a look at this and check it in if required? Thanks. - Mark "Fred Long" Sent by: biojava-dev-bounces at lists.open-bio.org 05/08/2007 03:15 PM To: cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] fixed and streamlined SmithWaterman.java I found that SmithWaterman was calling super() with the wrong parameters, which caused getMatch() to return the wrong value. While fixing that I removed a lot of the redundancy from SmithWaterman. Here is the patch file is anybody is interested. Disclaimer: I'm not a BioJava developer. FL ------------------------------------ *** old/NeedlemanWunsch.java 2007-05-08 00:05:20.000000000 -0700 --- NeedlemanWunsch.java 2007-05-08 00:05:38.000000000 -0700 *************** *** 63,69 **** protected SubstitutionMatrix subMatrix; protected Alignment pairalign; protected String alignment; ! private double insert, delete, gapExt, match, replace; /** Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm --- 63,69 ---- protected SubstitutionMatrix subMatrix; protected Alignment pairalign; protected String alignment; ! protected double insert, delete, gapExt, match, replace; /** Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm *************** *** 517,523 **** * target sequence * @return The score for the given substitution. */ ! private double matchReplace(Sequence query, Sequence subject, int i, int j) { try { return subMatrix.getValueAt(query.symbolAt(i), subject.symbolAt(j)); } catch (Exception exc) { --- 517,523 ---- * target sequence * @return The score for the given substitution. */ ! protected double matchReplace(Sequence query, Sequence subject, int i, int j) { try { return subMatrix.getValueAt(query.symbolAt(i), subject.symbolAt(j)); } catch (Exception exc) { *** old/SmithWaterman.java 2007-05-08 00:05:20.000000000 -0700 --- SmithWaterman.java 2007-05-08 00:05:38.000000000 -0700 *************** *** 53,141 **** public class SmithWaterman extends NeedlemanWunsch { - private double match, replace, insert, delete, gapExt; private double[][] scoreMatrix; /** Constructs the new SmithWaterman alignment object. Alignments are only performed, * if the alphabet of the given SubstitutionMatrix equals the alpabet of ! * both the query and the target Sequence. The alignment parameters here ! * are expenses and not scores as they are in the NeedlemanWunsch object. ! * scores are just given by multipliing the expenses with (-1). For example ! * you could use parameters like "-2, 5, 3, 3, 0". If the expenses for gap extension * are equal to the cost of starting a gap (delete or insert), no affine gap penalties * are used, which saves memory. * ! * @param match expenses for a match ! * @param replace expenses for a replace operation ! * @param insert expenses for a gap opening in the query sequence ! * @param delete expenses for a gap opening in the target sequence ! * @param gapExtend expenses for the extension of a gap which was started earlier. * @param matrix the SubstitutionMatrix object to use. */ public SmithWaterman(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix matrix) { ! super(insert, delete, gapExtend, match, replace, matrix); ! this.match = -match; ! this.replace = -replace; ! this.insert = -insert; ! this.delete = -delete; ! this.gapExt = -gapExtend; ! this.subMatrix = matrix; ! this.alignment = ""; } - /** Overrides the method inherited from the NeedlemanWunsch and - * sets the penalty for an insert operation to the specified value. - * Reason: internaly scores are used instead of penalties so that - * the value is muliplied with -1. - * @param ins costs for a single insert operation - */ - public void setInsert(double ins) { - this.insert = -ins; - } - - /** Overrides the method inherited from the NeedlemanWunsch and - * sets the penalty for a delete operation to the specified value. - * Reason: internaly scores are used instead of penalties so that - * the value is muliplied with -1. - * @param del costs for a single deletion operation - */ - public void setDelete(double del) { - this.delete = -del; - } - - /** Overrides the method inherited from the NeedlemanWunsch and - * sets the penalty for an extension of any gap (insert or delete) to the - * specified value. - * Reason: internaly scores are used instead of penalties so that - * the value is muliplied with -1. - * @param ge costs for any gap extension - */ - public void setGapExt(double ge) { - this.gapExt = -ge; - } - - /** Overrides the method inherited from the NeedlemanWunsch and - * sets the penalty for a match operation to the specified value. - * Reason: internaly scores are used instead of penalties so that - * the value is muliplied with -1. - * @param ma costs for a single match operation - */ - public void setMatch(double ma) { - this.match = -ma; - } - - /** Overrides the method inherited from the NeedlemanWunsch and - * sets the penalty for a replace operation to the specified value. - * Reason: internaly scores are used instead of penalties so that - * the value is muliplied with -1. - * @param rep costs for a single replace operation - */ - public void setReplace(double rep) { - this.replace = -rep; - } - /** Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. * It finds only the longest common subsequence. This is good for the beginning, but it might --- 53,79 ---- public class SmithWaterman extends NeedlemanWunsch { private double[][] scoreMatrix; /** Constructs the new SmithWaterman alignment object. Alignments are only performed, * if the alphabet of the given SubstitutionMatrix equals the alpabet of ! * both the query and the target Sequence. If the expenses for gap extension * are equal to the cost of starting a gap (delete or insert), no affine gap penalties * are used, which saves memory. * ! * @param match expenses for a match (usually < 0) ! * @param replace expenses for a replace operation (usually > 0) ! * @param insert expenses for a gap opening in the query sequence (usually > 0) ! * @param delete expenses for a gap opening in the target sequence (usually > 0) ! * @param gapExtend expenses for the extension of a gap which was started earlier (usually >= 0) * @param matrix the SubstitutionMatrix object to use. */ public SmithWaterman(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix matrix) { ! super(match, replace, insert, delete, gapExtend, matrix); } /** Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. * It finds only the longest common subsequence. This is good for the beginning, but it might *************** *** 186,193 **** for (i=1; i<=query.length(); i++) for (j=1; j<=subject.length(); j++) { ! E[i][j] = Math.max(E[i][j-1], scoreMatrix[i][j-1] + insert) + gapExt; ! F[i][j] = Math.max(F[i-1][j], scoreMatrix[i-1][j] + delete) + gapExt; scoreMatrix[i][j] = max(0.0, E[i][j], F[i][j], scoreMatrix[i-1][j-1] + matchReplace(query, subject, i, j)); if (scoreMatrix[i][j] > scoreMatrix[maxI][maxJ]) { --- 124,131 ---- for (i=1; i<=query.length(); i++) for (j=1; j<=subject.length(); j++) { ! E[i][j] = Math.max(E[i][j-1], scoreMatrix[i][j-1] - insert) - gapExt; ! F[i][j] = Math.max(F[i-1][j], scoreMatrix[i-1][j] - delete) - gapExt; scoreMatrix[i][j] = max(0.0, E[i][j], F[i][j], scoreMatrix[i-1][j-1] + matchReplace(query, subject, i, j)); if (scoreMatrix[i][j] > scoreMatrix[maxI][maxJ]) { *************** *** 223,229 **** // Insert || finish gap if extended gap is opened } else if (scoreMatrix[i][j] == E[i][j] || gap_extend[0]) { //check if gap has been extended or freshly opened ! gap_extend[0] = (E[i][j] != scoreMatrix[i][j-1] + insert + gapExt); align[0] = '-' + align[0]; align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; --- 161,167 ---- // Insert || finish gap if extended gap is opened } else if (scoreMatrix[i][j] == E[i][j] || gap_extend[0]) { //check if gap has been extended or freshly opened ! gap_extend[0] = (E[i][j] != scoreMatrix[i][j-1] - insert - gapExt); align[0] = '-' + align[0]; align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; *************** *** 232,238 **** // Delete || finish gap if extended gap is opened } else { //check if gap has been extended or freshly opened ! gap_extend[1] = (F[i][j] != scoreMatrix[i-1][j] + delete + gapExt); align[0] = st.tokenizeSymbol(query.symbolAt(i--)) + align[0]; align[1] = '-' + align[1]; --- 170,176 ---- // Delete || finish gap if extended gap is opened } else { //check if gap has been extended or freshly opened ! gap_extend[1] = (F[i][j] != scoreMatrix[i-1][j] - delete - gapExt); align[0] = st.tokenizeSymbol(query.symbolAt(i--)) + align[0]; align[1] = '-' + align[1]; *************** *** 257,264 **** scoreMatrix[i][j] = max( 0.0, ! scoreMatrix[i-1][j] + delete, ! scoreMatrix[i][j-1] + insert, scoreMatrix[i-1][j-1] + matchReplace(query, subject, i, j) ); --- 195,202 ---- scoreMatrix[i][j] = max( 0.0, ! scoreMatrix[i-1][j] - delete, ! scoreMatrix[i][j-1] - insert, scoreMatrix[i-1][j-1] + matchReplace(query, subject, i, j) ); *************** *** 291,297 **** align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; // Insert ! } else if (scoreMatrix[i][j] == scoreMatrix[i][j-1] + insert) { align[0] = '-' + align[0]; align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; path = ' ' + path; --- 229,235 ---- align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; // Insert ! } else if (scoreMatrix[i][j] == scoreMatrix[i][j-1] - insert) { align[0] = '-' + align[0]; align[1] = st.tokenizeSymbol(subject.symbolAt(j--)) + align[1]; path = ' ' + path; *************** *** 382,409 **** if ((y > z)) return y; return z; } - - /** This method computes the scores for the substution of the i-th symbol - * of query by the j-th symbol of subject. - * - * @param query The query sequence - * @param subject The target sequence - * @param i The position of the symbol under consideration within the - * query sequence (starting from one) - * @param j The position of the symbol under consideration within the - * target sequence - * @return The score for the given substitution. - */ - private double matchReplace(Sequence query, Sequence subject, int i, int j) { - try { - return subMatrix.getValueAt(query.symbolAt(i), subject.symbolAt(j)); - } catch (Exception exc) { - if (query.symbolAt(i).getMatches().contains(subject.symbolAt(j)) || - subject.symbolAt(j).getMatches().contains(query.symbolAt(i))) - return match; - return replace; - } - } - - } --- 320,323 ---- _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:03:39 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:03:39 -0400 Subject: [Biojava-dev] [Bug 2306] New: build.xml is in an unusable state Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2306 Summary: build.xml is in an unusable state Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at build.xml of the current biojava1.5-beta2 "complete download" has an incorrect classpath setting. Compiling is not possible. Unified Diff attached... -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:04:08 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:04:08 -0400 Subject: [Biojava-dev] [Bug 2306] build.xml is in an unusable state In-Reply-To: Message-ID: <200706061404.l56E48jC016660@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2306 ------- Comment #1 from brunner at imp.ac.at 2007-06-06 10:04 EST ------- Created an attachment (id=664) --> (http://bugzilla.open-bio.org/attachment.cgi?id=664&action=view) Unified diff -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:06:25 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:06:25 -0400 Subject: [Biojava-dev] [Bug 2307] New: biojava "complete download" redundant Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2307 Summary: biojava "complete download" redundant Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at The biojava 1.5-beta2 "complete download" contains a package of itself. This leads to longer download times. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:11:42 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:11:42 -0400 Subject: [Biojava-dev] [Bug 2308] New: More exact values for amino acid masses Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2308 Summary: More exact values for amino acid masses Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: symbol AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at With state-of-the-art high-resolution mass spectrometers, the current amino acid masses contain not enough digits. What about using the values from http://www.ionsource.com/Card/aatable/aatable_print.htm If nobody else wants to do this, I will attach an updated XML file for these symbols. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:18:05 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:18:05 -0400 Subject: [Biojava-dev] [Bug 2309] New: Digest.addDigestFeatures() does not work Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2309 Summary: Digest.addDigestFeatures() does not work Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: major Priority: P2 Component: bio AssignedTo: biojava-dev at biojava.org ReportedBy: brunner at imp.ac.at org.biojava.bio.proteomics.Digest not functional: Digesting protein sequences yields only one fragment (Feature). The problem seems to be in the Feature.compare() function. Individual peptides are not distinguished by the compare() function, leaving only one fragment in the features TreeMap. I will provide a patch in the next the if I can make it work. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:22:00 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:22:00 -0400 Subject: [Biojava-dev] [Bug 2307] biojava "complete download" redundant In-Reply-To: Message-ID: <200706061422.l56EM0kM017790@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2307 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |mark.schreiber at novartis.com ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:21 EST ------- Again for you Mark I think? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:22:05 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:22:05 -0400 Subject: [Biojava-dev] [Bug 2306] build.xml is in an unusable state In-Reply-To: Message-ID: <200706061422.l56EM5ml017827@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2306 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |mark.schreiber at novartis.com ------- Comment #2 from holland at ebi.ac.uk 2007-06-06 10:22 EST ------- Mark can you fix this? I assume you made the change? Looks like a relative path problem - it shouldn't need the lib/ prefixes in the classpath line. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:23:01 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:23:01 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706061423.l56EN1Z5017908@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:23 EST ------- If you could attach an updated XML file to this bug report then I will make the changes on your behalf. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 14:24:20 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 10:24:20 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061424.l56EOKYU018003@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from holland at ebi.ac.uk 2007-06-06 10:24 EST ------- Great stuff - looking forward to seeing the patch. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 15:28:34 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 11:28:34 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061528.l56FSYkL021929@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 ------- Comment #2 from brunner at imp.ac.at 2007-06-06 11:28 EST ------- Created an attachment (id=665) --> (http://bugzilla.open-bio.org/attachment.cgi?id=665&action=view) Proposed fix As I am quite new to biojava (only have downloaded it this week) I do not know whether the fix fits into the concept. But IMO features can also differ in respect to their location to qualify them as a distinct entity. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 6 16:05:40 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 6 Jun 2007 12:05:40 -0400 Subject: [Biojava-dev] [Bug 2309] Digest.addDigestFeatures() does not work In-Reply-To: Message-ID: <200706061605.l56G5eLu024438@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2309 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #3 from holland at ebi.ac.uk 2007-06-06 12:05 EST ------- OK, I found the problem - SimpleRichFeature by default sets a rank of 0. By setting it to have unique ranks instead, the location check suggested becomes unnecessary (it is feasible for two otherwise identical features to have different locations, when really only one of them should be present). Now all features are unique by default by virtue of having different ranks, Digest will produce correct results. Fixed in CVS (head). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From felipe.albrecht at gmail.com Thu Jun 7 04:01:13 2007 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Thu, 7 Jun 2007 01:01:13 -0300 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? Message-ID: Hello, im trying to convert a protein multiple alignment in fasta format to phylip format. The source is: BufferedReader br = new BufferedReader(new FileReader(args[0])); PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); RichSequenceIterator richSequenceIterator = IOTools.readFastaProtein(br, null); List l = new LinkedList(); Sequence seq = null; while (richSequenceIterator.hasNext()) { l.add(richSequenceIterator.nextSequence()); } builder.startFile(); builder.setSequenceCount(l.size()); builder.setSitesCount(seq.seqString().length()); for (Sequence sequence : l) { builder.setCurrentSequenceName(sequence.getName()); builder.receiveSequence(sequence.seqString()); } builder.endFile(); As I said, my input data is a protein multiple alignment. Running this source, this trace is showed: Exception in thread "main" org.biojava.bio.BioError: Something has gone badly wrong with DNA at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) at FastaParser.main(FastaParser.java:54) Caused by: org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: 'Q' at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) ... 