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jalview.git
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin... commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-2428 use 'correct' name for selected score model commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text... commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-1632 named parameters commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-2398 corrected BLOSUM62 C -> R score in resource... commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-2416 tests added for ScoreMatrix commit | commitdiff | tree | snapshot
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match... commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-2397 formatting only commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-1632 suppress PID parameter options in Tree/PCA... commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-838 class javadoc added commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre... commit | commitdiff | tree | snapshot
2017-03-23 gmungocJAL-2393 updated test for removal of PIDDistanceModel commit | commitdiff | tree | snapshot
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff | tree | snapshot
2017-03-22 kiramtJAL-2388 Reinstated original overview checks for annota... commit | commitdiff | tree | snapshot
2017-03-22 kiramtMerge remote-tracking branch bug/JAL-2436featureRendererThreading commit | commitdiff | tree | snapshot
2017-03-22 kiramtMerge remote-tracking branch 'origin/develop' into commit | commitdiff | tree | snapshot
2017-03-22 gmungocJAL-2311 suppress autocalc'd annotation to isolate... commit | commitdiff | tree | snapshot
2017-03-21 kiramtJAL-2307 Fixed SiftsClient unit test commit | commitdiff | tree | snapshot
2017-03-21 gmungocJAL-2306 assert no DAS sources commit | commitdiff | tree | snapshot
2017-03-21 gmungocJAL-2438 removed (non-functional) lastSeq, lastSequence... commit | commitdiff | tree | snapshot
2017-03-21 gmungocJAL-2243 update discovered features on opening structur... commit | commitdiff | tree | snapshot
2017-03-21 gmungocJAL-2438 check for null FeatureRenderer commit | commitdiff | tree | snapshot
2017-03-21 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... commit | commitdiff | tree | snapshot
2017-03-20 Jim ProcterMerge branch 'bug/JAL-2421overviewboxflicker' into... commit | commitdiff | tree | snapshot
2017-03-20 kiramtJAL-2388 Comment typo commit | commitdiff | tree | snapshot
2017-03-17 kiramtJAL-2388 ViewportRanges unit test commit | commitdiff | tree | snapshot
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests commit | commitdiff | tree | snapshot
2017-03-17 kiramtJAL-2388 Renamed column and row subtraction functions commit | commitdiff | tree | snapshot
2017-03-16 Jim ProcterMerge branch 'merges/develop_JAL2295setChimeraAttribute... commit | commitdiff | tree | snapshot
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity commit | commitdiff | tree | snapshot
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code commit | commitdiff | tree | snapshot
2017-03-16 kiramtJAL-2388 Renamed viewport position props to viewport... commit | commitdiff | tree | snapshot
2017-03-16 kiramtJAL-2388 Unit test update commit | commitdiff | tree | snapshot
2017-03-16 kiramtJAL-2388 Applet update for overview panel commit | commitdiff | tree | snapshot
2017-03-16 kiramtJAL-2439 Out-by-one in setting endRes/endSeq commit | commitdiff | tree | snapshot
2017-03-15 kiramtJAL-2388 Unit tests and tidies commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2443 push getResidueBoxColour inside getResidueColour commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2438 corrected getFeatureRenderer() commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2442 applet feature transparency also on overview... commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2438 handle null FeatureRenderer in FeatureColourFinder commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2438 refactored checks for 'no features displayed' commit | commitdiff | tree | snapshot
2017-03-15 gmungocJAL-2438 clarify code and javadoc, reinstate updateFeat... commit | commitdiff | tree | snapshot
2017-03-15 gmungocMerge branch 'develop' into bug/JAL-2436featureRenderer... commit | commitdiff | tree | snapshot
2017-03-15 kiramtMerge remote-tracking branch 'origin/develop' into... commit | commitdiff | tree | snapshot
2017-03-14 kiramtJAL-2388 Working overview panel commit | commitdiff | tree | snapshot
2017-03-14 kiramtJAL-2439 Fixes to out-by-one sequence indexing in gui... commit | commitdiff | tree | snapshot
2017-03-14 kiramtJAL-2388 New hidden cols/seqs functions to support... commit | commitdiff | tree | snapshot
2017-03-14 gmungocJAL-2438 unit test, fixes, Javadoc updates commit | commitdiff | tree | snapshot
