From Mark.Hoebeke at jouy.inra.fr Thu Apr 1 14:06:18 2004 From: Mark.Hoebeke at jouy.inra.fr (Hoebeke Mark) Date: Thu Apr 1 14:11:55 2004 Subject: [Biojava-l] Parsing GenBank files in Threads Message-ID: <1080846378.7089.14.camel@localhost> Hi, I was wondering if Sequence objects are thread-safe. In a pipeline I am developing I parse a set of GenBank flat files in several simultaneously executing threads (one file per thread, obviously), to feed them in a database. On execution I get erratic ArrayOutOfBoundsExceptions when invoking the SimpleSequence.getString() method. The indices in question are mostly negative. The SimpleSequence instance is created trough a SequenceIterator obtained with SeqIOTools.readGenbank(). When I prefix the method making this call with 'static synchronized' the errors disappear. I leafed through 6 months worth of mail archives looking for clues, to no avail. My guess is that there could be something odd happening in the SeqIOTools.readGenbank() method, which is declared as a static method. Any help would be greatly appreciated. Thanks in advance, Mark -- --------------------------Mark.Hoebeke@jouy.inra.fr---------------------- Unit? Statistique & G?nome Unit? MIG +33 (0)1 60 87 38 03 T?l. +33 (0)1 34 65 28 85 +33 (0)1 60 87 38 09 Fax. +33 (0)1 34 65 29 01 Tour Evry 2, 523 pl. des Terrasses INRA - Domaine de Vilvert F - 91000 Evry F - 78352 Jouy-en-Josas CEDEX From td2 at sanger.ac.uk Thu Apr 1 14:18:58 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Thu Apr 1 14:24:07 2004 Subject: [Biojava-l] Dazzle 1.00 release Message-ID: <6D3C3B22-8411-11D8-9B37-000A95C8B056@sanger.ac.uk> I've just put out a new release of the Dazzle modular DAS server. The new release features improvements to the plugin API, updates to work with the BioJava 1.4 release, and many minor fixes. You can download either source or a prebuilt web-application skeleton from: http://www.biojava.org/download/dazzle/ If you have the Subversion client available, you can also check it out from: http://www.derkholm.net/svn/repos/dazzle/tags/dazzle-1.00 Installation instructions can be found at: http://www.biojava.org/dazzle/deploy.html Please not that this release *will not* work with the old ensembl-das plugins. I've been working on a major re-write of the biojava-ensembl adaptors, including support for the schema changes in Ensembl release 20 and some substantially improved DAS plugins. There should be a release sometime next week. In the mean time, development code is available from the Subversion repository at: http://www.derkholm.net/svn/repos/biojava-ensembl/trunk Thomas. From matthew_pocock at yahoo.co.uk Thu Apr 1 14:31:56 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Thu Apr 1 14:37:08 2004 Subject: [Biojava-l] Parsing GenBank files in Threads In-Reply-To: <1080846378.7089.14.camel@localhost> References: <1080846378.7089.14.camel@localhost> Message-ID: <406C6E2C.8000508@yahoo.co.uk> Hi, The biojava policy on synchronization is that we try to make things safe if possible, but expect the user to synchronize sanely. Unfortunately, this is usually not documented anywhere. I could not guarantee that GenbankFormat is threadsafe - it would be sensible for it to be, but the particular implementation may not be. To help us track this, could you include some example stack traces of eratic behavior? Matthew Hoebeke Mark wrote: >Hi, > >I was wondering if Sequence objects are thread-safe. > >In a pipeline I am developing I parse a set of GenBank flat files in >several simultaneously executing threads (one file per thread, >obviously), to feed them in a database. > >On execution I get erratic ArrayOutOfBoundsExceptions when invoking the >SimpleSequence.getString() method. The indices in question are mostly >negative. The SimpleSequence instance is created trough a >SequenceIterator obtained with SeqIOTools.readGenbank(). > >When I prefix the method making this call with 'static synchronized' the >errors disappear. > >I leafed through 6 months worth of mail archives looking for clues, to >no avail. > >My guess is that there could be something odd happening in the >SeqIOTools.readGenbank() method, which is declared as a static method. > >Any help would be greatly appreciated. > >Thanks in advance, > >Mark > > > From Mark.Hoebeke at jouy.inra.fr Fri Apr 2 01:41:33 2004 From: Mark.Hoebeke at jouy.inra.fr (Hoebeke Mark) Date: Fri Apr 2 01:45:11 2004 Subject: [Biojava-l] Parsing GenBank files in Threads In-Reply-To: <406C6E2C.8000508@yahoo.co.uk> References: <1080846378.7089.14.camel@localhost> <406C6E2C.8000508@yahoo.co.uk> Message-ID: <1080888093.2186.19.camel@localhost> Hi Matthew, I just finished some further investigation, strengthening my feeling that using SeqIOTools.readGenbank() might not be thread-safe. The strongest point is that the errors appear less frequently on uniprocessor machines that on multiprocessor ones. As you requested, below is a snippet of the the exception stack whith the bio.