From ap3 at sanger.ac.uk Thu Nov 1 12:59:35 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 1 Nov 2007 16:59:35 +0000 Subject: [Biojava-dev] Biojava migrating to Subversion Message-ID: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> Hi all, Over the next weeks (until Christmas) BioJava will finally move the version control system from CVS to Subversion (svn). This is happening in parallel to the other open-bio projects. We will ensure that nothing gets lost during this migration. This means that all Biojava modules, branches, tags and the history of the files will be imported into the new repository. Over the next weeks we will A) Test the migration procedure to ensure nothing gets lost B) We will declare a CVS freeze at some point, giving all developers enough time to commit the latest code to CVS. C) After the freeze the final svn migration will happen. At this point we will also do a quick BioJava release (version 1.5.1) D) From that moment on all future Biojava development will happen via svn, CVS will remain frozen. Detailed instructions for how to check out and commit code using svn will be announced closer to the migration date. We will keep you informed about the details of these ongoings. There is also a wiki page which provides documentation for this: http://biojava.org/wiki/CVS_to_SVN_Migration 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 Tue Nov 6 05:15:43 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 06 Nov 2007 10:15:43 +0000 Subject: [Biojava-dev] [Biojava-l] Error while reading byte data for creating a Trace. In-Reply-To: <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> Message-ID: <47303ECF.4020806@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I suspect the byte array itself may contain inaccurate data. Internally, both the URL and File constructors read the data into a byte array and then pass it to the same method as is used by the byte[] constructor. So, something must be different between the byte array you have, and the byte array obtained by reading the file in. The File constructor uses the following code to read the file: byte[] bytes = null; ByteArrayOutputStream baos = new ByteArrayOutputStream(); FileInputStream fis = new FileInputStream(ABIFile); BufferedInputStream bis = new BufferedInputStream(fis); int b; while ((b = bis.read()) >= 0) { baos.write(b); } bis.close(); fis.close(); baos.close(); bytes = baos.toByteArray(); If the above code produces different results to your byte array when reading data from the same file as your code, then something has gone wrong with the construction of your byte array. Lastly, a full stack trace would help us pinpoint the line that is breaking, and hopefully provide a hint as to what is wrong with the contents of the byte array. If you could provide one that would be very helpful. cheers, Richard abhi232 at cc.gatech.edu wrote: > Hi all, > I am having a byte array which is having the data from an .ab1 file.The > biojava library provides a class called as ABITrace which takes as input > either a byte[] array , a file or a url.If i use the later parameters (the > file or the url )the program works but if I pass the byte array to the > constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a > problem with the ABITrace class or how can I bypass this particular error. > I am printing the length of the byte array and it comes to 144930...Can > that cause a problem in my code? > > Thanks in advance. > Abhinav > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHMD7P4C5LeMEKA/QRAmGIAJ9a/V6nZqMROz3H4u69ECQ+9iTgMgCeNZvr oe52S3khmTvi5BFCL1W4KHM= =5JAO -----END PGP SIGNATURE----- From holland at ebi.ac.uk Tue Nov 6 06:34:08 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 06 Nov 2007 11:34:08 +0000 Subject: [Biojava-dev] LGPL information forgotten at BlastLikeDataSetCollection.dtd ? In-Reply-To: References: Message-ID: <47305130.8040901@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 > The LICENSE file at biojava/LICENSE contains the text of version 2.1 of > the LPGL. > > We should make this explicit, by including "version 2.1", "version 2.1 or > any later version", "version 3", or "version 3 or any later version" in > the LICENSE file and all the license headers. my vote is for "version 2.1 or any later version". -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHMFEw4C5LeMEKA/QRAmLLAJ9a6Sge9aVukdtl72DJKsfzpLqyxgCeINRr jCjh/7bmvgnkZNNVhIhBOn0= =t6wF -----END PGP SIGNATURE----- From holland at ebi.ac.uk Tue Nov 6 06:35:47 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 06 Nov 2007 11:35:47 +0000 Subject: [Biojava-dev] [Fwd: BioJava 3 Proposal] In-Reply-To: References: Message-ID: <47305193.2070603@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 would you mind if i posted your comments to the wiki but without your name? that way everyone can read and comment as needed, but any politics involved with who said what are avoided. cheers, Richard Michael Heuer wrote: > Hello Richard, > > I'm not sure if I want any of this up on the wiki, but here are a few > of my thoughts... > > Immutable classes, not beans, are the safest and most efficient. > > Statements like "We would adhere rigidly to a common coding style and > heavily comment the code." only work if there is a way to measure and > enforce it. A better way to say this would be something like "All > committed code must have zero style errors as measured by Checkstyle with > our local checkstyle configuration, have zero coding errors as measured by > FindBugs with our local findbugs configuration, have 95% unit test > coverage as measured by Cobertura", and so on. > > Sequence features aught to align