From bugzilla-daemon at portal.open-bio.org Thu Jul 3 14:27:21 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jul 2008 14:27:21 -0400 Subject: [Biojava-dev] [Bug 2536] New: GenBankFormat Doesn't Support Bond Features Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2536 Summary: GenBankFormat Doesn't Support Bond Features Product: BioJava Version: 1.5 Platform: All OS/Version: Windows Status: NEW Severity: major Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: james at carmanconsulting.com I'm trying to parse the file: ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian12.protein.gpff.gz using: RichSequence.IOTools.readGenbankProtein() and I keep getting this error (the date column is from my build server which runs this "loader", sorry): [10:51:36]: org.biojava.bio.BioException: Could not read sequence [10:51:36]: at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) [10:51:36]: at com.pg.iip.loader.pubrec.RefSeqLoader.loadPublicRecords(RefSeqLoader.java:106) [10:51:36]: at com.pg.iip.loader.pubrec.PublicRecordLoader.doLoad(PublicRecordLoader.java:248) [10:51:36]: at com.pg.iip.loader.AbstractLoader.execute(AbstractLoader.java:56) [10:51:36]: at com.pg.iip.loader.LoaderUtils.executeLoader(LoaderUtils.java:20) [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [10:51:36]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) [10:51:36]: at com.pg.iip.loader.plugin.RunLoaderMojo.invoke(RunLoaderMojo.java:95) [10:51:36]: at com.pg.iip.loader.plugin.RunLoaderMojo.execute(RunLoaderMojo.java:142) [10:51:36]: at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:447) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:539) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:493) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:463) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:311) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:278) [10:51:36]: at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:143) [10:51:36]: at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:333) [10:51:36]: at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:126) [10:51:36]: at org.apache.maven.cli.MavenCli.main(MavenCli.java:282) [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [10:51:36]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) [10:51:36]: at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) [10:51:36]: at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) [10:51:36]: at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) [10:51:36]: at org.codehaus.classworlds.Launcher.main(Launcher.java:375) [10:51:36]: Caused by: org.biojava.bio.seq.io.ParseException: Could not understand position: bond(39,96 [10:51:36]: at org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285) [10:51:36]: at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:271) [10:51:36]: at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131) [10:51:36]: at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:490) [10:51:36]: at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) [10:51:36]: ... 28 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 Thu Jul 3 14:50:53 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jul 2008 14:50:53 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807031850.m63IorsM011751@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #1 from james at carmanconsulting.com 2008-07-03 14:50 EST ------- Created an attachment (id=967) --> (http://bugzilla.open-bio.org/attachment.cgi?id=967&action=view) A patch (with a unit test) which fixes the issue -- 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 Jul 3 15:18:41 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jul 2008 15:18:41 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807031918.m63JIf4b015073@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #2 from james at carmanconsulting.com 2008-07-03 15:18 EST ------- Ok, maybe it doesn't quite fix the issue. It still bugs out for some reason. -- 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 Jul 3 17:11:07 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jul 2008 17:11:07 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807032111.m63LB7iO023014@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #3 from james at carmanconsulting.com 2008-07-03 17:11 EST ------- The build doesn't fail when unit tests fail, so I assumed everything worked fine. I'll change that in the build.xml file and try to get the test case working. -- 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 Jul 3 18:58:02 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jul 2008 18:58:02 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807032258.m63Mw2KL027048@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #4 from james at carmanconsulting.com 2008-07-03 18:58 EST ------- Created an attachment (id=968) --> (http://bugzilla.open-bio.org/attachment.cgi?id=968&action=view) an updated 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 Fri Jul 4 04:28:23 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jul 2008 04:28:23 -0400 Subject: [Biojava-dev] [Bug 2510] Error when trying to retrieve a sequence assigned to a feature from BioSQL using Hibernate In-Reply-To: Message-ID: <200807040828.m648SNab025049@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2510 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from ap3 at sanger.ac.uk 2008-07-04 04:28 EST ------- Thanks for the patch, I applied it and committed the changes to SVN. Andreas -- 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 Jul 4 04:35:29 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jul 2008 04:35:29 -0400 Subject: [Biojava-dev] [Bug 2510] Error when trying to retrieve a sequence assigned to a feature from BioSQL using Hibernate In-Reply-To: Message-ID: <200807040835.m648ZTjb025577@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2510 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |REOPENED Resolution|FIXED | ------- Comment #2 from ap3 at sanger.ac.uk 2008-07-04 04:35 EST ------- weird, I tried to resolve bug #2536 but instead this one got resolved??? reopening it again. Andreas -- 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 Jul 4 04:37:47 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jul 2008 04:37:47 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807040837.m648blM1025743@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ap3 at sanger.