[Biojava-dev] biojava3 and forester question

[Chris Friedline]

I replied earlier to Olivier, but forgot to copy the list.  Here's the reply:

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Strange, I just looked at the biojava3-phylo source jar and saw an included forester package, with the phylogenyinference under it.  However, this refers to the evoinference package (and subpackages) in the actual forester source.  Given that forester is actively developed, should it really be inluded with the biojava3-phylo source in the first place?

The references in biojava3 are below:
CheckTreeAccuracy.java:import org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix;
CheckTreeAccuracy.java:import org.forester.phylogenyinference.DistanceMatrix;
TreeConstructor.java:import org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix;
TreeConstructor.java:import org.forester.phylogenyinference.DistanceMatrix;
TreeConstructor.java:import org.forester.phylogenyinference.NeighborJoining;

However, these classes are missing from the phylogenyinference package distributed with biojava3-phylo.  In forester itself, they are here:

./forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java
./forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java
./forester/java/src/org/forester/evoinference/distance/NeighborJoining.java

Seems like some clean-up/separation might be needed.

Chris

On May 25, 2012, at 8:43 AM, Olivier Sallou wrote:

> Hi,
> biojava3-phylo refers to package classes: org.forester.phylogenyinference.*
> 
> from maven dependency "forester"
> 
> Could you tell me where those sources comes from ?
> 
> I cannot find those in forester sources
> (http://code.google.com/p/forester/source/browse/#svn%2Fforester%2Fjava%2Fsrc%2Forg%2Fforester)
> 
> (not jar on their web site).
> 
> This prevent complete rebuild from source (still related to Debian
> packaging).
> 
> Thanks
> 
> Olivier
> 
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