with the Sequence Ontology (SO/SOFA). > The two top-level sequence feature types are Region (SO:0000001, "A > sequence_feature with an extent greater than zero.") and Junction > (SO:0000699, "A sequence_feature with an extent of zero."). > > Is there a role for biojava in any of > > Ontologies in OBO format > Ontologies in OWL format > BioPAX > MAGE-ML/SOFT/MINiML > FuGO/OBI > SMBL/CellML > Web services/BioMoby > etc. > > or is each best handled by their respective projects/tools? > > michael > > > Richard Holland wrote: > > Hi all. I'm planning on opening this wiki page to the general public > (ie. biojava-l) on Monday next week (Oct 29th). The email that will > accompany the public announcement is shown below. > > If you'd like to review it and add any further comments or suggestions > before everyone else gets to see it, please make those changes before > this coming weekend is over! > > The page will be made visible as-is, and will be left open for public > comment until January when I will distribute a summary of its contents > and start work on a plan of action. > > cheers, > Richard > > Here is the email that will be sent out on Monday: > > ---- > Dear BioJava users, > > The BioJava developers are considering options for the future > development of the BioJava toolkit. We consider that it needs > improvement in a few major areas to make it easier to use and > understand, and also faster and more scalable. > > The options are to either rewrite large parts of the existing code, > working within the existing interfaces and paradigms, or to develop a > new set of BioJava packages from the ground up in order to take > advantage of lessons learned from the design patterns of the existing code. > > The BioJava developers have spent the last couple of months discussing > ideas and proposals related to these options on a Wiki page, and would > now like to open this discussion to all users of BioJava and the > bioinformatics community in general. We would like to invite anyone who > has any ideas or suggestions to contribute these to the Wiki page, > and/or to comment on the ideas and suggestions that have already been > posted there. > > Here is a link to the Wiki page, and also a link to the associated Talk > page where much of the discussion has taken place so far: > > http://biojava.org/wiki/BioJava3_Proposal > http://biojava.org/wiki/Talk:BioJava3_Proposal > > It is our intention to leave the discussion open until early January > 2008 when we will summarise it and use it as the basis of a plan of > action. We will then distribute the summary and the action plan via the > BioJava website. > > We look forward to hearing your comments and ideas. Please do remember > to make them directly to the Wiki page so that they are preserved in > context, making it easier for us to summarise them later! > > cheers, > Richard > (on behalf of all BioJava developers) > ---- > >> > _______________________________________________ > 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 iD8DBQFHMFGT4C5LeMEKA/QRAkneAJ9TIRn8U9Bpmdt45R9UwV2ZrL3dcwCgmIcq SPkJmxfthlyTgbajDv9/lDc= =zpQK -----END PGP SIGNATURE----- From gwaldon at geneinfinity.org Tue Nov 6 12:37:23 2007 From: gwaldon at geneinfinity.org (george waldon) Date: Tue, 06 Nov 2007 09:37:23 -0800 Subject: [Biojava-dev] LGPL information forgotten at BlastLikeDataSetCollection.dtd ? Message-ID: <20071106173723.27225.qmail@mmm1924.dulles19-verio.com> Hi, I have a question here. It seems to me that to change the license in biojava, like going from LGPL 2.1 to LGPL 3, we need the agreement of all copyright holders, past and present (there is no copyright transfer agreement in biojava). Is-this really feasible? George > -----Original Message----- > From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev- > bounces at lists.open-bio.org] On Behalf Of Richard Holland > Sent: Tuesday, November 06, 2007 3:34 AM > To: Michael Heuer > Cc: biojava-dev at lists.open-bio.org; Steffen Moeller > Subject: Re: [Biojava-dev] LGPL information forgotten at > BlastLikeDataSetCollection.dtd ? > > > > The LICENSE file at biojava/LICENSE contains the text of version 2.1 of > > the LPGL. > > > > We should make this explicit, by including "version 2.1", "version 2.1 > or > > any later version", "version 3", or "version 3 or any later version" in > > the LICENSE file and all the license headers. > > my vote is for "version 2.1 or any later version". From ap3 at sanger.ac.uk Tue Nov 6 13:36:53 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 6 Nov 2007 18:36:53 +0000 Subject: [Biojava-dev] LGPL information forgotten at BlastLikeDataSetCollection.dtd ? In-Reply-To: <20071106173723.27225.qmail@mmm1924.dulles19-verio.com> References: <20071106173723.27225.qmail@mmm1924.dulles19-verio.com> Message-ID: We have about 50 people who ever did a CVS commit. It will be hard to get permission for any change from everybody who holds copyright, even if there was an agreement to change the license. Will be interesting to see how the Linux kernel will deal with the v3 issue, but I think Linus said that they are going to stay with v2. Andreas On 6 Nov 2007, at 17:37, george waldon wrote: > Hi, > > I have a question here. It seems to me that to change the license > in biojava, like going from LGPL 2.1 to LGPL 3, we need the > agreement of all copyright holders, past and present (there is no > copyright transfer agreement in biojava). Is-this really feasible? > > George > >> -----Original Message----- >> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev- >> bounces at lists.open-bio.org] On Behalf Of Richard Holland >> Sent: Tuesday, November 06, 2007 3:34 AM >> To: Michael