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2017-11-14 kjvdheideJAL-2805 viewport is passed along to the tree parser commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2795 added duplication check when calculated nodes... commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 added getters for hashmaps filled with associa... commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 added static method for logging duplications... commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 more sensible interface method params commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 finished up interface comments commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 re-enabled one2many checks commit | commitdiff | tree | snapshot
2017-11-14 kjvdheideJAL-2805 interface comments, progress on associating... commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 interface comments commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 some more name changes commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 more name changes for clarity commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 more interface name changing commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 name changed of interfaces for consistency commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 Jalview sequence binding interface expanded commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 TreeParser now interface based commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 Added tree building interface commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 name change commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 deleted old Aptx class for loading just Newick... commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 more interface work commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2794 removed unused interface commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 undid accidental double (buggy) binding, more... commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 warning messages added if Forester detects... commit | commitdiff | tree | snapshot
2017-11-13 kjvdheideJAL-2805 First try at loading tree through Forester... commit | commitdiff | tree | snapshot
2017-11-10 kjvdheideJAL-2794 reorganized node select code, added subtree... commit | commitdiff | tree | snapshot
2017-11-10 kjvdheideJAL-2794 comments comments comments commit | commitdiff | tree | snapshot
2017-11-10 kjvdheideJAL-2794 most method parameters/class variables made... commit | commitdiff | tree | snapshot
2017-11-10 kjvdheideJAL-2794 comments, selected node now doesn't have to... commit | commitdiff | tree | snapshot
2017-11-09 kjvdheideJAL-2794 PaintRefresher support, Aptx node selection... commit | commitdiff | tree | snapshot
2017-11-09 kjvdheideJAL-2794 interface comment commit | commitdiff | tree | snapshot
2017-11-09 kjvdheideJAL-2794 Made HashMap with Nodes as keys and sequences... commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 Aptx instances get their parent alignment... commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 Cleaning up tree conversion, sequences are... commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 getters and setters for finding nodes in fores... commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2795 created static class for forester conversions commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 Interface name change (oops) commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 made JalviewTreeViewerBinding an interface commit | commitdiff | tree | snapshot
2017-11-08 kjvdheideJAL-2794 Added getter for AlignmentViewport to TreeBuilder commit | commitdiff | tree | snapshot
2017-11-06 kjvdheideJAL-2794 simplified/clarified associating leaves to... commit | commitdiff | tree | snapshot
2017-11-03 kjvdheideJAL-2794 created tree viewer binding class commit | commitdiff | tree | snapshot
2017-11-03 kjvdheideJAL-2795 bunch of cleanup and comments commit | commitdiff | tree | snapshot
2017-11-02 kjvdheideJAL-2795 added back test loop for Aptx tree naming... commit | commitdiff | tree | snapshot
2017-11-02 kjvdheideJAL-2795 Reverted code changes needed to cluster from... commit | commitdiff | tree | snapshot
2017-11-02 kjvdheideJAL-2795 Forester now NJ-clusters the DistanceMatrix... commit | commitdiff | tree | snapshot
2017-11-02 kjvdheideJAL-2795 moved matrix conversion to the ForesterMatrix... commit | commitdiff | tree | snapshot
2017-11-01 kjvdheideJAL-2795 Sequence[] references now as SequenceI[] ... commit | commitdiff | tree | snapshot
2017-11-01 kjvdheideJAL-2795 removed sequences[] class variable, more comments commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 neater error message commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 added error catching for invalid identifier commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 changed getting index of identifier to Stream... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 rebuilt MatrixConverter to be purely static commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 finalized method arguments; commited forester... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 removed unneeded for loop (woops) and initiali... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 implemented getting/setting identifiers commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 added comments links from ForesterMatrix to... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 removed now unneeded values variable in Forest... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 add get for all matrix values to MatrixI ... commit | commitdiff | tree | snapshot
2017-10-30 kjvdheideJAL-2795 foresterMatrix now stores distance values... commit | commitdiff | tree | snapshot
2017-10-29 kjvdheideJAL-2795 more matrix implementations commit | commitdiff | tree | snapshot
2017-10-28 kjvdheideJAL-2795 moved ForesterMatrix to ext.forester commit | commitdiff | tree | snapshot
2017-10-28 kjvdheideJAL-2795 Added get and set values to the converted... commit | commitdiff | tree | snapshot
2017-10-27 kjvdheideJAL-2795 start of Jalview's Matrix conversion commit | commitdiff | tree | snapshot
2017-10-27 kjvdheideMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-10-27 gmungocJAL-2526 updated javadoc commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideStart of matrix converter commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideAdded proper title to aptx trees commit | commitdiff | tree | snapshot
2017-10-26 kjvdheidetest name change commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideMade FreeUpMemoryTest compatible with modified Calculat... commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2698 update version and cut release branch commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2546 release notes commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2488 patch causes of NPE during testStoreAndRecover... commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideAdded getters for scoremodel & scoreparams in TreeBuilder commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideTreeBuilder now stores the used ScoreModel and ScoreParams commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2036 2.10.3 release notes commit | commitdiff | tree | snapshot
2017-10-26 kjvdheidesmall name fixes in TreeBuilder commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideAdded TreeBuilder as parameter to the converter constructor commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideName changed of aptx treebuilder to treeconverter commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideadded getSeqData to TreeBuilder commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2793 cancelling font changed dialog didn't call... commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideAdded full names to the tree algorithm enum commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideadded abbreviations commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideadded enum for the different tree algorithms commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideCouple more thread names commit | commitdiff | tree | snapshot
2017-10-26 kjvdheidenamed most Jalview threads commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2548 release notes commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterMerge branch 'bug/JAL-2776toggleGroupColour' into develop commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2684 JAL-2685 release notes commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2685 tidy up html doc commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into... commit | commitdiff | tree | snapshot
2017-10-26 Jim ProcterJAL-2392 test asserts for progressbar creation on the... commit | commitdiff | tree | snapshot
2017-10-26 kjvdheideremoved accidental added enters, commented out broken... commit | commitdiff | tree | snapshot
2017-10-25 kjvdheidefinished up tests for trees made from jalview data commit | commitdiff | tree | snapshot
2017-10-25 kjvdheideMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-10-25 kjvdheideImplemented distance tests commit | commitdiff | tree | snapshot
2017-10-25 kjvdheideImplemented tree title test for tree made from Jalview commit | commitdiff | tree | snapshot
2017-10-25 kjvdheideAdded tree title test commit | commitdiff | tree | snapshot
2017-10-25 kjvdheideRemoved redundant annotations commit | commitdiff | tree | snapshot
2017-10-25 Jim ProcterJAL-2617 release notes commit | commitdiff | tree | snapshot
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2617mappedStopCodon' into develop commit | commitdiff | tree | snapshot
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