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Merge branch 'develop' into features/JAL-2435splitScreenFont
[jalview.git] / src /
2017-03-31 gmungocJAL-2430 code tidy, unit test for Jmol hidden column... tree | commitdiff
2017-03-31 gmungocJAL-2435 tidy code tree | commitdiff
2017-03-31 gmungocJAL-1608 unused method removed tree | commitdiff
2017-03-31 gmungocJAL-2435 slightly more sensible behaviour changing... tree | commitdiff
2017-03-30 gmungocMerge branch 'develop' into features/JAL-2435splitScree... tree | commitdiff
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-1608createGroups bug/JAL-1608createGroups tree | commitdiff
2017-03-30 gmungocJAL-1608 leave Create Group, Remove Group menu items... tree | commitdiff
2017-03-30 gmungocJAL-2401 code and help tidy for review comments tree | commitdiff
2017-03-30 gmungocJAL-2401 don't apply lower case colour to upper case tree | commitdiff
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2399textColour bug/JAL-2399textColour tree | commitdiff
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice tree | commitdiff
2017-03-29 gmungocMerge branch 'develop' into bug/JAL-1608createGroups tree | commitdiff
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme... tree | commitdiff
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle... tree | commitdiff
2017-03-29 gmungocJAL-2416 explicit constant for unknown/unknown identity... tree | commitdiff
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols... tree | commitdiff
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from... tree | commitdiff
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min... tree | commitdiff
2017-03-28 gmungocJAL-2416 more test coverage of matrix parser tree | commitdiff
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex... tree | commitdiff
2017-03-27 gmungocJAL-2416 class Javadoc updates prior to parsing changes tree | commitdiff
2017-03-27 gmungocJAL-2468 change score model in PCAModel when switching tree | commitdiff
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score... tree | commitdiff
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... tree | commitdiff
2017-03-27 gmungocJAL-2416 tooltip with descriptions for score models... tree | commitdiff
2017-03-27 gmungocJAL-2416 add score model description field for tooltip... tree | commitdiff
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a... tree | commitdiff
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices tree | commitdiff
2017-03-27 gmungocJAL-2428 unused method deleted tree | commitdiff
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by... tree | commitdiff
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input... tree | commitdiff
2017-03-24 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin... tree | commitdiff
2017-03-24 gmungocJAL-2428 use 'correct' name for selected score model tree | commitdiff
2017-03-24 Jim ProcterJAL-2360 fix applet build by separating castor XML... tree | commitdiff
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text... tree | commitdiff
2017-03-24 gmungocJAL-1632 named parameters tree | commitdiff
2017-03-24 kiramtJAL-2314 Tidy up tree | commitdiff
2017-03-24 gmungocJAL-2464 fix cancel tree print behaviour tree | commitdiff
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... tree | commitdiff
2017-03-23 kiramtJAL-2314 Tweaks to stop thread sync issues tree | commitdiff
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match... tree | commitdiff
2017-03-23 gmungocJAL-2397 formatting only tree | commitdiff
2017-03-23 gmungocJAL-1632 suppress PID parameter options in Tree/PCA... tree | commitdiff
2017-03-23 gmungocJAL-838 class javadoc added tree | commitdiff
2017-03-23 gmungocJAL-2464 fix cancel tree print behaviour tree | commitdiff
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre... tree | commitdiff
2017-03-23 kiramtJAL-2314 Tidies tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-22 kiramtJAL-2461 Removed DAS error stack trace, updated message tree | commitdiff
2017-03-22 kiramtJAL-2388 Reinstated original overview checks for annota... tree | commitdiff
