Commits

History for

onbiojava-4.2.4

Commits on Mar 9, 2016

More whitespace fixes
sbliven
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af59f90
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Removing template messages
sbliven
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2bb0271
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Remove trailing whitespace globally from .java files
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sbliven
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Running addlicense.sh
sbliven
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f4e725f
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Commits on Feb 3, 2016

Handle symmetry refinement Exceptions
lafita
committed
d66cc12
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Fix bugs in Phylogenetic tree display
lafita
committed
36b9bf2
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New feature, show phylogenetic trees for Multiple Structure Alignemnts
lafita
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b7f2ea9
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FastaWriter was throwing Exception instead of IOException
lafita
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b756496
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Commits on Jan 15, 2016

Unskip phylo tests
lafita
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a3d594d
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Commits on Nov 18, 2015

Ignore tests until forester update
lafita
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4cac1d5
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Tests failing until forester version updated
lafita
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f53f123
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Commits on Nov 17, 2015

More Testing for trees
lafita
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740df91
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Implement fractional dissimilarity score
lafita
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4a4c06d
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Create a Test for the distance tree evaluation
lafita
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85578cc
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Switch phylo and alignment dependencies back
lafita
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45a66c7
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Function to clone forester DistanceMatrix
lafita
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8a0da08
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Fix bug in distance matrix calculation
lafita
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9cabf41
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Create a Test for Wrapper functions
lafita
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7901603
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Commits on Nov 16, 2015

Implement the structural distance in phylo
lafita
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2a8487d
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Fix bug with the ConcurrencyTools usage
lafita
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fea2b4c
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Update path to Substitution Matrices (now in core)
lafita
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58adbd2
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Reshape the TreeConstructor class
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lafita
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6a1ebc8
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Create methods for distance matrix calculation
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lafita
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bc79c9e
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Rename the Tree Evaluator, specific for distance trees
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lafita
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231a155
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TreeConstructionAlgorithm renamed
lafita
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c485b29
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Remove unused classes
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lafita
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8a7ca13
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Create TreeConstructorType (replace TreeType)
lafita
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The TreeType means the optimization criteria used for tree building
lafita
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e596ce2
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The demo is only for tree construction
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lafita
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571ebb0
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Create a Wrapper class for conversion biojava-forester
lafita
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ea52fb6
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Remove the tree Logger Listeners
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lafita
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Formatting changes to Comparison class
lafita
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d527cf6
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Commits on Nov 10, 2015

Improve documentation in phylo module
lafita
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0073740
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Commits on Nov 9, 2015

Fix typo in demo TreeConstructor
lafita
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37ae6c2
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Port TreeConstructor.main to demo
lafita
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4485ea6
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