Heuer >> Cc: biojava-dev at lists.open-bio.org; Steffen Moeller >> Subject: Re: [Biojava-dev] LGPL information forgotten at >> BlastLikeDataSetCollection.dtd ? >> >> >>> The LICENSE file at biojava/LICENSE contains the text of version >>> 2.1 of >>> the LPGL. >>> >>> We should make this explicit, by including "version 2.1", >>> "version 2.1 >> or >>> any later version", "version 3", or "version 3 or any later >>> version" in >>> the LICENSE file and all the license headers. >> >> my vote is for "version 2.1 or any later version". > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Thu Nov 8 08:53:09 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Thu, 08 Nov 2007 13:53:09 +0000 Subject: [Biojava-dev] BioJava 3 Proposals Message-ID: <473314C5.8070207@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear BioJava users, The BioJava developers are considering options for the future development of the BioJava toolkit. We consider that it needs improvement in a few major areas to make it easier to use and understand, and also faster and more scalable. The options are to either rewrite large parts of the existing code, working within the existing interfaces and paradigms, or to develop a new set of BioJava packages from the ground up in order to take advantage of lessons learned from the design patterns of the existing code. The BioJava developers have spent the last couple of months discussing ideas and proposals related to these options on a Wiki page, and would now like to open this discussion to all users of BioJava and the bioinformatics community in general. We would like to invite anyone who has any ideas or suggestions to contribute these to the Wiki page, and/or to comment on the ideas and suggestions that have already been posted there. Here is a link to the Wiki page, and also a link to the associated Talk page where much of the discussion has taken place so far: http://biojava.org/wiki/BioJava3_Proposal http://biojava.org/wiki/Talk:BioJava3_Proposal It is our intention to leave the discussion open until mid-January 2008 when we will summarise it and use it as the basis of a plan of action. We will then distribute the summary and the action plan via the BioJava website. We look forward to hearing your comments and ideas. Please do remember to make them directly to the Wiki page so that they are preserved in context, making it easier for us to summarise them later! cheers, Richard (on behalf of all BioJava developers) PS. Just to reassure you, this is NOT a plan to drop the existing codebase. It will continue to exist, but the outcome of these discussions will determine whether we will continue to develop and support it or start afresh with a clean slate and a new codebase. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHMxTE4C5LeMEKA/QRAlGSAJwKzO0oAe3T2e8ibcG8uRReOVfh7wCdGlwn JkcVzA55Ye32o8Ry48LO+04= =oaaC -----END PGP SIGNATURE----- From gwaldon at geneinfinity.org Thu Nov 8 12:36:42 2007 From: gwaldon at geneinfinity.org (george waldon) Date: Thu, 08 Nov 2007 09:36:42 -0800 Subject: [Biojava-dev] Biojava license Message-ID: <20071108173642.2824.qmail@mmm1924.dulles19-verio.com> 50 developers is not a too large number and, even if a few could not be contacted, an agreement covering more than 95% or even 99% of the code is probably reachable at the present time. This will require some kind of organization. Isn't it more the role of the OBF to do such a think? Why not having a real copyright transfer agreement so that the OBF has copyright on the different projects, can operate license changes if necessary, and defends in case of copyright breach. George > -----Original Message----- > From: Andreas Prlic [mailto:ap3 at sanger.ac.uk] > Sent: Tuesday, November 06, 2007 10:37 AM > To: george waldon > Cc: biojava-dev at biojava.org > Subject: Re: [Biojava-dev] LGPL information forgotten at > BlastLikeDataSetCollection.dtd ? > > We have about 50 people who ever did a CVS commit. > It will be hard to get permission for any change from everybody who > holds copyright, even > if there was an agreement to change the license. > > Will be interesting to see how the Linux kernel will deal with the v3 > issue, > but I think Linus said that they are going to stay with v2. > > Andreas > > > > > > On 6 Nov 2007, at 17:37, george waldon wrote: > > > Hi, > > > > I have a question here. It seems to me that to change the license > > in biojava, like going from LGPL 2.1 to LGPL 3, we need the > > agreement of all copyright holders, past and present (there is no > > copyright transfer agreement in biojava). Is-this really feasible? > > > > George > > > >> -----Original Message----- > >> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev- > >> bounces at lists.open-bio.org] On Behalf Of Richard Holland > >> Sent: Tuesday, November 06, 2007 3:34 AM > >> To: Michael Heuer > >> Cc: biojava-dev at lists.open-bio.org; Steffen Moeller > >> Subject: Re: [Biojava-dev] LGPL information forgotten at > >> BlastLikeDataSetCollection.dtd ? > >> > >> > >>> The LICENSE file at biojava/LICENSE contains the text of version > >>> 2.1 of > >>> the LPGL. > >>> > >>> We should make this explicit, by including "version 2.1", > >>> "version 2.1 > >> or > >>> any later version", "version 3", or "version 3 or any later > >>> version" in > >>> the LICENSE file and all the license headers. > >> > >> my vote is for "version 2.1 or any later version". > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From gwaldon at geneinfinity.org Thu Nov 8 15:46:28 2007 From: gwaldon at geneinfinity.org (george waldon) Date: Thu, 08 Nov 2007 12:46:28 -0800 Subject: [Biojava-dev] Biojava license Message-ID: <20071108204628.9765.qmail@mmm1924.dulles19-verio.com> >From: cornell kay [mailto:cor154 at yahoo.com] >Sent: Thursday, November 08, 2007 11:47 AM >To: george waldon >Subject: Re: [Biojava-dev] Biojava license >send me an agreement. >thx I was reading through this article (http://producingoss.com/en/copyright-assignment.html) on copyright transfer agreement. The full transfer is complex and contributors might not want to give away their own rights. This sounds like a dead end for biojava indeed. - George From heuermh at acm.org Fri Nov 9 00:58:57 2007 From: heuermh at acm.org (Michael Heuer) Date: Fri, 9 Nov 2007 00:58:57 -0500 (EST) Subject: [Biojava-dev] BioJava 3 Proposals In-Reply-To: <473314C5.8070207@ebi.ac.uk> Message-ID: Hello, I have created a small example of how a biojava 3 might be built in a more modular fashion using maven2: > http://shell3.shore.net/~heuermh/biojava-maven.tar.gz There is a short readme with build instructions. It could use a bit more polish but I think it demonstrates the idea well enough. I forgot to mention before W3C Semantic Web Health Care and Life Sciences Interest Group > http://www.w3.org/2001/sw/hcls/ The group might welcome help implementing their recommendations and best practices. Plenty of interesting discussion at any rate. michael From bugzilla-daemon at portal.open-bio.org Wed Nov 14 11:20:01 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 14 Nov 2007 11:20:01 -0500 Subject: [Biojava-dev] [Bug 2400] New: add parsing of SSBOND records in PDB files Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2400 Summary: add parsing of SSBOND records in PDB files Product: BioJava Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: structure AssignedTo: biojava-dev at biojava.org ReportedBy: bmduggan at yahoo.com I would like to be able to use BioJava to pass the SSBOND records in the header of a PDB file. Currently these lines are not parsed. The information I would like to obtain would be a list of the pairs of residues involved in each disulfide bond in the structure. Each residue would probably have to be identified by residue number and chain. -- 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 Nov 14 11:28:11 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 14 Nov 2007 11:28:11 -0500 Subject: [Biojava-dev] [Bug 2400] add parsing of SSBOND records in PDB files In-Reply-To: Message-ID: <200711141628.lAEGSBIA014178@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2400 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biojava-dev at biojava.org |ap3 at sanger.ac.uk -- 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 Thu Nov 15 07:56:46 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 15 Nov 2007 07:56:46 -0500 Subject: [Biojava-dev] [Bug 2401] New: NullPointerException in SimpleNote.setTerm() Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2401 Summary: NullPointerException in SimpleNote.setTerm() Product: BioJava Version: 1.5 Platform: PC OS/Version: Linux Status: NEW Severity: blocker Priority: P1 Component: seq AssignedTo: biojava-dev at biojava.org ReportedBy: thomas at fkserv.ugent.be When loading a RichSequence from an EMBL file like this: RichSequenceIterator stream = IOTools.readEMBLDNA(br,RichObjectFactory.getDefaultNamespace()); ... RichSequence seq = stream.nextRichSequence(); ... and trying to save it: Session session = sessionFactory.openSession(); RichObjectFactory.connectToBioSQL(session); Transaction tx = session.beginTransaction(); ... session.save("Sequence", seq); tx.commit(); session.close(); A NullPointerException occurs in SimpleNote.setTerm(ComparableTerm term), because this.term appears to be null, so this.term.equals(term) obviously gives an error. I hope I didn't use a wrong method that caused this error, but it was easily fixed by replacing this code (in biojavax.SimpleNote) if (this.term.equals(term)) return; by if (this.term!=null && this.term.equals(term)) return; -- 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 Nov 15 09:01:58 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 15 Nov 2007 09:01:58 -0500 Subject: [Biojava-dev] [Bug 2401] NullPointerException in SimpleNote.setTerm() In-Reply-To: Message-ID: <200711151401.lAFE1wAT008349@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2401 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from holland at ebi.ac.uk 2007-11-15 09:01 EST ------- Thanks for this. I've fixed it on the head branch (development) of CVS so will be available if you check out the latest code from there. It'll also be present in the next release. -- 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 Nov 16 09:02:29 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:02:29 -0500 Subject: [Biojava-dev] [Bug 2402] New: Parsed genbank file lacks some annotations from original record Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2402 Summary: Parsed genbank file lacks some annotations from original record Product: BioJava Version: 1.5 Platform: PC OS/Version: Windows XP Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: p.troshin at dl.ac.uk Hi there, I am not sure whether this is a feature or a bug. I discovered that some annotation is not put in the Annotation object, however, there were clearly in the genbank file. Some Annotation seems to be always ignored like "db_xref" for instance. In the genBank protein record YP_006528 the source feature contains 5 annotations they are: /virion /isolate /specific_host /db_xref /organism BioJava annotation after parsing this file contains only the first 3, thereas db-xref and organism gets ignored. Here is a testcase for this bug. import java.io.BufferedReader; import java.io.StringReader; import java.util.Iterator; import junit.framework.TestCase; import org.biojava.bio.Annotation; import org.biojava.bio.seq.Feature; import org.biojava.bio.seq.FeatureFilter; import org.biojava.bio.seq.FeatureHolder; import org.biojava.bio.seq.ProteinTools; import org.biojava.bio.seq.io.SymbolTokenization; import org.biojavax.RichObjectFactory; import org.biojavax.bio.seq.RichSequence; import org.biojavax.bio.seq.RichSequenceIterator; import org.biojavax.bio.seq.io.RichSequenceBuilderFactory; public class BioJavaGenBankProteinParserForDev extends TestCase { RichSequence bio = null; static final String genBankProtein = " LOCUS YP_006528 398 aa linear PHG 25-JUL-2007\r\n" + "DEFINITION ParA [Enterobacteria phage P1].