* related part delimited by ===========. This pattern repeats itself for different Genbank files except for the actual value of the corrupt(?) index. Note that the problem is solved by prefixing the method calling Sequence.seqString() with static synchronized, but that takes all the fun out of the pipeline ;) If needed, I can hand you the complete source file but I thought I'd better not spam biojava-l with it. Thanks for your support. Mark [java] org.quartz.JobExecutionException: java.lang.Exception: Unable to extract sequence from entry BA000019 [See nested exception: java.lang.Exception: Unable to extract sequence from entry BA000019] [java] at pipeline.jobs.EntryFeeder.execute(EntryFeeder.java:241) [java] at org.quartz.core.JobRunShell.run(JobRunShell.java:178) [java] at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:487) [java] * Nested Exception (Underlying Cause) --------------- [java] java.lang.Exception: Unable to extract sequence from entry BA000019 [java] at pipeline.jobs.EntryFeeder.feedEntry(EntryFeeder.java:199) [java] at pipeline.jobs.EntryFeeder.execute(EntryFeeder.java:234) [java] at org.quartz.core.JobRunShell.run(JobRunShell.java:178) [java] at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:487) =========================================================================================================== [java] java.lang.ArrayIndexOutOfBoundsException: -17406 [java] at org.biojava.bio.symbol.PackedSymbolList.symbolAt(PackedSymbolList.java:275) [java] at org.biojava.bio.seq.io.ChunkedSymbolListFactory$ChunkedSymbolList.symbolAt(ChunkedSymbolListFactory.java:178) [java] at org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbolList.java:191) [java] at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTokenization.java:202) [java] at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenizeSymbolList(AlphabetManager.java:1378) [java] at org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:93) [java] at org.biojava.bio.seq.impl.SimpleSequence.seqString(SimpleSequence.java:89) ============================================================================================================= [java] at pipeline.jobs.EntryFeeder.feedEntry(EntryFeeder.java:194) [java] at pipeline.jobs.EntryFeeder.execute(EntryFeeder.java:234) [java] at org.quartz.core.JobRunShell.run(JobRunShell.java:178) [java] at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:487) [java] java.lang.Exception: Unable to extract sequence from entry AE004092 [java] at pipeline.jobs.EntryFeeder.feedEntry(EntryFeeder.java:199) [java] at pipeline.jobs.EntryFeeder.execute(EntryFeeder.java:234) [java] at org.quartz.core.JobRunShell.run(JobRunShell.java:178) [java] at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:487) [java] 2 avr. 2004 08:12:54 org.quartz.core.JobRunShell run Le jeu 01/04/2004 ? 21:31, Matthew Pocock a ?crit : > Hi, > > The biojava policy on synchronization is that we try to make things safe > if possible, but expect the user to synchronize sanely. Unfortunately, > this is usually not documented anywhere. I could not guarantee that > GenbankFormat is threadsafe - it would be sensible for it to be, but the > particular implementation may not be. To help us track this, could you > include some example stack traces of eratic behavior? > > Matthew -- --------------------------Mark.Hoebeke@jouy.inra.fr---------------------- Unit? Statistique & G?nome Unit? MIG +33 (0)1 60 87 38 03 T?l. +33 (0)1 34 65 28 85 +33 (0)1 60 87 38 09 Fax. +33 (0)1 34 65 29 01 Tour Evry 2, 523 pl. des Terrasses INRA - Domaine de Vilvert F - 91000 Evry F - 78352 Jouy-en-Josas CEDEX From r.bruskiewich at cgiar.org Fri Apr 2 06:42:16 2004 From: r.bruskiewich at cgiar.org (Richard Bruskiewich) Date: Fri Apr 2 06:37:36 2004 Subject: [Biojava-l] Anybody working on a Java binding to CHADO? Message-ID: Hi folks (especially Matt and Thomas...), I've finally decided to