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JAL-2685 score matrix in sysout formatted with sequence row/col numbers
[jalview.git]
/
src
/
jalview
/
2017-06-08
gmungoc
JAL-2386 JAL-2570 use ResidueShader copy constructor...
bug/JAL-2386groupConservationColouring
tree
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commitdiff
2017-06-08
kiramt
Merge branch 'bug/JAL-2586' into develop
tree
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commitdiff
2017-06-08
kiramt
JAL-2586 Clarification to URL link code
bug/JAL-2586
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 Made redraw flag in OverviewRenderer volatile
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 made redraw volatile
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 Refactor HiddenColumns to use ArrayList instea...
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 More HiddenColumns refactoring. Tests passing.
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Further refactoring (still incomplete)
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 More refactoring (incomplete)
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 updated HiddenColumns::findHiddenRegionPositio...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 ported to applet
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Overview changes ported to applet
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 More rationalising of hiddencols
tree
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commitdiff
2017-06-07
gmungoc
JAL-2386 ensure group conservation shading is applied...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Overview window update interrupts
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Increased granularity of overview panel update...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
tree
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commitdiff
2017-06-06
kiramt
JAL-2591 Removed getHiddenRegions()==null checks which...
tree
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commitdiff
2017-06-06
kiramt
JAL-2591 Added readwrite locking on HiddenColumns
tree
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commitdiff
2017-06-06
gmungoc
JAL-2589 correct colour for Gap in Score and User Defin...
tree
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commitdiff
2017-06-06
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2576'...
tree
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commitdiff
2017-06-05
Jim Procter
JAL-2590 patch for rendering eggnog trees with polytomi...
tree
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commitdiff
2017-06-05
Jim Procter
Merge branch 'bug/JAL-2576' into develop
tree
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commitdiff
2017-06-05
kiramt
JAL-2586 Checkstyle flagged fix of unintended fall...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2228 java 1.7 compliance
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 only hide/show columns intersecting with curre...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 get bitset representing hidden columns
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 use HiddenColumns.hideMarkedBits and take...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 method taking a BitSet for hiding columns
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 bug fix - BitSet.set is [start,end+1)
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 ‘Hide Insertions’ now operates on selection...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 SequenceI.getInsertionsAsBits for convenient...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 comment about IDs being lost if they resembl...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 recognise ENS…P peptide IDs and make two getPa...
tree
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commitdiff
2017-06-02
Jim Procter
Merge branch 'bug/JAL-2578' into develop
tree
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commitdiff
2017-06-02
Jim Procter
Merge branch 'bug/JAL-2577' into develop
tree
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commitdiff
2017-06-02
Jim Procter
Merge branch 'features/JAL-2228_featureSetCounts_minRan...
tree
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commitdiff
2017-06-02
tcofoegbu
JAL-2473 revised default minimum dimension for Alignmen...
tree
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commitdiff
2017-06-02
Jim Procter
JAL-2228 always create zero score annotations, since...
tree
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commitdiff
2017-06-02
Jim Procter
JAL-2228 always set minimum for count to zero for annot...
tree
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commitdiff
2017-06-02
kiramt
JAL-2576 Proposed fix
bug/JAL-2576
tree
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commitdiff
2017-06-02
kiramt
JAL-2577 Don't allow viewport ranges below 0. Unit...
bug/JAL-2577
tree
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commitdiff
2017-06-02
kiramt
JAL-2578 Moved hidden columns reveal to before selectio...
bug/JAL-2578
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
Jim Procter
Merge branch 'JAL-2571' into develop
tree
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commitdiff
2017-05-31
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
tree
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commitdiff
2017-05-31
gmungoc
JAL-2547 handle contact features 'around' a gap correctly
tree
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commitdiff
2017-05-30
kiramt
JAL-2573 Fixes for alignment < viewport width, and...
JAL-2571
tree
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commitdiff
2017-05-30
gmungoc
JAL-2547 tooltip/AmendFeatures on gap straddled by...
tree
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commitdiff
2017-05-30
kiramt
JAL-2571 Corrected alignment width/height checks to...
tree
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commitdiff
2017-05-30
gmungoc
JAL-2570 don't zap group colour scheme when mapping...
