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JAL-2805 Added tree building interface
[jalview.git]
/
src
/
jalview
/
2017-11-13
kjvdheide
JAL-2805 Added tree building interface
tree
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commitdiff
2017-11-13
kjvdheide
JAL-2805 name change
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commitdiff
2017-11-13
kjvdheide
JAL-2805 deleted old Aptx class for loading just Newick...
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commitdiff
2017-11-13
kjvdheide
JAL-2805 more interface work
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2017-11-13
kjvdheide
JAL-2794 removed unused interface
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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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commitdiff
2017-11-13
kjvdheide
JAL-2805 First try at loading tree through Forester...
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commitdiff
2017-11-10
kjvdheide
JAL-2794 reorganized node select code, added subtree...
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments comments comments
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commitdiff
2017-11-10
kjvdheide
JAL-2794 most method parameters/class variables made...
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments, selected node now doesn't have to...
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commitdiff
2017-11-09
kjvdheide
JAL-2794 PaintRefresher support, Aptx node selection...
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commitdiff
2017-11-09
kjvdheide
JAL-2794 interface comment
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commitdiff
2017-11-09
kjvdheide
JAL-2794 Made HashMap with Nodes as keys and sequences...
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Aptx instances get their parent alignment...
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Cleaning up tree conversion, sequences are...
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commitdiff
2017-11-08
kjvdheide
JAL-2795 created static class for forester conversions
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Interface name change (oops)
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commitdiff
2017-11-08
kjvdheide
JAL-2794 made JalviewTreeViewerBinding an interface
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Added getter for AlignmentViewport to TreeBuilder
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commitdiff
2017-11-06
kjvdheide
JAL-2794 simplified/clarified associating leaves to...
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commitdiff
2017-11-03
kjvdheide
JAL-2794 created tree viewer binding class
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commitdiff
2017-11-03
kjvdheide
JAL-2795 bunch of cleanup and comments
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commitdiff
2017-11-02
kjvdheide
JAL-2795 added back test loop for Aptx tree naming...
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Reverted code changes needed to cluster from...
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Forester now NJ-clusters the DistanceMatrix...
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commitdiff
2017-11-02
kjvdheide
JAL-2795 moved matrix conversion to the ForesterMatrix...
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commitdiff
2017-11-01
kjvdheide
JAL-2795 Sequence[] references now as SequenceI[] ...
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commitdiff
2017-11-01
kjvdheide
JAL-2795 removed sequences[] class variable, more comments
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added error catching for invalid identifier
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commitdiff
2017-10-30
kjvdheide
JAL-2795 changed getting index of identifier to Stream...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 rebuilt MatrixConverter to be purely static
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commitdiff
2017-10-30
kjvdheide
JAL-2795 finalized method arguments; commited forester...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed unneeded for loop (woops) and initiali...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 implemented getting/setting identifiers
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added comments links from ForesterMatrix to...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed now unneeded values variable in Forest...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 add get for all matrix values to MatrixI ...
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commitdiff
2017-10-30
kjvdheide
JAL-2795 foresterMatrix now stores distance values...
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commitdiff
2017-10-29
kjvdheide
JAL-2795 more matrix implementations
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commitdiff
2017-10-28
kjvdheide
JAL-2795 moved ForesterMatrix to ext.forester
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commitdiff
2017-10-28
kjvdheide
JAL-2795 Added get and set values to the converted...
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commitdiff
2017-10-27
kjvdheide
JAL-2795 start of Jalview's Matrix conversion
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commitdiff
2017-10-27
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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2017-10-27
gmungoc
JAL-2526 updated javadoc
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commitdiff
2017-10-26
kjvdheide
Start of matrix converter
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commitdiff
2017-10-26
kjvdheide
Added proper title to aptx trees
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commitdiff
2017-10-26
kjvdheide
Made FreeUpMemoryTest compatible with modified Calculat...
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commitdiff
2017-10-26
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-26
Jim Procter
JAL-2488 patch causes of NPE during testStoreAndRecover...