subscribe to this list since we're getting more heavily into Java here at IRRI. First question: who is working on a Java binding to CHADO? Cheers Richard Bruskiewich Bioinformatics Specialist International Rice Research Institute (IRRI) From smh1008 at cus.cam.ac.uk Fri Apr 2 07:20:13 2004 From: smh1008 at cus.cam.ac.uk (David Huen) Date: Fri Apr 2 07:25:28 2004 Subject: [Biojava-l] Anybody working on a Java binding to CHADO? In-Reply-To: References: Message-ID: <200404021320.13956.smh1008@cus.cam.ac.uk> On Friday 02 Apr 2004 12:42 pm, Richard Bruskiewich wrote: > Hi folks (especially Matt and Thomas...), > > I've finally decided to subscribe to this list since we're getting more > heavily into Java here at IRRI. > > First question: who is working on a Java binding to CHADO? > Hi Richard, I worked on one for some time before suspending my efforts. The main problem is that the fit between the Chado data model and the BioJava one is particularly poor. BioJava has a hierarachical feature model in which features have subfeatures etc. All features are associated with a location on a sequence. This made sense at the time BJ was being developed and is also inherent in a BioSQL type of world. Chado, however, unlinks features from sequences and from each other. Now, features can be associated with multiple locations on different sequences. Also, features have relationships to each other that are potentially non-hierarchical (DAG for example). The Chado data model is probably more powerful and expressive. I made one attempt to shoehorn Chado's predecessor into the Biojava by forcing particular relationships into particular positions in the BJ hierarchy but the results are ugly and fragile. With Chado being more generalised that its predecessor, the results have been even more messy. For example, BJ uses getParent() to move up the hierarchy but an attemtp to use this in Chado would be ambiguous - by what relationship would the other object be a parent? SImilarly, all our feature selection through filter() also fails. How do we traverse the feature relationships if they are not a hierarchy? Are we filtering by applying the FF on each individual feature or by traversing the hierarchy of a specific relationship? The inadequacies of our data model will need to be addressed in BioJava 2 ( and may that day come soon!) but for now, I would not suggest trying to bridge BJ1 to Chado. When BJ2 becomes available, i will certainly revisit Chado for Biojava. One aspect of Chado is that because it is so heavily denormalised, performance can be a real issue if you are attempting to use it as a datasource rather than as a reference data repository. Almost everything you could possibly want to do involves a large number of joins (e.g. feature->feature type - 1 join. -> location 1 join , thru relationship - 1 join, etc). As such I think you will need to explicitly denormalise it if you are intending to use it for analysis. You may want to investigate Flymine (flymine.org) - they have to Java-ize Chado for their own use. They have a transparent (to user) query optimisation that may be of help to you. You could try asking their liaison officer (Rachel Lyne) (rachel [at] flymine.org) for more details. Regards, David Huen -- David Huen, Ph.D. Email: smh1008@cus.cam.ac.uk Dept. of Genetics Fax : +44 1223 333992 University of Cambridge Phone: +44 1223 333982/766748 Cambridge, CB2 3UH U.K. From Mark.Hoebeke at jouy.inra.fr Fri Apr 2 08:11:51 2004 From: Mark.Hoebeke at jouy.inra.fr (Hoebeke Mark) Date: Fri Apr 2 08:15:29 2004 Subject: [Biojava-l] Parsing GenBank files in Threads In-Reply-To: <406C6E2C.8000508@yahoo.co.uk> References: <1080846378.7089.14.camel@localhost> <406C6E2C.8000508@yahoo.co.uk> Message-ID: <1080911510.2190.48.camel@localhost> Wow, replacing the biojava-1.3.1.jar with the one recompiled from the biojava-live CVS tree seems to solve the problem. Many thanks for suggesting just that, Matthew and sorry I didn't start checking that out. But heck, I'm a Biojava newbie after all. Mark -- --------------------------Mark.Hoebeke@jouy.inra.fr---------------------- Unit? Statistique & G?nome Unit? MIG +33 (0)1 60 87 38 03 T?l. +33 (0)1 34 65 28 85 +33 (0)1 60 87 38 09 Fax. +33 (0)1 34 65 29 01 Tour Evry 2, 523 pl. des Terrasses INRA - Domaine de Vilvert F - 91000 Evry F - 78352 Jouy-en-Josas CEDEX From Christian.Gruber at biomax.com Fri Apr 2 08:20:20 2004 From: Christian.Gruber at biomax.com (Christian Gruber) Date: Fri Apr 2 08:25:25 2004 Subject: [Biojava-l] Blast Parser oddity Message-ID: <406D6894.3030504@biomax.com> Hi! I am currently evaluating the XML output of NCBI Blast, and the ability of BioJava to parse this output. For this purpose, I have done twice the identical blastp and blastn (i.e. the same sequence against the same database with the same parameters), one time with the standard output, and one time with XML output ("-m 7"). I then parsed the files either with BlastLikeSAXParser (original output), or with BlastXMLParserFacade (XML output) and compared the outcome. Surprisingly, I got two different results... Here is a list of the fields that are different: SeqSimilaritySearchResult: Annotation: databaseId program queryId version SeqSimilaritySearchHit: subjectId queryStrand subjectStrand Annotation: subjectDescription subjectId SeqSimilaritySearchSubHit: queryStrand subjectStrand score numberOfIdentities numberOfPositives percentageIdentity score These are all rather important fields, for example subjectId, the description or score. After looking at it, I think that the output of BlastLikeSAXParser is OK, but the one of BlastXMLParserFacade is rotten. What now? I think that the parsing results are supposed to be identical (as good as it gets), but changing the parser might break existing code. If it's OK for you, I'd like to volunteer to change BlastXMLParserFacade so that the outcome resembles more the one of BlastLikeSAXParser. By the way, is there a guaranteed set of Annotation entries for these different classes? For example, I find percentageIdentity, but no percentagePositives. Greetings, Christian From Wiepert.Mathieu at mayo.edu Wed Apr 7 10:21:32 2004 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Wed Apr 7 10:26:41 2004 Subject: [Biojava-l] Blast Parser oddity Message-ID: <2F41CC6C9777D311ACBD009027B108EA06E9B43C@excsrv32.mayo.edu> Hi, The problem is likely with the Blastoutput and not the parsers. This was addressed in the bioperl list in January, and biojava lists back in 2002. Check out some of the postings at http://www.biojava.org/pipermail/biojava-l/2002-March/002311.html http://bioperl.org/pipermail/bioperl-l/2004-January/014749.html There are more postings on the bioperl archive for January as well, if you need more information http://bioperl.org/pipermail/bioperl-l/2004-January/ And note also Jason pointed out other difference http://bioperl.org/pipermail/bioperl-l/2004-February/014769.html HTH, -mat > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org]On Behalf Of Christian > Gruber > Sent: Friday, April 02, 2004 7:20 AM > To: biojava-l@open-bio.org > Subject: [Biojava-l] Blast Parser oddity > > > Hi! > > I am currently evaluating the XML output of NCBI Blast, and > the ability > of BioJava to parse this output. For this purpose, I have > done twice the > identical blastp and blastn (i.e. the same sequence against the same > database with the same parameters), one time with the > standard output, > and one time with XML output ("-m 7"). I then parsed the files either > with BlastLikeSAXParser (original output), or with > BlastXMLParserFacade > (XML output) and compared the outcome. Surprisingly, I got > two different > results... > > Here is a list of the fields that are different: > > SeqSimilaritySearchResult: > Annotation: > databaseId > program > queryId > version > > SeqSimilaritySearchHit: > subjectId > queryStrand > subjectStrand > Annotation: > subjectDescription > subjectId > > > SeqSimilaritySearchSubHit: > queryStrand > subjectStrand > score > numberOfIdentities > numberOfPositives > percentageIdentity > score > > These are all rather important fields, for example subjectId, the > description or score. After looking at it, I think that the output of > BlastLikeSAXParser is OK, but the one of BlastXMLParserFacade > is rotten. > > What now? I think that the parsing results are supposed to be > identical > (as good as it gets), but changing the parser might break > existing code. > If it's OK for you, I'd like to volunteer to change > BlastXMLParserFacade > so that the outcome resembles more the one of BlastLikeSAXParser. > > By the way, is there a guaranteed set of Annotation entries for these > different classes? For example, I find percentageIdentity, but no > percentagePositives. > > Greetings, > Christian > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From khalil.elmazouari at ablynx.com Thu