\r\n" + "ACCESSION YP_006528\r\n" + "VERSION YP_006528.1 GI:46401682\r\n" + "DBSOURCE REFSEQ: accession NC_005856.1\r\n" + "KEYWORDS .\r\n" + "SOURCE Enterobacteria phage P1\r\n" + " ORGANISM Enterobacteria phage P1\r\n" + " Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;\r\n" + " P1-like viruses.\r\n" + "REFERENCE 1 (residues 1 to 398)\r\n" + " AUTHORS Lobocka,M.B., Rose,D.J., Plunkett,G., Rusin,M., Samojedny,A.,\r\n" + " Lehnherr,H., Yarmolinsky,M.B. and Blattner,F.R.\r\n" + " TITLE Genome of bacteriophage p1\r\n" + " JOURNAL J. Bacteriol. 186 (21), 7032-7068 (2004)\r\n" + " PUBMED 15489417\r\n" + "REFERENCE 2 (residues 1 to 398)\r\n" + " CONSRTM NCBI Genome Project\r\n" + " TITLE Direct Submission\r\n" + " JOURNAL Submitted (06-APR-2006) National Center for Biotechnology\r\n" + " Information, NIH, Bethesda, MD 20894, USA\r\n" + "REFERENCE 3 (residues 1 to 398)\r\n" + " AUTHORS Lobocka,M.B.\r\n" + " TITLE Direct Submission\r\n" + " JOURNAL Submitted (14-FEB-2000) Department of Microbial Biochemistry,\r\n" + " Institute of Biochemistry and Biophysics of the Polish Academy of\r\n" + " Sciences, Ul. Pawinskiego 5A, Warsaw 02-106, Poland\r\n" + "REFERENCE 4 (residues 1 to 398)\r\n" + " AUTHORS Rusin,M. and Samojedny,A.\r\n" + " TITLE Direct Submission\r\n" + " JOURNAL Submitted (14-FEB-2000) Department of Tumor Biology, Centre of\r\n" + " Oncology, M. Sklodowska-Curie Memorial Institute, Ul. Wybrzeze AK\r\n" + " 15, Gliwice 44-101, Poland\r\n" + "COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final\r\n" + " NCBI review. The reference sequence was derived from AAQ14032.\r\n" + " Method: conceptual translation.\r\n" + "FEATURES Location/Qualifiers\r\n" + " source 1..398\r\n" + " /organism=\"Enterobacteria phage P1\"\r\n" + " /virion\r\n" + " /isolate=\"mod749::IS5 c1.100 mutant\"\r\n" + " /specific_host=\"Escherichia coli\"\r\n" + " /db_xref=\"taxon:10678\"\r\n" + " Protein 1..398\r\n" + " /product=\"ParA\"\r\n" + " /name=\"encodes ParA/SopA family protein involved in active\r\n" + " partitioning of P1 plasmid prophage at cell division\"\r\n" + " /calculated_mol_wt=44139\r\n" + " Region 108..393\r\n" + " /region_name=\"Soj\"\r\n" + " /note=\"ATPases involved in chromosome partitioning [Cell\r\n" + " division and chromosome partitioning]; COG1192\"\r\n" + " /db_xref=\"CDD:31385\"\r\n" + " Region 110..>154\r\n" + " /region_name=\"ParA\"\r\n" + " /note=\"ParA and ParB of Caulobacter crescentus belong to a\r\n" + " conserved family of bacterial proteins implicated in\r\n" + " chromosome segregation; cd02042\"\r\n" + " /db_xref=\"CDD:73302\"\r\n" + " Site 117..123\r\n" + " /site_type=\"other\"\r\n" + " /note=\"P-loop\"\r\n" + " /db_xref=\"CDD:73302\"\r\n" + " Site 123\r\n" + " /site_type=\"other\"\r\n" + " /note=\"Magnesium ion binding site\"\r\n" + " /db_xref=\"CDD:73302\"\r\n" + " Region <237..300\r\n" + " /region_name=\"ParA\"\r\n" + " /note=\"ParA and ParB of Caulobacter crescentus belong to a\r\n" + " conserved family of bacterial proteins implicated in\r\n" + " chromosome segregation; cd02042\"\r\n" + " /db_xref=\"CDD:73302\"\r\n" + " Site 251\r\n" + " /site_type=\"other\"\r\n" + " /note=\"Magnesium ion binding site\"\r\n" + " /db_xref=\"CDD:73302\"\r\n" + " CDS 1..398\r\n" + " /gene=\"parA\"\r\n" + " /locus_tag=\"P1_gp060\"\r\n" + " /coded_by=\"complement(NC_005856.1:60017..61213)\"\r\n" + " /note=\"weak ATPase, binds to par operator site to repress\r\n" + " transcription; 100 pct identical to previously predicted\r\n" + " product of parA of P1 Swissprot:PARA_ECOLI; similar to\r\n" + " partition ATPases of ParA/SopA family of many low copy\r\n" + " number plasmids and bacteria\"\r\n" + " /transl_table=11\r\n" + " /db_xref=\"GeneID:2777494\"\r\n" + "ORIGIN \r\n" + " 1 msdssqlhkv aqranrmlnv lteqvqlqkd elhanefyqv yakaalaklp lltranvdya\r\n" + " 61 vsemeekgyv fdkrpagssm kyamsiqnii diyehrgvpk yrdryseayv ifisnlkggv\r\n" + " 121 sktvstvsla hamrahphll medlrilvid ldpqssatmf lshkhsigiv natsaqamlq\r\n" + " 181 nvsreellee fivpsvvpgv dvmpasidda fiasdwrelc nehlpgqnih avlkenvidk\r\n" + " 241 lksdydfilv dsgphldafl knalasanil ftplppatvd fhsslkyvar lpelvklisd\r\n" + " 301 egcecqlatn igfmsklsnk adhkychsla kevfggdmld vflprldgfe rcgesfdtvi\r\n" + " 361 sanpatyvgs adalknaria aedfakavfd riefirsn\r\n" + "//\r\n" + "\r\n"; /** * @see junit.framework.TestCase#setUp() */ @Override protected void setUp() throws Exception { BufferedReader br = new BufferedReader(new StringReader(genBankProtein)); SymbolTokenization rParser = ProteinTools.getAlphabet().getTokenization("token"); RichSequenceIterator seqI = RichSequence.IOTools.readGenbank(br, rParser, RichSequenceBuilderFactory.FACTORY, RichObjectFactory.getDefaultNamespace()); bio = seqI.nextRichSequence(); } /** * @see junit.framework.TestCase#tearDown() */ @Override protected void tearDown() throws Exception { bio = null; } public void testFeatureList() { FeatureHolder cds = bio.filter(new FeatureFilter.ByType("source")); for (Iterator