From andreas at sdsc.edu Fri Oct 2 11:52:35 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 2 Oct 2009 08:52:35 -0700 Subject: [Biojava-dev] please don't send attachments to the biojava-lists Message-ID: <59a41c430910020852x2d119995j7787311a7aebad23@mail.gmail.com> Hi, We just had a couple of emails coming through to the biojava-l list that were sent months ago. This can happen if * emails are being sent from an address, that is not subscribed to the mailing list * the email contains an attachment. To avoid spam email, all incoming messages that meet any of these criteria are being filtered out by the mail server and put on hold. Going through this list is no fun for the admins, because of the large nr of spam mails. In short, please don't mail attachments to the list. If you want to share a patch, upload it to bugzilla or send it directly to one of the developers, so they can svn commit it. If you notice that your message is on hold (there is a notification from the mail server about that) please re-send your mail without attachment. Thanks, Andreas From mark.schreiber at novartis.com Tue Oct 6 23:30:25 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 7 Oct 2009 11:30:25 +0800 Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: Hi - Could I suggest that the biosql code be factored out into it's own module? The main argument for this is that it currently uses fairly old Hibernate specific ORM bindings. The more modern way to do this would be to use JPA (either inside or outside a container) which could then use any ORM provider (Hibernate, EclipseLink, JDO etc etc) in a uniform way. This could be a new BioSQL module that could replace the old one allowing a simple migration from the current ORM code to a JPA compliant ORM code without having to rip apart the core module. Best regards, - Mark biojava-dev-bounces at lists.open-bio.org wrote on 08/31/2009 09:23:03 AM: > Hi, > > I started to split up biojava into submodules and am mavenizing the > build process. The new SVN location is emerging here: > > http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > or in your browser: > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava > > A few questions so far from my side. > > 1) bytecode.jar: at the present the core module depends on this. So > far it is in the /jars subfolder of the module and needs to be > installed by hand. What is the best way to deal with this in SVN? > > 2) Sequence module (Richard's original biojava v.3 branch) Since this > consists of sub-modules I have set it up as a few hierarchically > organized submodules. There is some biosql code there as well. > Richard/Mark not sure now to arrange this. I think it would be good to > have a biosql module. Shall I refactor the current biosql code out of > core into a new biosql module or will the current code be obsoleted > and replaced with the new code in the sequence module? > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to 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 the sender immediately by e-mail and delete the material from any computer. Thank you. From andreas at sdsc.edu Wed Oct 7 00:01:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 6 Oct 2009 21:01:36 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: <59a41c430910062101p5a1ad421s83e56cbad5fd6350@mail.gmail.com> Hi Mark, That's already done. ;-) Have a look at new biosql module and let us know if it works for you. Andreas On Tue, Oct 6, 2009 at 8:30 PM, wrote: > > Hi - > > Could I suggest that the biosql code be factored out into it's own module? > > The main argument for this is that it currently uses fairly old Hibernate > specific ORM bindings. The more modern way to do this would be to use JPA > (either inside or outside a container) which could then use any ORM provider > (Hibernate, EclipseLink, JDO etc etc) in a uniform way. This could be a new > BioSQL module that could replace the old one allowing a simple migration > from the current ORM code to a JPA compliant ORM code without having to rip > apart the core module. > > Best regards, > > - Mark > > biojava-dev-bounces at lists.open-bio.org wrote on 08/31/2009 09:23:03 AM: > > > > Hi, > > > > I started to split up biojava into submodules and am mavenizing the > > build process. The new SVN location is emerging here: > > > > > http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > > or in your browser: > > > > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava > > > > A few questions so far from my side. > > > > 1) bytecode.jar: at the present the core module depends on this. So > > far it is in the /jars subfolder of the module and needs to be > > installed by hand. What is the best way to deal with this in SVN? > > > > 2) Sequence module (Richard's original biojava v.3 branch) Since this > > consists of sub-modules I have set it up as a few hierarchically > > organized submodules. There is some biosql code there as well. > > Richard/Mark not sure now to arrange this. I think it would be good to > > have a biosql module. Shall I refactor the current biosql code out of > > core into a new biosql module or will the current code be obsoleted > > and replaced with the new code in the sequence module? > > > > Andreas > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient, > or the employee or agent responsible for delivery of the message to 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 the sender > immediately by e-mail and delete the material from any computer. Thank you. > From gwaldon at geneinfinity.org Wed Oct 7 14:29:30 2009 From: gwaldon at geneinfinity.org (George Waldon) Date: Wed, 07 Oct 2009 14:29:30 -0400 Subject: [Biojava-dev] new build questions Message-ID: <20091007182930.28200.qmail@mxw1102.verio-web.com> Hi, Is-there any reason to have still some