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #5 from ap3 at sanger.ac.uk 2008-07-04 04:37 EST ------- Thanks for the patch, I applied it and committed the changes to SVN. You can run the unit tests individually if you do a and -Dtest.subtree=org/biojavax/bio/seq/** runtests If you use eclipse just do "Run As Junit test" on the test you are interested in. Andreas -- 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 Jul 4 08:36:23 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jul 2008 08:36:23 -0400 Subject: [Biojava-dev] [Bug 2536] GenBankFormat Doesn't Support Bond Features In-Reply-To: Message-ID: <200807041236.m64CaNFT008279@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2536 ------- Comment #6 from james at carmanconsulting.com 2008-07-04 08:36 EST ------- I figured out *how* to run the tests. The problem is that if a test fails, the Ant build is still successful. You really should change that. -- 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 Jul 10 06:27:55 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 10 Jul 2008 06:27:55 -0400 Subject: [Biojava-dev] [Bug 2540] New: RichSequenceIterator does not skip sequence when exception is thrown Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2540 Summary: RichSequenceIterator does not skip sequence when exception is thrown Product: BioJava Version: 1.5 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: martin.jones at ed.ac.uk I have a file containing GenBank records, and I want to process them thus: RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(myReader, null); while (seqs.hasNext()) { RichSequence seq = seqs.nextRichSequence(); // processing code } however, some records cannot be parsed by biojava... this is to be expected as I'm processing half a million records - some are bound to be wonky. So I use a try-catch to skip over troublesome records: RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(myReader, null); while (seqs.hasNext()) { try{ RichSequence seq = seqs.nextRichSequence(); // processing code } catch (BioException e){ System.out.println("record count not be parsed!"); } } However, it seems that the position in the input file is not changed if an exception is thrown during parsing. If I run the above code on a file containing a single un-parseable record, it gets stuck in a non-terminating loop - i.e. each time seqs.nextRichSequence() is called, an exception is thrown, but seqs.hasNext() still returns true. This may be true for other parsers. -- 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 HardmanC at medimmune.com Thu Jul 10 09:15:11 2008 From: HardmanC at medimmune.com (Hardman, Colin) Date: Thu, 10 Jul 2008 14:15:11 +0100 Subject: [Biojava-dev] Missing licence on BlastLikeDataSetCollection.dtd Message-ID: <3F2692AFAA9C6046AC392822E9BDF767C1BD52@UK2EV001.medimmune.com> Biojava developers, Steffen Moller has contacted me about BlastLikeDataSetCollection.dtd missing the GNU Lesser General Public License header which is stopping it's inclusion in the Debian distribution. The original omission was purely accidental - it was always intended to be under that license - just like the rest of the CAT contributions. As I don't have/can't remember my cvs access any more would it be possible for one you to make the change for me so biojava can be included in free software distributions? Cheers, Colin -- Colin Hardman Head of Informatics MedImmune ( Formally Cambridge Antibody Technology ) >> Dear Simon, >> >> I just contacted Tim Dilks in my role of a developer for the Debian >> Linux distribution because of a problem that I have with the file >> dtd/BlastLikeDataSetCollection.dtd that you are the primary author >> of. It has all rights reserved to CAT without mentionning the free >> license of BioJava of any sort. My Debian package was rejected by the >> administratives of Debian for that reason. >> >> Since my email to the BioJava mailing list about a year ago left the >> problem untreated, may I ask you to add that license information to >> the source? I know your time is precious and you may not even have >> BioJava checked out anywhere anymore, but maybe you could send an >> email to the developers list and ask to have the license information added. >> >> With many thanks and best regards, >> >> Steffen >> >> >> > > Hi Steffen, > > I'm not at CAT anymore, so I don't have the (moral) authority to make > the changes in terms of dealing with license issues. However, the > missing FOSS license information was simply an oversight on my part, > so I'm sure there won't be an issue. > > For information, CAT doesn't actually exist as an entity anymore - the > company was acquired by AstraZeneca and then merged with a company > called MedImmune. I suggest you contact Colin Hardman at MedImmune - > he should have the authority to make/request the changes you need. > > > Hope this helps, > > Simon To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. From bugzilla-daemon at portal.open-bio.org Thu Jul 10 10:05:27 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 10 Jul 2008 10:05:27 -0400 Subject: [Biojava-dev] [Bug 2541] New: Exception is thrown when trying to parse a valid GenBank file Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2541 Summary: Exception is thrown when trying to parse a valid GenBank file Product: BioJava Version: 1.5 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: martin.jones at ed.ac.uk org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at readgbtest.GenBankReader$GenBankSequenceReader.processRecord(GenBankReader.java:333) at readgbtest.GenBankReader$GenBankSequenceReader.run(GenBankReader.java:416) 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.GenbankFormat Accession=AB000109 Id=4958873 Comments=Section key was null Parse_block=null Stack trace follows .... at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:289) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 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 Thu Jul 10 10:06:33 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 10 Jul 2008 10:06:33 -0400 Subject: [Biojava-dev] [Bug 2541] Exception is thrown when trying to parse a valid GenBank file In-Reply-To: Message-ID: <200807101406.m6AE6XaB004320@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2541 ------- Comment #1 from martin.jones at ed.ac.uk 2008-07-10 10:06 EST ------- Created an attachment (id=970) --> (http://bugzilla.open-bio.org/attachment.cgi?id=970&action=view) genbank record that causes the parse failure -- 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 ap3 at sanger.ac.uk Thu Jul 10 09:53:01 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 10 Jul 2008 14:53:01 +0100 (BST) Subject: [Biojava-dev] Missing licence on BlastLikeDataSetCollection.dtd In-Reply-To: <3F2692AFAA9C6046AC392822E9BDF767C1BD52@UK2EV001.medimmune.com> References: <3F2692AFAA9C6046AC392822E9BDF767C1BD52@UK2EV001.medimmune.com> Message-ID: Hi Colin, Thanks for the info, I updated the file in the SVN repository to contain the missing LGPL information. Andreas -------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK On Thu, 10 Jul 2008, Hardman, Colin wrote: > > > Biojava developers, > > > > Steffen Moller has contacted me about BlastLikeDataSetCollection.dtd > missing the GNU Lesser General Public License header which is stopping > it's inclusion in the Debian distribution. > > > > The original omission was purely accidental - it was always intended to > be under that license - just like the rest of the CAT contributions. As > I don't have/can't remember my cvs access any more would it be possible > for one you to make the change for me so biojava can be included in free > software distributions? > > > > Cheers, > > > > Colin > > -- > > Colin Hardman > > Head of Informatics > > MedImmune ( Formally Cambridge Antibody Technology ) > > > > > > > > > >>> Dear Simon, > >>> > >>> I just contacted Tim Dilks in my role of a developer for the Debian > >>> Linux distribution because of a problem that I have with the file > >>> dtd/BlastLikeDataSetCollection.dtd that you are the primary author > >>> of. It has all rights reserved to CAT without mentionning the free > >>> license of BioJava of any sort. My Debian package was rejected by the > > >>> administratives of Debian for that