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Merge branch 'develop' into releases/Release_2_11_Branch
[jalview.git]
/
src
/
jalview
/
io
/
2017-05-08
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch
tree
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commitdiff
2017-05-05
tcofoegbu
JAL-2484 adjusted default cache settings panel's left...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-05-04
tcofoegbu
JAL-1648 improvements: enter key closes the popup and...
tree
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commitdiff
2017-05-04
tcofoegbu
JAL-1648 resolved CR-JAL-41 review issues
tree
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commitdiff
2017-05-04
Jim Procter
fix for JAL-2509 - don’t replace all bracket types...
tree
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commitdiff
2017-05-04
Jim Procter
fix for JAL-2507 - resolve stockholm per residue annota...
tree
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commitdiff
2017-05-02
gmungoc
JAL-2499 JAL-2403 push 'configure for view' inside...
tree
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commitdiff
2017-05-02
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-05-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-01
gmungoc
JAL-2489 JAL-2371 reinstate calls to
tree
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commitdiff
2017-04-28
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-04-27
gmungoc
JAL-2492 use SequenceFeatures.getNonPositionalFeatures()
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-26
gmungoc
JAL-2490 findFeaturesAtRes with performant feature...
tree
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commitdiff
2017-04-25
tcofoegbu
JAL-2489 bug fix
tree
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commitdiff
2017-04-25
kiramt
JAL-2388 Working hidden regions hide/show in desktop
tree
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commitdiff
2017-04-24
tcofoegbu
JAL-1648 House keeping
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Finished split of hidden columns and selected...
tree
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commitdiff
2017-04-24
tcofoegbu
JAL-1648 added unit test for AppCache
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping and code docs
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 added improvement to enable clearing cache...
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-1648 refactored and improved caching architecture...
tree
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commitdiff
2017-04-11
tcofoegbu
JAL-1648 Fix review issue - remove usage of String...
tree
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commitdiff
2017-04-03
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-04-03
tcofoegbu
JAL-1648 Added improvement to persist cache items to...
tree
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commitdiff
2017-03-28
gmungoc
JAL-2416 more test coverage of matrix parser
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 parse score matrices in either NCBI or AAindex...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 class Javadoc updates prior to parsing changes
tree
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commitdiff
2017-03-24
gmungoc
JAL-2428 simplify TreeModel constructors, add getOrigin...
tree
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commitdiff
2017-03-24
gmungoc
JAL-1632 TreeChooser renamed CalculationChooser, text...
tree
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commitdiff
2017-03-23
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-03-13
gmungoc
JAL-2438 FeatureColourFinder refactored from FeatureRen...
tree
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commitdiff
2017-03-06
gmungoc
JAL-2428 separate TreeModel from TreeBuilder/NJTree...
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 similarity options on TreeChooser panel affect...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 support roundtrip print/parse of ScoreMatrix
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 allow space in score matrix name
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 constants for "NJ", "AV"
tree
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commitdiff
2017-02-14
gmungoc
Parsing moved to (new) ScoreMatrixFile, drag and drop...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-26
gmungoc
JAL-2344 test fix and code tidy for review comments
tree
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commitdiff
2017-01-25
gmungoc
JAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-12
gmungoc
JAL-2344 now flagging formats as 'identifiable' instead...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 separated AlignmentFileI into AlignmentFileRea...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 FileFormats singleton for formats, FileFormatI...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 addSequence() method added to support Groovy...
tree
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commitdiff
2017-01-06
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-06
gmungoc
JAL-2360 findColour() with no args removed from ColourS...
tree
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commitdiff
2017-01-04
gmungoc
JAL-2371 CollectionColourScheme wraps ColourSchemeI
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 tidy spelling and file contents order only
tree
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commitdiff
2016-12-16
Jim Procter
JAL-2360 report line number when threshold cannot be...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2360 getColour() renamed to getColourScheme(),...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2360 refactoring for JalviewColourScheme enum,
tree
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commitdiff
2016-12-08
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-12-07
gmungoc
JAL-2344 handle null format, simplify JalviewFileChoose...
tree
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commitdiff
2016-12-02
tcofoegbu
JAL-1648 made further abstraction and createda new...
tree
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commitdiff
2016-12-01
tcofoegbu
JAL-1648 Implemented in-memory caching for FTS (Uniprot...
tree
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commitdiff
2016-11-29
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-29
gmungoc
JAL-2344 FileFormat.isStructureFile replaces
tree
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commitdiff
2016-11-28
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-28
tcofoegbu
Merge branch 'features/JAL-2326_JOptionPane-refactoring...
tree
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commitdiff
2016-11-28
gmungoc
JAL-2344 added FileFormatI.isStructureFile()
tree
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commitdiff
2016-11-28
gmungoc
JAL-2345 cache generated ImageIcon per file path
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 dynamically determine recognised extensions...
tree
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commitdiff
2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 override to ignore (obsolete?) JalviewFileView
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 use .equals() to compare FileFormatI objects
tree
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commitdiff
2016-11-24
gmungoc
Distinguish text-only output formats and others (.jar...
tree
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 updated references of JOptionPane to JvOptionPane
tree
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commitdiff
2016-11-24
gmungoc
Further tweaks to get tests passing
tree
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commitdiff
2016-11-24
gmungoc
FileFormatI further tweaks, clean compile
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'bug/JAL-2323disulfideOverview' into develop
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'documentation/JAL-2325_release2101' into...
tree
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commitdiff
2016-11-23
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-22
Jim Procter
JAL-2197 changed tooltip for Jnet annotation rows to...
tree
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commitdiff
2016-11-22
tcofoegbu
Merge branch 'bug/JAL-2277_refactorPrintUnwrapped'...
tree
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commitdiff
2016-11-22
tcofoegbu
JAL-2322 added runnable interface to HTMLOutput class...
tree
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commitdiff
2016-11-22
gmungoc
JAL-2277 refactored AlignmentPanel.printUnwrapped to...
tree
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commitdiff
2016-11-21
gmungoc
Merge branch 'develop' into bug/JAL-2323disulfideOverview
tree
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commitdiff
2016-11-17
gmungoc
JAL-2327 disulfide bond abstracted to SequenceFeature...
tree
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commitdiff
2016-11-16
Jim Procter
Merge branch 'features/JAL-1723_sequenceReport' into...
tree
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commitdiff
2016-11-16
tcofoegbu
JAL-2322 JAL-2309 replaced references to isheadless...
tree
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commitdiff
2016-11-16
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-14
tcofoegbu
JAL-2322 Refactored unified architecture for data ...
tree
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commitdiff
2016-11-11
tcofoegbu
JAL-2277 Refactored out duplicated method - printUnwrap...
tree
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commitdiff
2016-11-09
gmungoc
JAL-2295 single constant for "RESNUM" feature name
tree
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commitdiff
2016-11-02
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2282'...
tree
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commitdiff
2016-11-02
gmungoc
JAL-98 JAL-1854 encapsulate 'magic number' threshold...
tree
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commitdiff
2016-11-01
tcofoegbu
JAL-2280 refactored and improved structure file identif...
tree
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commitdiff
2016-11-01
kiramt
JAL-2282 Refactor SequenceAnnotationReport to use refac...
tree
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commitdiff
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