modules with a 1.0-SNAPSHOT version in the new Maven build (gui and biosql modules)? Also the gui module pom.xml file refers to an 1.0-SNAPSHOT version of the sequencing module that does not exist and prevents the Netbeans IDE to make a full build. If this is OK with everybody, I'd like to correct those. - George From andreas.prlic at gmail.com Wed Oct 7 14:44:36 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Wed, 7 Oct 2009 11:44:36 -0700 Subject: [Biojava-dev] new build questions In-Reply-To: <20091007182930.28200.qmail@mxw1102.verio-web.com> References: <20091007182930.28200.qmail@mxw1102.verio-web.com> Message-ID: <59a41c430910071144r20462e1bgafe84ca5e81b99dc@mail.gmail.com> yea that is wrong. Please go ahead and fix this. Thanks, Andreas On Wed, Oct 7, 2009 at 11:29 AM, George Waldon wrote: > Hi, > > Is-there any reason to have still some modules with a 1.0-SNAPSHOT version > in the new Maven build (gui and biosql modules)? Also the gui module pom.xml > file refers to an 1.0-SNAPSHOT version of the sequencing module that does > not exist and prevents the Netbeans IDE to make a full build. If this is OK > with everybody, I'd like to correct those. > > - George > _______________________________________________ > 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 Wed Oct 21 03:54:39 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 21 Oct 2009 08:54:39 +0100 Subject: [Biojava-dev] Hackathon Message-ID: <733F010A-8D6A-4F57-82A7-24EE175339CE@eaglegenomics.com> Hi all - just a reminder that there will be a BioJava hackathon held in Cambridge January 18th-22nd 2010, at the Wellcome Trust Genome Campus. I'm collecting names of those who will definitely be attending so if you plan to come along, please let me know. The room we book will depend on numbers attending so it's important I know that you're coming! So far I have 4 people, plus myself. cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From forumjspro at gmail.com Wed Oct 21 17:03:05 2009 From: forumjspro at gmail.com (forumjspro at gmail.com) Date: Wed, 21 Oct 2009 23:03:05 +0200 Subject: [Biojava-dev] Biojava and biomanycores Message-ID: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Dear all, I'm one of the people who is trying to develop the biomanycores project (www.biomanycores.org) which aims to give access to efficient parallel algorithms developed for GPUs to bioinformaticians. To reach this goal we want to provide interfaces to those algorithms through Bio* frameworks. People will have to change only some lines in their Bio* code to use more efficient tools. In order to realize such interfaces, it is necessary to launch the command line tool and to retrieve results. I didn't see in the BioJava API a class enabling to do such a thing although a mechanism seems to exist in BioPython or BioPerl. I would like to know if I miss something in the API and, if it is not the case, what could be the best way to launch external programs to stay in the spirit of BioJava. For the moment, I use the trilead package to launch commands on distant computers and the Runtime class in the standard API to launch local commands. But may be it is completely irrelevant to add such functionalities to BioJava. Please let me know what do you think about it. Best regards Jean-Stephane Jean-Stephane Varre http://www.lifl.fr/~varre http://www.lifl.fr/SEQUOIA http://bioinfo.lifl.fr From mark.schreiber at novartis.com Thu Oct 22 03:41:36 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Thu, 22 Oct 2009 15:41:36 +0800 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: Hi - I think this is a historical hangover from the days when Java was not actually very good at launching external processes. There are actually two frameworks in biojava that attempted to overcome these shortcomings although both are now deprecated by the existence the ProcessBuilder (since JDK version 1.5). Below is an example of calling the Linux/Unix command "ls". Typically for Java much of the biolerplate is setting up the stream readers and handling exceptions but you get the idea. You can do much more advanced things such as launching long running jobs, monitoring them and cancelling them. List cmd = new ArrayList(); cmd.add("/bin/ls"); ProcessBuilder builder = new ProcessBuilder(cmd); try { final Process process = builder.start(); InputStream is = process.getInputStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); String line; StringBuffer sb = new StringBuffer(); while ((line = br.readLine()) != null) { sb.append(line); } return sb.toString(); } catch (Exception e) { return e.getMessage(); } Using this basic template you could theoretically launch any program, in your case these would be presumably be compiled to use GPUs or have command line options for these (the first item in the cmd list is the program and all other items are command line arguments). You can do this with much less work in Groovy which can be run as a stand alone script or compiled to a class file and called from another Java class. Process proc = "ls -l ".execute() proc.waitFor() result = proc.in.text If you want to get really "Groovy" you could even set up a Java program that executes Groovy script on the fly, you could then have all your scripts that lauch command line programs in text files that can be changed during runtime (no compilation required). Given that this is all quite easy now in java it would be good if someone could add some of these to biojava. Best regards, - Mark biojava-dev-bounces at lists.open-bio.org wrote on 10/22/2009 05:03:05 AM: > Dear all, > > I'm one of the people who is trying to develop the biomanycores > project (www.biomanycores.org) which aims to give access to efficient > parallel algorithms developed for GPUs to bioinformaticians. > > To reach this goal we