reason. > >>> > >>> Since my email to the BioJava mailing list about a year ago left the > >>> problem untreated, may I ask you to add that license information to > >>> the source? I know your time is precious and you may not even have > >>> BioJava checked out anywhere anymore, but maybe you could send an > >>> email to the developers list and ask to have the license information > added. > >>> > >>> With many thanks and best regards, > >>> > >>> Steffen > >>> > >>> > >>> > >> > >> Hi Steffen, > >> > >> I'm not at CAT anymore, so I don't have the (moral) authority to make > >> the changes in terms of dealing with license issues. However, the > >> missing FOSS license information was simply an oversight on my part, > >> so I'm sure there won't be an issue. > >> > >> For information, CAT doesn't actually exist as an entity anymore - the > > >> company was acquired by AstraZeneca and then merged with a company > >> called MedImmune. I suggest you contact Colin Hardman at MedImmune - > >> he should have the authority to make/request the changes you need. > >> > >> > >> Hope this helps, > >> > >> Simon > > > > > To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From ap3 at sanger.ac.uk Sun Jul 13 07:54:49 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Sun, 13 Jul 2008 12:54:49 +0100 (BST) Subject: [Biojava-dev] Missing licence on BlastLikeDataSetCollection.dtd In-Reply-To: <4879DAF4.5000305@gmx.de> References: <3F2692AFAA9C6046AC392822E9BDF767C1BD52@UK2EV001.medimmune.com> <4879DAF4.5000305@gmx.de> Message-ID: Hi Steffen, > I was just going through last year's work on the packaging and found > that you are happily using libjgraphT now and (as it just had to be) I > ran into problem. Could you just indicate to me what version of that > library you are using? not exactly sure which version is being used, therefore CCing the dev list, where Richard might be able to help. As far as I know, this is an optional dependency, which is only required for the new nexus parser. > I am trying to use the Debian package of > libjgraphT, which is of version 0.6.0 (0.7.x are incompatible with > another program and was hence not yet update). Please also state this > dependency somehere on your wiki pages. That's true, it was missing from the docu there. I added it to the list of support libraries at the Download page in the wiki. > > On a sidenote, I know it to be common practice to ship the external jar > files together with the local source. For the packagers however this is > then always a bit difficult since one needs to amend everything to the > versions that area already available locally.If would be preferable, in > my view, to have the jar files distributed separatedly for those who > want them, and with explicit instructions on how to retrieve them from > external sources or even how to rebuild them from source. We try to make life as easy as possible for the users. As such we provide a biojava-all jar file that contains the complete source code, javadocs and all jar files that biojava is dependent on as well as the biojava.jar. It should be easy to extract whatever you need from that download. Let me know if anything is missing for you. Additionally, if you only want the biojava.jar you can get that from the download site as well. We have not discussed bundling the dependencies separately, but my feeling is that this would add another step in the installation process, and just getting it all in one download might be the easiest. Would a Maven setup be useful for you? Andreas -- 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 simpleyrx at 163.com Sun Jul 13 22:44:13 2008 From: simpleyrx at 163.com (simpleyrx) Date: Mon, 14 Jul 2008 10:44:13 +0800 (CST) Subject: [Biojava-dev] can biojava calculate pseudo amino acid composition ? Message-ID: <9483751.323861216003453070.JavaMail.coremail@bj163app72.163.com> Dear friends, I wonder that does biojava can biojava calculate pseudo amino acid composition ? -- yan From dicknetherlands at gmail.com Mon Jul 14 11:15:26 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Mon, 14 Jul 2008 16:15:26 +0100 Subject: [Biojava-dev] can biojava calculate pseudo amino acid composition ? In-Reply-To: <9483751.323861216003453070.JavaMail.coremail@bj163app72.163.com> References: <9483751.323861216003453070.JavaMail.coremail@bj163app72.163.com> Message-ID: Nobody's written any code for that yet, no. If you come up with something we'd love to see it! cheers, Richard 2008/7/14 simpleyrx : > > Dear friends, > > I wonder that does biojava can biojava calculate pseudo amino acid composition ? > > > > > -- > > > yan > > > > _______________________________________________ > 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 Mon Jul 14 20:57:49 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 15 Jul 2008 08:57:49 +0800 Subject: [Biojava-dev] can biojava calculate pseudo amino acid composition ? In-Reply-To: <9483751.323861216003453070.JavaMail.coremail@bj163app72.163.com> References: <9483751.323861216003453070.JavaMail.coremail@bj163app72.163.com> Message-ID: <93b45ca50807141757n444e4e33ncfac098befa4f412@mail.gmail.com> Hi - Not sure what you mean by Pseudo amino acid composition? However, BioJava has very flexible Symbol and Distribution API's so anything that can be represented by a Symbol can be counted by a Distribution. - Mark On 7/14/08, simpleyrx wrote: > > Dear friends, > > I wonder that does biojava can biojava calculate pseudo amino acid composition ? > > > > > -- > > > yan > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From ap3 at sanger.ac.uk Thu Jul 17 08:21:19 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 17 Jul 2008 13:21:19 +0100 Subject: [Biojava-dev] [Biojava-l] biojava 1.6 released In-Reply-To: <48032123.7010803@psb.ugent.be> References: <0A060667-C24C-4D41-8D10-ED1D449A5F62@sanger.ac.uk> <48032123.7010803@psb.ugent.be> Message-ID: <81230DAA-B03B-4BDC-A353-B3072DB03C4F@sanger.ac.uk> Hi Thomas, Your mail from April only arrived at the mailing list today, (most likely you are not subscribed to the list with this email and hence your mail was stuck in the moderation loop until now. This is to avoid getting spam through...) This issue has been reported by somebody else as well and I believe it should work fine now. Let me know if there are any other problems. Cheers, Andreas On 14 Apr 2008, at 10:17, Thomas Van Parys wrote: > Andreas Prlic schreef: >> Biojava 1.6 has been released and is available from http:// >> biojava.org/wiki/BioJava:Download > > Hi, > > Thanks for the new release, but is there any chance that there's > something wrong with the download? > Firefox hangs when trying to download and wget gives me a jar file > that doesn't contain the source code. > > http://www.biojava.org/download/bj16/all/biojava-1.6-all.jar > > > regards, > Thomas > > -- > ================================================================== > Thomas Van Parys > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > thomas.vanparys at psb.ugent.be http://bioinformatics.psb.ugent.be > ================================================================== > _______________________________________________ > 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 markjschreiber at gmail.com Thu Jul 17 08:33:11 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 17 Jul 2008 20:33:11 +0800 Subject: [Biojava-dev] [Fwd: large