jalview.git
2017-11-16 kjvdheideJAL-2805 expanded tree and treenode interfaces
2017-11-16 kjvdheideJAL-2805 loads of file reorganizing, interfaces expanded
2017-11-15 kjvdheideJAL-2805 functional binding on loading associated trees
2017-11-14 kjvdheideJAL-2805 viewport is passed along to the tree parser
2017-11-14 kjvdheideJAL-2795 added duplication check when calculated nodes...
2017-11-14 kjvdheideJAL-2805 added getters for hashmaps filled with associa...
2017-11-14 kjvdheideJAL-2805 added static method for logging duplications...
2017-11-14 kjvdheideJAL-2805 more sensible interface method params
2017-11-14 kjvdheideJAL-2805 finished up interface comments
2017-11-14 kjvdheideJAL-2805 re-enabled one2many checks
2017-11-14 kjvdheideJAL-2805 interface comments, progress on associating...
2017-11-13 kjvdheideJAL-2805 interface comments
2017-11-13 kjvdheideJAL-2805 some more name changes
2017-11-13 kjvdheideJAL-2805 more name changes for clarity
2017-11-13 kjvdheideJAL-2805 more interface name changing
2017-11-13 kjvdheideJAL-2805 name changed of interfaces for consistency
2017-11-13 kjvdheideJAL-2805 Jalview sequence binding interface expanded
2017-11-13 kjvdheideJAL-2805 TreeParser now interface based
2017-11-13 kjvdheideJAL-2805 Added tree building interface
2017-11-13 kjvdheideJAL-2805 name change
2017-11-13 kjvdheideJAL-2805 deleted old Aptx class for loading just Newick...
2017-11-13 kjvdheideJAL-2805 more interface work
2017-11-13 kjvdheideJAL-2794 removed unused interface
2017-11-13 kjvdheideJAL-2805 undid accidental double (buggy) binding, more...
2017-11-13 kjvdheideJAL-2805 warning messages added if Forester detects...
2017-11-13 kjvdheideJAL-2805 First try at loading tree through Forester...
2017-11-10 kjvdheideJAL-2794 reorganized node select code, added subtree...
2017-11-10 kjvdheideJAL-2794 comments comments comments
2017-11-10 kjvdheideJAL-2794 most method parameters/class variables made...
2017-11-10 kjvdheideJAL-2794 comments, selected node now doesn't have to...
2017-11-09 kjvdheideJAL-2794 PaintRefresher support, Aptx node selection...
2017-11-09 kjvdheideJAL-2794 interface comment
2017-11-09 kjvdheideJAL-2794 Made HashMap with Nodes as keys and sequences...
2017-11-08 kjvdheideJAL-2794 Aptx instances get their parent alignment...
2017-11-08 kjvdheideJAL-2794 Cleaning up tree conversion, sequences are...
2017-11-08 kjvdheideJAL-2794 getters and setters for finding nodes in fores...
2017-11-08 kjvdheideJAL-2795 created static class for forester conversions
2017-11-08 kjvdheideJAL-2794 Interface name change (oops)
2017-11-08 kjvdheideJAL-2794 made JalviewTreeViewerBinding an interface
2017-11-08 kjvdheideJAL-2794 Added getter for AlignmentViewport to TreeBuilder
2017-11-06 kjvdheideJAL-2794 simplified/clarified associating leaves to...
2017-11-03 kjvdheideJAL-2794 created tree viewer binding class
2017-11-03 kjvdheideJAL-2795 bunch of cleanup and comments
2017-11-02 kjvdheideJAL-2795 added back test loop for Aptx tree naming...
2017-11-02 kjvdheideJAL-2795 Reverted code changes needed to cluster from...
2017-11-02 kjvdheideJAL-2795 Forester now NJ-clusters the DistanceMatrix...
2017-11-02 kjvdheideJAL-2795 moved matrix conversion to the ForesterMatrix...
2017-11-01 kjvdheideJAL-2795 Sequence[] references now as SequenceI[] ...