want to provide interfaces to those algorithms > through Bio* frameworks. People will have to change only some lines in > their Bio* code to use more efficient tools. In order to realize such > interfaces, it is necessary to launch the command line tool and to > retrieve results. I didn't see in the BioJava API a class enabling to > do such a thing although a mechanism seems to exist in BioPython or > BioPerl. > > I would like to know if I miss something in the API and, if it is not > the case, what could be the best way to launch external programs to > stay in the spirit of BioJava. For the moment, I use the trilead > package to launch commands on distant computers and the Runtime class > in the standard API to launch local commands. But may be it is > completely irrelevant to add such functionalities to BioJava. > > Please let me know what do you think about it. > > Best regards > > Jean-Stephane > > Jean-Stephane Varre > http://www.lifl.fr/~varre > http://www.lifl.fr/SEQUOIA > http://bioinfo.lifl.fr > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to 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 the sender immediately by e-mail and delete the material from any computer. Thank you. From holland at eaglegenomics.com Wed Oct 21 17:20:10 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 21 Oct 2009 22:20:10 +0100 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> BioJava does have a facility for launching local processes - check out this page: http://www.biojava.org/docs/api/org/biojava/utils/ExecRunner.html All the BioJava code does is wrap Runtime in some nice programmer- friendly cotton wool. The best bit is the part that kills the process if it overruns a predetermined time limit (this has to be set explicitly - by default there is no time limit). cheers, Richard On 21 Oct 2009, at 22:03, forumjspro at gmail.com wrote: > Dear all, > > I'm one of the people who is trying to develop the biomanycores > project (www.biomanycores.org) which aims to give access to > efficient parallel algorithms developed for GPUs to bioinformaticians. > > To reach this goal we want to provide interfaces to those algorithms > through Bio* frameworks. People will have to change only some lines > in their Bio* code to use more efficient tools. In order to realize > such interfaces, it is necessary to launch the command line tool and > to retrieve results. I didn't see in the BioJava API a class > enabling to do such a thing although a mechanism seems to exist in > BioPython or BioPerl. > > I would like to know if I miss something in the API and, if it is > not the case, what could be the best way to launch external programs > to stay in the spirit of BioJava. For the moment, I use the trilead > package to launch commands on distant computers and the Runtime > class in the standard API to launch local commands. But may be it is > completely irrelevant to add such functionalities to BioJava. > > Please let me know what do you think about it. > > Best regards > > Jean-Stephane > > Jean-Stephane Varre > http://www.lifl.fr/~varre > http://www.lifl.fr/SEQUOIA > http://bioinfo.lifl.fr > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From forumjspro at gmail.com Fri Oct 23 11:32:10 2009 From: forumjspro at gmail.com (forumjspro at gmail.com) Date: Fri, 23 Oct 2009 17:32:10 +0200 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> Message-ID: Thank you for the answers from Richard and Mark. I will use ExecRunner in the next release. Jean-Stephane Le 21 oct. 09 ? 23:20, Richard Holland a ?crit : > BioJava does have a facility for launching local processes - check > out this page: > > http://www.biojava.org/docs/api/org/biojava/utils/ExecRunner.html > > All the BioJava code does is wrap Runtime in some nice programmer- > friendly cotton wool. The best bit is the part that kills the > process if it overruns a predetermined time limit (this has to be > set explicitly - by default there is no time limit). > > cheers, > Richard > > On 21 Oct 2009, at 22:03, forumjspro at gmail.com wrote: > >> Dear all, >> >> I'm one of the people who is trying to develop the biomanycores >> project (www.biomanycores.org) which aims to give access to >> efficient parallel algorithms developed for GPUs to >> bioinformaticians. >> >> To reach this goal we want to provide interfaces to those >> algorithms through Bio* frameworks. People will have to change only >> some lines in their Bio* code to use more efficient tools. In order >> to realize such interfaces, it is necessary to launch the command >> line tool and to retrieve results. I didn't see in the BioJava API >> a class enabling to do such a thing although a mechanism seems to >> exist in BioPython or BioPerl. >> >> I would like to know if I miss something in the API and, if it is >> not the case, what could be the best way to launch external >> programs to stay in the spirit of BioJava. For the moment, I use >> the trilead package to launch commands on distant computers and the >> Runtime class in the standard API to launch local commands. But may >> be it is completely irrelevant to add such functionalities to >> BioJava. >> >> Please let me know what do you think about it. >> >> Best regards >> >> Jean-Stephane >> >> Jean-Stephane Varre >> http://www.lifl.fr/~varre >> http://www.lifl.fr/SEQUOIA >> http://bioinfo.lifl.fr >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > From phidias51 at gmail.com Fri Oct 23 16:03:14 2009 From: phidias51 at gmail.com (Mark Fortner) Date: Fri, 23 Oct 2009 13:03:14 -0700 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: <6e1d61f50910231303w7f525df7k58853def421ecc8e@mail.gmail.com> As an aside there's the start of a BioGroovy cook site here: http://biogroovy.open-bio.org. You can learn more about using Groovy for those tasks that you