genbank data] In-Reply-To: <483E0CA2.4010906@asti.dost.gov.ph> References: <483E0CA2.4010906@asti.dost.gov.ph> Message-ID: <93b45ca50807170533k24af6231s89b257bce5c740ad@mail.gmail.com> Hi - Is the code throwing an exception or running out of memory?? Can you send an example program and the problem you encounter to the list. - Mark On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia wrote: > > > -------- Original Message -------- > Subject: large genbank data > Date: Wed, 28 May 2008 18:02:48 +0800 > From: Rey Vincent Babilonia > To: biojava-l at biojava.org > > hi, > > anybody tried uploading a large genbank data (e.g. > ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? > load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and > it can't read the sequence (maybe because it has 30000+ sequences). > > thanks. > > -- > /** > * @author Rey Vincent P. Babilonia > * @number +63 2 426 9760 local 1302 > * @pgp 0x383454CF pgp.mit.edu > * @project Philippine Bioinformatics Solutions > * @program Philippine e-Science Grid > * @division Research and Development Division > * @agency Advanced Science and Technology Institute > * @url http://www.psigrid.gov.ph > */ > > > -- > /** > * @author Rey Vincent P. Babilonia > * @number +63 2 426 9760 local 1302 > * @pgp 0x383454CF pgp.mit.edu > * @project Philippine Bioinformatics Solutions > * @program Philippine e-Science Grid > * @division Research and Development Division > * @agency Advanced Science and Technology Institute > * @url http://www.psigrid.gov.ph > */ > > No virus found in this outgoing message. > Checked by AVG. > Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: 5/28/2008 5:33 PM > > _______________________________________________ > 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 Thu Jul 17 08:34:44 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 17 Jul 2008 20:34:44 +0800 Subject: [Biojava-dev] biojavax src? In-Reply-To: <061220080206.12993.485084AE000E1EFF000032C122230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net> References: <061220080206.12993.485084AE000E1EFF000032C122230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net> Message-ID: <93b45ca50807170534p2ec2c70nf855b7e818605b36@mail.gmail.com> Hi - The code for biojavax should be in the src directory under that packages starting with org.biojavax.* - Mark On Thu, Jun 12, 2008 at 10:06 AM, wrote: > Greetings, > > I'd like to know if the full source code is available for biojavax. I could > not find in my download... > > http://www.biojava.org/download/bj16/all/biojava-1.6-all.jar > > Please forgive my error, if any. > > > Regards, > Carl > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From ap3 at sanger.ac.uk Thu Jul 17 08:49:41 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 17 Jul 2008 13:49:41 +0100 Subject: [Biojava-dev] biojava mailing lists Message-ID: <66377475-9986-4824-820F-A36F4AC979D9@sanger.ac.uk> Hi, You might have noticed a number of emails getting through to the mailing lists today with big delay. This happens if you post to the mailing list, without being subscribed to it. In order to avoid spam both lists only accept postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail will get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam). 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 markjschreiber at gmail.com Thu Jul 17 08:50:15 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Thu, 17 Jul 2008 20:50:15 +0800 Subject: [Biojava-dev] Important notice about email handling on BioJava lists Message-ID: <93b45ca50807170550y722ebdc2qd4a1bb36b3b32206@mail.gmail.com> Hi - A lot of old emails just got posted to the list. This usually happens because messages that contain attachments or HTML get blocked by our aggressive spam filter. When our overworked admins get around to confirming they are not spam they eventually get through but probably too late to be of much help to you. Therefore... For prompt service when asking for help: 1) USE ONLY TEXT FORMAT EMAIL (NO HTML) 2) DON'T ADD ATTACHMENTS. If you want to post code just copy it in the body of the email. Although this might be a bit draconian we used to get badly spammed on the list so this is one of the easiest ways around it. Thanks, - Mark From dicknetherlands at gmail.com Thu Jul 17 15:06:54 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Thu, 17 Jul 2008 20:06:54 +0100 Subject: [Biojava-dev] tbl2gff? In-Reply-To: <061220080206.13462.485084B9000C35630000349622230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net> References: <061220080206.13462.485084B9000C35630000349622230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net> Message-ID: No not yet but if you have one or are going to write one, keep us posted! cheers, Richard 2008/6/12 : > Greetings again, > > Is there any tool for converting a .tbl file to .gff format? > > Regards, > Carl > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From rvincent at asti.dost.gov.ph Thu Jul 17 21:59:47 2008 From: rvincent at asti.dost.gov.ph (Rey Vincent Babilonia) Date: Fri, 18 Jul 2008 09:59:47 +0800 Subject: [Biojava-dev] [Fwd: large genbank data] In-Reply-To: <93b45ca50807170533k24af6231s89b257bce5c740ad@mail.gmail.com> References: <483E0CA2.4010906@asti.dost.gov.ph> <93b45ca50807170533k24af6231s89b257bce5c740ad@mail.gmail.com> Message-ID: <487FF913.6090504@asti.dost.gov.ph> Hi Mark, At first it throws an out of memory exception. My workaround is to subdivide the sequence file into individual GenBank files. The error now is that if a GenBank sequence has an 'empty alphabet', it does not get loaded to BioSQL. My workaround is to check if sequence.getAlphabet().getName() is DNA. Thanks. Mark Schreiber wrote: > Hi - > > Is the code throwing an exception or running out of memory?? > > Can you send an example program and the problem you encounter to the list. > - Mark > > On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia > wrote: >> >> -------- Original Message -------- >> Subject: large genbank data >> Date: Wed, 28 May 2008 18:02:48 +0800 >> From: Rey Vincent Babilonia >> To: biojava-l at biojava.org >> >> hi, >> >> anybody tried uploading a large genbank data (e.g. >> ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? >> load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and >> it can't read the sequence (maybe because it has 30000+ sequences). >> >> thanks. >> >> -- >> /** >> * @author Rey Vincent P. Babilonia >> * @number +63 2 426 9760 local 1302 >> * @pgp 0x383454CF pgp.mit.edu >> * @project Philippine Bioinformatics Solutions >> * @program Philippine e-Science Grid >> * @division Research and Development Division >> * @agency Advanced Science and Technology Institute >> * @url http://www.psigrid.gov.ph >> */ >> >> >> -- >> /** >> * @author Rey Vincent P. Babilonia >> * @number +63 2 426 9760 local 1302 >> * @pgp 0x383454CF pgp.mit.edu >> * @project Philippine Bioinformatics Solutions >> * @program Philippine e-Science Grid >> * @division Research and Development Division >> * @agency Advanced Science and Technology Institute >> * @url http://www.psigrid.gov.ph >> */ >> >> No virus found in this outgoing message. >> Checked by AVG. >> Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: 5/28/2008 5:33 PM >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -- /** * @author Rey Vincent P. Babilonia * @number +63 2 426 9760 local 1302 * @pgp 0x383454CF pgp.mit.edu * @project Philippine Bioinformatics Solutions * @program Philippine e-Science Grid * @division Research and Development Division * @agency Advanced Science and Technology Institute * @url http://www.psigrid.gov.ph */ From rvincent at asti.dost.gov.ph Fri Jul 18 04:12:15 2008 From: rvincent at asti.dost.gov.ph (Rey Vincent Babilonia) Date: Fri, 18 Jul 2008 16:12:15 +0800 Subject: [Biojava-dev] [Biojava-l] [Fwd: large genbank data] In-Reply-To: <487FF913.6090504@asti.dost.gov.ph> References: <483E0CA2.4010906@asti.dost.gov.ph> <93b45ca50807170533k24af6231s89b257bce5c740ad@mail.gmail.com> <487FF913.6090504@asti.dost.gov.ph> Message-ID: <4880505F.7010308@asti.dost.gov.ph> Hi Mark, What is the maximum sequence length that a RichSequence can handle? java -Xms1024m -Xmx1256m -jar loader.jar . 