2017-03-14 gmungocJAL-2438 unit tests for FeatureColourFinder (transparen... commit | commitdiff | tree | snapshot
2017-03-14 gmungocJAL-2438 Javadoc updates commit | commitdiff | tree | snapshot
2017-03-14 gmungocJAL-2438 comment/Javadoc tidies commit | commitdiff | tree | snapshot
2017-03-13 gmungocJAL-2438 corrected handling of default colour commit | commitdiff | tree | snapshot
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen... commit | commitdiff | tree | snapshot
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding... commit | commitdiff | tree | snapshot
2017-03-10 kiramtJAL-2388 Moving some alignment panel logic into overvie... commit | commitdiff | tree | snapshot
2017-03-09 kiramtJAL-2426 Checks on conservation thread in case we are... commit | commitdiff | tree | snapshot
2017-03-09 kiramtJAL-2426 Removal of NPE in conservation thread when... commit | commitdiff | tree | snapshot
2017-03-09 kiramtJAL-2388 Minor fix for annotation graph, removed unit... commit | commitdiff | tree | snapshot
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on... commit | commitdiff | tree | snapshot
2017-03-08 gmungocJAL-2295 avoid quotes breaking attribute value parsing commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2388 Fixed inherited&new out-by-one errors; further... commit | commitdiff | tree | snapshot
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set... commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2388 Additional unit tests commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2388 Missed commit commit | commitdiff | tree | snapshot
2017-03-07 kiramtMerge remote-tracking branch 'origin/develop' into... commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2429 Messed something up, merged conflicts commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2429 findColumnPosition returns 0 for cols in regio... commit | commitdiff | tree | snapshot
2017-03-07 kiramtJAL-2429 Additional fix to ColumnSelection when hidden... commit | commitdiff | tree | snapshot
2017-03-06 kiramtJAL-2388 Dependency tidy commit | commitdiff | tree | snapshot
2017-03-06 kiramtJAL-2388 Remove OverviewDimensions dependency on gui... commit | commitdiff | tree | snapshot
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters() commit | commitdiff | tree | snapshot
2017-03-06 kiramtJAL-2388 Corrected overview panel behaviour, updated... commit | commitdiff | tree | snapshot
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... commit | commitdiff | tree | snapshot
2017-03-03 kiramtJAL-2429 Fix to ColumnSelection::findColumnPosition commit | commitdiff | tree | snapshot
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags commit | commitdiff | tree | snapshot
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of... commit | commitdiff | tree | snapshot
2017-03-02 gmungocJAL-2295 tweak order and wording of Superpose menu... commit | commitdiff | tree | snapshot
2017-03-02 gmungocJAL-2295 make 'Jmol' menu appear; enable/disable Superp... commit | commitdiff | tree | snapshot
2017-03-01 kiramtJAL-2388 Reverted to previous commit | commitdiff | tree | snapshot
2017-03-01 gmungocJAL-1264 smarter way to skip autocalc'd annotations... commit | commitdiff | tree | snapshot
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... commit | commitdiff | tree | snapshot
2017-03-01 kiramtJAL-2388 Preliminary refactor check-in, does not compile commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel... commit | commitdiff | tree | snapshot
2017-02-28 kiramtJAL-2426 Removal of NPE in conservation thread when... commit | commitdiff | tree | snapshot
2017-02-28 kiramtJAL-2388 Removing sources of non-determinism in unit... commit | commitdiff | tree | snapshot
2017-02-28 kiramtJAL-2388 First move of endRes etc out of AlignmentViewp... commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-1632 disable parameters not applicable for score... commit | commitdiff | tree | snapshot
2017-02-28 kiramtJAL-2426 Checks on conservation thread in case we are... commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-838 Javadoc tidy commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams! commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options commit | commitdiff | tree | snapshot
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 dialog to calculate either Tree or PCA commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... commit | commitdiff | tree | snapshot
2017-02-27 kiramtJAL-2388 Minor refactoring commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... commit | commitdiff | tree | snapshot
2017-02-27 kiramtJAL-2388 Unit tests take 2 commit | commitdiff | tree | snapshot
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