used to do in Perl. :-) Feel free to add your own recipes. Regards, Mark Fortner On Thu, Oct 22, 2009 at 12:41 AM, wrote: > Hi - > > I think this is a historical hangover from the days when Java was not > actually very good at launching external processes. There are actually > two frameworks in biojava that attempted to overcome these shortcomings > although both are now deprecated by the existence the ProcessBuilder > (since JDK version 1.5). > > Below is an example of calling the Linux/Unix command "ls". Typically for > Java much of the biolerplate is setting up the stream readers and handling > exceptions but you get the idea. You can do much more advanced things > such as launching long running jobs, monitoring them and cancelling them. > > List cmd = new ArrayList(); > > cmd.add("/bin/ls"); > > ProcessBuilder builder = new ProcessBuilder(cmd); > > try { > final Process process = builder.start(); > InputStream is = process.getInputStream(); > InputStreamReader isr = new InputStreamReader(is); > BufferedReader br = new BufferedReader(isr); > String line; > StringBuffer sb = new StringBuffer(); > while ((line = br.readLine()) != null) { > sb.append(line); > } > return sb.toString(); > } catch (Exception e) { > return e.getMessage(); > } > > Using this basic template you could theoretically launch any program, in > your case these would be presumably be compiled to use GPUs or have > command line options for these (the first item in the cmd list is the > program and all other items are command line arguments). > > You can do this with much less work in Groovy which can be run as a stand > alone script or compiled to a class file and called from another Java > class. > > Process proc = "ls -l ".execute() > proc.waitFor() > result = proc.in.text > > If you want to get really "Groovy" you could even set up a Java program > that executes Groovy script on the fly, you could then have all your > scripts that lauch command line programs in text files that can be changed > during runtime (no compilation required). > > Given that this is all quite easy now in java it would be good if someone > could add some of these to biojava. > > Best regards, > > - Mark > > biojava-dev-bounces at lists.open-bio.org wrote on 10/22/2009 05:03:05 AM: > > > Dear all, > > > > I'm one of the people who is trying to develop the biomanycores > > project (www.biomanycores.org) which aims to give access to efficient > > parallel algorithms developed for GPUs to bioinformaticians. > > > > To reach this goal we want to provide interfaces to those algorithms > > through Bio* frameworks. People will have to change only some lines in > > their Bio* code to use more efficient tools. In order to realize such > > interfaces, it is necessary to launch the command line tool and to > > retrieve results. I didn't see in the BioJava API a class enabling to > > do such a thing although a mechanism seems to exist in BioPython or > > BioPerl. > > > > I would like to know if I miss something in the API and, if it is not > > the case, what could be the best way to launch external programs to > > stay in the spirit of BioJava. For the moment, I use the trilead > > package to launch commands on distant computers and the Runtime class > > in the standard API to launch local commands. But may be it is > > completely irrelevant to add such functionalities to BioJava. > > > > Please let me know what do you think about it. > > > > Best regards > > > > Jean-Stephane > > > > Jean-Stephane Varre > > http://www.lifl.fr/~varre > > http://www.lifl.fr/SEQUOIA > > http://bioinfo.lifl.fr > > > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to 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 the sender immediately by e-mail and delete the material from any > computer. Thank you. > _______________________________________________ > 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 bugzilla-daemon at portal.open-bio.org Sat Oct 31 11:17:43 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 31 Oct 2009 11:17:43 -0400 Subject: [Biojava-dev] [Bug 2941] New: NEXUS parser fails with tree nodes called p[0-9]+ Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2941 Summary: NEXUS parser fails with tree nodes called p[0-9]+ Product: BioJava Version: unspecified Platform: All OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: tiagoantao at gmail.com The Nexus parser fails to return a weighted graph if a tree node is called p[0-9+]. This happens because the internal representation creates nodes with this name pattern. Example Tree : tree tree2 = ((1:0.1,2:0.2):0.15,p1:0.3); Note the p1 node at the end. Typical error: Exception in thread "main" java.lang.IllegalArgumentException: loops not allowed at org.jgrapht.graph.AbstractBaseGraph.addEdge(Unknown Source) at org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:547) This happens on 1.7 (there is no version 1.7 on bugzilla, by the way) -- 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 andreas.prlic at gmail.com Thu Oct 1 03:48:11 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Wed, 30 Sep 2009 20:48:11 -0700 Subject: [Biojava-dev] what is the default parameters of In-Reply-To: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> References: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> Message-ID: <59a41c430909302048g14712d53tefdef1f1d64edfb3@mail.gmail.com> Hi, That depends on several things. E.g. on the substitution matrix being used, also on what you want to align. Here a site that suggests a combination of substitution matrix and gap penalties: ( BLOSUM62 matrix with gap opening penalty of 10 and a gap extension penalty of 0.5) http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 To also advertise some related, but ancient work of myself ;-) see: at: http://peds.oxfordjournals.org/cgi/content/full/13/8/545 Andreas http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 2009/9/29 simpleyrx : > > Dear experts, > > > NeedlemanWunsch's constructive funtion in biojava is as below: > public NeedlemanWunsch(short?match, > ? ? ? ? ? ? ? ? ? ? ? short?replace, > ? ? ? ? ? ? ? ? ? ? ? short?insert, > ? ? ? ? ? ? ? ? ? ? ? short?delete, > ? ? ? ? ? ? ? ? ? ? ? short?gapExtend, > ? ? ? ? ? ? ? ? ? ? ? SubstitutionMatrix?subMat) > I would like to know what are the default values to used NeedlemanWunsch. Such as how select match ,replace,insert,delete,gapExtend or subMat parameters ? > > > -- > > > Renxiang Yan > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From andreas at sdsc.edu Fri Oct 2 15:52:35 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 2 Oct 2009 08:52:35 -0700 Subject: [Biojava-dev] please don't send attachments to the biojava-lists Message-ID: <59a41c430910020852x2d119995j7787311a7aebad23@mail.gmail.com> Hi, We just had a couple of emails coming through to the biojava-l list that were sent months ago. This can happen if * emails are being sent from an address, that is not subscribed to the mailing list * the email contains an attachment. To avoid spam email, all incoming messages that meet any of these criteria are being filtered out by the mail server and put on hold. Going through this list is no fun for the admins, because of the large nr of spam mails. In short, please don't mail attachments to the list. If you want to share a patch, upload it to bugzilla or send it directly to one of the developers, so they can svn commit it. If you notice that your message is on hold (there is a notification from the mail server about that) please re-send your mail without attachment. Thanks, Andreas From mark.schreiber at novartis.com Wed Oct 7 03:30:25 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 7 Oct 2009 11:30:25 +0800 Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: Hi - Could I suggest that the biosql code be factored out into it's own module? The main argument for this is that it currently uses fairly old Hibernate specific ORM bindings. The more modern way to do this would be to use JPA (either inside or outside a container) which could then use any ORM provider (Hibernate, EclipseLink, JDO etc etc) in a uniform way. This could be a new BioSQL module that could replace the old one allowing a simple migration from the current ORM code to a JPA compliant ORM code without having to rip apart the core module. Best regards, - Mark biojava-dev-bounces at lists.open-bio.org wrote on 08/31/2009 09:23:03 AM: > Hi, > > I started to split up biojava into submodules and am mavenizing the > build process. The new SVN location is emerging here: > > http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > or in your browser: > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava > > A few questions so far from my side. > > 1) bytecode.jar: at the present the core module depends on this. So > far it is in the /jars subfolder of the module and needs to be > installed by hand. What is the best way to deal with this in SVN? > > 2) Sequence module (Richard's original biojava v.3 branch) Since this > consists of sub-modules I have set it up as a few hierarchically > organized submodules. There is some biosql code there as well. > Richard/Mark not sure now to arrange this. I think it would be good to > have a biosql module. Shall I refactor the current biosql code out of > core into a new biosql module or will the current code be obsoleted > and replaced with the new code in the sequence module? > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to 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 the sender immediately by e-mail and delete the material from any computer. Thank you. From andreas at sdsc.edu Wed Oct 7 04:01:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 6 Oct 2009 21:01:36 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: <59a41c430910062101p5a1ad421s83e56cbad5fd6350@mail.gmail.com> Hi Mark, That's already done. ;-) Have a look at new biosql module and let us know if it works for you. Andreas On Tue, Oct 6, 2009 at 8:30 PM, wrote: > > Hi - > > Could I suggest that the biosql code be factored out into it's own module? > > The main argument for this is that it currently uses fairly old Hibernate > specific ORM bindings. The more modern way to do this would be to use JPA > (either inside or outside a container) which could then use any ORM provider > (Hibernate, EclipseLink, JDO etc etc) in a uniform way. This could be a new > BioSQL module that could replace the old one allowing a simple migration > from the current ORM code to a JPA compliant ORM code without having to rip > apart the core module. > > Best regards, > > - Mark > > biojava-dev-bounces at lists.open-bio.org wrote on 08/31/2009 09:23:03 AM: > > > > Hi, > > > > I started to split up biojava into submodules and am mavenizing the > > build process. The new SVN location is emerging here: > > > > > http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > > or in your browser: > > > > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava > > > > A few questions so far from my side. > > > > 1) bytecode.jar: at the present the core module depends on this. So > > far it is in the /jars subfolder of the module and needs to be > > installed by hand. What is the best way to deal with this in SVN? > > > > 2) Sequence module (Richard's original biojava v.3 branch) Since this > > consists of sub-modules I have set it up as a few hierarchically > > organized submodules. There is some biosql code there as well. > > Richard/Mark not sure now to arrange this. I think it would be good to > > have a biosql module. Shall I refactor the current biosql code out of > > core into a new