kiramt [Thu, 27 Jul 2017 10:34:37 +0000 (12:34 +0200)]
JAL-2611 Missed merge from JAL-147
kiramt [Sat, 22 Jul 2017 09:18:41 +0000 (11:18 +0200)]
Merge branch 'develop' into feature/JAL-2611
Conflicts:
src/jalview/gui/OverviewPanel.java
src/jalview/viewmodel/OverviewDimensionsHideHidden.java
src/jalview/viewmodel/OverviewDimensionsShowHidden.java
kiramt [Tue, 18 Jul 2017 14:44:30 +0000 (15:44 +0100)]
JAL-2611 unit tests
kiramt [Tue, 18 Jul 2017 13:45:38 +0000 (14:45 +0100)]
JAL-2611 Tidies, initial unit tests
gmungoc [Tue, 18 Jul 2017 13:44:27 +0000 (14:44 +0100)]
JAL-147 don't scroll up beyond startRes = 0
gmungoc [Tue, 18 Jul 2017 12:02:15 +0000 (13:02 +0100)]
JAL-147 corrected calculation of vertical scroll position and max
gmungoc [Tue, 18 Jul 2017 12:01:46 +0000 (13:01 +0100)]
JAL-147 draw up to last position of wrapped alignment!
kiramt [Tue, 18 Jul 2017 11:12:23 +0000 (12:12 +0100)]
JAL-2611 Better
gmungoc [Mon, 17 Jul 2017 15:20:37 +0000 (16:20 +0100)]
Merge branch 'develop' into bug/JAL-147scrollWrappedView
kiramt [Mon, 17 Jul 2017 15:02:03 +0000 (16:02 +0100)]
JAL-2611 Still not happy with behaviour
gmungoc [Mon, 17 Jul 2017 11:25:04 +0000 (12:25 +0100)]
JAL-1648 JAL-2447 Spanish translations
kiramt [Fri, 14 Jul 2017 13:31:51 +0000 (14:31 +0100)]
JAL-2611 First pass, not thrilled with hidden column behaviour
kiramt [Fri, 14 Jul 2017 09:01:25 +0000 (10:01 +0100)]
Merge branch 'feature/JAL-2613' into feature/JAL-2611
Conflicts:
src/jalview/viewmodel/OverviewDimensions.java
kiramt [Fri, 14 Jul 2017 08:59:38 +0000 (09:59 +0100)]
JAL-2611 Pre-merge checkin
kiramt [Fri, 14 Jul 2017 06:59:45 +0000 (07:59 +0100)]
JAL-2611 More unit tests
kiramt [Fri, 14 Jul 2017 06:41:09 +0000 (07:41 +0100)]
JAL-2613 Missed unit test
kiramt [Thu, 13 Jul 2017 15:54:22 +0000 (16:54 +0100)]
JAL-2611 Added overview dimensions test for position in box
kiramt [Thu, 13 Jul 2017 14:52:20 +0000 (15:52 +0100)]
JAL-2613 Unit tests and a fix. Phew.
kiramt [Wed, 12 Jul 2017 13:58:03 +0000 (14:58 +0100)]
JAL-2613 Centre alignment at click point
gmungoc [Thu, 6 Jul 2017 14:59:43 +0000 (15:59 +0100)]
JAL-147 prevent vertical Overview box movement in wrapped mode
gmungoc [Thu, 6 Jul 2017 14:59:09 +0000 (15:59 +0100)]
JAL-147 unit test for hide/show sequences update ViewportRanges
gmungoc [Thu, 6 Jul 2017 14:03:24 +0000 (15:03 +0100)]
JAL-2605 ensure correct scale width calculation
gmungoc [Wed, 5 Jul 2017 12:43:48 +0000 (13:43 +0100)]
JAL-147 don't update overview for column selection (applet)
gmungoc [Wed, 5 Jul 2017 12:37:26 +0000 (13:37 +0100)]
JAL-147 additions to unit test, check for negative array index
gmungoc [Wed, 5 Jul 2017 10:34:50 +0000 (11:34 +0100)]
JAL-147 prevent overview box move up over hidden first sequence
gmungoc [Tue, 4 Jul 2017 15:51:34 +0000 (16:51 +0100)]
JAL-147 revised update of startSeq, endSeq on unhide sequences
gmungoc [Tue, 4 Jul 2017 15:20:03 +0000 (16:20 +0100)]
JAL-147 unit tests added, unused setEndRes removed
gmungoc [Tue, 4 Jul 2017 10:23:32 +0000 (11:23 +0100)]
JAL-147 corrected update of ViewportRanges for show/hide sequences
gmungoc [Tue, 4 Jul 2017 10:05:15 +0000 (11:05 +0100)]
JAL-147 update ViewportRanges height after show/hide sequences
gmungoc [Tue, 4 Jul 2017 09:26:43 +0000 (10:26 +0100)]
JAL-147 remove redundant calls to update overview panel
gmungoc [Tue, 4 Jul 2017 08:35:01 +0000 (09:35 +0100)]
JAL-2608 tidy up OverviewPanel when closed
