| 2017-11-17 |
kjvdheide | JAL-2805 code refactor (actionPerformed cleaned up...
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| 2017-11-17 |
kjvdheide | JAL-2805 reorganized code, tree building goes through...
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| 2017-11-17 |
kjvdheide | JAL-2795 removed unneeded distancematrix length/width...
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| 2017-11-17 |
kjvdheide | JAL-2844 changed Aptx config to make all cladogram...
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| 2017-11-17 |
kjvdheide | Merge branch 'kjvdh/features/PhylogenyViewer' of
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| 2017-11-17 |
kjvdheide | JAL-2805 couple of method name changes
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| 2017-11-17 |
kjvdheide | JAL-281 added menu items and listeners to load from...
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| 2017-11-17 |
kjvdheide | JAL-281 changed load associated tree GUI item to menu...
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| 2017-11-16 |
kjvdheide | JAL-2805 expanded tree and treenode interfaces
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| 2017-11-16 |
kjvdheide | JAL-2805 loads of file reorganizing, interfaces expanded
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| 2017-11-15 |
kjvdheide | JAL-2805 functional binding on loading associated trees
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| 2017-11-14 |
kjvdheide | JAL-2805 viewport is passed along to the tree parser
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| 2017-11-14 |
kjvdheide | JAL-2795 added duplication check when calculated nodes...
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| 2017-11-14 |
kjvdheide | JAL-2805 added getters for hashmaps filled with associated...
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| 2017-11-14 |
kjvdheide | JAL-2805 added static method for logging duplications...
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| 2017-11-14 |
kjvdheide | JAL-2805 more sensible interface method params
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| 2017-11-14 |
kjvdheide | JAL-2805 finished up interface comments
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commit | commitdiff | tree |
| 2017-11-14 |
kjvdheide | JAL-2805 re-enabled one2many checks
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| 2017-11-14 |
kjvdheide | JAL-2805 interface comments, progress on associating...
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 interface comments
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 some more name changes
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 more name changes for clarity
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 more interface name changing
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 name changed of interfaces for consistency
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 Jalview sequence binding interface expanded
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 TreeParser now interface based
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 Added tree building interface
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 name change
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 deleted old Aptx class for loading just Newick...
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 more interface work
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2794 removed unused interface
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commit | commitdiff | tree |
| 2017-11-13 |
kjvdheide | JAL-2805 undid accidental double (buggy) binding, more...
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| 2017-11-13 |
kjvdheide | JAL-2805 warning messages added if Forester detects...
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| 2017-11-13 |
kjvdheide | JAL-2805 First try at loading tree through Forester...
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| 2017-11-10 |
kjvdheide | JAL-2794 reorganized node select code, added subtree...
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commit | commitdiff | tree |
| 2017-11-10 |
kjvdheide | JAL-2794 comments comments comments
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| 2017-11-10 |
kjvdheide | JAL-2794 most method parameters/class variables made...
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commit | commitdiff | tree |
| 2017-11-10 |
kjvdheide | JAL-2794 comments, selected node now doesn't have to...
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| 2017-11-09 |
kjvdheide | JAL-2794 PaintRefresher support, Aptx node selection...
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commit | commitdiff | tree |
| 2017-11-09 |
kjvdheide | JAL-2794 interface comment
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commit | commitdiff | tree |
| 2017-11-09 |
kjvdheide | JAL-2794 Made HashMap with Nodes as keys and sequences...
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commit | commitdiff | tree |
| 2017-11-08 |
kjvdheide | JAL-2794 Aptx instances get their parent alignment...
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| 2017-11-08 |
kjvdheide | JAL-2794 Cleaning up tree conversion, sequences are...
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| 2017-11-08 |
kjvdheide | JAL-2794 getters and setters for finding nodes in forester...
