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Merge remote-tracking branch 'origin/develop' into kjvdh/features/PhylogenyViewer
[jalview.git]
/
src
/
2017-11-13
Jim Procter
JAL-2810 auto search checkbox state stored as user...
tree
|
commitdiff
2017-11-13
gmungoc
JAL-2679 example accession changed to CAD01290
tree
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commitdiff
2017-11-13
Jim Procter
JAL-2810 mainFramTabs -> tabs
tree
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commitdiff
2017-11-10
Jim Procter
JAL-2828 allow CalcId to match on String equivalence...
doc/JAL-2494_JAL-2828_mergefindAnnotation
tree
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commitdiff
2017-11-10
Jim Procter
JAL-2828 refactored duplicate code for searching lists...
tree
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commitdiff
2017-11-10
gmungoc
JAL-2829 fixes and unit tests
bug/JAL-2829deleteCharsWithGaps
tree
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commitdiff
2017-11-10
gmungoc
JAL-2562 updated findPosition javadoc to match behaviour
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 reorganized node select code, added subtree...
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments comments comments
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 most method parameters/class variables made...
tree
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commitdiff
2017-11-10
kjvdheide
JAL-2794 comments, selected node now doesn't have to...
tree
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commitdiff
2017-11-10
kiramt
JAL-2827 related fixes for stem and non-canonical annot...
bug/JAL-2827
tree
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commitdiff
2017-11-09
kiramt
JAL-2827 Fix notched repaint of helix annotation when...
tree
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commitdiff
2017-11-09
kjvdheide
JAL-2794 PaintRefresher support, Aptx node selection...
tree
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commitdiff
2017-11-09
kjvdheide
JAL-2794 interface comment
tree
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commitdiff
2017-11-09
kjvdheide
JAL-2794 Made HashMap with Nodes as keys and sequences...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Aptx instances get their parent alignment...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Cleaning up tree conversion, sequences are...
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2795 created static class for forester conversions
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Interface name change (oops)
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 made JalviewTreeViewerBinding an interface
tree
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commitdiff
2017-11-08
kjvdheide
JAL-2794 Added getter for AlignmentViewport to TreeBuilder
tree
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commitdiff
2017-11-08
Jim Procter
Merge branch 'develop' into bug/JAL-2225mapMultipleChains
tree
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commitdiff
2017-11-07
Jim Procter
Merge branch 'imp/JAL-2775' into develop
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2810 i18n tab label
tree
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commitdiff
2017-11-07
kiramt
JAL-2774 Added javadoc for new event parameters
imp/JAL-2774
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2810 ‘Close’ is now ‘Cancel’ in SequenceFetcher...
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2810 working back button shown for bulk ID retrieva...
tree
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commitdiff
2017-11-07
kiramt
JAL-2774 Fix fastpaint of wrapped alignment
tree
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commitdiff
2017-11-07
kiramt
JAL-2821 refactored drawPartialGroupOutline
bug/JAL-2821
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2810 bulk fetch for PDB IDs
tree
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commitdiff
2017-11-06
kjvdheide
JAL-2794 simplified/clarified associating leaves to...
tree
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commitdiff
2017-11-03
kjvdheide
JAL-2794 created tree viewer binding class
tree
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commitdiff
2017-11-03
kjvdheide
JAL-2795 bunch of cleanup and comments
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 added back test loop for Aptx tree naming...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Reverted code changes needed to cluster from...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 Forester now NJ-clusters the DistanceMatrix...
tree
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commitdiff
2017-11-02
kjvdheide
JAL-2795 moved matrix conversion to the ForesterMatrix...
tree
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commitdiff
2017-11-01
kjvdheide
JAL-2795 Sequence[] references now as SequenceI[] ...
