[Biojava-l] Biojava Dependency on Forester

[Scooter Willis]

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" <tmc46 at cornell.edu>
To: "Scooter Willis" <HWillis at scripps.edu>
Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
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 <HWillis at scripps.edu> 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" <andreas.prlic at gmail.com>
> To: "Terry Casstevens" <tmc46 at cornell.edu>
> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
> "biojava-l at biojava.org" <biojava-l at biojava.org>
> 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 <tmc46 at cornell.edu>
> 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
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