16:09:00,173 INFO Loader:296 - D:\AE005174.gbk is readable. 16:09:06,704 INFO Loader:326 - Loading sequence AE005174 with identifier 56384585, length 5528445 and alphabet DNA... org.hibernate.PropertyAccessException: Exception occurred inside getter of org.biojavax.bio.seq.SimpleRichSequence.sequenceLength Rey Vincent Babilonia wrote: > Hi Mark, > > At first it throws an out of memory exception. My workaround is to > subdivide the sequence file into individual GenBank files. > > The error now is that if a GenBank sequence has an 'empty alphabet', it > does not get loaded to BioSQL. My workaround is to check if > sequence.getAlphabet().getName() is DNA. > > Thanks. > > Mark Schreiber wrote: >> Hi - >> >> Is the code throwing an exception or running out of memory?? >> >> Can you send an example program and the problem you encounter to the >> list. >> - Mark >> >> On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia >> wrote: >>> >>> -------- Original Message -------- >>> Subject: large genbank data >>> Date: Wed, 28 May 2008 18:02:48 +0800 >>> From: Rey Vincent Babilonia >>> To: biojava-l at biojava.org >>> >>> hi, >>> >>> anybody tried uploading a large genbank data (e.g. >>> ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? >>> load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and >>> it can't read the sequence (maybe because it has 30000+ sequences). >>> >>> thanks. >>> >>> -- >>> /** >>> * @author Rey Vincent P. Babilonia >>> * @number +63 2 426 9760 local 1302 >>> * @pgp 0x383454CF pgp.mit.edu >>> * @project Philippine Bioinformatics Solutions >>> * @program Philippine e-Science Grid >>> * @division Research and Development Division >>> * @agency Advanced Science and Technology Institute >>> * @url http://www.psigrid.gov.ph >>> */ >>> >>> >>> -- >>> /** >>> * @author Rey Vincent P. Babilonia >>> * @number +63 2 426 9760 local 1302 >>> * @pgp 0x383454CF pgp.mit.edu >>> * @project Philippine Bioinformatics Solutions >>> * @program Philippine e-Science Grid >>> * @division Research and Development Division >>> * @agency Advanced Science and Technology Institute >>> * @url http://www.psigrid.gov.ph >>> */ >>> >>> No virus found in this outgoing message. >>> Checked by AVG. >>> Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: >>> 5/28/2008 5:33 PM >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> > -- /** * @author Rey Vincent P. Babilonia * @number +63 2 426 9760 local 1302 * @pgp 0x383454CF pgp.mit.edu * @project Philippine Bioinformatics Solutions * @program Philippine e-Science Grid * @division Research and Development Division * @agency Advanced Science and Technology Institute * @url http://www.psigrid.gov.ph */ From dicknetherlands at gmail.com Fri Jul 18 04:47:08 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Fri, 18 Jul 2008 09:47:08 +0100 Subject: [Biojava-dev] [Biojava-l] [Fwd: large genbank data] In-Reply-To: <4880505F.7010308@asti.dost.gov.ph> References: <483E0CA2.4010906@asti.dost.gov.ph> <93b45ca50807170533k24af6231s89b257bce5c740ad@mail.gmail.com> <487FF913.6090504@asti.dost.gov.ph> <4880505F.7010308@asti.dost.gov.ph> Message-ID: In order to persist to BioSQL, BioJava has to convert the symbol list into a string so that it can pass it to JDBC via Hibernate. Therefore the maximum length of a sequence you wish to persist to BioSQL is the maximum length of a string in Java, which is 65536 (2^16) if you are working in a UTF-8 environment. 2008/7/18 Rey Vincent Babilonia : > Hi Mark, > > What is the maximum sequence length that a RichSequence can handle? > > java -Xms1024m -Xmx1256m -jar loader.jar > . > 16:09:00,173 INFO Loader:296 - D:\AE005174.gbk is readable. > 16:09:06,704 INFO Loader:326 - Loading sequence AE005174 with identifier > 56384585, length 5528445 and alphabet DNA... > org.hibernate.PropertyAccessException: Exception occurred inside getter of > org.biojavax.bio.seq.SimpleRichSequence.sequenceLength > > Rey Vincent Babilonia wrote: >> >> Hi Mark, >> >> At first it throws an out of memory exception. My workaround is to >> subdivide the sequence file into individual GenBank files. >> >> The error now is that if a GenBank sequence has an 'empty alphabet', it >> does not get loaded to BioSQL. My workaround is to check if >> sequence.getAlphabet().getName() is DNA. >> >> Thanks. >> >> Mark Schreiber wrote: >>> >>> Hi - >>> >>> Is the code throwing an exception or running out of memory?? >>> >>> Can you send an example program and the problem you encounter to the >>> list. >>> - Mark >>> >>> On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia >>> wrote: >>>> >>>> -------- Original Message -------- >>>> Subject: large genbank data >>>> Date: Wed, 28 May 2008 18:02:48 +0800 >>>> From: Rey Vincent Babilonia >>>> To: biojava-l at biojava.org >>>> >>>> hi, >>>> >>>> anybody tried uploading a large genbank data (e.g. >>>> ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? >>>> load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and >>>> it can't read the sequence (maybe because it has 30000+ sequences). >>>> >>>> thanks. >>>> >>>> -- >>>> /** >>>> * @author Rey Vincent P. Babilonia >>>> * @number +63 2 426 9760 local 1302 >>>> * @pgp 0x383454CF pgp.mit.edu >>>> * @project Philippine Bioinformatics Solutions >>>> * @program Philippine e-Science Grid >>>> * @division Research and Development Division >>>> * @agency Advanced Science and Technology Institute >>>> * @url http://www.psigrid.gov.ph >>>> */ >>>> >>>> >>>> -- >>>> /** >>>> * @author Rey Vincent P. Babilonia >>>> * @number +63 2 426 9760 local 1302 >>>> * @pgp 0x383454CF pgp.mit.edu >>>> * @project Philippine Bioinformatics Solutions >>>> * @program Philippine e-Science Grid >>>> * @division Research and Development Division >>>> * @agency Advanced Science and Technology Institute >>>> * @url http://www.psigrid.gov.ph >>>> */ >>>> >>>> No virus found in this outgoing message. >>>> Checked by AVG. >>>> Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: >>>> 5/28/2008 5:33 PM >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >> > > -- > /** > * @author Rey Vincent P. Babilonia > * @number +63 2 426 9760 local 1302 > * @pgp 0x383454CF pgp.mit.edu > * @project Philippine Bioinformatics Solutions > * @program Philippine e-Science Grid > * @division Research and Development Division > * @agency Advanced Science and Technology Institute > * @url http://www.psigrid.gov.ph > */ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From holland at eaglegenomics.com Mon Jul 21 05:28:46 2008 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 21 Jul 2008 10:28:46 +0100 Subject: [Biojava-dev] BioJava3 Use Cases Message-ID: Hi guys, I'd like to repeat an earlier request for use cases to guide the new BioJava 3 development work. We have a wiki page for this but it hasn't seen many updates: http://biojava.org/wiki/BioJava_3_Use_Cases Could anyone who has a task which BioJava cannot currently achieve, or does not achieve correctly, please add that task to this wiki page, so that we can try and implement it in the new code. A template for a use case has been provided on that same wiki page which you should follow when submitting your own suggestions. Basically the rule is that saying something like 'I want microarray support' isn't likely to get much of a response, but asking for a specific function, e.g. 