tree
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commitdiff
2017-11-01
kjvdheide
JAL-2795 removed sequences[] class variable, more comments
tree
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commitdiff
2017-11-01
kiramt
Merge branch 'develop' into imp/JAL-2775
imp/JAL-2775
tree
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commitdiff
2017-10-31
kiramt
JAL-2774 Fix repaint artefacts
tree
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commitdiff
2017-10-31
kiramt
JAL-2774 Fixed merge issues
tree
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commitdiff
2017-10-31
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-10-31
Jim Procter
JAL-2810 checkbox label for Autosearch
tree
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commitdiff
2017-10-31
Jim Procter
JAL-2810 default border colour
tree
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commitdiff
2017-10-31
kiramt
JAL-2756 update for new EBI https link
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added error catching for invalid identifier
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 changed getting index of identifier to Stream...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 rebuilt MatrixConverter to be purely static
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 finalized method arguments; commited forester...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed unneeded for loop (woops) and initiali...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 implemented getting/setting identifiers
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 added comments links from ForesterMatrix to...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 removed now unneeded values variable in Forest...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 add get for all matrix values to MatrixI ...
tree
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commitdiff
2017-10-30
kjvdheide
JAL-2795 foresterMatrix now stores distance values...
tree
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commitdiff
2017-10-29
kjvdheide
JAL-2795 more matrix implementations
tree
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commitdiff
2017-10-28
kjvdheide
JAL-2795 moved ForesterMatrix to ext.forester
tree
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commitdiff
2017-10-28
kjvdheide
JAL-2795 Added get and set values to the converted...
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2810 prototype retrieve ID tab for the Uniprot...
tree
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commitdiff
2017-10-27
kjvdheide
JAL-2795 start of Jalview's Matrix conversion
tree
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commitdiff
2017-10-27
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2804 update search results when enter pressed or...
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2804 checkbox to enable/disable auto search (with...
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2804 kludge method to test if last key event handle...
tree
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commitdiff
2017-10-27
gmungoc
JAL-2526 updated javadoc
tree
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commitdiff
2017-10-26
kjvdheide
Start of matrix converter
tree
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commitdiff
2017-10-26
kjvdheide
Added proper title to aptx trees
tree
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commitdiff
2017-10-26
kjvdheide
Made FreeUpMemoryTest compatible with modified Calculat...
tree
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commitdiff
2017-10-26
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-26
Jim Procter
JAL-2488 patch causes of NPE during testStoreAndRecover...
tree
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commitdiff
2017-10-26
kjvdheide
Added getters for scoremodel & scoreparams in TreeBuilder
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'feature/JAL-2488finalize' into develop
tree
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commitdiff
2017-10-26
kjvdheide
TreeBuilder now stores the used ScoreModel and ScoreParams
tree
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commitdiff
2017-10-26
kjvdheide
small name fixes in TreeBuilder
tree
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commitdiff
2017-10-26
kjvdheide
Added TreeBuilder as parameter to the converter constructor
tree
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commitdiff
2017-10-26
kjvdheide
Name changed of aptx treebuilder to treeconverter
tree
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commitdiff
2017-10-26
kjvdheide
added getSeqData to TreeBuilder
tree
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commitdiff
2017-10-26
Jim Procter
JAL-2793 cancelling font changed dialog didn't call...
tree
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commitdiff
2017-10-26
kjvdheide
Added full names to the tree algorithm enum
tree
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commitdiff
2017-10-26
kjvdheide
added abbreviations
tree
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commitdiff
2017-10-26
kjvdheide
added enum for the different tree algorithms
tree
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commitdiff
2017-10-26
kjvdheide
Couple more thread names
tree
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commitdiff
2017-10-26
kjvdheide
named most Jalview threads
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'bug/JAL-2776toggleGroupColour' into develop
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'features/JAL-2685pairwiseSeqLimits' into...
tree
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commitdiff
2017-10-26
kjvdheide
removed accidental added enters, commented out broken...
tree
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commitdiff
2017-10-25
kjvdheide
finished up tests for trees made from jalview data
tree
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2617mappedStopCodon' into develop
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2667mouseWheelWrapped' into develop
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2727closeAllFreeMemory' into...
tree
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commitdiff
2017-10-25
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bugs/JAL-2779_osx_dialogsequencingbroke...
tree
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commitdiff
2017-10-25
Jim Procter
JAL-2779 remove empty block and if statement
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
tree
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commitdiff
2017-10-25
Jim Procter
JAL-2790 provide a cancel button for JABAWS and AACon...
tree
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commitdiff
2017-10-25
Jim Procter
JAL-2392 auto boxing rather than explicit Long as key
tree
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commitdiff
2017-10-24
gmungoc
JAL-2495 highlight all mapped sequences from structure...
tree
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commitdiff
next