Apr 8 12:38:52 2004 From: khalil.elmazouari at ablynx.com (Khalil El Mazouari) Date: Thu Apr 8 12:41:08 2004 Subject: [Biojava-l] RestrictionEnzymeManager Message-ID: <4075801C.6070002@ablynx.com> Hi I am trying to use the RestrictionEnzymeManager with a new REBASE file. I followed the recommendation concerning the RestrictionEnzymeManager.properties file and the CLASSPATH, but the RestrictionEnzymeManager still load the default RestrictionEnzymeManager.properties file that came with biojava. Any idea on what is going wrong? Thank you. Khalil ----------------------------------------------------------------------- THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. ----------------------------------------------------------------------- From dfenger at amylin.com Thu Apr 8 17:52:19 2004 From: dfenger at amylin.com (Fenger, Doug) Date: Thu Apr 8 17:57:17 2004 Subject: [Biojava-l] Problem parsing Genbank files Message-ID: Hi, I've been using biojava-1.3.1 to parse some Genbank files, similar to the FilterEMBLBySpecies code at BioJava in Anger. The problem is that with some Genbank files I get an IllegalArgumentException. I believe it's caused when the Feature has a single base for a Location (such as in Genbank records AY197155 and M19699), like this: tRNA <1 The problem goes away when I change it to tRNA <1..457 I also get an error message if there's a newline in the feature, as in record L32753: /note=" 50 bp gap between spans; putative" Here's the code I've been using to test it: import java.io.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; public class TestSeqIOTools { public static void main(String[] args) { if (args.length != 1) { System.out.println("Usage: java TestSeqIOTools "); System.exit(1); } try { BufferedReader fin = new BufferedReader(new FileReader(args[0])); SequenceIterator stream = SeqIOTools.readGenbank(fin); while(stream.hasNext()) { Sequence seq = stream.nextSequence(); } fin.close(); } catch(Exception e) { System.err.println("Exception: " + e.getMessage()); } } } Thanks for any suggestions, Doug p.s. I get similar errors if I use EMBL files instead. From gwu at molbio.mgh.harvard.edu Mon Apr 12 13:42:40 2004 From: gwu at molbio.mgh.harvard.edu (Gang Wu) Date: Mon Apr 12 13:47:25 2004 Subject: [Biojava-l] How to pull out the detailed information in Genbank feature table Message-ID: Following is a piece of code I used to retrieve the gene information in the feature table of GeneBank flat file. Seems "location" is the only inforamtion stored in Feature class. Is there a way to retrieve other detailed informaiton like "/note", "/locus_tag" etc? Thanks public static void main (String [] args) { BufferedReader br = new BufferedReader(new FileReader("GenBankFilePath")); SequenceIterator stream = SeqIOTools.readGenbank(br); Sequence seq = stream.nextSequence(); printGenes(seq.features()); } public static void printGenes(Iterator features) { while(features.hasNext()) { Feature f = (Feature) features.next(); if (f.getType().equalsIgnoreCase("gene")) { System.out.print(f.getType() + " at " + f.getLocation().toString()); printGenes(f.features()); } } } From gwu at molbio.mgh.harvard.edu Mon Apr 12 16:37:31 2004 From: gwu at molbio.mgh.harvard.edu (Gang Wu) Date: Mon Apr 12 16:42:16 2004 Subject: [Biojava-l] How to pull out the detailed information in Genbankfeature table In-Reply-To: Message-ID: Sorry for the naive question. Just found out by adding several rows in the printGenes() to dig out the gene annotation information. public static void printGenes(Iterator features) { while(features.hasNext()) { Feature f = (Feature) features.next(); if (f.getType().equalsIgnoreCase("gene")) { System.out.print(f.getType() + " at " + f.getLocation().toString()); Annotation geneAnnotation = f.getAnnotation(); java.util.Set theKeys = geneAnnotation.keys(); java.util.Iterator keyIterator = theKeys.iterator(); while (keyIterator.hasNext()) { String key = (String) keyIterator.next(); System.out.println("\t" + key + " = " + geneAnnotation.getProperty(key).toString()); } printGenes(f.features()); } } } -----Original Message----- From: biojava-l-bounces@portal.open-bio.org [mailto:biojava-l-bounces@portal.open-bio.org]On Behalf Of Gang Wu Sent: Monday, April 12, 2004 1:43 PM To: Bio-Java Subject: [Biojava-l] How to pull out the detailed information in Genbankfeature table Following is a piece of code I used to retrieve the gene information in the feature table of