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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git] / src /
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport tree | commitdiff
2017-03-21 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... tree | commitdiff
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress 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 kiramtJAL-2388 Unit tests and tidies 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
2017-03-10 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-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
2017-03-06 kiramtJAL-2388 Corrected overview panel behaviour, updated... tree | commitdiff
2017-03-03 kiramtJAL-2429 Fix to ColumnSelection::findColumnPosition tree | commitdiff
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of... tree | commitdiff
2017-03-02 gmungocJAL-2295 tweak order and wording of Superpose menu... tree | commitdiff
2017-03-02 gmungocJAL-2295 make 'Jmol' menu appear; enable/disable Superp... tree | commitdiff
2017-03-01 kiramtJAL-2388 Reverted to previous tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-03-01 kiramtJAL-2388 Preliminary refactor check-in, does not compile tree | commitdiff
2017-02-28 kiramtJAL-2426 Removal of NPE in conservation thread when... tree | commitdiff
2017-02-28 kiramtJAL-2388 First move of endRes etc out of AlignmentViewp... tree | commitdiff
2017-02-28 kiramtJAL-2426 Checks on conservation thread in case we are... tree | commitdiff
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private... tree | commitdiff
2017-02-27 kiramtJAL-2388 Minor refactoring tree | commitdiff
2017-02-23 kiramtJAL-2388 Unit tests in progress tree | commitdiff
2017-02-21 kiramtMerge branch 'bug/JAL-2421overviewboxflicker' into tree | commitdiff
2017-02-21 kiramtMerge branch 'develop' into features/JAL-2388OverviewWindow tree | commitdiff
2017-02-21 kiramtJAL-2421 Unit test tree | commitdiff
2017-02-20 Jim ProcterMerge branch 'features/JAL-2379pcaMemory' into develop tree | commitdiff
2017-02-17 kiramtJAL-2388 Incomplete unit tests tree | commitdiff
2017-02-17 kiramtJAL-2421 Fix to alignment panel scroll values, and... tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 JAL-2419 - TODO suspiciously redundant nested... bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu tree | commitdiff
2017-02-15 Jim Procterfix for JAL-2419 - don’t trash the current selection tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 don’t search twice for containing group to... tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 javadoc - qualify that sequence argument to... tree | commitdiff
2017-02-14 kiramtJAL-2388 Removed unnecessary CommandListener interface... tree | commitdiff
2017-02-10 gmungocJAL-2371 small move of code, typo correction tree | commitdiff
2017-02-09 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-02-09 kiramtJAL-2388 Initial refactor of OverviewPanel tree | commitdiff
2017-02-09 Jim ProcterMerge branch 'develop' into features/JAL-2316 features/JAL-2316 tree | commitdiff
2017-02-09 gmungocJAL-2401 change 'Lower Case Colour' to checkbox with... tree | commitdiff
2017-02-09 gmungocJAL-2371 ensure some colour scheme (may be None) is... tree | commitdiff
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory tree | commitdiff
2017-02-09 gmungocJAL-2371 skip upper-casing consensus as it already is tree | commitdiff
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... tree | commitdiff
2017-02-09 gmungocJAL-2405 set initial selection group alignment context tree | commitdiff
2017-02-09 gmungocJAL-2405 enable nucleotide/peptide colour schemes in... tree | commitdiff
2017-02-08 gmungocJAL-2405 set context on selection group for tailored... tree | commitdiff
2017-02-08 gmungocJAL-2401 fix for NPE on selectedButtons, tweak for... tree | commitdiff
2017-02-08 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-02-08 Jim ProcterJAL-2366 updated default URL to jalview.org/services... tree | commitdiff
2017-02-07 Jim ProcterMerge branch 'features/JAL-2371collectionColourScheme... tree | commitdiff
2017-02-07 gmungocJAL-2401 Lower Case Colour toggleable, help text added tree | commitdiff
2017-02-07 gmungocJAL-2379 removed unused commented code tree | commitdiff
2017-02-07 gmungocJAL-2397 flag provided for 2.10.1 PCA gap calculation... tree | commitdiff
2017-02-07 gmungocJAL-2397 PCA gap cost uses last column of score matrix tree | commitdiff
2017-02-07 gmungocJAL-2398 corrected entry for C->R in Blosum62 matrix tree | commitdiff
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix tree | commitdiff
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA... tree | commitdiff
2017-02-01 gmungocJAL-2371 (slight!) simplification of isApplicableTo() tree | commitdiff
2017-01-31 gmungocJAL-2371 commented code removed only tree | commitdiff
2017-01-31 gmungocJAL-2371 rename global/viewportColourScheme to residueS... tree | commitdiff
2017-01-31 gmungocJAL-2385 more tests/bug fixes mostly for gui.SliderPane... tree | commitdiff
2017-01-27 gmungocJAL-2379 commented out code removed tree | commitdiff
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader... tree | commitdiff
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1 tree | commitdiff
2017-01-27 kiramtJAL-2366 Removed unneeded setEnabled calls tree | commitdiff
2017-01-26 gmungocJAL-2360 corrected comment tree | commitdiff
2017-01-26 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-26 kiramtJAL-2316 Updated to use identifiers jalview service tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory tree | commitdiff
2017-01-26 gmungocJAL-2344 test fix and code tidy for review comments tree | commitdiff
2017-01-26 gmungocJAL-2380 code tidy after review tree | commitdiff
2017-01-25 gmungocJAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid... tree | commitdiff
2017-01-23 gmungocJAL-2379 made SparseMatrix.divide() so as to exactly... tree | commitdiff
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