jalview.git
2017-03-27 gmungocJAL-2416 add score model description field for tooltip...
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a...
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices
2017-03-27 gmungocJAL-2428 unused method deleted
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by...
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input...
2017-03-24 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin...
2017-03-24 gmungocJAL-2428 use 'correct' name for selected score model
2017-03-24 Jim ProcterJAL-2360 fix applet build by separating castor XML...
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text...
2017-03-24 gmungocJAL-1632 named parameters
2017-03-24 gmungocJAL-2398 corrected BLOSUM62 C -> R score in resource...
2017-03-24 gmungocJAL-2416 tests added for ScoreMatrix
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca...
2017-03-23 kiramtMerge branch 'develop' of https://source.jalview.org...
2017-03-23 kiramtJAL-2388 unit test initialisation fix for running full...
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match...
2017-03-23 gmungocJAL-2397 formatting only
2017-03-23 gmungocJAL-1632 suppress PID parameter options in Tree/PCA...
2017-03-23 gmungocJAL-838 class javadoc added
2017-03-23 gmungocJAL-2464 fix cancel tree print behaviour
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre...
2017-03-23 gmungocJAL-2393 updated test for removal of PIDDistanceModel
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-22 kiramtJAL-2388 Reinstated original overview checks for annota...
2017-03-22 kiramtMerge remote-tracking branch bug/JAL-2436featureRendererThreading
2017-03-22 kiramtMerge remote-tracking branch 'origin/develop' into
2017-03-22 gmungocJAL-2311 suppress autocalc'd annotation to isolate...
2017-03-21 kiramtJAL-2307 Fixed SiftsClient unit test
2017-03-21 gmungocJAL-2306 assert no DAS sources
2017-03-21 gmungocJAL-2438 removed (non-functional) lastSeq, lastSequence...
2017-03-21 gmungocJAL-2243 update discovered features on opening structur...
2017-03-21 gmungocJAL-2438 check for null FeatureRenderer
2017-03-21 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into...
2017-03-20 Jim ProcterMerge branch 'bug/JAL-2421overviewboxflicker' into...
2017-03-20 kiramtJAL-2388 Comment typo
2017-03-17 kiramtJAL-2388 ViewportRanges unit test
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests
2017-03-17 kiramtJAL-2388 Renamed column and row subtraction functions
2017-03-16 Jim ProcterMerge branch 'merges/develop_JAL2295setChimeraAttribute...
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code
2017-03-16 kiramtJAL-2388 Renamed viewport position props to viewport...
2017-03-16 kiramtJAL-2388 Unit test update
2017-03-16 kiramtJAL-2388 Applet update for overview panel
2017-03-16 kiramtJAL-2439 Out-by-one in setting endRes/endSeq
2017-03-15 kiramtJAL-2388 Unit tests and tidies
2017-03-15 gmungocJAL-2443 push getResidueBoxColour inside getResidueColour
2017-03-15 gmungocJAL-2438 corrected getFeatureRenderer()
2017-03-15 gmungocJAL-2442 applet feature transparency also on overview...
2017-03-15 gmungocJAL-2438 handle null FeatureRenderer in FeatureColourFinder
2017-03-15 gmungocJAL-2438 refactored checks for 'no features displayed'
2017-03-15 gmungocJAL-2438 clarify code and javadoc, reinstate updateFeat...
2017-03-15 gmungocMerge branch 'develop' into bug/JAL-2436featureRenderer...
2017-03-15 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-03-14 kiramtJAL-2388 Working overview panel
2017-03-14 kiramtJAL-2439 Fixes to out-by-one sequence indexing in gui...
2017-03-14 kiramtJAL-2388 New hidden cols/seqs functions to support...
2017-03-14 gmungocJAL-2438 unit test, fixes, Javadoc updates
2017-03-14 gmungocJAL-2438 unit tests for FeatureColourFinder (transparen...
2017-03-14 gmungocJAL-2438 Javadoc updates
2017-03-14 gmungocJAL-2438 comment/Javadoc tidies
2017-03-13 gmungocJAL-2438 corrected handling of default colour
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen...
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding...
2017-03-10 kiramtJAL-2388 Moving some alignment panel logic into overvie...
2017-03-09 kiramtJAL-2426 Checks on conservation thread in case we are...
2017-03-09 kiramtJAL-2426 Removal of NPE in conservation thread when...
2017-03-09 kiramtJAL-2388 Minor fix for annotation graph, removed unit...
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on...
2017-03-08 gmungocJAL-2295 avoid quotes breaking attribute value parsing
2017-03-07 kiramtJAL-2388 Fixed inherited&new out-by-one errors; further...
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set...
2017-03-07 kiramtJAL-2388 Additional unit tests
2017-03-07 kiramtJAL-2388 Missed commit
2017-03-07 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-03-07 kiramtJAL-2429 Messed something up, merged conflicts
2017-03-07 kiramtJAL-2429 findColumnPosition returns 0 for cols in regio...
2017-03-07 kiramtJAL-2429 Additional fix to ColumnSelection when hidden...
2017-03-06 kiramtJAL-2388 Dependency tidy
2017-03-06 kiramtJAL-2388 Remove OverviewDimensions dependency on gui...
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters()
2017-03-06 kiramtJAL-2388 Corrected overview panel behaviour, updated...
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree...
2017-03-03 kiramtJAL-2429 Fix to ColumnSelection::findColumnPosition
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of...
2017-03-02 gmungocJAL-2295 tweak order and wording of Superpose menu...
2017-03-02 gmungocJAL-2295 make 'Jmol' menu appear; enable/disable Superp...
2017-03-01 kiramtJAL-2388 Reverted to previous
2017-03-01 gmungocJAL-1264 smarter way to skip autocalc'd annotations...
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes...
2017-03-01 kiramtJAL-2388 Preliminary refactor check-in, does not compile
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel...
2017-02-28 kiramtJAL-2426 Removal of NPE in conservation thread when...
2017-02-28 kiramtJAL-2388 Removing sources of non-determinism in unit...
2017-02-28 kiramtJAL-2388 First move of endRes etc out of AlignmentViewp...
2017-02-28 gmungocJAL-1632 disable parameters not applicable for score...
2017-02-28 kiramtJAL-2426 Checks on conservation thread in case we are...
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