'I want to be able to parse MAGE files' or 'I want to use XYZ technique to analyse my own chip designs', will get you a lot further. I'm setting a cut-off date for the initial list of use-cases at August 1st. Whatever's on the page at that point will be considered for implementation in the first phase of development over the next 6 months, along with updates or transfers of functionality from the existing code base where appropriate. Anything that gets added to the list after that date will only get implemented in the second later phase, date indeterminate as yet, unless whoever submits the use case also chooses to submit their own code to solve it! cheers, Richard -- Richard Holland Bioinformatics Software Developer Eagle Genomics http://www.eaglegenomics.com/ From elee at berkeleybop.org Fri Jul 25 20:25:36 2008 From: elee at berkeleybop.org (Ed Lee) Date: Fri, 25 Jul 2008 17:25:36 -0700 Subject: [Biojava-dev] GBOL (Chado based API) page Message-ID: <1217031936.7746.12.camel@fruitless.lbl.gov> Hello everyone, As discussed, I've set up a page for GBOL (GMOD Bio Object Layer) on the GMOD wiki. Right now it's just a brain dump on the design. We highly encourage the community to contribute their thoughts on what the Biological layer should encompass, as well as help refine the best practices for how data should be stored. The GBOL page is located at: http://www.gmod.org/wiki/index.php/Gbol Cheers, Ed From heuermh at acm.org Tue Jul 29 01:04:32 2008 From: heuermh at acm.org (Michael Heuer) Date: Tue, 29 Jul 2008 01:04:32 -0400 (EDT) Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: Message-ID: Richard Holland wrote: > Hi guys, > > I'd like to repeat an earlier request for use cases to guide the new > BioJava 3 development work. We have a wiki page for this but it hasn't > seen many updates: > > http://biojava.org/wiki/BioJava_3_Use_Cases > > Could anyone who has a task which BioJava cannot currently achieve, or > does not achieve correctly, please add that task to this wiki page, so > that we can try and implement it in the new code. > > A template for a use case has been provided on that same wiki page > which you should follow when submitting your own suggestions. > Basically the rule is that saying something like 'I want microarray > support' isn't likely to get much of a response, but asking for a > specific function, e.g. 'I want to be able to parse MAGE files' or 'I > want to use XYZ technique to analyse my own chip designs', will get > you a lot further. > > I'm setting a cut-off date for the initial list of use-cases at August > 1st. Whatever's on the page at that point will be considered for > implementation in the first phase of development over the next 6 > months, along with updates or transfers of functionality from the > existing code base where appropriate. Anything that gets added to the > list after that date will only get implemented in the second later > phase, date indeterminate as yet, unless whoever submits the use case > also chooses to submit their own code to solve it! Hello Richard, Very brief notes from the Biojava BOF session at BOSC 2008 are up at http://biojava.org/wiki/BOSC2008_Presentation Much of the conversation was about how to make Biojava more convenient to use rather than about what features were missing. michael From holland at eaglegenomics.com Tue Jul 29 02:33:11 2008 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 29 Jul 2008 07:33:11 +0100 Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: References: Message-ID: That's what I've thought too... ease of use (and ease of extension) seems to be people's highest priority. I'll give it till the 1st as promised then make a summary. cheers, Richard 2008/7/29 Michael Heuer : > Richard Holland wrote: > >> Hi guys, >> >> I'd like to repeat an earlier request for use cases to guide the new >> BioJava 3 development work. We have a wiki page for this but it hasn't >> seen many updates: >> >> http://biojava.org/wiki/BioJava_3_Use_Cases >> >> Could anyone who has a task which BioJava cannot currently achieve, or >> does not achieve correctly, please add that task to this wiki page, so >> that we can try and implement it in the new code. >> >> A template for a use case has been provided on that same wiki page >> which you should follow when submitting your own suggestions. >> Basically the rule is that saying something like 'I want microarray >> support' isn't likely to get much of a response, but asking for a >> specific function, e.g. 'I want to be able to parse MAGE files' or 'I >> want to use XYZ technique to analyse my own chip designs', will get >> you a lot further. >> >> I'm setting a cut-off date for the initial list of use-cases at August >> 1st. Whatever's on the page at that point will be considered for >> implementation in the first phase of development over the next 6 >> months, along with updates or transfers of functionality from the >> existing code base where appropriate. Anything that gets added to the >> list after that date will only get implemented in the second later >> phase, date indeterminate as yet, unless whoever submits the use case >> also chooses to submit their own code to solve it! > > Hello Richard, > > Very brief notes from the Biojava BOF session at BOSC 2008 are up at > > http://biojava.org/wiki/BOSC2008_Presentation > > Much of the conversation was about how to make Biojava more convenient to > use rather than about what features were missing. > > michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland Bioinformatics Software Developer Eagle Genomics http://www.eaglegenomics.com/ From phidias51 at gmail.com Tue Jul 29 10:24:51 2008 From: phidias51 at gmail.com (Mark Fortner) Date: Tue, 29 Jul 2008 07:24:51 -0700 Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: References: Message-ID: <6e1d61f50807290724v665f975eqd624d9793926b5bc@mail.gmail.com> Along the lines of ease-of-use, I've been using BioJava for the past few weeks in conjunction with the Groovy scripting language. It's easy to setup, and works wherever Java works. It also makes it easy to leverage any Java libraries. You can use either Java syntax or Groovy syntax, and the scripts can either be compiled to Java bytecode or interpreted. You can make the scripts either procedural or object-oriented to suit your needs. You can find out more about Groovy here: http://groovy.codehaus.org Regards, Mark On Mon, Jul 28, 2008 at 11:33 PM, Richard Holland wrote: > That's what I've thought too... ease of use (and ease of extension) > seems to be people's highest priority. I'll give it till the 1st as > promised then make a summary. > > cheers, > Richard > > 2008/7/29 Michael Heuer : > > Richard Holland wrote: > > > >> Hi guys, > >> > >> I'd like to repeat an earlier request for use cases to guide the new > >> BioJava 3 development work. We have a wiki page for this but it hasn't > >> seen many updates: > >> > >> http://biojava.org/wiki/BioJava_3_Use_Cases > >> > >> Could anyone who has a task which BioJava cannot currently achieve, or > >> does not achieve correctly, please add that task to this wiki page, so > >> that we can try and implement it in the new code. > >> > >> A template for a use case has been provided on that same wiki page > >> which you should follow when submitting your own suggestions. > >> Basically the rule is that saying something like 'I want microarray > >> support' isn't likely to get much of a response, but asking for a > >> specific function, e.g. 