5 more IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method createSequence , where is done: try { DNATools.createGappedDNASequence(sequence, name); } catch (IllegalSymbolException e) { isDNA = false; } Where is execpeted that DNATools.CreateGappedDNASequence throws a IllegalSymbolException , but seeking this method, in the file DNAToos.java line 198: } catch (BioException se) { throw new BioError("Something has gone badly wrong with DNA", se); } Being the IllegalSymbolException subclass of the BioError, they is "catched" and a new exception is created and in NATools.createSequences they arent catched. I solved this problem adding: } catch (IllegalSymbolException ie) { throw ie; } in createDNASequence, but it's a workaround for the exception be catched. A better solution, is check the type of the sequence. Exist a method for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses it, also the exceptions must be used when occurs an exception and dont for flow control. PS: Im using the biojava source code downloaded today from http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz Thanks and Im waiting opinions. Felipe Albrecht From felipe.albrecht at gmail.com Thu Jun 7 04:02:55 2007 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Thu, 7 Jun 2007 01:02:55 -0300 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? In-Reply-To: References: Message-ID: Sorry, from my example file, substitute the line builder.setSitesCount(seq.seqString().length()); to builder.setSitesCount(l.get(l.size()-1).seqString().length()); Thanks Felipe Albrecht On 6/7/07, Felipe Albrecht wrote: > Hello, im trying to convert a protein multiple alignment in fasta > format to phylip format. > > The source is: > > BufferedReader br = new BufferedReader(new FileReader(args[0])); > PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); > RichSequenceIterator richSequenceIterator = > IOTools.readFastaProtein(br, null); > List l = new LinkedList(); > Sequence seq = null; > while (richSequenceIterator.hasNext()) { > l.add(richSequenceIterator.nextSequence()); > } > builder.startFile(); > builder.setSequenceCount(l.size()); > builder.setSitesCount(seq.seqString().length()); > for (Sequence sequence : l) { > builder.setCurrentSequenceName(sequence.getName()); > builder.receiveSequence(sequence.seqString()); > } > builder.endFile(); > > As I said, my input data is a protein multiple alignment. > > Running this source, this trace is showed: > > Exception in thread "main" org.biojava.bio.BioError: Something has > gone badly wrong with DNA > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) > at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) > at FastaParser.main(FastaParser.java:54) > Caused by: org.biojava.bio.symbol.IllegalSymbolException: This > tokenization doesn't contain character: 'Q' > at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) > at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) > at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) > at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) > ... 5 more > > IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method > createSequence , where is done: > try { > DNATools.createGappedDNASequence(sequence, name); > } catch (IllegalSymbolException e) { > isDNA = false; > } > > Where is execpeted that DNATools.CreateGappedDNASequence throws a > IllegalSymbolException , but seeking this method, in the file > DNAToos.java line 198: > } catch (BioException se) { > throw new BioError("Something has gone badly wrong with DNA", se); > } > Being the IllegalSymbolException subclass of the BioError, they is > "catched" and a new exception is created and in > NATools.createSequences they arent catched. > > > I solved this problem adding: > } catch (IllegalSymbolException ie) { > throw ie; > } > > in createDNASequence, but it's a workaround for the exception be catched. > > A better solution, is check the type of the sequence. Exist a method > for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses > it, also the exceptions must be used when occurs an exception and dont > for flow control. > > PS: Im using the biojava source code downloaded today from > http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz > > Thanks and Im waiting opinions. > > Felipe Albrecht > From bugzilla-daemon at portal.open-bio.org Thu Jun 7 04:07:47 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 00:07:47 -0400 Subject: [Biojava-dev] [Bug 2311] New: Bug in PHYLIPFileBuilder with protein sequences Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2311 Summary: Bug in PHYLIPFileBuilder with protein sequences Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: minor Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: felipe.albrecht at gmail.com Hello, im trying to convert a protein multiple alignment in fasta format to phylip format. The source is: BufferedReader br = new BufferedReader(new FileReader(args[0])); PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); RichSequenceIterator richSequenceIterator = IOTools.readFastaProtein(br, null); List l = new LinkedList(); Sequence seq = null; while (richSequenceIterator.hasNext()) { l.add(richSequenceIterator.nextSequence()); } builder.startFile(); builder.setSequenceCount(l.size()); builder.setSitesCount(seq.seqString().length()); for (Sequence sequence : l) { builder.setCurrentSequenceName(sequence.getName()); builder.receiveSequence(sequence.seqString()); } builder.endFile(); As I said, my input data is a protein multiple alignment. Running this source, this trace is showed: Exception in thread "main" org.biojava.bio.BioError: Something has gone badly wrong with DNA at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) at FastaParser.main(FastaParser.java:54) Caused by: org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: 'Q' at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) ... 5 more IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method createSequence , where is done: try { DNATools.createGappedDNASequence(sequence, name); } catch (IllegalSymbolException e) { isDNA = false; } Where is execpeted that DNATools.CreateGappedDNASequence throws a IllegalSymbolException , but seeking this method, in the file DNAToos.java line 198: } catch (BioException se) { throw new BioError("Something has gone badly wrong with DNA", se); } Being the IllegalSymbolException subclass of the BioError, they is "catched" and a new exception is created and in NATools.createSequences they arent catched. I solved this problem adding: } catch (IllegalSymbolException ie) { throw ie; } in createDNASequence, but it's a workaround for the exception be catched. A better solution, is check the type of the sequence. Exist a method for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses it, also the exceptions must be used when occurs an exception and dont for flow control. PS: Im using the biojava source code downloaded today from http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 7 04:08:37 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 00:08:37 -0400 Subject: [Biojava-dev] [Bug 2311] Bug in PHYLIPFileBuilder with protein sequences In-Reply-To: Message-ID: <200706070408.l5748b2u027260@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2311 ------- Comment #1 from felipe.albrecht at gmail.com 2007-06-07 00:08 EST ------- Created an attachment (id=666) --> (http://bugzilla.open-bio.org/attachment.cgi?id=666&action=view) Source that reproduce the error -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 7 07:51:35 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 7 Jun 2007 03:51:35 -0400 Subject: [Biojava-dev] [Bug 2311] Bug in PHYLIPFileBuilder with protein sequences In-Reply-To: Message-ID: <200706070751.l577pZZO004077@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2311 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from holland at ebi.ac.uk 2007-06-07 03:51 EST ------- This was a silly bug in DNATools - the createDNASequence() method said it threw IllegalSymybolException, but in fact it was catching all occurrences of this and converting them to BioException which is uncatchable. The fix for this was to stop the unnecessary conversion and therefore make the code behave exactly as its signature and JavaDocs say it will. Fixed in CVS (head). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From holland at ebi.ac.uk Thu Jun 7 08:22:15 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 07 Jun 2007 09:22:15 +0100 Subject: [Biojava-dev] http://bugzilla.open-bio.org/show_bug.cgi?id=2311 In-Reply-To: References: Message-ID: <4667C037.7070703@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The PHYLIPFileFormat code already does that. The problem was that the exception it catches to determine non-DNA-ness was not happening because DNATools was not throwing it. There is no easy way to determine a sequence file's type short of reading the whole file in and scanning through it in advance to spot symbol combinations that are unique to a particular alphabet, then repeating the read of the file to do the actual parsing. As BioJava uses mostly stream-based parsers which don't expect to be able to repeatedly read the same data, they have to rely on other methods. They make good guesses wherever they can but obviously they don't always get that guess right. Wherever the API allows it is always a good idea to specify the type of sequence in advance. PHYLIPFileFormat is not an API that allows this though, although there's nothing saying it couldn't be modified to do so by some willing volunteer! :) cheers, Richard Felipe Albrecht wrote: > Hello, > > about http://bugzilla.open-bio.org/show_bug.cgi?id=2311 > > isnt better check the sequence before create the DNA/RNA/Protein sequence? > That is: dont wait for an exception, but view what is the type. > > Felipe Albrecht -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGZ8A24C5LeMEKA/QRAginAJ40bL5YJl4pUgmRb1yBf9jDXz72bQCbBssO k24Us468mhs8wCx/f/gnU68= =4xYe -----END PGP SIGNATURE----- From markjschreiber at gmail.com Thu Jun 7 10:46:47 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 7 Jun 2007 18:46:47 +0800 Subject: [Biojava-dev] Bug in PHYLIPFileBuilder? In-Reply-To: References: Message-ID: <93b45ca50706070346o5a52c1d8t68cb95217e835f37@mail.gmail.com> Hi - BioJava's phylogenetics support is very experimental right now. However, this would be something that our Google SOC student might want to take a look at. - Mark On 6/7/07, Felipe Albrecht wrote: > Sorry, > from my example file, substitute the line > builder.setSitesCount(seq.seqString().length()); > to > builder.setSitesCount(l.get(l.size()-1).seqString().length()); > > Thanks > > Felipe Albrecht > > > On 6/7/07, Felipe Albrecht wrote: > > Hello, im trying to convert a protein multiple alignment in fasta > > format to phylip format. > > > > The source is: > > > > BufferedReader br = new BufferedReader(new FileReader(args[0])); > > PHYLIPFileBuilder builder = new PHYLIPFileBuilder(); > > RichSequenceIterator richSequenceIterator = > > IOTools.readFastaProtein(br, null); > > List l = new LinkedList(); > > Sequence seq = null; > > while (richSequenceIterator.hasNext()) { > > l.add(richSequenceIterator.nextSequence()); > > } > > builder.startFile(); > > builder.setSequenceCount(l.size()); > > builder.setSitesCount(seq.seqString().length()); > > for (Sequence sequence : l) { > > builder.setCurrentSequenceName(sequence.getName()); > > builder.receiveSequence(sequence.seqString()); > > } > > builder.endFile(); > > > > As I said, my input data is a protein multiple alignment. > > > > Running this source, this trace is showed: > > > > Exception in thread "main" org.biojava.bio.BioError: Something has > > gone badly wrong with DNA > > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:199) > > at org.biojava.bio.seq.DNATools.createGappedDNASequence(DNATools.java:207) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.createSequences(PHYLIPFileBuilder.java:121) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.buildAlignment(PHYLIPFileBuilder.java:94) > > at org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.endFile(PHYLIPFileBuilder.java:63) > > at FastaParser.main(FastaParser.java:54) > > Caused by: org.biojava.bio.symbol.IllegalSymbolException: This > > tokenization doesn't contain character: 'Q' > > at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175) > > at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246) > > at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:178) > > at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:173) > > at org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:195) > > ... 5 more > > > > IMHO, the bug is at the line 121 of PHYLIPFileBuilder.java, method > > createSequence , where is done: > > try { > > DNATools.createGappedDNASequence(sequence, name); > > } catch (IllegalSymbolException e) { > > isDNA = false; > > } > > > > Where is execpeted that DNATools.CreateGappedDNASequence throws a > > IllegalSymbolException , but seeking this method, in the file > > DNAToos.java line 198: > > } catch (BioException se) { > > throw new BioError("Something has gone badly wrong with DNA", se); > > } > > Being the IllegalSymbolException subclass of the BioError, they is > > "catched" and a new exception is created and in > > NATools.createSequences they arent catched. > > > > > > I solved this problem adding: > > } catch (IllegalSymbolException ie) { > > throw ie; > > } > > > > in createDNASequence, but it's a workaround for the exception be catched. > > > > A better solution, is check the type of the sequence. Exist a method > > for discover is the sequence is DNA/RNA/Protein/mistake? If yes, uses > > it, also the exceptions must be used when occurs an exception and dont > > for flow control. > > > > PS: Im using the biojava source code downloaded today from > > http://www.biojava.org/download/bj15b/all/biojava-1.5-beta2.tar.gz > > > > Thanks and Im waiting opinions. > > > > Felipe Albrecht > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > 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-dev] 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 bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:00:02 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:00:02 -0400 Subject: [Biojava-dev] [Bug 2315] New: UniProtFormat fail on long protein sequence. Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2315 Summary: UniProtFormat fail on long protein sequence. Product: BioJava Version: live (CVS source) Platform: PC OS/Version: All Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: miyabe at port4.info It seems some errors in the renewal of the symbol buffer of org.biojava.bio.seq.io.ChunkedSymbolListFactory. Here is a stacktrace. -- Exception in thread "main" org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at jp.co.maze.intact.RestructMain.exec(RestructMain.java:90) at jp.co.maze.intact.RestructMain.main(RestructMain.java:42) Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.UniProtFormat Accession=Q8WXI7 Id= Comments= Parse_block=SQ MLKPSGLPGS SSPTRSLMTG SRSTKATPEM DSGLTGATLS PKTSTGAIVV TEHTLPFTSP DKTLASPTSS VVGRTTQSLG VMSSALPEST SRGMTHSEQR TSPSLSPQVN GTPSRNYPAT SMVSGLSSPR TRTSSTEGNF TKEASTYTLT VETTSGPVTE KYTVPTETST TEGDSTETPW DTRYIPVKIT SPMKTFADST ASKENAPVSM TPAETTVTDS HTPGRTNPSF GTLYSSFLDL SPKGTPNSRG ETSLELILST TGYPFSSPEP GSAGHSRIST SAPLSSSASV LDNKISETSI FSGQSLTSPL SPGVPEARAS TMPNSAIPFS MTLSNAETSA ERVRSTISSL GTPSISTKQT AETILTFHAF AETMDIPSTH IAKTLASEWL GSPGTLGGTS TSALTTTSPS TTLVSEETNT HHSTSGKETE GTLNTSMTPL ETSAPGEESE MTATLVPTLG FTTLDSKIRS PSQVSSSHPT RELRTTGSTS GRQSSSTAAH GSSDILRATT SSTSKASSWT SESTAQQFSE PQHTQWVETS PSMKTERPPA STSVAAPITT SVPSVVSGFT TLKTSSTKGI WLEETSADTL IGESTAGPTT HQFAVPTGIS MTGGSSTRGS QGTTHLLTRA TASSETSADL TLATNGVPVS VSPAVSKTAA GSSPPGGTKP SYTMVSSVIP ETSSLQSSAF REGTSLGLTP LNTRHPFSSP EPDSAGHTKI STSIPLLSSA SVLEDKVSAT STFSHHKATS SITTGTPEIS TKTKPSSAVL SSMTLSNAAT SPERVRNATS PLTHPSPSGE ETAGSVLTLS TSAETTDSPN IHPTGTLTSE SSESPSTLSL PSVSGVKTTF SSSTPSTHLF TSGEETEETS NPSVSQPETS VSRVRTTLAS TSVPTPVFPT MDTWPTRSAQ FSSSHLVSEL RATSSTSVTN STGSALPKIS HLTGTATMSQ TNRDTFNDSA APQSTTWPET SPRFKTGLPS ATTTVSTSAT SLSATVMVSK FTSPATSSME ATSIREPSTT ILTTETTNGP GSMAVASTNI PIGKGYITEG RLDTSHLPIG TTASSETSMD FTMAKESVSM SVSPSQSMDA AGSSTPGRTS QFVDTFSDDV YHLTSREITI PRDGTSSALT PQMTATHPPS PDPGSARSTW LGILSSSPSS PTPKVTMSST FSTQRVTTSM IMDTVETSRW NMPNLPSTTS LTPSNIPTSG AIGKSTLVPL DTPSPATSLE ASEGGLPTLS TYPESTNTPS IHLGAHASSE SPSTIKLTMA SVVKPGSYTP LTFPSIETHI HVSTARMAYS SGSSPEMTAP GETNTGSTWD PTTYITTTDP KDTSSAQVST PHSVRTLRTT ENHPKTESAT PAAYSGSPKI SSSPNLTSPA TKAWTITDTT EHSTQLHYTK LAEKSSGFET QSAPGPVSVV IPTSPTIGSS TLELTSDVPG EPLVLAPSEQ TTITLPMATW LSTSLTEEMA STDLDISSPS SPMSTFAIFP PMSTPSHELS KSEADTSAIR NTDSTTLDQH LGIRSLGRTG DLTTVPITPL TTTWTSVIEH STQAQDTLSA TMSPTHVTQS LKDQTSIPAS ASPSHLTEVY PELGTQGRSS SEATTFWKPS TDTLSREIET GPTNIQSTPP MDNTTTGSSS SGVTLGIAHL PIGTSSPAET STNMALERRS STATVSMAGT MGLLVTSAPG RSISQSLGRV SSVLSESTTE GVTDSSKGSS PRLNTQGNTA LSSSLEPSYA EGSQMSTSIP LTSSPTTPDV EFIGGSTFWT KEVTTVMTSD ISKSSARTES SSATLMSTAL GSTENTGKEK LRTASMDLPS PTPSMEVTPW ISLTLSNAPN TTDSLDLSHG VHTSSAGTLA TDRSLNTGVT RASRLENGSD TSSKSLSMGN STHTSMTDTE KSEVSSSIHP RPETSAPGAE TTLTSTPGNR AISLTLPFSS IPVEEVISTG ITSGPDINSA PMTHSPITPP TIVWTSTGTI EQSTQPLHAV SSEKVSVQTQ STPYVNSVAV SASPTHENSV SSGSSTSSPY SSASLESLDS TISRRNAITS WLWDLTTSLP TTTWPSTSLS EALSSGHSGV SNPSSTTTEF PLFSAASTSA AKQRNPETET HGPQNTAAST LNTDASSVTG LSETPVGASI SSEVPLPMAI TSRSDVSGLT SESTANPSLG TASSAGTKLT RTISLPTSES LVSFRMNKDP WTVSIPLGSH PTTNTETSIP VNSAGPPGLS TVASDVIDTP SDGAESIPTV SFSPSPDTEV TTISHFPEKT THSFRTISSL THELTSRVTP IPGDWMSSAM STKPTGASPS ITLGERRTIT SAAPTTSPIV LTASFTETST VSLDNETTVK TSDILDARKT NELPSDSSSS SDLINTSIAS STMDVTKTAS ISPTSISGMT ASSSPSLFSS DRPQVPTSTT ETNTATSPSV SSNTYSLDGG SNVGGTPSTL PPFTITHPVE TSSALLAWSR PVRTFSTMVS TDTASGENPT SSNSVVTSVP APGTWASVGS TTDLPAMGFL KTSPAGEAHS LLASTIEPAT AFTPHLSAAV VTGSSATSEA SLLTTSESKA IHSSPQTPTT PTSGANWETS ATPESLLVVT ETSDTTLTSK ILVTDTILFS TVSTPPSKFP STGTLSGASF PTLLPDTPAI PLTATEPTSS LATSFDSTPL VTIASDSLGT VPETTLTMSE TSNGDALVLK TVSNPDRSIP GITIQGVTES PLHPSSTSPS KIVAPRNTTY EGSITVALST LPAGTTGSLV FSQSSENSET TALVDSSAGL ERASVMPLTT GSQGMASSGG IRSGSTHSTG TKTFSSLPLT MNPGEVTAMS EITTNRLTAT QSTAPKGIPV KPTSAESGLL TPVSASSSPS KAFASLTTAP PSTWGIPQST LTFEFSEVPS LDTKSASLPT PGQSLNTIPD SDASTASSSL SKSPEKNPRA RMMTSTKAIS ASSFQSTGFT ETPEGSASPS MAGHEPRVPT SGTGDPRYAS ESMSYPDPSK ASSAMTSTSL ASKLTTLFST GQAARSGSSS SPISLSTEKE TSFLSPTAST SRKTSLFLGP SMARQPNILV HLQTSALTLS PTSTLNMSQE EPPELTSSQT IAEEEGTTAE TQTLTFTPSE TPTSLLPVSS PTEPTARRKS SPETWASSIS VPAKTSLVET TDGTLVTTIK MSSQAAQGNS TWPAPAEETG TSPAGTSPGS PEVSTTLKIM SSKEPSISPE IRSTVRNSPW KTPETTVPME TTVEPVTLQS TALGSGSTSI SHLPTGTTSP TKSPTENMLA TERVSLSPSP PEAWTNLYSG TPGGTRQSLA TMSSVSLESP TARSITGTGQ QSSPELVSKT TGMEFSMWHG STGGTTGDTH VSLSTSSNIL EDPVTSPNSV SSLTDKSKHK TETWVSTTAI PSTVLNNKIM AAEQQTSRSV DEAYSSTSSW SDQTSGSDIT LGASPDVTNT LYITSTAQTT SLVSLPSGDQ GITSLTNPSG GKTSSASSVT SPSIGLETLR ANVSAVKSDI APTAGHLSQT SSPAEVSILD VTTAPTPGIS TTITTMGTNS ISTTTPNPEV GMSTMDSTPA TERRTTSTEH PSTWSSTAAS DSWTVTDMTS NLKVARSPGT ISTMHTTSFL ASSTELDSMS TPHGRITVIG TSLVTPSSDA SAVKTETSTS ERTLSPSDTT ASTPISTFSR VQRMSISVPD ILSTSWTPSS TEAEDVPVSM VSTDHASTKT DPNTPLSTFL FDSLSTLDWD TGRSLSSATA TTSAPQGATT PQELTLETMI SPATSQLPFS IGHITSAVTP AAMARSSGVT FSRPDPTSKK AEQTSTQLPT TTSAHPGQVP RSAATTLDVI PHTAKTPDAT FQRQGQTALT TEARATSDSW NEKEKSTPSA PWITEMMNSV SEDTIKEVTS SSSVLKDPEY AGHKLGIWDD FIPKFGKAAH MRELPLLSPP QDKEAIHPST NTVETTGWVT SSEHASHSTI PAHSASSKLT SPVVTTSTRE QAIVSMSTTT WPESTRARTE PNSFLTIELR DVSPYMDTSS TTQTSIISSP GSTAITKGPR TEITSSKRIS SSFLAQSMRS SDSPSEAITR LSNFPAMTES GGMILAMQTS PPGATSLSAP TLDTSATASW TGTPLATTQR FTYSEKTTLF SKGPEDTSQP SPPSVEETSS SSSLVPIHAT TSPSNILLTS QGHSPSSTPP VTSVFLSETS GLGKTTDMSR ISLEPGTSLP PNLSSTAGEA LSTYEASRDT KAIHHSADTA VTNMEATSSE YSPIPGHTKP SKATSPLVTS HIMGDITSST SVFGSSETTE IETVSSVNQG LQERSTSQVA SSATETSTVI THVSSGDATT HVTKTQATFS SGTSISSPHQ FITSTNTFTD VSTNPSTSLI MTESSGVTIT TQTGPTGAAT QGPYLLDTST MPYLTETPLA VTPDFMQSEK TTLISKGPKD VTWTSPPSVA ETSYPSSLTP FLVTTIPPAT STLQGQHTSS PVSATSVLTS GLVKTTDMLN TSMEPVTNSP QNLNNPSNEI LATLAATTDI ETIHPSINKA VTNMGTASSA HVLHSTLPVS SEPSTATSPM VPASSMGDAL ASISIPGSET TDIEGEPTSS LTAGRKENST LQEMNSTTES NIILSNVSVG AITEATKMEV PSFDATFIPT PAQSTKFPDI FSVASSRLSN SPPMTISTHM TTTQTGSSGA TSKIPLALDT STLETSAGTP SVVTEGFAHS KITTAMNNDV KDVSQTNPPF QDEASSPSSQ APVLVTTLPS SVAFTPQWHS TSSPVSMSSV LTSSLVKTAG KVDTSLETVT SSPQSMSNTL DDISVTSAAT TDIETTHPSI NTVVTNVGTT GSAFESHSTV SAYPEPSKVT SPNVTTSTME DTTISRSIPK SSKTTRTETE TTSSLTPKLR ETSISQEITS STETSTVPYK ELTGATTEVS RTDVTSSSST SFPGPDQSTV SLDISTETNT RLSTSPIMTE SAEITITTQT GPHGATSQDT FTMDPSNTTP QAGIHSAMTH GFSQLDVTTL MSRIPQDVSW TSPPSVDKTS SPSSFLSSPA MTTPSLISST LPEDKLSSPM TSLLTSGLVK ITDILRTRLE PVTSSLPNFS STSDKILATS KDSKDTKEIF PSINTEETNV KANNSGHESH SPALADSETP KATTQMVITT TVGDPAPSTS MPVHGSSETT NIKREPTYFL TPRLRETSTS QESSFPTDTS FLLSKVPTGT ITEVSSTGVN SSSKISTPDH DKSTVPPDTF TGEIPRVFTS SIKTKSAEMT ITTQASPPES ASHSTLPLDT STTLSQGGTH STVTQGFPYS EVTTLMGMGP GNVSWMTTPP