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jalview.git
2017-03-30 gmungocJAL-728 offer choice of substitution matrix for Quality... features/JAL-728alternateQuality commit | commitdiff | tree | snapshot
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme... commit | commitdiff | tree | snapshot
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle... commit | commitdiff | tree | snapshot
2017-03-29 gmungocJAL-2416 explicit constant for unknown/unknown identity... commit | commitdiff | tree | snapshot
2017-03-28 gmungocJAL-2416 format matrix more readably commit | commitdiff | tree | snapshot
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols... commit | commitdiff | tree | snapshot
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from... commit | commitdiff | tree | snapshot
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min... commit | commitdiff | tree | snapshot
2017-03-28 gmungocJAL-2416 more test coverage of matrix parser commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 amended to AAindex format commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 amended to (as near as possible) strict NCBI... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 class Javadoc updates prior to parsing changes commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2468 change score model in PCAModel when switching commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 tooltip with descriptions for score models... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 add score model description field for tooltip... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2428 unused method deleted commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by... commit | commitdiff | tree | snapshot
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input... commit | commitdiff | tree | snapshot
2017-03-24 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff | tree | snapshot
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 Jim ProcterJAL-2360 fix applet build by separating castor XML... 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 kiramtMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-03-23 kiramtJAL-2388 unit test initialisation fix for running full... 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-2464 fix cancel tree print behaviour 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
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