gmungoc [Tue, 4 Jul 2017 08:12:49 +0000 (09:12 +0100)]
JAL-147 call method that sets visible width when drawing wrapped panel
gmungoc [Tue, 4 Jul 2017 08:12:13 +0000 (09:12 +0100)]
JAL-147 extract local variable for ease of debugging
gmungoc [Mon, 3 Jul 2017 14:39:09 +0000 (15:39 +0100)]
Merge branch 'develop' into bug/JAL-147scrollWrappedView
gmungoc [Mon, 3 Jul 2017 14:27:01 +0000 (15:27 +0100)]
JAL-147 correct width out-by-one drawing ids
gmungoc [Mon, 3 Jul 2017 14:26:33 +0000 (15:26 +0100)]
JAL-147 don't scroll Overview box outside panel dimensions
gmungoc [Mon, 3 Jul 2017 14:25:48 +0000 (15:25 +0100)]
JAL-147 ViewportRanges calculate wrapped vertical scroll position
gmungoc [Mon, 3 Jul 2017 14:17:27 +0000 (15:17 +0100)]
JAL-147 don't draw ScalePanel when in wrapped mode
gmungoc [Mon, 3 Jul 2017 13:54:11 +0000 (14:54 +0100)]
JAL-2034 don't refresh Overview for selection in id panel
gmungoc [Fri, 30 Jun 2017 14:06:50 +0000 (15:06 +0100)]
JAL-2602 unit test added
gmungoc [Fri, 30 Jun 2017 13:49:13 +0000 (14:49 +0100)]
JAL-147 don't page up above origin, repaint ids for scroll in wrapped
mode
gmungoc [Fri, 30 Jun 2017 12:00:56 +0000 (13:00 +0100)]
Merge branch 'bug/JAL-2597' into develop
gmungoc [Fri, 30 Jun 2017 10:48:15 +0000 (11:48 +0100)]
JAL-2602 pulled up identical methods to base class
gmungoc [Fri, 30 Jun 2017 10:44:27 +0000 (11:44 +0100)]
JAL-2602 same fix for applet
Jim Procter [Fri, 30 Jun 2017 08:02:30 +0000 (09:02 +0100)]
Merge branch 'bugs/JAL-2606_broken_jabaws22_IADependency' into develop
Jim Procter [Fri, 30 Jun 2017 08:00:41 +0000 (09:00 +0100)]
JAL-2606 updated IA build for changed dependency due to JAL-2549
gmungoc [Thu, 29 Jun 2017 18:59:08 +0000 (19:59 +0100)]
JAL-147 improved wrapped scrolling (including Overview) with
ViewportRanges
kiramt [Thu, 29 Jun 2017 13:02:45 +0000 (14:02 +0100)]
JAL-2597 Fix and unit test
gmungoc [Thu, 29 Jun 2017 11:20:15 +0000 (12:20 +0100)]
JAL-2605 exclude left/right scale in sequence column calculation
gmungoc [Wed, 28 Jun 2017 14:16:17 +0000 (15:16 +0100)]
Merge branch 'bug/JAL-2600resizeflicker' into develop
kiramt [Wed, 28 Jun 2017 11:49:17 +0000 (12:49 +0100)]
JAL-2600 Tidies
kiramt [Wed, 28 Jun 2017 11:45:50 +0000 (12:45 +0100)]
JAL-2600 updates following review
kiramt [Tue, 27 Jun 2017 13:18:01 +0000 (14:18 +0100)]
JAL-2600 Tidies
kiramt [Tue, 27 Jun 2017 13:16:56 +0000 (14:16 +0100)]
JAL-2600 Abandoned fastpaint for resize; now full repaint, single call
gmungoc [Tue, 27 Jun 2017 13:03:09 +0000 (14:03 +0100)]
JAL-2602 check for null or empty description when copying consensus
kiramt [Tue, 27 Jun 2017 08:36:37 +0000 (09:36 +0100)]
JAL-2600 Add in IdCanvas and checks for 0 size images
kiramt [Tue, 27 Jun 2017 07:12:00 +0000 (08:12 +0100)]
JAL-2600 vertical fast paint too
kiramt [Tue, 27 Jun 2017 06:47:55 +0000 (07:47 +0100)]
JAL-2600 fast painting on resize
kiramt [Mon, 26 Jun 2017 13:33:15 +0000 (14:33 +0100)]
JAL-2600 reinstate original behaviour
gmungoc [Thu, 15 Jun 2017 13:22:11 +0000 (14:22 +0100)]
JAL-2563 test updated for fix
gmungoc [Thu, 15 Jun 2017 13:08:32 +0000 (14:08 +0100)]
Merge branch 'bug/JAL-2386groupConservationColouring' into develop
kiramt [Thu, 15 Jun 2017 10:54:40 +0000 (11:54 +0100)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2591
gmungoc [Thu, 15 Jun 2017 10:34:37 +0000 (11:34 +0100)]
JAL-2418 typos
gmungoc [Thu, 15 Jun 2017 09:26:40 +0000 (10:26 +0100)]