2017-11-01 kjvdheideJAL-2795 removed sequences[] class variable, more comments
2017-10-30 kjvdheideJAL-2795 neater error message
2017-10-30 kjvdheideJAL-2795 added error catching for invalid identifier
2017-10-30 kjvdheideJAL-2795 changed getting index of identifier to Stream...
2017-10-30 kjvdheideJAL-2795 rebuilt MatrixConverter to be purely static
2017-10-30 kjvdheideJAL-2795 finalized method arguments; commited forester...
2017-10-30 kjvdheideJAL-2795 removed unneeded for loop (woops) and initiali...
2017-10-30 kjvdheideJAL-2795 implemented getting/setting identifiers
2017-10-30 kjvdheideJAL-2795 added comments links from ForesterMatrix to...
2017-10-30 kjvdheideJAL-2795 removed now unneeded values variable in Forest...
2017-10-30 kjvdheideJAL-2795 add get for all matrix values to MatrixI ...
2017-10-30 kjvdheideJAL-2795 foresterMatrix now stores distance values...
2017-10-29 kjvdheideJAL-2795 more matrix implementations
2017-10-28 kjvdheideJAL-2795 moved ForesterMatrix to ext.forester
2017-10-28 kjvdheideJAL-2795 Added get and set values to the converted...
2017-10-27 kjvdheideJAL-2795 start of Jalview's Matrix conversion
2017-10-27 kjvdheideMerge branch 'develop' of https://source.jalview.org...
2017-10-27 gmungocJAL-2526 updated javadoc
2017-10-26 kjvdheideStart of matrix converter
2017-10-26 kjvdheideAdded proper title to aptx trees
2017-10-26 kjvdheidetest name change
2017-10-26 kjvdheideMade FreeUpMemoryTest compatible with modified Calculat...
2017-10-26 kjvdheideMerge branch 'develop' of https://source.jalview.org...
2017-10-26 Jim ProcterJAL-2698 update version and cut release branch
2017-10-26 Jim ProcterJAL-2546 release notes
2017-10-26 Jim ProcterJAL-2488 patch causes of NPE during testStoreAndRecover...
2017-10-26 kjvdheideAdded getters for scoremodel & scoreparams in TreeBuilder
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop
2017-10-26 kjvdheideTreeBuilder now stores the used ScoreModel and ScoreParams
2017-10-26 Jim ProcterJAL-2036 2.10.3 release notes
2017-10-26 kjvdheidesmall name fixes in TreeBuilder
2017-10-26 kjvdheideAdded TreeBuilder as parameter to the converter constructor
2017-10-26 kjvdheideName changed of aptx treebuilder to treeconverter
2017-10-26 kjvdheideadded getSeqData to TreeBuilder
2017-10-26 Jim ProcterJAL-2793 cancelling font changed dialog didn't call...
2017-10-26 kjvdheideAdded full names to the tree algorithm enum
2017-10-26 kjvdheideadded abbreviations
2017-10-26 kjvdheideadded enum for the different tree algorithms
2017-10-26 kjvdheideCouple more thread names
2017-10-26 kjvdheidenamed most Jalview threads
2017-10-26 Jim ProcterJAL-2548 release notes
2017-10-26 Jim ProcterMerge branch 'bug/JAL-2776toggleGroupColour' into develop
2017-10-26 Jim ProcterJAL-2684 JAL-2685 release notes
2017-10-26 Jim ProcterJAL-2685 tidy up html doc
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into...
2017-10-26 Jim ProcterJAL-2392 test asserts for progressbar creation on the...
2017-10-26 kjvdheideremoved accidental added enters, commented out broken...
2017-10-25 kjvdheidefinished up tests for trees made from jalview data
2017-10-25 kjvdheideMerge branch 'develop' of https://source.jalview.org...
2017-10-25 kjvdheideImplemented distance tests
2017-10-25 kjvdheideImplemented tree title test for tree made from Jalview
2017-10-25 kjvdheideAdded tree title test
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