GeneBank flat file. Seems "location" is the only inforamtion stored in Feature class. Is there a way to retrieve other detailed informaiton like "/note", "/locus_tag" etc? Thanks public static void main (String [] args) { BufferedReader br = new BufferedReader(new FileReader("GenBankFilePath")); SequenceIterator stream = SeqIOTools.readGenbank(br); Sequence seq = stream.nextSequence(); printGenes(seq.features()); } public static void printGenes(Iterator features) { while(features.hasNext()) { Feature f = (Feature) features.next(); if (f.getType().equalsIgnoreCase("gene")) { System.out.print(f.getType() + " at " + f.getLocation().toString()); printGenes(f.features()); } } } _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From max_dipl at web.de Mon Apr 12 19:17:48 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Mon Apr 12 19:22:22 2004 Subject: [Biojava-l] LabelledSequenceRenderer: OutofBounds exception on window resize References: <4062F91A.8020306@web.de> <4063093D.1010709@yahoo.co.uk> <406C2276.7020009@web.de> <406C29D4.7080304@yahoo.co.uk> Message-ID: <407B239C.1070006@web.de> Hi everyone, when I modify BeadDemo and wrap a LabelledSequenceRenderer around the MultiLineRenderer, a lot of "java.lang.IndexOutOfBoundsException: max must exceed min: min=1, max=-728" keep showing on the console, as soon as I resize the window. I don't know how to debug this as it is executed by paint and I don't have an idea neither which bounds are meant nor why this occurs only on a window resize... I appreciate any ideas, as my own programs throws these exceptions all the time in the LabelledSequenceRenderer. BTW: Recently, there was discussion here about the speed difference between TranslatedSequencePanel and its SequencePanel-counterpart. Any new results? Max From max_dipl at web.de Mon Apr 12 19:23:04 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Mon Apr 12 19:27:27 2004 Subject: [Biojava-l] Re: Speed TranslatedSequenceRenderer References: <40693877.40107@genpat.uu.se> <406C25E4.6040903@web.de> Message-ID: <407B24D8.70000@web.de> Oups, this didn't make it to the list two weeks ago... > I can support David's and Keith's opinion: Using 12 > FeatureBeadRenderers (each having 2 filters attached), 6 > symbolrenderers and > 6 rulerrenderers and the Labelledsequencerenderers (a set that fits > nicely on a 800x600 screen) and on my 1ghz-machine it is so slow that > my program has become nearly "unscrollable"... (I might have missed > some options to speed it up) > I am wondering where the speed difference comes from. The > SequencePanel is not rendering anything that is off-screen, right? > Just like the Translated one... > Kalle Naslund wrote: >> I dont know if he has fixed issue number 1 aswell, but i will try to >> take a look >> at that later on today, and see if i can see the rendering errors >> with the CVS >> version of SequencePanel. > I am using the CVS version from yesterday. Max From Christian.Gruber at biomax.com Tue Apr 13 10:06:57 2004 From: Christian.Gruber at biomax.com (Christian Gruber) Date: Tue Apr 13 10:11:42 2004 Subject: [Biojava-l] blast parser alignment middle line Message-ID: <407BF401.6030301@biomax.com> Hello! Is there a way to get the middle line of an alignment that I parse out of the blast output? In the example below, it would be the "S++VGTR..." line. In the Alignment of the SeqSimilaritySearchSubHit, I only find a Sequence entry for Query and Sbjct. Query: 2 SFEVGTRCWYPHKELGWIGAEVIKNEFNDGKYHLEL... S++VGTR W P GW+ +EV+K + K L ... Sbjct: 4 SYDVGTRAWQPDPTEGWVASEVVKKTVDGNKVTLIF... Thanks, Christian From hz5 at njit.edu Tue Apr 13 17:25:14 2004 From: hz5 at njit.edu (hz5@njit.edu) Date: Tue Apr 13 17:29:57 2004 Subject: [Biojava-l] bioperl graph - different glyph on the same track In-Reply-To: <407BF401.6030301@biomax.com> References: <407BF401.6030301@biomax.com> Message-ID: <1081891514.407c5aba49479@webmail.njit.edu> Hi everybody, I want to generate something like this: _________ ____________ ----| |-----------| |----- --------- ------------- segments are colored differently, if I use cds, or segments glyph type, the whole thing is one feature, cannot be colored differently, also the line will ends where the box(HSP or exon) ends, it won't extent to indicate the full length of the sequence. if I use a set of features for each segments and display them on one track, then they can be colored differently, but the lines cannot be displayed, if I