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2034contextchange' into develop
tree
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commitdiff
2017-05-29
tcofoegbu
JAL-1648 improvement on finder searchbox keyboard contr...
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
2017-05-29
tcofoegbu
JAL-1648 code fix - enter key should pick selected...
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2536' into develop
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2536 tweak javadoc wording
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2517cancelAppletColour' into...
tree
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commitdiff
2017-05-27
Jim Procter
Merge branch 'bug/JAL-2491' into develop
tree
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commitdiff
2017-05-27
Jim Procter
Merge branch 'bug/JAL-2547tooltipOnGap' into develop
tree
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commitdiff
2017-05-27
Jim Procter
JAL-2526 test and documentation for SeqPanel.setStatus...
tree
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commitdiff
2017-05-27
Jim Procter
JAL-2562 javadoc TODO
tree
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commitdiff
2017-05-26
kiramt
JAL-2491 Missed port to applet from JAL-1691
bug/JAL-2491
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
2017-05-26
tcofoegbu
Merge branch 'features/JAL-1648_cache_user_inputs'...
tree
|
commitdiff
2017-05-26
tcofoegbu
JAL-1648 fix to transfer focus back to alignment frame...
tree
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commitdiff
2017-05-25
Jim Procter
Merge branch 'develop' into features/JAL-1648_cache_use...
tree
|
commitdiff
2017-05-25
kiramt
JAl-2034 Ported to applet
bug/JAL-2034contextchange
tree
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commitdiff
2017-05-25
kiramt
JAL-2034 don't update overview after click without...
tree
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commitdiff
2017-05-25
kiramt
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
tree
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commitdiff
2017-05-24
kiramt
JAL-2551 Fix to group colouring when group extent is...
bug/JAL-2551
tree
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commitdiff
2017-05-24
kiramt
JAL-2034 Added isDefined flag to SequenceGroup
tree
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commitdiff
2017-05-23
Jim Procter
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2547 don't show features in tooltip over a gap
bug/JAL-2547tooltipOnGap
tree
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commitdiff
2017-05-22
gmungoc
JAL-2504 update the right feature colour when creating...
bug/JAL-2510amendFeatures
tree
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commitdiff
2017-05-22
gmungoc
JAL-2544 check feature overlaps selection region
tree
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commitdiff
2017-05-22
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2256'...
tree
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commitdiff
2017-05-22
Jim Procter
JAL-2418 patch build - broken htsjdk import
tree
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commitdiff
2017-05-19
gmungoc
JAL-2526 removed redundant call to Sequence.findPosition()
tree
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commitdiff
2017-05-18
Jim Procter
JAL-2388 return empty hidden columns for fully visible...
tree
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commitdiff
2017-05-18
kiramt
JAL-2256 Corrected AllCols/Rows iterator behaviour...
bug/JAL-2256
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'bug/JAL-2510amendFeatures' into develop
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'features/JAL-2447experimentalFlag' into...
tree
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commitdiff
2017-05-17
gmungoc
JAL-2504 use (and update) defaults for new feature...
tree
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commitdiff
2017-05-17
gmungoc
Merge branch 'develop' into bug/JAL-2510amendFeatures
tree
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commitdiff
2017-05-16
kiramt
JAL-2536 Overview window sizing not subject to min...
bug/JAL-2536
tree
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commitdiff
2017-05-16
gmungoc
JAL-2517 restore complex colour scheme on Cancel in...
bug/JAL-2517cancelAppletColour
tree
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commitdiff
2017-05-16
gmungoc
JAL-2403 simplify instantiation / configuration of...
tree
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commitdiff
2017-05-16
kiramt
JAL-2522 Missed fix to applet
tree
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commitdiff
2017-05-16
kiramt
JAL-2388 Rationalised hashCode method in HiddenColumns
tree
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commitdiff
2017-05-16
kiramt
Merge branch 'develop' into bug/JAL-2491
tree
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commitdiff
2017-05-16
kiramt
JAL-2491 Better merge
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
gmungoc
JAL-2532 new feature types and colour changes from...
tree
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commitdiff
next