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
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