biosql module or will the current code be obsoleted > > and replaced with the new code in the sequence module? > > > > Andreas > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient, > or the employee or agent responsible for delivery of the message to 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 the sender > immediately by e-mail and delete the material from any computer. Thank you. > From gwaldon at geneinfinity.org Wed Oct 7 18:29:30 2009 From: gwaldon at geneinfinity.org (George Waldon) Date: Wed, 07 Oct 2009 14:29:30 -0400 Subject: [Biojava-dev] new build questions Message-ID: <20091007182930.28200.qmail@mxw1102.verio-web.com> Hi, Is-there any reason to have still some modules with a 1.0-SNAPSHOT version in the new Maven build (gui and biosql modules)? Also the gui module pom.xml file refers to an 1.0-SNAPSHOT version of the sequencing module that does not exist and prevents the Netbeans IDE to make a full build. If this is OK with everybody, I'd like to correct those. - George From andreas.prlic at gmail.com Wed Oct 7 18:44:36 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Wed, 7 Oct 2009 11:44:36 -0700 Subject: [Biojava-dev] new build questions In-Reply-To: <20091007182930.28200.qmail@mxw1102.verio-web.com> References: <20091007182930.28200.qmail@mxw1102.verio-web.com> Message-ID: <59a41c430910071144r20462e1bgafe84ca5e81b99dc@mail.gmail.com> yea that is wrong. Please go ahead and fix this. Thanks, Andreas On Wed, Oct 7, 2009 at 11:29 AM, George Waldon wrote: > Hi, > > Is-there any reason to have still some modules with a 1.0-SNAPSHOT version > in the new Maven build (gui and biosql modules)? Also the gui module pom.xml > file refers to an 1.0-SNAPSHOT version of the sequencing module that does > not exist and prevents the Netbeans IDE to make a full build. If this is OK > with everybody, I'd like to correct those. > > - George > _______________________________________________ > 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 Wed Oct 21 07:54:39 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 21 Oct 2009 08:54:39 +0100 Subject: [Biojava-dev] Hackathon Message-ID: <733F010A-8D6A-4F57-82A7-24EE175339CE@eaglegenomics.com> Hi all - just a reminder that there will be a BioJava hackathon held in Cambridge January 18th-22nd 2010, at the Wellcome Trust Genome Campus. I'm collecting names of those who will definitely be attending so if you plan to come along, please let me know. The room we book will depend on numbers attending so it's important I know that you're coming! So far I have 4 people, plus myself. cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From forumjspro at gmail.com Wed Oct 21 21:03:05 2009 From: forumjspro at gmail.com (forumjspro at gmail.com) Date: Wed, 21 Oct 2009 23:03:05 +0200 Subject: [Biojava-dev] Biojava and biomanycores Message-ID: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Dear all, I'm one of the people who is trying to develop the biomanycores project (www.biomanycores.org) which aims to give access to efficient parallel algorithms developed for GPUs to bioinformaticians. To reach this goal we want to provide interfaces to those algorithms through Bio* frameworks. People will have to change only some lines in their Bio* code to use more efficient tools. In order to realize such interfaces, it is necessary to launch the command line tool and to retrieve results. I didn't see in the BioJava API a class enabling to do such a thing although a mechanism seems to exist in BioPython or BioPerl. I would like to know if I miss something in the API and, if it is not the case, what could be the best way to launch external programs to stay in the spirit of BioJava. For the moment, I use the trilead package to launch commands on distant computers and the Runtime class in the standard API to launch local commands. But may be it is completely irrelevant to add such functionalities to BioJava. Please let me know what do you think about it. Best regards Jean-Stephane Jean-Stephane Varre http://www.lifl.fr/~varre http://www.lifl.fr/SEQUOIA http://bioinfo.lifl.fr From mark.schreiber at novartis.com Thu Oct 22 07:41:36 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Thu, 22 Oct 2009 15:41:36 +0800 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: Hi - I think this is a historical hangover from the days when Java was not actually very good at launching external processes. There are actually two frameworks in biojava that attempted to overcome these shortcomings although both are now deprecated by the existence the ProcessBuilder (since JDK version 1.5). Below is an example of calling the Linux/Unix command "ls". Typically for Java much of the biolerplate is setting up the stream readers and handling exceptions but you get the idea. You can do much more advanced things such as launching long running jobs, monitoring them and cancelling them. List cmd = new ArrayList(); cmd.add("/bin/ls"); ProcessBuilder builder = new ProcessBuilder(cmd); try { final Process process = builder.start(); InputStream is = process.getInputStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); String line; StringBuffer sb = new StringBuffer(); while ((line = br.readLine()) != null) { sb.append(line); } return sb.toString(); } catch (Exception e) { return e.getMessage(); } Using this basic template you could theoretically launch any program, in your case these would be presumably be compiled to use GPUs or have command line options for these (the first item in the cmd list is the program and all other items are command line arguments). You can do this with much less work in Groovy which can be run as a stand alone script or compiled to a class file and called from another Java class. Process proc = "ls -l ".execute() proc.waitFor() result = proc.in.text If you want to