iterator = cds.features(); iterator.hasNext();) { Feature f = (Feature) iterator.next(); assertEquals("GenBank", f.getSource()); assertEquals("source", f.getType()); Annotation annot = f.getAnnotation(); assertTrue(annot.containsProperty("virion")); assertTrue(annot.containsProperty("specific_host")); assertTrue(annot.containsProperty("isolate")); assertTrue(annot.containsProperty("organism")); assertTrue(annot.containsProperty("db_xref")); } } } Thank you for your help. Peter -- 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 Nov 16 09:03:48 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:03:48 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161403.lAGE3mxI009543@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 ------- Comment #1 from p.troshin at dl.ac.uk 2007-11-16 09:03 EST ------- Created an attachment (id=811) --> (http://bugzilla.open-bio.org/attachment.cgi?id=811&action=view) JUnit testcase -- 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 Nov 16 09:22:38 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:22:38 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161422.lAGEMct4010867@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |INVALID ------- Comment #2 from holland at ebi.ac.uk 2007-11-16 09:22 EST ------- Thanks for taking the time to report this. What you have observed is definitely the intended behaviour. The db_xref has gone into the CrossRef part of the object model for the parsed sequence, and the organism has gone into the taxonomy part. If you explore the object model of the RichSequence you'll discover the information. The reason for this is that RichSequence is loosely based on the BioSQL schema, and if it can assign a piece of information it finds in the annotations to a good 1:1 match with a BioSQL concept, then it will do so. If you write the sequence back out, you'll see the annotations reappear, as the format is clever enough to gather back together the reorganised information from the various parts of the RichSequence object model and write it out in the manner defined by the GenBank format. -- 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 Nov 16 09:32:00 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:32:00 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161432.lAGEW0VE011267@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 ------- Comment #3 from p.troshin at dl.ac.uk 2007-11-16 09:32 EST ------- Thank you for your prompt answers, and excuse me my ignorance, but if the db_xfer has gone to CrossRef part of the object why is it empty? Am I just getting the cross references in a wrong way? If you add this RichSequence bio =.... assertFalse(bio.getRankedCrossRefs().isEmpty()); to the testcase posted earlier it will fail. Many thanks, Peter -- 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 Nov 16 09:41:26 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:41:26 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161441.lAGEfQXg011790@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 ------- Comment #4 from holland at ebi.ac.uk 2007-11-16 09:41 EST ------- Annotations in GenBank are all associated with features (in this case, the 'source' feature), and so it will be found in the CrossRefs of the feature it is associated with. -- 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 Nov 16 09:46:19 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 09:46:19 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161446.lAGEkJh5012097@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 ------- Comment #5 from holland at ebi.ac.uk 2007-11-16 09:46 EST ------- P.S. I forgot to mention also that 'taxon' and 'organism' db_xrefs aren't stored in crossrefs at all, they are combined to provide the taxonomy info instead. -- 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 Nov 16 10:10:52 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 16 Nov 2007 10:10:52 -0500 Subject: [Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record In-Reply-To: Message-ID: <200711161510.lAGFAqHS013650@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2402 ------- Comment #6 from p.troshin at dl.ac.uk 2007-11-16 10:10 EST ------- Thank you very much. I've just discovered that from RichFeature there are cross references available indeed. This was not the case with the Feature. This is something i was not using. I am sorted now. -- 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 Tue Nov 20 06:38:11 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 20 Nov 2007 06:38:11 -0500 Subject: [Biojava-dev] [Bug 2404] New: PSI-Blast flat file parsing for 2.2.17 Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2404 Summary: PSI-Blast flat file parsing for 2.2.17 Product: BioJava Version: live (CVS source) Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: bio AssignedTo: biojava-dev at biojava.org ReportedBy: jimp at compbio.dundee.ac.uk PSI Blast output is not properly supported. The attached file breaks the parser (causes an infinite loop). Andreas Prlic has outlined the necessary steps required for patching/enhancing the exisiting parser: * add PSI-Blast to BlastLikeVersionSupport * add a PSIBlastSummaryLineHelper implements SumaryLineHelperIF * hook it into BlastSAXParser in the IN_SUmmary section * check for Sequences with E-value WORSE lines and ignore it (or do something with them) * check for hitSectionReached and call this method everything up to here should be quickly possible. Some may be implementable as independent filters (note added by me JBP). The thing which looks a bit scarier at the moment is the next step: * the hitSectionReach delegates the parsing to HitSectionSAXParser - this needs to be extended to support psiblast or an independent implementation for Psi blast needs to be written... finally: * run the Junit tests to make sure the other Blast file are still parsed correctly * write a Junit test to make sure other changes in the parser won't break the support for this one -- 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 Tue Nov 20 06:51:38 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 20 Nov 2007 06:51:38 -0500 Subject: [Biojava-dev] [Bug 2404] PSI-Blast flat file parsing for 2.2.17 In-Reply-To: Message-ID: <200711201151.lAKBpcIC015388@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2404 jimp at compbio.dundee.