VEETSSVSSL MSSPAMTSPS PVSSTSPQSI PSSPLPVTAL PTSVLVTTTD VLGTTSPESV TSSPPNLSSI THERPATYKD TAHTEAAMHH STNTAVTNVG TSGSGHKSQS SVLADSETSK ATPLMSTTST LGDTSVSTST PNISQTNQIQ TEPTASLSPR LRESSTSEKT SSTTETNTAF SYVPTGAITQ ASRTEISSSR TSISDLDRPT IAPDISTGMI TRLFTSPIMT KSAEMTVTTQ TTTPGATSQG ILPWDTSTTL FQGGTHSTVS QGFPHSEITT LRSRTPGDVS WMTTPPVEET SSGFSLMSPS MTSPSPVSST SPESIPSSPL PVTALLTSVL VTTTNVLGTT SPETVTSSPP NLSSPTQERL TTYKDTAHTE AMHASMHTNT AVANVGTSIS GHESQSSVPA DSHTSKATSP MGITFAMGDT SVSTSTPAFF ETRIQTESTS SLIPGLRDTR TSEEINTVTE TSTVLSEVPT TTTTEVSRTE VITSSRTTIS GPDHSKMSPY ISTETITRLS TFPFVTGSTE MAITNQTGPI GTISQATLTL DTSSTASWEG THSPVTQRFP HSEETTTMSR STKGVSWQSP PSVEETSSPS SPVPLPAITS HSSLYSAVSG SSPTSALPVT SLLTSGRRKT IDMLDTHSEL VTSSLPSASS FSGEILTSEA STNTETIHFS ENTAETNMGT TNSMHKLHSS VSIHSQPSGH TPPKVTGSMM EDAIVSTSTP GSPETKNVDR DSTSPLTPEL KEDSTALVMN STTESNTVFS SVSLDAATEV SRAEVTYYDP TFMPASAQST KSPDISPEAS SSHSNSPPLT ISTHKTIATQ TGPSGVTSLG QLTLDTSTIA TSAGTPSART QDFVDSETTS VMNNDLNDVL KTSPFSAEEA NSLSSQAPLL VTTSPSPVTS TLQEHSTSSL VSVTSVPTPT LAKITDMDTN LEPVTRSPQN LRNTLATSEA TTDTHTMHPS INTAMANVGT TSSPNEFYFT VSPDSDPYKA TSAVVITSTS GDSIVSTSMP RSSAMKKIES ETTFSLIFRL RETSTSQKIG SSSDTSTVFD KAFTAATTEV SRTELTSSSR TSIQGTEKPT MSPDTSTRSV TMLSTFAGLT KSEERTIATQ TGPHRATSQG TLTWDTSITT SQAGTHSAMT HGFSQLDLST LTSRVPEYIS GTSPPSVEKT SSSSSLLSLP AITSPSPVPT TLPESRPSSP VHLTSLPTSG LVKTTDMLAS VASLPPNLGS TSHKIPTTSE DIKDTEKMYP STNIAVTNVG TTTSEKESYS SVPAYSEPPK VTSPMVTSFN IRDTIVSTSM PGSSEITRIE MESTFSVAHG LKGTSTSQDP IVSTEKSAVL HKLTTGATET SRTEVASSRR TSIPGPDHST ESPDISTEVI PSLPISLGIT ESSNMTIITR TGPPLGSTSQ GTFTLDTPTT SSRAGTHSMA TQEFPHSEMT TVMNKDPEIL SWTIPPSIEK TSFSSSLMPS PAMTSPPVSS TLPKTIHTTP SPMTSLLTPS LVMTTDTLGT SPEPTTSSPP NLSSTSHVIL TTDEDTTAIE AMHPSTSTAA TNVETTCSGH GSQSSVLTDS EKTKATAPMD TTSTMGHTTV STSMSVSSET TKIKRESTYS LTPGLRETSI SQNASFSTDT SIVLSEVPTG TTAEVSRTEV TSSGRTSIPG PSQSTVLPEI STRTMTRLFA SPTMTESAEM TIPTQTGPSG STSQDTLTLD TSTTKSQAKT HSTLTQRFPH SEMTTLMSRG PGDMSWQSSP SLENPSSLPS LLSLPATTSP PPISSTLPVT ISSSPLPVTS LLTSSPVTTT DMLHTSPELV TSSPPKLSHT SDERLTTGKD TTNTEAVHPS TNTAASNVEI PSFGHESPSS ALADSETSKA TSPMFITSTQ EDTTVAISTP HFLETSRIQK ESISSLSPKL RETGSSVETS SAIETSAVLS EVSIGATTEI SRTEVTSSSR TSISGSAEST MLPEISTTRK IIKFPTSPIL AESSEMTIKT QTSPPGSTSE STFTLDTSTT PSLVITHSTM TQRLPHSEIT TLVSRGAGDV PRPSSLPVEE TSPPSSQLSL SAMISPSPVS STLPASSHSS SASVTSPLTP GQVKTTEVLD ASAEPETSSP PSLSSTSVEI LATSEVTTDT EKIHPFPNTA VTKVGTSSSG HESPSSVLPD SETTKATSAM GTISIMGDTS VSTLTPALSN TRKIQSEPAS SLTTRLRETS TSEETSLATE ANTVLSKVST GATTEVSRTE AISFSRTSMS GPEQSTMSQD ISIGTIPRIS ASSVLTESAK MTITTQTGPS ESTLESTLNL NTATTPSWVE THSIVIQGFP HPEMTTSMGR GPGGVSWPSP PFVKETSPPS SPLSLPAVTS PHPVSTTFLA HIPPSPLPVT SLLTSGPATT TDILGTSTEP GTSSSSSLST TSHERLTTYK DTAHTEAVHP STNTGGTNVA TTSSGYKSQS SVLADSSPMC TTSTMGDTSV LTSTPAFLET RRIQTELASS LTPGLRESSG SEGTSSGTKM STVLSKVPTG ATTEISKEDV TSIPGPAQST ISPDISTRTV SWFSTSPVMT ESAEITMNTH TSPLGATTQG TSTLATSSTT SLTMTHSTIS QGFSHSQMST LMRRGPEDVS WMSPPLLEKT RPSFSLMSSP ATTSPSPVSS TLPESISSSP LPVTSLLTSG LAKTTDMLHK SSEPVTNSPA NLSSTSVEIL ATSEVTTDTE KTHPSSNRTV TDVGTSSSGH ESTSFVLADS QTSKVTSPMV ITSTMEDTSV STSTPGFFET SRIQTEPTSS LTLGLRKTSS SEGTSLATEM STVLSGVPTG ATAEVSRTEV TSSSRTSISG FAQLTVSPET STETITRLPT SSIMTESAEM MIKTQTDPPG STPESTHTVD ISTTPNWVET HSTVTQRFSH SEMTTLVSRS PGDMLWPSQS SVEETSSASS LLSLPATTSP SPVSSTLVED FPSASLPVTS LLTPGLVITT DRMGISREPG TSSTSNLSST SHERLTTLED TVDTEDMQPS THTAVTNVRT SISGHESQSS VLSDSETPKA TSPMGTTYTM GETSVSISTS DFFETSRIQI EPTSSLTSGL RETSSSERIS SATEGSTVLS EVPSGATTEV SRTEVISSRG TSMSGPDQFT ISPDISTEAI TRLSTSPIMT ESAESAITIE TGSPGATSEG TLTLDTSTTT FWSGTHSTAS PGFSHSEMTT LMSRTPGDVP WPSLPSVEEA SSVSSSLSSP AMTSTSFFSA LPESISSSPH PVTALLTLGP VKTTDMLRTS SEPETSSPPN LSSTSAEILA TSEVTKDREK IHPSSNTPVV NVGTVIYKHL SPSSVLADLV TTKPTSPMAT TSTLGNTSVS TSTPAFPETM MTQPTSSLTS GLREISTSQE TSSATERSAS LSGMPTGATT KVSRTEALSL GRTSTPGPAQ STISPEISTE TITRISTPLT TTGSAEMTIT PKTGHSGASS QGTFTLDTSS RASWPGTHSA ATHRSPHSGM TTPMSRGPED VSWPSRPSVE KTSPPSSLVS LSAVTSPSPL YSTPSESSHS SPLRVTSLFT PVMMKTTDML DTSLEPVTTS PPSMNITSDE SLATSKATME TEAIQLSENT AVTQMGTISA RQEFYSSYPG LPEPSKVTSP VVTSSTIKDI VSTTIPASSE ITRIEMESTS TLTPTPRETS TSQEIHSATK PSTVPYKALT SATIEDSMTQ VMSSSRGPSP DQSTMSQDIS SEVITRLSTS PIKAESTEMT ITTQTGSPGA TSRGTLTLDT STTFMSGTHS TASQGFSHSQ MTALMSRTPG DVPWLSHPSV EEASSASFSL SSPVMTSSSP VSSTLPDSIH SSSLPVTSLL TSGLVKTTEL LGTSSEPETS SPPNLSSTSA EILATTEVTT DTEKLEMTNV VTSGYTHESP SSVLADSVTT KATSSMGITY PTGDTNVLTS TPAFSDTSRI QTKSKLSLTP GLMETSISEE TSSATEKSTV LSSVPTGATT EVSRTEAISS SRTSIPGPAQ STMSSDTSME TITRISTPLT RKESTDMAIT PKTGPSGATS QGTFTLDSSS TASWPGTHSA TTQRFPQSVV TTPMSRGPED VSWPSPLSVE KNSPPSSLVS SSSVTSPSPL YSTPSGSSHS SPVPVTSLFT SIMMKATDML DASLEPETTS APNMNITSDE SLATSKATTE TEAIHVFENT AASHVETTSA TEELYSSSPG FSEPTKVISP VVTSSSIRDN MVSTTMPGSS GITRIEIESM SSLTPGLRET RTSQDITSST ETSTVLYKMS SGATPEVSRT EVMPSSRTSI PGPAQSTMSL DISDEVVTRL STSPIMTESA EITITTQTGY SLATSQVTLP LGTSMTFLSG THSTMSQGLS HSEMTNLMSR GPESLSWTSP RFVETTRSSS SLTSLPLTTS LSPVSSTLLD SSPSSPLPVT SLILPGLVKT TEVLDTSSEP KTSSSPNLSS TSVEIPATSE IMTDTEKIHP SSNTAVAKVR TSSSVHESHS SVLADSETTI TIPSMGITSA VDDTTVFTSN PAFSETRRIP TEPTFSLTPG FRETSTSEET TSITETSAVL YGVPTSATTE VSMTEIMSSN RTHIPDSDQS TMSPDIITEV ITRLSSSSMM SESTQMTITT QKSSPGATAQ STLTLATTTA PLARTHSTVP PRFLHSEMTT LMSRSPENPS WKSSPFVEKT SSSSSLLSLP VTTSPSVSST LPQSIPSSSF SVTSLLTPGM VKTTDTSTEP GTSLSPNLSG TSVEILAASE VTTDTEKIHP SSSMAVTNVG TTSSGHELYS SVSIHSEPSK ATYPVGTPSS MAETSISTSM PANFETTGFE AEPFSHLTSG FRKTNMSLDT SSVTPTNTPS SPGSTHLLQS SKTDFTSSAK TSSPDWPPAS QYTEIPVDII TPFNASPSIT ESTGITSFPE SRFTMSVTES THHLSTDLLP SAETISTGTV MPSLSEAMTS FATTGVPRAI SGSGSPFSRT ESGPGDATLS TIAESLPSST PVPFSSSTFT TTDSSTIPAL HEITSSSATP YRVDTSLGTE SSTTEGRLVM VSTLDTSSQP GRTSSTPILD TRMTESVELG TVTSAYQVPS LSTRLTRTDG IMEHITKIPN EAAHRGTIRP VKGPQTSTSP ASPKGLHTGG TKRMETTTTA LKTTTTALKT TSRATLTTSV YTPTLGTLTP LNASRQMAST ILTEMMITTP YVFPDVPETT SSLATSLGAE TSTALPRTTP SVLNRESETT ASLVSRSGAE RSPVIQTLDV SSSEPDTTAS WVIHPAETIP TVSKTTPNFF HSELDTVSST ATSHGADVSS AIPTNISPSE LDALTPLVTI SGTDTSTTFP TLTKSPHETE TRTTWLTHPA ETSSTIPRTI PNFSHHESDA TPSIATSPGA ETSSAIPIMT VSPGAEDLVT SQVTSSGTDR NMTIPTLTLS PGEPKTIASL VTHPEAQTSS AIPTSTISPA VSRLVTSMVT SLAAKTSTTN RALTNSPGEP ATTVSLVTHP AQTSPTVPWT TSIFFHSKSD TTPSMTTSHG AESSSAVPTP TVSTEVPGVV TPLVTSSRAV ISTTIPILTL SPGEPETTPS MATSHGEEAS SAIPTPTVSP GVPGVVTSLV TSSRAVTSTT IPILTFSLGE PETTPSMATS HGTEAGSAVP TVLPEVPGMV TSLVASSRAV TSTTLPTLTL SPGEPETTPS MATSHGAEAS STVPTVSPEV PGVVTSLVTS SSGVNSTSIP TLILSPGELE TTPSMATSHG AEASSAVPTP TVSPGVSGVV TPLVTSSRAV TSTTIPILTL SSSEPETTPS MATSHGVEAS SAVLTVSPEV PGMVTSLVTS SRAVTSTTIP TLTISSDEPE TTTSLVTHSE AKMISAIPTL AVSPTVQGLV TSLVTSSGSE TSAFSNLTVA SSQPETIDSW VAHPGTEASS VVPTLTVSTG EPFTNISLVT HPAESSSTLP RTTSRFSHSE LDTMPSTVTS PEAESSSAIS TTISPGIPGV LTSLVTSSGR DISATFPTVP ESPHESEATA SWVTHPAVTS TTVPRTTPNY SHSEPDTTPS IATSPGAEAT SDFPTITVSP DVPDMVTSQV TSSGTDTSIT IPTLTLSSGE PETTTSFITY SETHTSSAIP TLPVSPGASK MLTSLVISSG TDSTTTFPTL TETPYEPETT AIQLIHPAET NTMVPKTTPK FSHSKSDTTL PVAITSPGPE ASSAVSTTTI SPDMSDLVTS LVPSSGTDTS TTFPTLSETP YEPETTVTWL THPAETSTTV SGTIPNFSHR GSDTAPSMVT SPGVDTRSGV PTTTIPPSIP GVVTSQVTSS ATDTSTAIPT LTPSPGEPET TASSATHPGT QTGFTVPIRT VPSSEPDTMA SWVTHPPQTS TPVSRTTSSF SHSSPDATPV MATSPRTEAS SAVLTTISPG APEMVTSQIT SSGAATSTTV PTLTHSPGMP ETTALLSTHP RTGTSKTFPA STVFPQVSET TASLTIRPGA ETSTALPTQT TSSLFTLLVT GTSRVDLSPT ASPGVSAKTA PLSTHPGTET STMIPTSTLS LGLLETTGLL ATSSSAETST STLTLTVSPA VSGLSSASIT TDKPQTVTSW NTETSPSVTS VGPPEFSRTV TGTTMTLIPS EMPTPPKTSH GEGVSPTTIL RTTMVEATNL ATTGSSPTVA KTTTTFNTLA GSLFTPLTTP GMSTLASESV TSRTSYNHRS WISTTSSYNR RYWTPATSTP VTSTFSPGIS TSSIPSSTAA TVPFMVPFTL NFTITNLQYE EDMRHPGSRK FNATERELQG LLKPLFRNSS LEYLYSGCRL ASLRPEKDSS AMAVDAICTH RPDPEDLGLD RERLYWELSN LTNGIQELGP YTLDRNSLYV NGFTHRSSMP TTSTPGTSTV DVGTSGTPSS SPSPTAAGPL LMPFTLNFTI TNLQYEEDMR RTGSRKFNTM ESVLQGLLKP LFKNTSVGPL YSGCRLTLLR PEKDGAATGV DAICTHRLDP KSPGLNREQL YWELSKLTND IEELGPYTLD RNSLYVNGFT HQSSVSTTST PGTSTVDLRT SGTPSSLSSP TIMAAGPLLV PFTLNFTITN LQYGEDMGHP GSRKFNTTER VLQGLLGPIF KNTSVGPLYS GCRLTSLRSE KDGAATGVDA ICIHHLDPKS PGLNRERLYW ELSQLTNGIK ELGPYTLDRN SLYVNGFTHR TSVPTTSTPG TSTVDLGTSG TPFSLPSPAT AGPLLVLFTL NFTITNLKYE EDMHRPGSRK FNTTERVLQT LLGPMFKNTS VGLLYSGCRL TLLRSEKDGA ATGVDAICTH RLDPKSPGLD REQLYWELSQ LTNGIKELGP YTLDRNSLYV NGFTHWIPVP TSSTPGTSTV DLGSGTPSSL PSPTAAGPLL VPFTLNFTIT NLQYEEDMHH PGSRKFNTTE RVLQGLLGPM FKNTSVGLLY SGCRLTLLRS EKDGAATGVD AICTHRLDPK SPGVDREQLY WELSQLTNGI KELGPYTLDR NSLYVNGFTH QTSAPNTSTP GTSTVDLGTS GTPSSLPSPT SAGPLLVPFT LNFTITNLQY EEDMRHPGSR KFNTTERVLQ GLLKPLFKST SVGPLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGV DREQLYWELS QLTNGIKELG PYTLDRNSLY VNGFTHQTSA PNTSTPGTST VDLGTSGTPS SLPSPTSAGP LLVPFTLNFT ITNLQYEEDM HHPGSRKFNT TERVLQGLLG PMFKNTSVGL LYSGCRLTLL RPEKNGAATG MDAICSHRLD PKSPGLNREQ LYWELSQLTH GIKELGPYTL DRNSLYVNGF THRSSVAPTS TPGTSTVDLG TSGTPSSLPS PTTAVPLLVP FTLNFTITNL QYGEDMRHPG SRKFNTTERV LQGLLGPLFK NSSVGPLYSG CRLISLRSEK DGAATGVDAI CTHHLNPQSP GLDREQLYWQ LSQMTNGIKE LGPYTLDRNS LYVNGFTHRS SGLTTSTPWT STVDLGTSGT PSPVPSPTTA GPLLVPFTLN FTITNLQYEE DMHRPGSRKF NTTERVLQGL LSPIFKNSSV GPLYSGCRLT SLRPEKDGAA TGMDAVCLYH PNPKRPGLDR EQLYWELSQL THNITELGPY SLDRDSLYVN GFTHQNSVPT TSTPGTSTVY WATTGTPSSF PGHTEPGPLL IPFTFNFTIT NLHYEENMQH PGSRKFNTTE RVLQGLLKPL FKNTSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY WELSQLTHNI TELGPYSLDR DSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT EPGPLLIPFT FNFTITNLHY EENMQHPGSR KFNTTERVLQ GLLKPLFKNT SVGPLYSGCR LTLLRPEKHE AATGVDTICT HRVDPIGPGL DRERLYWELS QLTNSITELG PYTLDRDSLY VNGFNPRSSV PTTSTPGTST VHLATSGTPS SLPGHTAPVP LLIPFTLNFT ITNLHYEENM QHPGSRKFNT TERVLQGLLK PLFKNTSVGP LYSGCRLTLL RPEKHEAATG VDTICTHRVD PIGPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTSAGPLLVP FTLNFTITNL QYEEDMHHPG SRKFNTTERV LQGLLGPMFK NTSVGLLYSG CRLTLLRPEK NGAATGMDAI CSHRLDPKSP GLDREQLYWE LSQLTHGIKE LGPYTLDRNS LYVNGFTHRS SVAPTSTPGT STVDLGTSGT PSSLPSPTTA VPLLVPFTLN FTITNLQYGE DMRHPGSRKF NTTERVLQGL LGPLFKNSSV GPLYSGCRLI SLRSEKDGAA TGVDAICTHH LNPQSPGLDR EQLYWQLSQM