get really "Groovy" you could even set up a Java program that executes Groovy script on the fly, you could then have all your scripts that lauch command line programs in text files that can be changed during runtime (no compilation required). Given that this is all quite easy now in java it would be good if someone could add some of these to biojava. Best regards, - Mark biojava-dev-bounces at lists.open-bio.org wrote on 10/22/2009 05:03:05 AM: > Dear all, > > I'm one of the people who is trying to develop the biomanycores > project (www.biomanycores.org) which aims to give access to efficient > parallel algorithms developed for GPUs to bioinformaticians. > > To reach this goal we want to provide interfaces to those algorithms > through Bio* frameworks. People will have to change only some lines in > their Bio* code to use more efficient tools. In order to realize such > interfaces, it is necessary to launch the command line tool and to > retrieve results. I didn't see in the BioJava API a class enabling to > do such a thing although a mechanism seems to exist in BioPython or > BioPerl. > > I would like to know if I miss something in the API and, if it is not > the case, what could be the best way to launch external programs to > stay in the spirit of BioJava. For the moment, I use the trilead > package to launch commands on distant computers and the Runtime class > in the standard API to launch local commands. But may be it is > completely irrelevant to add such functionalities to BioJava. > > Please let me know what do you think about it. > > Best regards > > Jean-Stephane > > Jean-Stephane Varre > http://www.lifl.fr/~varre > http://www.lifl.fr/SEQUOIA > http://bioinfo.lifl.fr > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to 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 the sender immediately by e-mail and delete the material from any computer. Thank you. From holland at eaglegenomics.com Wed Oct 21 21:20:10 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 21 Oct 2009 22:20:10 +0100 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> BioJava does have a facility for launching local processes - check out this page: http://www.biojava.org/docs/api/org/biojava/utils/ExecRunner.html All the BioJava code does is wrap Runtime in some nice programmer- friendly cotton wool. The best bit is the part that kills the process if it overruns a predetermined time limit (this has to be set explicitly - by default there is no time limit). cheers, Richard On 21 Oct 2009, at 22:03, forumjspro at gmail.com wrote: > Dear all, > > I'm one of the people who is trying to develop the biomanycores > project (www.biomanycores.org) which aims to give access to > efficient parallel algorithms developed for GPUs to bioinformaticians. > > To reach this goal we want to provide interfaces to those algorithms > through Bio* frameworks. People will have to change only some lines > in their Bio* code to use more efficient tools. In order to realize > such interfaces, it is necessary to launch the command line tool and > to retrieve results. I didn't see in the BioJava API a class > enabling to do such a thing although a mechanism seems to exist in > BioPython or BioPerl. > > I would like to know if I miss something in the API and, if it is > not the case, what could be the best way to launch external programs > to stay in the spirit of BioJava. For the moment, I use the trilead > package to launch commands on distant computers and the Runtime > class in the standard API to launch local commands. But may be it is > completely irrelevant to add such functionalities to BioJava. > > Please let me know what do you think about it. > > Best regards > > Jean-Stephane > > Jean-Stephane Varre > http://www.lifl.fr/~varre > http://www.lifl.fr/SEQUOIA > http://bioinfo.lifl.fr > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From forumjspro at gmail.com Fri Oct 23 15:32:10 2009 From: forumjspro at gmail.com (forumjspro at gmail.com) Date: Fri, 23 Oct 2009 17:32:10 +0200 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> <7EFABCE3-AA2B-46D9-B4E5-38B74277E52E@eaglegenomics.com> Message-ID: Thank you for the answers from Richard and Mark. I will use ExecRunner in the next release. Jean-Stephane Le 21 oct. 09 ? 23:20, Richard Holland a ?crit : > BioJava does have a facility for launching local processes - check > out this page: > > http://www.biojava.org/docs/api/org/biojava/utils/ExecRunner.html > > All the BioJava code does is wrap Runtime in some nice programmer- > friendly cotton wool. The best bit is the part that kills the > process if it overruns a predetermined time limit (this has to be > set explicitly - by default there is no time limit). > > cheers, > Richard > > On 21 Oct 2009, at 22:03, forumjspro at gmail.com wrote: > >> Dear all, >> >> I'm one of the people who is trying to develop the biomanycores >> project (www.biomanycores.org) which aims to give access to >> efficient parallel algorithms developed for GPUs to >> bioinformaticians. >> >> To reach this goal we want to provide interfaces to those >> algorithms through Bio* frameworks. People will have to change only >> some lines in their Bio* code to use more efficient tools. In order >> to realize such interfaces, it is necessary to launch the command >> line tool and to retrieve results. I didn't see in the BioJava API >> a class enabling to do such a thing although a mechanism seems to >> exist in BioPython or BioPerl. >> >> I would like to know if I miss something in the API and, if it is >> not the case, what could be the best way to launch external >> programs to stay in the spirit of BioJava. For the moment, I use >> the trilead package to launch commands on distant computers and the >> Runtime class in the standard API to launch local commands. But