Awesome, Mark, Thanks for fixing this! Andreas
On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <[email protected]> wrote: > biojava3-alignment and biojava3-phylo have both been updated to use the > latest forester release: 1.005. The jar file is in our maven repository, > and changes are committed to the SVN and git repositories. > > Enjoy! > Mark > > > > On 10/11/2012 02:50 PM, Scooter Willis wrote: >> >> Andreas >> >> Looks like the alignment code is using the distance matrix from forester >> and that has changed. Any chance the developer who did the MSA code could >> get this working with the latest forester code. It is probably a refactoring >> problem. >> >> Scooter >> >> ----- Reply message ----- >> From: "Terry Casstevens" <[email protected]> >> To: "Scooter Willis" <[email protected]> >> Cc: "Andreas Prlic" <[email protected]>, "Peter Bradbury" >> <[email protected]>, "Jeff Glaubitz" <[email protected]>, "Ed Buckler" >> <[email protected]>, "[email protected]" <[email protected]> >> Subject: [Biojava-l] Biojava Dependency on Forester >> Date: Thu, Oct 11, 2012 2:56 pm >> >> >> >> Hi Scooter, Andreas, >> >> Thank you again for the responses. >> >> This is one problem we are seeing. org/forester/phylogenyinference >> does not exist in Forester version 1.005. >> >> Exception in thread "main" java.lang.NoClassDefFoundError: >> org/forester/phylogenyinference/DistanceMatrix >> at >> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176) >> at >> net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306) >> at >> net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183) >> at >> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417) >> at >> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347) >> at >> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107) >> at >> net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36) >> at >> net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41) >> Caused by: java.lang.ClassNotFoundException: >> org.forester.phylogenyinference.DistanceMatrix >> at java.net.URLClassLoader$1.run(URLClassLoader.java:366) >> at java.net.URLClassLoader$1.run(URLClassLoader.java:355) >> at java.security.AccessController.doPrivileged(Native Method) >> at java.net.URLClassLoader.findClass(URLClassLoader.java:354) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:423) >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:356) >> >> >> Thank you, >> >> Terry >> >> >> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <[email protected]> >> wrote: >>> >>> If forester has maven repository we can unhook the local depedency. We >>> use >>> forester for NJ and should only be a needed in one model. Let me know the >>> issue/conflict and I can see what I can do to clean up. >>> >>> Thanks >>> >>> Scooter >>> >>> >>> ----- Reply message ----- >>> From: "Andreas Prlic" <[email protected]> >>> To: "Terry Casstevens" <[email protected]> >>> Cc: "Peter Bradbury" <[email protected]>, "Jeff Glaubitz" >>> <[email protected]>, "Ed Buckler" <[email protected]>, >>> "[email protected]" <[email protected]> >>> Subject: [Biojava-l] Biojava Dependency on Forester >>> Date: Thu, Oct 11, 2012 2:33 pm >>> >>> >>> >>> Hi Terry, >>> >>> Biojava depends on forester version 0.955. There are no plans to get >>> rid of this dependency, as far as I know. However we can try to >>> upgrade to a newer version if that helps. >>> >>> If you are working in a Maven environment and you pull in BioJava that >>> way, you can add an exclusion to your config. Something like the XML >>> below. This forces your project to ignore the older forester library >>> configured in biojava. Is this a suitable workaround for your problem? >>> >>> Andreas >>> >>> >>> <dependency> >>> <groupId>org.biojava</groupId> >>> <artifactId>biojava3-phylo</artifactId> >>> <version>3.0.4</version> >>> <exclusions> >>> <exclusion> >>> <groupId>org</groupId> >>> >>> <artifactId>forester</artifactId> >>> </exclusion> >>> </exclusions> >>> </dependency> >>> >>> >>> >>> >>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <[email protected]> >>> wrote: >>>> >>>> Dear Andreas, >>>> >>>> I am the lead developer of the software Tassel. >>>> http://www.maizegenetics.net/tassel >>>> >>>> We currently use Biojava 3.0. And we are >>>> wanting to use the latest release of Forester. >>>> Since Biojava has a dependency on an older >>>> release of Forester, we are running into conflicts. >>>> Can you help explain Biojava's dependency on >>>> Forester? >>>> >>>> What version of Forester does Biojava 3.0 require? >>>> It looks like version 0.955 >>>> >>>> What version of Forester does Biojava 3.0.4 require? >>>> >>>> Does any Biojava jar files include Forester classes? >>>> Or just references? >>>> >>>> Are there plans to remove Biojava's dependency >>>> on Forester? >>>> >>>> >>>> Thank you, >>>> >>>> Terry Casstevens >>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