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commitdiff
2017-10-26
kjvdheide
Added getters for scoremodel & scoreparams in TreeBuilder
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commitdiff
2017-10-26
Jim Procter
Merge branch 'feature/JAL-2488finalize' into develop
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commitdiff
2017-10-26
kjvdheide
TreeBuilder now stores the used ScoreModel and ScoreParams
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commitdiff
2017-10-26
kjvdheide
small name fixes in TreeBuilder
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commitdiff
2017-10-26
kjvdheide
Added TreeBuilder as parameter to the converter constructor
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commitdiff
2017-10-26
kjvdheide
Name changed of aptx treebuilder to treeconverter
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commitdiff
2017-10-26
kjvdheide
added getSeqData to TreeBuilder
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commitdiff
2017-10-26
Jim Procter
JAL-2793 cancelling font changed dialog didn't call...
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commitdiff
2017-10-26
kjvdheide
Added full names to the tree algorithm enum
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commitdiff
2017-10-26
kjvdheide
added abbreviations
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commitdiff
2017-10-26
kjvdheide
added enum for the different tree algorithms
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commitdiff
2017-10-26
kjvdheide
Couple more thread names
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commitdiff
2017-10-26
kjvdheide
named most Jalview threads
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commitdiff
2017-10-26
Jim Procter
Merge branch 'bug/JAL-2776toggleGroupColour' into develop
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commitdiff
2017-10-26
Jim Procter
Merge branch 'features/JAL-2685pairwiseSeqLimits' into...
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commitdiff
2017-10-26
kjvdheide
removed accidental added enters, commented out broken...
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commitdiff
2017-10-25
kjvdheide
finished up tests for trees made from jalview data
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2617mappedStopCodon' into develop
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2667mouseWheelWrapped' into develop
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2727closeAllFreeMemory' into...
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bugs/JAL-2779_osx_dialogsequencingbroke...
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commitdiff
2017-10-25
Jim Procter
JAL-2779 remove empty block and if statement
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
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commitdiff
2017-10-25
Jim Procter
JAL-2790 provide a cancel button for JABAWS and AACon...
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commitdiff
2017-10-25
Jim Procter
JAL-2392 auto boxing rather than explicit Long as key
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commitdiff
2017-10-24
gmungoc
JAL-2495 highlight all mapped sequences from structure...
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commitdiff
2017-10-24
Jim Procter
Merge branch 'features/JAL-2608closeOverview' into...
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commitdiff
2017-10-24
kjvdheide
Tests for Aptx tree created from a Phylogeny object...
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commitdiff
2017-10-24
gmungoc
JAL-2788 corrected merge error in propertyChange
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commitdiff
2017-10-24
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2609attemptedmerge' into develop
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commitdiff
2017-10-23
Jim Procter
JAL-2609 remove unused AlignPanel.fastPaint flag and...
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2609attemptedmerge' into develop
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2739' into develop
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2682parseId' into develop
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commitdiff
2017-10-23
gmungoc
JAL-2776 repaint everything on toggle group colour
bug/JAL-2776toggleGroupColour
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
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commitdiff
2017-10-23
gmungoc
JAL-1854 keep fallthrough but with comment to suppress...
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commitdiff
2017-10-23
gmungoc
JAL-1854 remove fallthrough of switch case (Checkstyle...
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commitdiff
2017-10-20
Jim Procter
JAL-2779 keep a reference to original Aqua manager...
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commitdiff
2017-10-20
Jim Procter
JAL-2779 remove OSX platform specific import (not neede...
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commitdiff
2017-10-20
gmungoc
JAL-2253 pull up constant, additional unit test
bug/JAL-2253
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commitdiff
2017-10-20
gmungoc
JAL-2609 fully erase scale above, tidy code change
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commitdiff
2017-10-19
gmungoc
JAL-2609 adjustments for test findings
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commitdiff
2017-10-19
kiramt
Merge branch 'develop' into bug/JAL-2609attemptedmerge
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commitdiff
2017-10-18
Jim Procter
JAL-2779 switch order for updating the current alignmen...
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commitdiff
2017-10-18
Jim Procter
JAL-2779 remove dead code
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