may >> be it is completely irrelevant to add such functionalities to >> BioJava. >> >> Please let me know what do you think about it. >> >> Best regards >> >> Jean-Stephane >> >> Jean-Stephane Varre >> http://www.lifl.fr/~varre >> http://www.lifl.fr/SEQUOIA >> http://bioinfo.lifl.fr >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > From phidias51 at gmail.com Fri Oct 23 20:03:14 2009 From: phidias51 at gmail.com (Mark Fortner) Date: Fri, 23 Oct 2009 13:03:14 -0700 Subject: [Biojava-dev] Biojava and biomanycores In-Reply-To: References: <0D96EDBF-2A05-4DFE-9AD0-A1B6CA6E368E@gmail.com> Message-ID: <6e1d61f50910231303w7f525df7k58853def421ecc8e@mail.gmail.com> As an aside there's the start of a BioGroovy cook site here: http://biogroovy.open-bio.org. You can learn more about using Groovy for those tasks that you used to do in Perl. :-) Feel free to add your own recipes. Regards, Mark Fortner On Thu, Oct 22, 2009 at 12:41 AM, wrote: > Hi - > > I think this is a historical hangover from the days when Java was not > actually very good at launching external processes. There are actually > two frameworks in biojava that attempted to overcome these shortcomings > although both are now deprecated by the existence the ProcessBuilder > (since JDK version 1.5). > > Below is an example of calling the Linux/Unix command "ls". Typically for > Java much of the biolerplate is setting up the stream readers and handling > exceptions but you get the idea. You can do much more advanced things > such as launching long running jobs, monitoring them and cancelling them. > > List cmd = new ArrayList(); > > cmd.add("/bin/ls"); > > ProcessBuilder builder = new ProcessBuilder(cmd); > > try { > final Process process = builder.start(); > InputStream is = process.getInputStream(); > InputStreamReader isr = new InputStreamReader(is); > BufferedReader br = new BufferedReader(isr); > String line; > StringBuffer sb = new StringBuffer(); > while ((line = br.readLine()) != null) { > sb.append(line); > } > return sb.toString(); > } catch (Exception e) { > return e.getMessage(); > } > > Using this basic template you could theoretically launch any program, in > your case these would be presumably be compiled to use GPUs or have > command line options for these (the first item in the cmd list is the > program and all other items are command line arguments). > > You can do this with much less work in Groovy which can be run as a stand > alone script or compiled to a class file and called from another Java > class. > > Process proc = "ls -l ".execute() > proc.waitFor() > result = proc.in.text > > If you want to get really "Groovy" you could even set up a Java program > that executes Groovy script on the fly, you could then have all your > scripts that lauch command line programs in text files that can be changed > during runtime (no compilation required). > > Given that this is all quite easy now in java it would be good if someone > could add some of these to biojava. > > Best regards, > > - Mark > > biojava-dev-bounces at lists.open-bio.org wrote on 10/22/2009 05:03:05 AM: > > > Dear all, > > > > I'm one of the people who is trying to develop the biomanycores > > project (www.biomanycores.org) which aims to give access to efficient > > parallel algorithms developed for GPUs to bioinformaticians. > > > > To reach this goal we want to provide interfaces to those algorithms > > through Bio* frameworks. People will have to change only some lines in > > their Bio* code to use more efficient tools. In order to realize such > > interfaces, it is necessary to launch the command line tool and to > > retrieve results. I didn't see in the BioJava API a class enabling to > > do such a thing although a mechanism seems to exist in BioPython or > > BioPerl. > > > > I would like to know if I miss something in the API and, if it is not > > the case, what could be the best way to launch external programs to > > stay in the spirit of BioJava. For the moment, I use the trilead > > package to launch commands on distant computers and the Runtime class > > in the standard API to launch local commands. But may be it is > > completely irrelevant to add such functionalities to BioJava. > > > > Please let me know what do you think about it. > > > > Best regards > > > > Jean-Stephane > > > > Jean-Stephane Varre > > http://www.lifl.fr/~varre > > http://www.lifl.fr/SEQUOIA > > http://bioinfo.lifl.fr > > > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to 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 the sender immediately by e-mail and delete the material from any > computer. Thank you. > _______________________________________________ > 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 bugzilla-daemon at portal.open-bio.org Sat Oct 31 15:17:43 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 31 Oct 2009 11:17:43 -0400 Subject: [Biojava-dev] [Bug 2941] New: NEXUS parser fails with tree nodes called p[0-9]+ Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2941 Summary: NEXUS parser fails with tree nodes called p[0-9]+ Product: BioJava Version: unspecified Platform: All OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: tiagoantao at gmail.com The Nexus parser fails to return a weighted graph if a tree node is called p[0-9+]. This happens because the internal representation creates nodes with this name pattern. Example Tree : tree tree2 = ((1:0.1,2:0.2):0.15,p1:0.3); Note the p1 node at the end. Typical error: Exception in thread "main" java.lang.IllegalArgumentException: loops not allowed at org.jgrapht.graph.AbstractBaseGraph.addEdge(Unknown Source) at org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:547) This happens on 1.7 (there is no version 1.7 on bugzilla, by the way) -- 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.