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JAL-2826 added action performed for hiding collapsed sequences
[jalview.git]
/
src
/
jalview
/
io
/
2018-01-18
kjvdheide
JAL-2805 disabled Nexus file identification(as its...
tree
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commitdiff
2018-01-17
kjvdheide
JAL-281 added initialising trees to FileLoader if filef...
tree
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commitdiff
2018-01-17
kjvdheide
JAL-281 added isTreeFile() boolean
tree
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commitdiff
2018-01-10
kjvdheide
JAL-1953 named various threads
tree
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commitdiff
2018-01-09
kjvdheide
JAL-2805 file identifying lines are turned to lowercase...
tree
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commitdiff
2018-01-09
kjvdheide
JAL-2805 broke off the phylogenetic file formats into...
tree
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commitdiff
2018-01-06
kjvdheide
JAL-281 first line also checked for PhyloXML identification
tree
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commitdiff
2018-01-04
kjvdheide
JAL-281 ForesterParser factory methods added
tree
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commitdiff
2017-12-21
kjvdheide
JAL-281 added file identify criteria for PhyloXML and...
tree
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commitdiff
2017-12-20
kjvdheide
JAL-281 split up TreeParser into separate format parsers
tree
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commitdiff
2017-12-19
kjvdheide
JAL-281 added phyloxml and nexus to jalview fileformats
tree
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commitdiff
2017-12-05
kjvdheide
JAL-2847 Strings for the various tree databases added
tree
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commitdiff
2017-12-05
kjvdheide
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-11-30
Jim Procter
JAL-2849 fix
tree
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commitdiff
2017-11-20
kjvdheide
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2017-11-13
Jim Procter
Merge branch 'imp/JAL-2810_ftsIDtab' into develop
tree
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commitdiff
2017-11-13
gmungoc
JAL-2176 removed unused Sequence.index
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2804 kludge method to test if last key event handle...
tree
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commitdiff
2017-10-26
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'feature/JAL-2488finalize' into develop
tree
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commitdiff
2017-10-26
kjvdheide
named most Jalview threads
tree
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commitdiff
2017-10-24
kjvdheide
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-10-12
Jim Procter
JAL-2773 add new flag to paintAlignment(updateOverview...
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
tree
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commitdiff
2017-09-27
kjvanderheide
proof of concept for passing tree data to archaeopteryx
tree
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commitdiff
2017-09-01
gmungoc
JAL-2488 remove finalize methods
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Hidden columns regions can be output to string...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
tree
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commitdiff
2017-06-02
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-01
Jim Procter
Merge branch 'features/JAL-1648_cache_user_inputs'...
tree
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commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
tree
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commitdiff
2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 Improvement to re-instate storing recently...
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 fix to prevent files loaded from the system...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
tree
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commitdiff
2017-05-25
Jim Procter
Merge branch 'develop' into features/JAL-1648_cache_use...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2490 test coverage of empty and null feature group...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 find features for export as GFF, JAL-2548...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 tidy code and tests for feature export in...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 improved lookup of features for Export Feature...
tree
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commitdiff
2017-05-22
gmungoc
JAL-2505 use setter not direct access to sf.description
tree
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commitdiff
2017-05-22
gmungoc
JAL-2543 identify as JSON before HTML
tree
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commitdiff
2017-05-22
gmungoc
JAL-2546 JAL-2490 efficient lookup of features, correct...
tree
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commitdiff
2017-05-19
gmungoc
JAL-2490 refactored test for 'hasFeatures'
tree
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commitdiff
2017-05-16
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 refactor to set type and group in SequenceFeat...
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 capitalisation for annotation lines generated...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 case insensitive recognition of annotation...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2535 quick hack to implement posterior probabilitie...
tree
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commitdiff
2017-05-15
tcofoegbu
JAL-2520 improvement to use URL leaf name for creating...
tree
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commitdiff
2017-05-15
tcofoegbu
JAL-2533 improvement to prune off file extension when...
tree
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commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2509 JAL-2507 allow whitespace in GS annotation...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2509 extend set of brackets recognised by stockholm...
tree
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commitdiff
2017-05-09
tcofoegbu
JAL-2520 improvement to download and update structure...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 output secondary structure regardless of prese...
tree
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commitdiff
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
tree
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commitdiff
2017-05-08
gmungoc
JAL-2505 set type,desc,begin,end,group,score in Sequenc...
tree
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commitdiff
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
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