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commit | commitdiff | tree |
| 2017-11-08 |
kjvdheide | JAL-2795 created static class for forester conversions
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commit | commitdiff | tree |
| 2017-11-08 |
kjvdheide | JAL-2794 Interface name change (oops)
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commit | commitdiff | tree |
| 2017-11-08 |
kjvdheide | JAL-2794 made JalviewTreeViewerBinding an interface
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| 2017-11-08 |
kjvdheide | JAL-2794 Added getter for AlignmentViewport to TreeBuilder
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commit | commitdiff | tree |
| 2017-11-06 |
kjvdheide | JAL-2794 simplified/clarified associating leaves to...
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commit | commitdiff | tree |
| 2017-11-03 |
kjvdheide | JAL-2794 created tree viewer binding class
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commit | commitdiff | tree |
| 2017-11-03 |
kjvdheide | JAL-2795 bunch of cleanup and comments
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commit | commitdiff | tree |
| 2017-11-02 |
kjvdheide | JAL-2795 added back test loop for Aptx tree naming...
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| 2017-11-02 |
kjvdheide | JAL-2795 Reverted code changes needed to cluster from...
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| 2017-11-02 |
kjvdheide | JAL-2795 Forester now NJ-clusters the DistanceMatrix...
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| 2017-11-02 |
kjvdheide | JAL-2795 moved matrix conversion to the ForesterMatrix...
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commit | commitdiff | tree |
| 2017-11-01 |
kjvdheide | JAL-2795 Sequence[] references now as SequenceI[] ...
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| 2017-11-01 |
kjvdheide | JAL-2795 removed sequences[] class variable, more comments
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 neater error message
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 added error catching for invalid identifier
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 changed getting index of identifier to Stream...
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 rebuilt MatrixConverter to be purely static
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 finalized method arguments; commited forester...
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 removed unneeded for loop (woops) and initialized...
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 implemented getting/setting identifiers
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 added comments links from ForesterMatrix to...
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 removed now unneeded values variable in ForesterMatrix
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commit | commitdiff | tree |
| 2017-10-30 |
kjvdheide | JAL-2795 add get for all matrix values to MatrixI ...
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| 2017-10-30 |
kjvdheide | JAL-2795 foresterMatrix now stores distance values...
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commit | commitdiff | tree |
| 2017-10-29 |
kjvdheide | JAL-2795 more matrix implementations
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commit | commitdiff | tree |
| 2017-10-28 |
kjvdheide | JAL-2795 moved ForesterMatrix to ext.forester
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commit | commitdiff | tree |
| 2017-10-28 |
kjvdheide | JAL-2795 Added get and set values to the converted...
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commit | commitdiff | tree |
| 2017-10-27 |
kjvdheide | JAL-2795 start of Jalview's Matrix conversion
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commit | commitdiff | tree |
| 2017-10-27 |
kjvdheide | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Start of matrix converter
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Added proper title to aptx trees
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | test name change
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Made FreeUpMemoryTest compatible with modified CalculationCh...
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Added getters for scoremodel & scoreparams in TreeBuilder
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | TreeBuilder now stores the used ScoreModel and ScoreParams
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | small name fixes in TreeBuilder
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Added TreeBuilder as parameter to the converter constructor
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Name changed of aptx treebuilder to treeconverter
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | added getSeqData to TreeBuilder
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Added full names to the tree algorithm enum
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | added abbreviations
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | added enum for the different tree algorithms
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | Couple more thread names
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | named most Jalview threads
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commit | commitdiff | tree |
| 2017-10-26 |
kjvdheide | removed accidental added enters, commented out broken...
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | finished up tests for trees made from jalview data
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Implemented distance tests
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Implemented tree title test for tree made from Jalview
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Added tree title test
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Removed redundant annotations
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Added branch name tests
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2017-10-25 |
kjvdheide | Added abstract class for tree viewer testing, rearranged...
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commit | commitdiff | tree |
| 2017-10-24 |
kjvdheide | Tests for Aptx tree created from a Phylogeny object...
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commit | commitdiff | tree |
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