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #814 is|0 |1 obsolete| | ------- Comment #1 from jimp at compbio.dundee.ac.uk 2007-11-20 06:51 EST ------- Created an attachment (id=815) --> (http://bugzilla.open-bio.org/attachment.cgi?id=815&action=view) ncbi 2.2.17 flat file and XML psi blast output (sourced from NCBI web interface) -- 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 Tue Nov 20 07:11:24 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 20 Nov 2007 07:11:24 -0500 Subject: [Biojava-dev] [Bug 2404] PSI-Blast flat file parsing for 2.2.17 In-Reply-To: Message-ID: <200711201211.lAKCBOGV016380@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2404 ------- Comment #2 from ap3 at sanger.ac.uk 2007-11-20 07:11 EST ------- I added a mini-patch to CVS which fixes the indefinite loop and prints a warning that this looks like a PSI blast file. This still does not change the fact that the parser does not support psi blast. -- 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 Nov 21 12:22:09 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 21 Nov 2007 12:22:09 -0500 Subject: [Biojava-dev] [Bug 2407] New: BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2407 Summary: BlastParser cannot parse the result of blastall using '- n' (MegaBlast Search) argument Product: BioJava Version: 1.5 Platform: All OS/Version: All Status: NEW Severity: critical Priority: P1 Component: seq AssignedTo: biojava-dev at biojava.org ReportedBy: iridiumcao at gmail.com There is a problem to parse the output result of blastall using the argument '-n' (MegaBlast Search). The query sequence ID and hit-start/end positions are inconsistent with the blast result text. Two blastall output files are attached, one is generated by blastall not using the argument '-n' (MegaBlast Search), parsed correctly; the other is generated using the argument '-n' (MegaBlast Search), parsed woronglg. -- 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 Nov 21 12:24:36 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 21 Nov 2007 12:24:36 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711211724.lALHOaat007074@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 ------- Comment #1 from iridiumcao at gmail.com 2007-11-21 12:24 EST ------- Created an attachment (id=821) --> (http://bugzilla.open-bio.org/attachment.cgi?id=821&action=view) This file can be parsed correctly. -- 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 Nov 21 12:26:13 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 21 Nov 2007 12:26:13 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711211726.lALHQDqr007191@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 ------- Comment #2 from iridiumcao at gmail.com 2007-11-21 12:26 EST ------- Created an attachment (id=822) --> (http://bugzilla.open-bio.org/attachment.cgi?id=822&action=view) This file is wrongly parsed -- 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 Nov 26 07:57:36 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 07:57:36 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261257.lAQCvanr018062@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #821|application/x-msdownload |text/plain mime type| | -- 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 Nov 26 07:57:59 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 07:57:59 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261257.lAQCvx2f018118@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #822|application/x-msdownload |text/plain mime type| | -- 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 Nov 26 07:58:51 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 07:58:51 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261258.lAQCwppF018196@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #3 from holland at ebi.ac.uk 2007-11-26 07:58 EST ------- The two files appear to be identical - I cannot tell which is which. Can you check and resubmit them? -- 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 Nov 26 08:12:19 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 08:12:19 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261312.lAQDCJJ1019160@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 ------- Comment #4 from iridiumcao at gmail.com 2007-11-26 08:12 EST ------- Created an attachment (id=827) --> (http://bugzilla.open-bio.org/attachment.cgi?id=827&action=view) the file which is wrongly parsed -- 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 Nov 26 08:13:46 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 08:13:46 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261313.lAQDDkBk019251@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 iridiumcao at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Attachment #822|This file is wrongly parsed |This file can be parsed description| |correctly. -- 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 Nov 26 08:15:10 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 26 Nov 2007 