'I want to be able to parse MAGE files' or 'I > >> want to use XYZ technique to analyse my own chip designs', will get > >> you a lot further. > >> > >> I'm setting a cut-off date for the initial list of use-cases at August > >> 1st. Whatever's on the page at that point will be considered for > >> implementation in the first phase of development over the next 6 > >> months, along with updates or transfers of functionality from the > >> existing code base where appropriate. Anything that gets added to the > >> list after that date will only get implemented in the second later > >> phase, date indeterminate as yet, unless whoever submits the use case > >> also chooses to submit their own code to solve it! > > > > Hello Richard, > > > > Very brief notes from the Biojava BOF session at BOSC 2008 are up at > > > > http://biojava.org/wiki/BOSC2008_Presentation > > > > Much of the conversation was about how to make Biojava more convenient to > > use rather than about what features were missing. > > > > michael > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > > > -- > Richard Holland > Bioinformatics Software Developer > Eagle Genomics > http://www.eaglegenomics.com/ > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Mark Fortner blog: http://feeds.feedburner.com/jroller/ideafactory From kono at ucsd.edu Tue Jul 29 18:26:56 2008 From: kono at ucsd.edu (Keiichiro Ono) Date: Tue, 29 Jul 2008 15:26:56 -0700 Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: <6e1d61f50807290724v665f975eqd624d9793926b5bc@mail.gmail.com> References: <6e1d61f50807290724v665f975eqd624d9793926b5bc@mail.gmail.com> Message-ID: <61056a720807291526n43acbfacyde8945a728c61be0@mail.gmail.com> Hi everyone. Is support for network/graph model a part of BioJava 3? I'm working on a project called Cytoscape: http://www.cytoscape.org/ and we are re-designing internal graph model now for Cytoscape 3. http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0 http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/api/src/main/java/org/cytoscape/model/network/ I'm curious because if BioJava supports data models for protein-protein interactions, I want to support it somehow. Also, we are trying to support technologies including scripting languages (http://www.cytoscape.org/cgi-bin/moin.cgi/ScriptingPlugins), Spring Framework, pluggable rendering engine (like using Processing as Cytoscape's rendering engine), so if we can cooperate in some topics, it would be great. Thanks. Kei -- Keiichiro Ono kono at ucsd.edu Cytoscape Core Developer Team: http://www.cytoscape.org/ UCSD Bioengineering Ideker Lab: http://chianti.ucsd.edu/idekerlab/ From heuermh at acm.org Tue Jul 29 22:45:22 2008 From: heuermh at acm.org (Michael Heuer) Date: Tue, 29 Jul 2008 22:45:22 -0400 (EDT) Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: <61056a720807291526n43acbfacyde8945a728c61be0@mail.gmail.com> Message-ID: Keiichiro Ono wrote: > Hi everyone. > > Is support for network/graph model a part of BioJava 3? I'm working > on a project called Cytoscape: > > http://www.cytoscape.org/ > > and we are re-designing internal graph model now for Cytoscape 3. > > http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0 > http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/api/src/main/java/org/cytoscape/model/network/ > > I'm curious because if BioJava supports data models for > protein-protein interactions, I want to support it somehow. > > > Also, we are trying to support technologies including scripting > languages (http://www.cytoscape.org/cgi-bin/moin.cgi/ScriptingPlugins), > Spring Framework, pluggable rendering engine (like using Processing as > Cytoscape's rendering engine), so if we can cooperate in some topics, > it would be great. > > Thanks. > Kei Hello Kei, I believe most of the Biojava devs are familiar with Cytoscape. I welcome cooperation with the Cytoscape project. I should also mention, that as a dev and project admin of the newly "opened" Piccolo2D project, an older version of which Cytoscape's current rendering engine is based on, I welcome cooperation in that area as well. http://piccolo2d.org michael From phidias51 at gmail.com Thu Jul 31 11:06:05 2008 From: phidias51 at gmail.com (Mark Fortner) Date: Thu, 31 Jul 2008 08:06:05 -0700 Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: References: <61056a720807291526n43acbfacyde8945a728c61be0@mail.gmail.com> Message-ID: <6e1d61f50807310806k55584c9jbd28a23543adda6c@mail.gmail.com> Hi Richard, I started to writeup a use-case, and realized that what I was thinking about was more than just a single use-case, and might be beyond the scope of what biojava should handle. So I thought I would ask before writing it up. It seems that we have a need for a generic parsing and dataloading framework. Something that encompasses not only Mark Schreiber's use-case, but could also handle data from a variety of different instrument files -- everything from MAGE files, ABI trace files, CSV, Excel, or text flat files. I've been thinking about creating a semantic data loader. This would be part framework and part GUI application. It would allow the user to map elements of data files to an ontology, and also map parts of an ontology to different databases. The user would be able to create a parser definition, which would parse and load data, verify the data against rules stored in the ontology and then load the data into the database using the data's ontology tags as a guide. A first step in the implementation, might be to retrofit the BioSQL and parsing code. Is this within the scope of BioJava? Is it something that the community would find interesting and useful in the everyday work they do? It it something to which people would like to contribute? Regards, -- Mark Fortner blog: http://feeds.feedburner.com/jroller/ideafactory From holland at eaglegenomics.com Thu Jul 31 11:47:37 2008 From: holland at eaglegenomics.com (Richard Holland) Date: Thu, 31 Jul 2008 16:47:37 +0100 Subject: [Biojava-dev] BioJava3 Use Cases In-Reply-To: <6e1d61f50807310806k55584c9jbd28a23543adda6c@mail.gmail.com> References: <61056a720807291526n43acbfacyde8945a728c61be0@mail.gmail.com> <6e1d61f50807310806k55584c9jbd28a23543adda6c@mail.gmail.com> Message-ID: In many ways that is what exists already, save an actual ontology, and I was definitely hoping to build on the existing methods in BJ3. The current system parses files by translating them into a common object model, which itself is based on the BioSQL object model, and then persists to BioSQL pretty much on a 1:1 basis. It would not be difficult to extend this to translate any format to this common layer, then transfer that common layer onto a database. Ontologies are a good way of doing it. However, you soon run into the issue of what makes a good intermediate object layer (i.e. an object model which can be described using the ontology, and suits every possible data format without losing any information from any of them). This is where it gets hard and you have to start compromising, at which point there's always someone out there that goes 'but why doesn't it parse my favourite tag?'