TNGIKELGPY TLDRNSLYVN GFTHRSSGLT TSTPWTSTVD LGTSGTPSPV PSPTTAGPLL VPFTLNFTIT NLQYEEDMHR PGSRKFNATE RVLQGLLSPI FKNSSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY WELSQLTHNI TELGPYSLDR DSLYVNGFTH QSSMTTTRTP DTSTMHLATS RTPASLSGPT TASPLLVLFT INCTITNLQY EEDMRRTGSR KFNTMESVLQ GLLKPLFKNT SVGPLYSGCR LTLLRPKKDG AATGVDAICT HRLDPKSPGL NREQLYWELS KLTNDIEELG PYTLDRNSLY VNGFTHQSSV STTSTPGTST VDLRTSGTPS SLSSPTIMXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTERVLQGL LRPLFKNTSV SSLYSGCRLT LLRPEKDGAA TRVDAACTYR PDPKSPGLDR EQLYWELSQL THSITELGPY TLDRVSLYVN GFNPRSSVPT TSTPGTSTVH LATSGTPSSL PGHTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE RVLQGLLKPL FRNSSLEYLY SGCRLASLRP EKDSSAMAVD AICTHRPDPE DLGLDRERLY WELSNLTNGI QELGPYTLDR NSLYVNGFTH RSSGLTTSTP WTSTVDLGTS GTPSPVPSPT TAGPLLVPFT LNFTITNLQY EEDMHRPGSR RFNTTERVLQ GLLTPLFKNT SVGPLYSGCR LTLLRPEKQE AATGVDTICT HRVDPIGPGL DRERLYWELS QLTNSITELG PYTLDRDSLY VNGFNPWSSV PTTSTPGTST VHLATSGTPS SLPGHTAPVP LLIPFTLNFT ITDLHYEENM QHPGSRKFNT TERVLQGLLK PLFKSTSVGP LYSGCRLTLL RPEKHGAATG VDAICTLRLD PTGPGLDRER LYWELSQLTN SVTELGPYTL DRDSLYVNGF THRSSVPTTS IPGTSAVHLE TSGTPASLPG HTAPGPLLVP FTLNFTITNL QYEEDMRHPG SRKFSTTERV LQGLLKPLFK NTSVSSLYSG CRLTLLRPEK DGAATRVDAV CTHRPDPKSP GLDRERLYWK LSQLTHGITE LGPYTLDRHS LYVNGFTHQS SMTTTRTPDT STMHLATSRT PASLSGPTTA SPLLVLFTIN FTITNLRYEE NMHHPGSRKF NTTERVLQGL LRPVFKNTSV GPLYSGCRLT TLRPKKDGAA TKVDAICTYR PDPKSPGLDR EQLYWELSQL THSITELGPY TQDRDSLYVN GFTHRSSVPT TSIPGTSAVH LETSGTPASL PGHTAPGPLL VPFTLNFTIT NLQYEEDMRH PGSRKFNTTE RVLQGLLKPL FKSTSVGPLY SGCRLTLLRP EKRGAATGVD TICTHRLDPL NPGLDREQLY WELSKLTRGI IELGPYLLDR GSLYVNGFTH RTSVPTTSTP GTSTVDLGTS GTPFSLPSPA XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTERVLQ TLLGPMFKNT SVGLLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGV DREQLYWELS QLTNGIKELG PYTLDRNSLY VNGFTHWIPV PTSSTPGTST VDLGSGTPSS LPSPTTAGPL LVPFTLNFTI TNLKYEEDMH CPGSRKFNTT ERVLQSLLGP MFKNTSVGPL YSGCRLTLLR SEKDGAATGV DAICTHRLDP KSPGVDREQL YWELSQLTNG IKELGPYTLD RNSLYVNGFT HQTSAPNTST PGTSTVDLGT SGTPSSLPSP TXXXPLLXPF TXNXTITNLX XXXXMXXPGS RKFNTTEXVL QGLLXPXFKN XSVGXLYSGC RLTXLRXEKX GAATGXDAIC XHXXXPKXPG LXXEXLYWEL SXLTXXIXEL GPYTLDRXSL YVNGFTHWIP VPTSSTPGTS TVDLGSGTPS SLPSPTTAGP LLVPFTLNFT ITNLKYEEDM HCPGSRKFNT TERVLQSLLG PMFKNTSVGP LYSGCRLTSL RSEKDGAATG VDAICTHRVD PKSPGVDREQ LYWELSQLTN GIKELGPYTL DRNSLYVNGF THQTSAPNTS TPGTSTVXXG TSGTPSSXPX XTSAGPLLVP FTLNFTITNL QYEEDMHHPG SRKFNTTERV LQGLLGPMFK NTSVGLLYSG CRLTLLRPEK NGATTGMDAI CTHRLDPKSP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHXX SXPTTSTPGT STVXXGTSGT PSSXPXXTXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTERVLQGL LKPLFRNSSL EYLYSGCRLA SLRPEKDSSA MAVDAICTHR PDPEDLGLDR ERLYWELSNL TNGIQELGPY TLDRNSLYVN GFTHRSSMPT TSTPGTSTVD VGTSGTPSSS PSPTTAGPLL IPFTLNFTIT NLQYGEDMGH PGSRKFNTTE RVLQGLLGPI FKNTSVGPLY SGCRLTSLRS EKDGAATGVD AICIHHLDPK SPGLNRERLY WELSQLTNGI KELGPYTLDR NSLYVNGFTH RTSVPTTSTP GTSTVDLGTS GTPFSLPSPA TAGPLLVLFT LNFTITNLKY EEDMHRPGSR KFNTTERVLQ TLLGPMFKNT SVGLLYSGCR LTLLRSEKDG AATGVDAICT HRLDPKSPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHXXSX PTTSTPGTST VXXGTSGTPS SXPXXTXXXP LLXPFTXNXT ITNLXXXXXM XXPGSRKFNT TERVLQGLLR PVFKNTSVGP LYSGCRLTLL RPKKDGAATK VDAICTYRPD PKSPGLDREQ LYWELSQLTH SITELGPYTQ DRDSLYVNGF THRSSVPTTS IPGTSAVHLE TTGTPSSFPG HTEPGPLLIP FTFNFTITNL RYEENMQHPG SRKFNTTERV LQGLLTPLFK NTSVGPLYSG CRLTLLRPEK QEAATGVDTI CTHRVDPIGP GLDRERLYWE LSQLTNSITE LGPYTLDRDS LYVDGFNPWS SVPTTSTPGT STVHLATSGT PSPLPGHTAP VPLLIPFTLN FTITDLHYEE NMQHPGSRKF NTTERVLQGL LKPLFKSTSV GPLYSGCRLT LLRPEKHGAA TGVDAICTLR LDPTGPGLDR ERLYWELSQL TNSITELGPY TLDRDSLYVN GFNPWSSVPT TSTPGTSTVH LATSGTPSSL PGHTTAGPLL VPFTLNFTIT NLKYEEDMHC PGSRKFNTTE RVLQSLHGPM FKNTSVGPLY SGCRLTLLRS EKDGAATGVD AICTHRLDPK SPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH XXSXPTTSTP GTSTVXXGTS GTPSSXPXXT XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTEXVLQ GLLXPXFKNX SVGXLYSGCR LTXLRXEKXG AATGXDAICX HXXXPKXPGL XXEXLYWELS XLTNSITELG PYTLDRDSLY VNGFTHRSSM PTTSIPGTSA VHLETSGTPA SLPGHTAPGP LLVPFTLNFT ITNLQYEEDM RHPGSRKFNT TERVLQGLLK PLFKSTSVGP LYSGCRLTLL RPEKRGAATG VDTICTHRLD PLNPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTXXXPLLXP FTXNXTITNL XXXXXMXXPG SRKFNTTEXV LQGLLXPXFK NXSVGXLYSG CRLTXLRXEK XGAATGXDAI CXHXXXPKXP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFHPRS SVPTTSTPGT STVHLATSGT PSSLPGHTAP VPLLIPFTLN FTITNLHYEE NMQHPGSRKF NTTERVLQGL LGPMFKNTSV GLLYSGCRLT LLRPEKNGAA TGMDAICSHR LDPKSPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHXXSXPT TSTPGTSTVX XGTSGTPSSX PXXTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE XVLQGLLXPX FKNXSVGXLY SGCRLTXLRX EKXGAATGXD AICXHXXXPK XPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT EPGPLLIPFT FNFTITNLHY EENMQHPGSR KFNTTERVLQ GLLTPLFKNT SVGPLYSGCR LTLLRPEKQE AATGVDTICT HRVDPIGPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHXXSX PTTSTPGTST VXXGTSGTPS SXPXXTXXXP LLXPFTXNXT ITNLXXXXXM XXPGSRKFNT TEXVLQGLLX PXFKNXSVGX LYSGCRLTXL RXEKXGAATG XDAICXHXXX PKXPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THRSSVPTTS SPGTSTVHLA TSGTPSSLPG HTAPVPLLIP FTLNFTITNL HYEENMQHPG SRKFNTTERV LQGLLKPLFK STSVGPLYSG CRLTLLRPEK HGAATGVDAI CTLRLDPTGP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHXX SXPTTSTPGT STVXXGTSGT PSSXPXXTXX XPLLXPFTXN XTITNLXXXX XMXXPGSRKF NTTEXVLQGL LXPXFKNXSV GXLYSGCRLT XLRXEKXGAA TGXDAICXHX XXPKXPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHRTSVPT TSTPGTSTVH LATSGTPSSL PGHTAPVPLL IPFTLNFTIT NLQYEEDMHR PGSRKFNTTE RVLQGLLSPI FKNSSVGPLY SGCRLTSLRP EKDGAATGMD AVCLYHPNPK RPGLDREQLY CELSQLTHNI TELGPYSLDR DSLYVNGFTH QNSVPTTSTP GTSTVYWATT GTPSSFPGHT XXXPLLXPFT XNXTITNLXX XXXMXXPGSR KFNTTEXVLQ GLLXPXFKNX SVGXLYSGCR LTXLRXEKXG AATGXDAICX HXXXPKXPGL XXEXLYWELS XLTXXIXELG PYTLDRXSLY VNGFTHWSSG LTTSTPWTST VDLGTSGTPS PVPSPTTAGP LLVPFTLNFT ITNLQYEEDM HRPGSRKFNA TERVLQGLLS PIFKNTSVGP LYSGCRLTLL RPEKQEAATG VDTICTHRVD PIGPGLXXEX LYWELSXLTX XIXELGPYTL DRXSLYVNGF THXXSXPTTS TPGTSTVXXG TSGTPSSXPX XTXXXPLLXP FTXNXTITNL XXXXXMXXPG SRKFNTTEXV LQGLLXPXFK NXSVGXLYSG CRLTXLRXEK XGAATGXDAI CXHXXXPKXP GLXXEXLYWE LSXLTXXIXE LGPYTLDRXS LYVNGFTHRS FGLTTSTPWT STVDLGTSGT PSPVPSPTTA GPLLVPFTLN FTITNLQYEE DMHRPGSRKF NTTERVLQGL LTPLFRNTSV SSLYSGCRLT LLRPEKDGAA TRVDAVCTHR PDPKSPGLXX EXLYWELSXL TXXIXELGPY TLDRXSLYVN GFTHXXSXPT TSTPGTSTVX XGTSGTPSSX PXXTXXXPLL XPFTXNXTIT NLXXXXXMXX PGSRKFNTTE XVLQGLLXPX FKNXSVGXLY SGCRLTXLRX EKXGAATGXD AICXHXXXPK XPGLXXEXLY WELSXLTXXI XELGPYTLDR XSLYVNGFTH WIPVPTSSTP GTSTVDLGSG TPSSLPSPTT AGPLLVPFTL NFTITNLQYG EDMGHPGSRK FNTTERVLQG LLGPIFKNTS VGPLYSGCRL TSLRSEKDGA ATGVDAICIH HLDPKSPGLX XEXLYWELSX LTXXIXELGP YTLDRXSLYV NGFTHXXSXP TTSTPGTSTV XXGTSGTPSS XPXXTXXXPL LXPFTXNXTI TNLXXXXXMX XPGSRKFNTT EXVLQGLLXP XFKNXSVGXL YSGCRLTXLR XEKXGAATGX DAICXHXXXP KXPGLXXEXL YWELSXLTXX IXELGPYTLD RXSLYVNGFT HQTFAPNTST PGTSTVDLGT SGTPSSLPSP TSAGPLLVPF TLNFTITNLQ YEEDMHHPGS RKFNTTERVL QGLLGPMFKN TSVGLLYSGC RLTLLRPEKN GAATRVDAVC THRPDPKSPG LXXEXLYWEL SXLTXXIXEL GPYTLDRXSL YVNGFTHXXS XPTTSTPGTS TVXXGTSGTP SSXPXXTAPV PLLIPFTLNF TITNLHYEEN MQHPGSRKFN TTERVLQGLL KPLFKSTSVG PLYSGCRLTL LRPEKHGAAT GVDAICTLRL DPTGPGLDRE RLYWELSQLT NSVTELGPYT LDRDSLYVNG FTQRSSVPTT SIPGTSAVHL ETSGTPASLP GHTAPGPLLV PFTLNFTITN LQYEVDMRHP GSRKFNTTER VLQGLLKPLF KSTSVGPLYS GCRLTLLRPE KRGAATGVDT ICTHRLDPLN PGLDREQLYW ELSKLTRGII ELGPYLLDRG SLYVNGFTHR NFVPITSTPG TSTVHLGTSE TPSSLPRPIV PGPLLVPFTL NFTITNLQYE EAMRHPGSRK FNTTERVLQG LLRPLFKNTS IGPLYSSCRL TLLRPEKDKA ATRVDAICTH HPDPQSPGLN REQLYWELSQ LTHGITELGP YTLDRDSLYV DGFTHWSPIP TTSTPGTSIV NLGTSGIPPS LPETTXXXPL LXPFTXNXTI TNLXXXXXMX XPGSRKFNTT ERVLQGLLKP LFKSTSVGPL YSGCRLTLLR PEKDGVATRV DAICTHRPDP KIPGLDRQQL YWELSQLTHS ITELGPYTLD RDSLYVNGFT QRSSVPTTST PGTFTVQPET SETPSSLPGP TATGPVLLPF TLNFTITNLQ YEEDMHRPGS RKFNTTERVL QGLLMPLFKN TSVSSLYSGC RLTLLRPEKD GAATRVDAVC THRPDPKSPG LDRERLYWKL SQLTHGITEL GPYTLDRHSL YVNGFTHQSS MTTTRTPDTS TMHLATSRTP ASLSGPTTAS PLLVLFTINF TITNLRYEEN MHHPGSRKFN TTERVLQGLL RPVFKNTSVG PLYSGCRLTL LRPKKDGAAT KVDAICTYRP DPKSPGLDRE QLYWELSQLT HSITELGPYT LDRDSLYVNG FTQRSSVPTT SIPGTPTVDL GTSGTPVSKP GPSAASPLLV LFTLNFTITN LRYEENMQHP GSRKFNTTER VLQGLLRSLF KSTSVGPLYS GCRLTLLRPE KDGTATGVDA ICTHHPDPKS PRLDREQLYW ELSQLTHNIT ELGHYALDND SLFVNGFTHR SSVSTTSTPG TPTVYLGASK TPASIFGPSA ASHLLILFTL NFTITNLRYE ENMWPGSRKF NTTERVLQGL LRPLFKNTSV GPLYSGSRLT LLRPEKDGEA TGVDAICTHR PDPTGPGLDR EQLYLELSQL THSITELGPY TLDRDSLYVN GFTHRSSVPT TSTGVVSEEP FTLNFTINNL RYMADMGQPG SLKFNITDNV MKHLLSPLFQ RSSLGARYTG CRVIALRSVK NGAETRVDLL CTYLQPLSGP GLPIKQVFHE LSQQTHGITR LGPYSLDKDS LYLNGYNEPG LDEPPTTPKP ATTFLPPLSE ATTAMGYHLK TLTLNFTISN LQYSPDMGKG SATFNSTEGV LQHLLRPLFQ KSSMGPFYLG CQLISLRPEK DGAATGVDTT CTYHPDPVGP GLDIQQLYWE LSQLTHGVTQ LGFYVLDRDS LFINGYAPQN LSIRGEYQIN FHIVNWNLSN PDPTSSEYIT LLRDIQDKVT TLYKGSQLHD TFRFCLVTNL TMDSVLVTVK ALFSSNLDPS LVEQVFLDKT LNASFHWLGS TYQLVDIHVT EMESSVYQPT SSSSTQHFYL NFTITNLPYS QDKAQPGTTN YQRNKRNIED ALNQLFRNSS IKSYFSDCQV STFRSVPNRH HTGVDSLCNF SPLARRVDRV AIYEEFLRMT RNGTQLQNFT LDRSSVLVDG YSPNRNEPLT GNSDLPFWAV ILIGLAGLLG LITCLICGVL VTTRRRKKEG EYNVQQQCPG YYQSHLDLED LQ Stack trace follows .... at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:609) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: org.biojava.bio.symbol.IllegalAlphabetException: Can't handle this in the general case: PROTEIN-TERM at org.biojava.bio.symbol.PackingFactory.getPacking(PackingFactory.java:75) at org.biojava.bio.symbol.PackedSymbolListFactory.makeSymbolList(PackedSymbolListFactory.java:88) at org.biojava.bio.seq.io.ChunkedSymbolListFactory.addSymbols(ChunkedSymbolListFactory.java:220) at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.addSymbols(SimpleRichSequenceBuilder.java:256) at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:604) ... 3 more -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:14:03 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:14:03 -0400 Subject: [Biojava-dev] [Bug 2316] New: UniProtFormat fail on read RX record. Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2316 Summary: UniProtFormat fail on read RX record. Product: BioJava Version: live (CVS source) Platform: PC OS/Version: All Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: miyabe at port4.info Isn't the delimiter not ";" but "; "? I changed row #481 of UniProtFormat to below and it works. String[] refs = val.split("; "); -- Exception in thread "main" org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at jp.co.maze.intact.RestructMain.exec(RestructMain.java:90) at jp.co.maze.intact.RestructMain.main(RestructMain.java:42) Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.UniProtFormat Accession=Q13362 Id= Comments= Parse_block=RN [6]RP IDENTIFICATION AS A RENAL CANCER ANTIGEN.RC TISSUE=Renal cell carcinoma;RX MEDLINE=99438124; PubMed=10508479; DOI=10.1002/(SICI)1097-0215(19991112)83:4<456::AID-IJC4>3.0.CO;2-5;RA Scanlan M.J., Gordan J.D., Williamson B., Stockert E., Bander N.H., Jongeneel C.V., Gure A.O., Jaeger D., Jaeger E., Knuth A., Chen Y.-T., Old L.J.;RT "Antigens recognized by autologous antibody in patients with renal- cell carcinoma.";RL Int. J. Cancer 83:456-464(1999). Stack trace follows .... at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:615) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 1 at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:486) ... 3 more -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:28:35 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:28:35 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706110928.l5B9SZGD031197@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 ------- Comment #2 from brunner at imp.ac.at 2007-06-11 05:28 EST ------- Created an attachment (id=673) --> (http://bugzilla.open-bio.org/attachment.cgi?id=673&action=view) More exact values for some AA masses -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:32:52 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:32:52 -0400 Subject: [Biojava-dev] [Bug 2315] UniProtFormat fail on long protein sequence. In-Reply-To: Message-ID: <200706110932.l5B9WqZJ032294@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2315 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:33:00 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:00 -0400 Subject: [Biojava-dev] [Bug 2316] UniProtFormat fail on read RX record. In-Reply-To: Message-ID: <200706110933.l5B9X0IB032352@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2316 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:33:26 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:26 -0400 Subject: [Biojava-dev] [Bug 2315] UniProtFormat fail on long protein sequence. In-Reply-To: Message-ID: <200706110933.l5B9XQdu032525@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2315 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |holland at ebi.ac.uk Status|ASSIGNED |NEW -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 09:33:34 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 05:33:34 -0400 Subject: [Biojava-dev] [Bug 2316] UniProtFormat fail on read RX record. In-Reply-To: Message-ID: <200706110933.l5B9XYFi032578@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2316 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |holland at ebi.ac.uk Status|ASSIGNED |NEW -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 14:47:30 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 10:47:30 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706111447.l5BElUwF016411@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |NEW ------- Comment #3 from holland at ebi.ac.uk 2007-06-11 10:47 EST ------- Done on head of CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 11 14:47:41 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Jun 2007 10:47:41 -0400 Subject: [Biojava-dev] [Bug 2308] More exact values for amino acid masses In-Reply-To: Message-ID: <200706111447.l5BElfdT016435@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2308 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from holland at ebi.ac.uk 2007-06-11 10:47 EST ------- Done on head of CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 13 08:28:49 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 13 Jun 2007 04:28:49 -0400 Subject: [Biojava-dev] [Bug 2301] Initialization error of org.biojava.bio.alignment.NeedlemanWunsch when considering affine gap penalty In-Reply-To: Message-ID: <200706130828.l5D8SnSD032089@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2301 mark.schreiber at novartis.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from mark.schreiber at novartis.com 2007-06-13 04:28 EST ------- fixed in CVS -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From markjschreiber at gmail.com Wed Jun 13 08:43:57 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 13 Jun 2007 16:43:57 +0800 Subject: [Biojava-dev] Problem with Phylo Code in CVS Message-ID: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Hi = CVS is currently unbuildable because of recent commits of phylo code. There are two problems. 1) The code has a reliance on JGraphT. This needs to be commited in the appropriate place and added to the classpath etc in the ant build file. 2) The code contains java 1.5 reliant code (generics) that won't compile with the biojava standard JDK (1.4.2). This is not really an issue as I am about to do a final BioJava 1.5 build after which we switch to JDK1.5 (or maybe even 1.6). Can someone checkin JGraphT and make the appropriate changes to the build XML? Please also ensure the licenses are acceptable and properly replicated. - Mark From holland at ebi.ac.uk Wed Jun 13 09:01:45 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 10:01:45 +0100 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Message-ID: <466FB279.5090506@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 JGraphT is LGPL. I have added the current JGraphT JAR file (Java 1.5) and modified build.xml. Can you temporarily omit JGraphT and the phylo packages from the 1.5 build process? cheers, Richard Mark Schreiber wrote: > Hi = > > CVS is currently unbuildable because of recent commits of phylo code. > There are two problems. > > 1) The code has a reliance on JGraphT. This needs to be commited in > the appropriate place and added to the classpath etc in the ant build > file. > > 2) The code contains java 1.5 reliant code (generics) that won't > compile with the biojava standard JDK (1.4.2). This is not really an > issue as I am about to do a final BioJava 1.5 build after which we > switch to JDK1.5 (or maybe even 1.6). > > Can someone checkin JGraphT and make the appropriate changes to the > build XML? Please also ensure the licenses are acceptable and properly > replicated. > > - Mark > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGb7J54C5LeMEKA/QRAofUAJ9fhc2CffT63qasVhmoy8hHz9j4+wCbB1eg JWLke1WXeYDxq4ijBDDVDLY= =zWib -----END PGP SIGNATURE----- From markjschreiber at gmail.com Wed Jun 13 09:15:54 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 13 Jun 2007 17:15:54 +0800 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <466FB279.5090506@ebi.ac.uk> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> <466FB279.5090506@ebi.ac.uk> Message-ID: <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> Yes, I will omit the phylo package as it is not stable (or finished). Also noticed that the MassCalcTest fails after the update of the new Mass values. Does no-one attempt to run tests before commiting?? I will commit a patch to the test today. - Mark On 6/13/07, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > JGraphT is LGPL. > > I have added the current JGraphT JAR file (Java 1.5) and modified build.xml. > > Can you temporarily omit JGraphT and the phylo packages from the 1.5 > build process? > > cheers, > Richard > > Mark Schreiber wrote: > > Hi = > > > > CVS is currently unbuildable because of recent commits of phylo code. > > There are two problems. > > > > 1) The code has a reliance on JGraphT. This needs to be commited in > > the appropriate place and added to the classpath etc in the ant build > > file. > > > > 2) The code contains java 1.5 reliant code (generics) that won't > > compile with the biojava standard JDK (1.4.2). This is not really an > > issue as I am about to do a final BioJava 1.5 build after which we > > switch to JDK1.5 (or maybe even 1.6). > > > > Can someone checkin JGraphT and make the appropriate changes to the > > build XML? Please also ensure the licenses are acceptable and properly > > replicated. > > > > - Mark > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGb7J54C5LeMEKA/QRAofUAJ9fhc2CffT63qasVhmoy8hHz9j4+wCbB1eg > JWLke1WXeYDxq4ijBDDVDLY= > =zWib > -----END PGP SIGNATURE----- > From ap3 at sanger.ac.uk Wed Jun 13 09:41:06 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 13 Jun 2007 10:41:06 +0100 Subject: [Biojava-dev] after this release In-Reply-To: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> Message-ID: <17b17e8f8f538b2068d81eafaff69ac8@sanger.ac.uk> Hi Mark, > This is not really an > issue as I am about to do a final BioJava 1.5 build after which we > switch to JDK1.5 (or maybe even 1.6). Thanks for all your work in getting this release out. A while ago we also were discussing to move to Subversion after this release. Is this still on? Greetings, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Wed Jun 13 12:16:43 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 13:16:43 +0100 Subject: [Biojava-dev] Problem with Phylo Code in CVS In-Reply-To: <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> References: <93b45ca50706130143p289742ffvebcece17ccc07d24@mail.gmail.com> <466FB279.5090506@ebi.ac.uk> <93b45ca50706130215qcb247ccrd25f899bef320cc3@mail.gmail.com> Message-ID: <466FE02B.7080006@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I did notice it failed but wasn't sure what to do about it. What is the fix? cheers, Richard Mark Schreiber wrote: > Yes, I will omit the phylo package as it is not stable (or finished). > > Also noticed that the MassCalcTest fails after the update of the new > Mass values. Does no-one attempt to run tests before commiting?? I > will commit a patch to the test today. > > - Mark > > On 6/13/07, Richard Holland wrote: > JGraphT is LGPL. > > I have added the current JGraphT JAR file (Java 1.5) and modified > build.xml. > > Can you temporarily omit JGraphT and the phylo packages from the 1.5 > build process? > > cheers, > Richard > > Mark Schreiber wrote: >> Hi = > >> CVS is currently unbuildable because of recent commits of phylo code. >> There are two problems. > >> 1) The code has a reliance on JGraphT. This needs to be commited in >> the appropriate place and added to the classpath etc in the ant build >> file. > >> 2) The code contains java 1.5 reliant code (generics) that won't >> compile with the biojava standard JDK (1.4.2). This is not really an >> issue as I am about to do a final BioJava 1.5 build after which we >> switch to JDK1.5 (or maybe even 1.6). > >> Can someone checkin JGraphT and make the appropriate changes to the >> build XML? Please also ensure the licenses are acceptable and properly >> replicated. > >> - Mark >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGb+Ar4C5LeMEKA/QRAlwHAJ41XTBBd5PvLRoTRg2rZB34fmT3LACfc6FL QOWkjIVahdkoBjMoNBHJjxk= =ywTL -----END PGP SIGNATURE----- From holland at ebi.ac.uk Wed Jun 13 15:15:48 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 13 Jun 2007 16:15:48 +0100 Subject: [Biojava-dev] BioJava 1.5 Released Message-ID: <46700A24.4040305@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 iD4DBQFGcAoj4C5LeMEKA/QRAvZiAJjhHGWvq5nrj8aanmUtCpA8U8dpAJ0bsxzy tv5LVdSEtAuA7gp12nLMCA== =/Wbu -----END PGP SIGNATURE----- From bugzilla-daemon at portal.open-bio.org Wed Jun 13 15:52:20 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 13 Jun 2007 11:52:20 -0400 Subject: [Biojava-dev] [Bug 2318] New: NPE in org.biojavax.bio.seq.io.EMBLxmlFormat Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2318 Summary: NPE in org.biojavax.bio.seq.io.EMBLxmlFormat Product: BioJava Version: unspecified Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: dmitry.repchevski at bsc.es Hi! Using RichSequence.IOTools.readStream() I got a Null Pointer Exception in EMBLxmlFormat when the sequence is not an xml and less than 2 lines: Here is a stack: ***************************************** SEVERE: java.lang.NullPointerException at java.util.regex.Matcher.getTextLength(Unknown Source) at java.util.regex.Matcher.reset(Unknown Source) at java.util.regex.Matcher.(Unknown Source) at java.util.regex.Pattern.matcher(Unknown Source) at org.biojavax.bio.seq.io.EMBLxmlFormat.canRead(EMBLxmlFormat.java:238) at org.biojavax.bio.seq.RichSequence$IOTools.readStream(RichSequence.java:683) at org.biojavax.bio.seq.RichSequence$IOTools.readStream(RichSequence.java:705) ... ***************************************** Looking into the code I can see ***************************************** public boolean canRead(BufferedInputStream stream) throws IOException { stream.mark(2000); // some streams may not support this BufferedReader br = new BufferedReader(new InputStreamReader(stream)); br.readLine(); // skip first line boolean readable = xmlSchema.matcher(br.readLine()).matches(); // check on second line ... ***************************************** that there is no br.readLine() == null check. the same with [public boolean canRead(File file)] method. the method supposed to check if the stream is an EMBL XML format... thank you in advance. Dmitry -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Jun 14 09:00:15 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 14 Jun 2007 05:00:15 -0400 Subject: [Biojava-dev] [Bug 2318] NPE in org.biojavax.bio.seq.io.EMBLxmlFormat In-Reply-To: Message-ID: <200706140900.l5E90FoJ006653@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2318 ------- Comment #1 from dmitry.repchevski at bsc.es 2007-06-14 05:00 EST ------- The same with UniProtXMLFormat -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 15 14:52:09 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 15 Jun 2007 10:52:09 -0400 Subject: [Biojava-dev] [Bug 2318] NPE in org.biojavax.bio.seq.io.EMBLxmlFormat In-Reply-To: Message-ID: <200706151452.l5FEq9cN001674@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2318 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from holland at ebi.ac.uk 2007-06-15 10:52 EST ------- Fixed in head on CVS. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From blee34 at mail.gatech.edu Tue Jun 19 17:50:23 2007 From: blee34 at mail.gatech.edu (blee34 at mail.gatech.edu) Date: Tue, 19 Jun 2007 13:50:23 -0400 Subject: [Biojava-dev] Helps needed for NexusParser Message-ID: <1182275423.4678175fe5775@webmail.mail.gatech.edu> Dear group, Hi, I'm a GSOC student Bohyun participating in BioJava project (as a part of NESCent phyloinformatics work) for this summer! I need some helps using (Nexus) TAXA Block Parser (which were included in BioJava1.5-beta2). Can anyone give me a sample code for Parsing a TAXA Block? What I am trying to do now is to parse a TAXA block and construct a phylo tree by using methods like UPGMA, Neighbor-Joining. (http://biojava.org/wiki/BioJava:PhyloSOC07) Also, I'd appreciate if there's anyone who can tell me where to find javadoc pages for biojavax.phylo package. (It was there on the wiki with Biojava1.5-beta2 release. I heard that It's been temporarily omitted for the BioJava1.5 version, but I'd like to get those files for the reference.) Thank you very much for your help. Best regards, Bohyun From markjschreiber at gmail.com Wed Jun 20 01:11:26 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 20 Jun 2007 09:11:26 +0800 Subject: [Biojava-dev] Helps needed for NexusParser In-Reply-To: <1182275423.4678175fe5775@webmail.mail.gatech.edu> References: <1182275423.4678175fe5775@webmail.mail.gatech.edu> Message-ID: <93b45ca50706191811y4ff9dc72k49f9b5139ade3932@mail.gmail.com> Hi - The phylo package was omitted from the biojava1.5 build but it is still accessible form the biojava-live distribution on CVS. If you have CVS access you should be able to get it. Additionally you can build any docs using JavaDoc or better yet build the entire package with Ant using the build.xml file. - Mark On 6/20/07, blee34 at mail.gatech.edu wrote: > > Dear group, > > Hi, I'm a GSOC student Bohyun participating in BioJava project (as a part of > NESCent phyloinformatics work) for this summer! > > I need some helps using (Nexus) TAXA Block Parser (which were included in > BioJava1.5-beta2). Can anyone give me a sample code for Parsing a TAXA Block? > > What I am trying to do now is to parse a TAXA block and construct a phylo tree > by > using methods like UPGMA, Neighbor-Joining. > (http://biojava.org/wiki/BioJava:PhyloSOC07) > > Also, I'd appreciate if there's anyone who can tell me where to find javadoc > pages for biojavax.phylo package. (It was there on the wiki with > Biojava1.5-beta2 release. I heard that It's been temporarily omitted for the > BioJava1.5 version, but I'd like to get those files for the reference.) > > Thank you very much for your help. > > Best regards, > Bohyun > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From bugzilla-daemon at portal.open-bio.org Mon Jun 25 12:35:10 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 25 Jun 2007 08:35:10 -0400 Subject: [Biojava-dev] [Bug 2260] Bug in UkkonenSuffixTree In-Reply-To: Message-ID: <200706251235.l5PCZAZM026974@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2260 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from holland at ebi.ac.uk 2007-06-25 08:35 EST ------- Fixed now in CVS on the head. Problem was quite simple - the loop that iterated over portions of a multiple string was identifying the end of each portion but lumping in the whole of the preceding portions with each one. Net effect was this: Input: aaa$bbb$ccc Sequences: aaa, aaa$bbb, aaa$bbb$ccc The corrected behaviour is this: Input: aaa$bbb$ccc Sequences: aaa, bbb, ccc -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From kannanbimatics at yahoo.com Mon Jun 25 09:15:10 2007 From: kannanbimatics at yahoo.com (kannan kannan) Date: Mon, 25 Jun 2007 09:15:10 -0000 Subject: [Biojava-dev] Requesting for project Message-ID: <322810.71032.qm@web57415.mail.re1.yahoo.com> Respected SIR / MADAM, I very much pleased to introduce myself as V.S Kannan, pursuing II M.Sc.bioinformatics, at kongunadu arts & science College, Coimbatore, Tamilnadu. I have completed my graduation in Biochemistry from Periyar University. As part of my curriculum, I have to do a project for a period of 4-6 months during December 2007-April 2008. I am very much interested in computational biology and have developed bioinformatics tools PERL,BIOJAVA and C. I have also completed two projects on Development of database for Signal peptide Database and Restriction site tracer using Oracle and Visual Basic. From the website I came to know about the projects done at your Institution and I am very much interested to do my project under your guidance. I kindly request you to consider my application and I assure you to put in my best efforts during the project. I have enclosed a copy of my resume for your kind perusal. Anticipating a favourable reply. Thanking you Regards, kannan --------------------------------- Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! 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