08:15:10 -0500 Subject: [Biojava-dev] [Bug 2407] BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument In-Reply-To: Message-ID: <200711261315.lAQDFAH7019470@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2407 iridiumcao at gmail.com 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 jcope at cableone.net Thu Nov 29 12:10:55 2007 From: jcope at cableone.net (Jeff Cope) Date: Thu, 29 Nov 2007 10:10:55 -0700 Subject: [Biojava-dev] BioJava Development Message-ID: <000001c832aa$cde19000$6402a8c0@roadrunner> Hello all, My name is Jeff Cope, and I am currently an undergraduate developer working as a research assistant on project where we are calculating some values for various protein sequences like isoelectric point, instability index, aromaticity, etc. (found here: http://trac.boisestate.edu/protcalc/ for those who are interested). As it stands right now we have implemented an applet client to server system to communicate the data because we have had to wrap the BioPython library on the server side. I have not been able to find the matching functionality in the BioJava Library, although I recognize that I might have missed it somewhere in there. I am currently signed up for the BioJava developer mailing list, and thought that I would offer to help with implementing this functionality in your library, then bring that library into our project rather than implementing it on our own individually. If I can help out, just let me know. Thanks, Jeff From will.stott at acm.org Thu Nov 29 12:57:24 2007 From: will.stott at acm.org (Will Stott) Date: Thu, 29 Nov 2007 18:57:24 +0100 Subject: [Biojava-dev] Essential skills for contributors - jUnit, CVS, what else? Message-ID: <001801c832b1$4c631060$e5293120$@stott@acm.org> I've just joined this community and would like to make some form of contribution to the BioJava code base. How do I get started, or is it a closed-shop? What are the essential skills developers need? Do you follow any sort of development process? Where can I get information about such matters? Will From gwaldon at geneinfinity.org Thu Nov 29 19:56:57 2007 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 29 Nov 2007 16:56:57 -0800 Subject: [Biojava-dev] Essential skills for contributors - jUnit, CVS, what else? Message-ID: <20071130005658.57059.qmail@mmm1924.dulles19-verio.com> Hello Will, Welcome aboard! I would suggest to start by checking a recent thread on the future of biojava at http://www.biojava.org/pipermail/biojava-dev/2007-September/003285.html that was initiated on this list by Richard Holland. Check also the multiple continuations of this thread in October and November on the dev mailing list. There is a summary on the biojava website at http://biojava.org/wiki/BioJava3_Proposal. - George From gwaldon at geneinfinity.org Thu Nov 29 20:18:57 2007 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 29 Nov 2007 17:18:57 -0800 Subject: [Biojava-dev] BioJava Development Message-ID: <20071130011857.63227.qmail@mmm1924.dulles19-verio.com> Hello Jeff, First, welcome on this list. Contributions are always welcome and proteins properties is certainly an area where work is needed. Check the proteomics package org.biojava.bio.proteomics. We already have code to compute molecular masses and isoelectric points. Also consult the file org.biojava.bio.symbol.ResidueProperties.xml. I have added recently the hydropathicity values. There is a pattern for residue properties involving the class org.biojava.bio.symbol.SymbolPropertyTable (see also ProteinTools). Please, do not hesitate to ask advice on this list. Personally, I think it is important to give a precise literature reference when biological constants and methods are used. - George > -----Original Message----- > From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev- > bounces at lists.open-bio.org] On Behalf Of Jeff Cope > Sent: Thursday, November 29, 2007 9:11 AM > To: biojava-dev at lists.open-bio.org > Subject: [Biojava-dev] BioJava Development > > Hello all, > > > > My name is Jeff Cope, and I am currently an undergraduate > developer working as a research assistant on project where we are > calculating some values for various protein sequences like isoelectric > point, instability index, aromaticity, etc. (found here: > http://trac.boisestate.edu/protcalc/ for those who are interested). > > > > As it stands right now we have implemented an applet client to > server system to communicate the data because we have had to wrap the > BioPython library on the server side. I have not been able to find the > matching functionality in the BioJava Library, although I recognize that I > might have missed it somewhere in there. > From abhi232 at cc.gatech.edu Mon Nov 5 13:28:31 2007 From: abhi232 at cc.gatech.edu (abhi232 at cc.gatech.edu) Date: Mon, 05 Nov 2007 18:28:31 -0000 Subject: [Biojava-dev] Error while reading byte data for creating a Trace. In-Reply-To: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> References: <6EDA8DA0-39B2-40A3-B3B3-DB5F3463DB51@sanger.ac.uk> Message-ID: <2839.130.207.66.142.1194285555.squirrel@webmail.cc.gatech.edu> Hi all, I am having a byte array which is having the data from an .ab1 file.The biojava library provides a class called as ABITrace which takes as input either a byte[] array , a file or a url.If i use the later parameters (the file or the url )the program works but if I pass the byte array to the constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a problem with the ABITrace class or how can I bypass this particular error. I am printing the length of the byte array and it comes to 144930...Can that cause a problem in my code? Thanks in advance. Abhinav