. Mark Schreiber has suggested INSDseq as a good intermediate format for sequence data, but that of course doesn't cater for microarrays etc. So, I was heading towards making each parser use its own format-specific object model, within which a user can explore exactly as if it were the file itself. Each database format supported would also have its own object model matching the schema. Then, I wanted to provide a set of translators that can map between them. How those translators work is uncertain, and would probably be on a specific format-to-format basis, one for each combo, but your ontology method is a possible alternative solution. There's also a tool out there called Dozer which can translate any bean into any other bean based on a mapping definition. I was hoping we could make use of that. So... nice idea, and I can see where you're coming from, but it suffers the same problem as our existing model does - how do you define a common ontology/object model that can cater for everything. Answers on a postcard please...! cheers, Richard 2008/7/31 Mark Fortner : > Hi Richard, > I started to writeup a use-case, and realized that what I was thinking about > was more than just a single use-case, and might be beyond the scope of what > biojava should handle. So I thought I would ask before writing it up. > > It seems that we have a need for a generic parsing and dataloading > framework. Something that encompasses not only Mark Schreiber's use-case, > but could also handle data from a variety of different instrument files -- > everything from MAGE files, ABI trace files, CSV, Excel, or text flat files. > > I've been thinking about creating a semantic data loader. This would be > part framework and part GUI application. It would allow the user to map > elements of data files to an ontology, and also map parts of an ontology to > different databases. The user would be able to create a parser definition, > which would parse and load data, verify the data against rules stored in the > ontology and then load the data into the database using the data's ontology > tags as a guide. > > A first step in the implementation, might be to retrofit the BioSQL and > parsing code. > > Is this within the scope of BioJava? Is it something that the community > would find interesting and useful in the everyday work they do? It it > something to which people would like to contribute? > > Regards, > > -- > Mark Fortner > > blog: http://feeds.feedburner.com/jroller/ideafactory > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland Bioinformatics Software Developer Eagle Genomics http://www.eaglegenomics.com/ From dicknetherlands at gmail.com Mon Jul 21 05:27:06 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Mon, 21 Jul 2008 10:27:06 +0100 Subject: [Biojava-dev] BioJava3 Use Cases Message-ID: Hi guys, I'd like to repeat an earlier request for use cases to guide the new BioJava 3 development work. We have a wiki page for this but it hasn't seen many updates: http://biojava.org/wiki/BioJava_3_Use_Cases Could anyone who has a task which BioJava cannot currently achieve, or does not achieve correctly, please add that task to this wiki page, so that we can try and implement it in the new code. A template for a use case has been provided on that same wiki page which you should follow when submitting your own suggestions. Basically the rule is that saying something like 'I want microarray support' isn't likely to get much of a response, but asking for a specific function, e.g. 'I want to be able to parse MAGE files' or 'I want to use XYZ technique to analyse my own chip designs', will get you a lot further. I'm setting a cut-off date for the initial list of use-cases at August 1st. Whatever's on the page at that point will be considered for implementation in the first phase of development over the next 6 months, along with updates or transfers of functionality from the existing code base where appropriate. Anything that gets added to the list after that date will only get implemented in the second later phase, date indeterminate as yet, unless whoever submits the use case also chooses to submit their own code to solve it! cheers, Richard -- Richard Holland Bioinformatics Software Developer Eagle Genomics http://www.eaglegenomics.com/ From sudhasadhasivam at yahoo.com Tue Jul 22 03:34:08 2008 From: sudhasadhasivam at yahoo.com (sudha sadhasivam) Date: Tue, 22 Jul 2008 00:34:08 -0700 (PDT) Subject: [Biojava-dev] Error Message-ID: <481940.27310.qm@web51103.mail.re2.yahoo.com> Respected Sir I am herewith attaching the error report on executing a simple prgm in biojava. I am working as an Asst Prof in CSE dept, PSGCT, INDIA. We are trying to use biojava for sequence alignment examples in ME(CSE) ? Please clarify our doubt at the earliest ? Thanking you with regards Dr G Sudha Sadasivam -------------- next part -------------- A non-text attachment was scrubbed... Name: error.doc Type: application/octet-stream Size: 22016 bytes Desc: not available URL: From sudhasadhasivam at yahoo.com Tue Jul 22 04:39:14 2008 From: sudhasadhasivam at yahoo.com (sudha sadhasivam) Date: Tue, 22 Jul 2008 01:39:14 -0700 (PDT) Subject: [Biojava-dev] error Message-ID: <702887.88659.qm@web51106.mail.re2.yahoo.com> Respected Sir We are herewith attaching the errors when we ran biojava in windows We are not able to identify the mistake. Kindly identify the same Thanking you with regards Dr G Sudha Sadasivam -------------- next part -------------- A non-text attachment was scrubbed... Name: error.doc Type: application/msword Size: 22016 bytes Desc: not available URL: From cjm at berkeleybop.org Fri Jul 25 21:42:31 2008 From: cjm at berkeleybop.org (Chris Mungall) Date: Fri, 25 Jul 2008 18:42:31 -0700 Subject: [Biojava-dev] [GMOD-devel] GBOL (Chado based API) page In-Reply-To: <1217031936.7746.12.camel@fruitless.lbl.gov> References: <1217031936.7746.12.camel@fruitless.lbl.gov> Message-ID: <7DF53633-4684-4F45-8ACB-C0AB55331C04@berkeleybop.org> Thanks Ed! Should we have a dedicated email list for this? gmod-gbol On Jul 25, 2008, at 5:25 PM, Ed Lee wrote: > Hello everyone, > > As discussed, I've set up a page for GBOL (GMOD Bio Object Layer) on > the > GMOD wiki. Right now it's just a brain dump on the design. We highly > encourage the community to contribute their thoughts on what the > Biological layer should encompass, as well as help refine the best > practices for how data should be stored. > > The GBOL page is located at: > > http://www.gmod.org/wiki/index.php/Gbol > > Cheers, > Ed > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Gmod-devel mailing list > Gmod-devel at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-devel >