render lines as features as well, glyph type will be line, then they cannot occupy the same track. How should I do it? I am sure other people have this problem before, sorry for ask again. Thanks! haibo From Russell.Smithies at agresearch.co.nz Thu Apr 15 16:41:18 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu Apr 15 16:46:04 2004 Subject: [Biojava-l] Bioinfo book review Message-ID: For those interested, Sebastian Bassi's book "Bioinformatics: Sequence and Genome Analysis" was reviewed on freshmeat.com yesterday. http://freshmeat.net/articles/view/865/ Russell Smithies Bioinformatics Software Developer AgResearch Invermay Private Bag 50034 Puddle Alley Mosgiel New Zealand Tel: +64 3 489 9171 Fax: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From max_dipl at web.de Thu Apr 22 09:31:07 2004 From: max_dipl at web.de (Maximilian Haeussler) Date: Thu Apr 22 09:35:47 2004 Subject: [Fwd: Re: [Biojava-l] Displaying many SequencePanels References: <40693877.40107@genpat.uu.se> <40803583.9080001@web.de> <40851442.4010101@genpat.uu.se> Message-ID: <4087C91B.1080106@web.de> Kalle wrote: (dialog about how to render a couple of SequencePanels, if SequencePanel starts throwing OutofBounds exceptions after a while...) > 2) if all you want is to display several sequences, There realy isnt > any need for several SequencePanels. Just build an Alignment of the > Sequences and use an AlignmentRenderer setup, so the SequencePanel > renders all sequences I have no idea what AlignmentRenderer is. There is no javadoc for it and I don't understand the sourcecode. Can anyone give me a hint on what an AlignmentRenderer really is, except that it renders an alignment? :-) Max From kalle.naslund at genpat.uu.se Fri Apr 23 07:59:00 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Fri Apr 23 08:00:12 2004 Subject: [Fwd: Re: [Biojava-l] Displaying many SequencePanels In-Reply-To: <4087C91B.1080106@web.de> References: <40693877.40107@genpat.uu.se> <40803583.9080001@web.de> <40851442.4010101@genpat.uu.se> <4087C91B.1080106@web.de> Message-ID: <40890504.9020603@genpat.uu.se> Maximilian Haeussler wrote: > Kalle wrote: > > (dialog about how to render a couple of SequencePanels, if > SequencePanel starts throwing OutofBounds exceptions after a while...) > >> 2) if all you want is to display several sequences, There realy isnt >> any need for several SequencePanels. Just build an Alignment of the >> Sequences and use an AlignmentRenderer setup, so the SequencePanel >> renders all sequences > > > I have no idea what AlignmentRenderer is. There is no javadoc for it > and I don't understand the sourcecode. Can anyone give me a hint on > what an AlignmentRenderer really is, except that it renders an > alignment? :-) > I am pretty sure AlignmentRenderer is described in the javadocs, atleast my javadocs include it. The full name is org.biojava.bio.gui.sequence.AlignmentRenderer. To get a better understanding on how to use it, you can take a look at a the mailinglist archive, http://biojava.org/pipermail/biojava-l/2003-May/003801.html gives a quick explanation that hopefully should get you started. > Max > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From matthew_pocock at yahoo.co.uk Mon Apr 26 10:45:12 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Apr 26 10:51:40 2004 Subject: [Biojava-l] biojava survey Message-ID: <408D2078.5080007@yahoo.co.uk> Hi guys, I have put together a short survey about BioJava. If you have a minute, could you pop over to http://polwarth.ncl.ac.uk/ and fill it out? Any/all sudgestions welcome. Thanks, Matthew From dlondon at ebi.ac.uk Thu Apr 29 04:39:05 2004 From: dlondon at ebi.ac.uk (Darin London) Date: Thu Apr 29 04:43:23 2004 Subject: [Biojava-l] BOSC 2nd Call For Papers (fwd) Message-ID: SECOND CALL FOR SPEAKERS BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2004/ * Email: bosc@open-bio.org * Online registration: https://www.cteusa.com/iscb3/ The program committee is currently seeking abstracts for talks at BOSC 2004. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2004, please send us: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. *** Abstracts for formal presentations must be recieved by 5-May-2004. *** LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2004. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2004. If you are interested in giving a software demonstration at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php