[Biojava-l] Biojava Dependency on Forester

[Andreas Prlic]

Awesome, Mark, Thanks for fixing this!

Andreas

On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> 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" <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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