2017-03-22 kiramtMerge remote-tracking branch 'origin/develop' into tree | commitdiff
2017-03-21 gmungocJAL-2438 removed (non-functional) lastSeq, lastSequence... tree | commitdiff
2017-03-21 gmungocJAL-2243 update discovered features on opening structur... tree | commitdiff
2017-03-21 gmungocJAL-2438 check for null FeatureRenderer tree | commitdiff
2017-03-21 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... tree | commitdiff
2017-03-20 Jim ProcterMerge branch 'bug/JAL-2421overviewboxflicker' into... tree | commitdiff
2017-03-20 kiramtJAL-2388 Comment typo tree | commitdiff
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests tree | commitdiff
2017-03-17 kiramtJAL-2388 Renamed column and row subtraction functions tree | commitdiff
2017-03-16 Jim ProcterMerge branch 'merges/develop_JAL2295setChimeraAttribute... tree | commitdiff
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity tree | commitdiff
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code tree | commitdiff
2017-03-16 kiramtJAL-2388 Renamed viewport position props to viewport... tree | commitdiff
2017-03-16 kiramtJAL-2388 Applet update for overview panel tree | commitdiff
2017-03-16 kiramtJAL-2439 Out-by-one in setting endRes/endSeq tree | commitdiff
2017-03-15 gmungocJAL-2431 show cDNA consensus after New View in split... tree | commitdiff
2017-03-15 kiramtJAL-2388 Unit tests and tidies tree | commitdiff
2017-03-15 gmungocJAL-2443 push getResidueBoxColour inside getResidueColour tree | commitdiff
2017-03-15 gmungocJAL-2438 corrected getFeatureRenderer() tree | commitdiff
2017-03-15 gmungocJAL-2442 applet feature transparency also on overview... tree | commitdiff
2017-03-15 gmungocJAL-2438 handle null FeatureRenderer in FeatureColourFinder tree | commitdiff
2017-03-15 gmungocJAL-2438 refactored checks for 'no features displayed' tree | commitdiff
2017-03-15 gmungocJAL-2438 clarify code and javadoc, reinstate updateFeat... tree | commitdiff
2017-03-15 gmungocMerge branch 'develop' into bug/JAL-2436featureRenderer... tree | commitdiff
2017-03-14 kiramtJAL-2388 Working overview panel tree | commitdiff
2017-03-14 kiramtJAL-2439 Fixes to out-by-one sequence indexing in gui... tree | commitdiff
2017-03-14 kiramtJAL-2388 New hidden cols/seqs functions to support... tree | commitdiff
2017-03-14 gmungocJAL-2438 unit test, fixes, Javadoc updates tree | commitdiff
2017-03-14 gmungocJAL-2438 Javadoc updates tree | commitdiff
2017-03-14 gmungocJAL-2438 comment/Javadoc tidies tree | commitdiff
2017-03-13 gmungocJAL-2438 corrected handling of default colour tree | commitdiff
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen... tree | commitdiff
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding... tree | commitdiff
2017-03-10 kiramtJAL-2388 Moving some alignment panel logic into overvie... tree | commitdiff
2017-03-09 kiramtJAL-2426 Checks on conservation thread in case we are... tree | commitdiff
2017-03-09 kiramtJAL-2426 Removal of NPE in conservation thread when... tree | commitdiff
2017-03-09 kiramtJAL-2388 Minor fix for annotation graph, removed unit... tree | commitdiff
2017-03-08 gmungocJAL-2435 copy font changes across split screen tree | commitdiff
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on... tree | commitdiff
2017-03-08 gmungocJAL-2295 avoid quotes breaking attribute value parsing tree | commitdiff
2017-03-07 kiramtJAL-2388 Fixed inherited&new out-by-one errors; further... tree | commitdiff
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set... tree | commitdiff
2017-03-07 kiramtJAL-2388 Additional unit tests tree | commitdiff
2017-03-07 kiramtJAL-2388 Missed commit tree | commitdiff
2017-03-07 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-03-07 kiramtJAL-2429 findColumnPosition returns 0 for cols in regio... tree | commitdiff
2017-03-07 kiramtJAL-2429 Additional fix to ColumnSelection when hidden... tree | commitdiff
2017-03-06 kiramtJAL-2388 Dependency tidy tree | commitdiff
2017-03-06 kiramtJAL-2388 Remove OverviewDimensions dependency on gui... tree | commitdiff
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