Merge branch 'bug/JAL-2589gapColour' into develop
gmungoc [Mon, 12 Jun 2017 16:11:27 +0000 (17:11 +0100)]
JAL-2577 mirror select/hide by annotation in split frame applet, and on
Cancel
kiramt [Mon, 12 Jun 2017 15:00:20 +0000 (16:00 +0100)]
JAL-2591 Updates following code review
gmungoc [Mon, 12 Jun 2017 09:36:36 +0000 (10:36 +0100)]
JAL-2577 mirror hide/select columns by annotation across split frame
Jim Procter [Sun, 11 Jun 2017 02:24:29 +0000 (12:24 +1000)]
JAL-2418 updated release branch/version and release date before forking release branch
gmungoc [Fri, 9 Jun 2017 14:21:35 +0000 (15:21 +0100)]
JAL-2589 render colour scheme gap colour in overview
gmungoc [Fri, 9 Jun 2017 09:58:52 +0000 (10:58 +0100)]
JAL-2594 avoid stack trace creating feature on gapped region
gmungoc [Thu, 8 Jun 2017 14:19:04 +0000 (15:19 +0100)]
JAL-2386 JAL-2570 use ResidueShader copy constructor in SequenceGroup
copy constructor for 'like but yet unlike' colouring of new group
kiramt [Thu, 8 Jun 2017 14:01:35 +0000 (15:01 +0100)]
Merge branch 'bug/JAL-2586' into develop
kiramt [Thu, 8 Jun 2017 14:01:02 +0000 (15:01 +0100)]
JAL-2586 Clarification to URL link code
kiramt [Thu, 8 Jun 2017 10:38:08 +0000 (11:38 +0100)]
JAL-2591 made redraw volatile
kiramt [Thu, 8 Jun 2017 10:15:28 +0000 (11:15 +0100)]
JAL-2591 Refactor HiddenColumns to use ArrayList instead of Vector
kiramt [Thu, 8 Jun 2017 09:55:52 +0000 (10:55 +0100)]
JAL-2591 More HiddenColumns refactoring. Tests passing.
kiramt [Wed, 7 Jun 2017 17:04:43 +0000 (18:04 +0100)]
JAL-2591 Further refactoring (still incomplete)
kiramt [Wed, 7 Jun 2017 14:32:30 +0000 (15:32 +0100)]
JAL-2591 More refactoring (incomplete)
kiramt [Wed, 7 Jun 2017 10:32:20 +0000 (11:32 +0100)]
JAL-2591 Hidden columns regions can be output to string + test
kiramt [Wed, 7 Jun 2017 09:58:04 +0000 (10:58 +0100)]
JAL-2591 updated HiddenColumns::findHiddenRegionPositions + test
kiramt [Wed, 7 Jun 2017 09:25:18 +0000 (10:25 +0100)]
JAL-2591 Overview changes ported to applet
kiramt [Wed, 7 Jun 2017 09:25:03 +0000 (10:25 +0100)]
JAL-2591 More rationalising of hiddencols
gmungoc [Wed, 7 Jun 2017 09:22:24 +0000 (10:22 +0100)]
JAL-2386 ensure group conservation shading is applied from slider
kiramt [Wed, 7 Jun 2017 07:14:48 +0000 (08:14 +0100)]
JAL-2591 Increased granularity of overview panel update checks
kiramt [Wed, 7 Jun 2017 06:58:34 +0000 (07:58 +0100)]
JAL-2591 simplifying hidden columns usage
kiramt [Tue, 6 Jun 2017 14:56:04 +0000 (15:56 +0100)]
JAL-2591 Removed getHiddenRegions()==null checks which are always false
kiramt [Tue, 6 Jun 2017 14:44:04 +0000 (15:44 +0100)]
JAL-2591 Added readwrite locking on HiddenColumns
gmungoc [Tue, 6 Jun 2017 14:00:25 +0000 (15:00 +0100)]
JAL-2589 correct colour for Gap in Score and User Defined schemes
kiramt [Tue, 6 Jun 2017 06:35:27 +0000 (07:35 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2576' into bug/JAL-2591
Jim Procter [Mon, 5 Jun 2017 20:53:25 +0000 (21:53 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 5 Jun 2017 20:51:05 +0000 (21:51 +0100)]
JAL-2590 release notes
Jim Procter [Mon, 5 Jun 2017 20:49:36 +0000 (21:49 +0100)]
Merge branch 'bug/JAL-2590' into develop
Jim Procter [Mon, 5 Jun 2017 20:49:14 +0000 (21:49 +0100)]
JAL-2590 patch for rendering eggnog trees with polytomies (also see
Jim Procter [Mon, 5 Jun 2017 20:06:40 +0000 (21:06 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 5 Jun 2017 20:06:22 +0000 (21:06 +0100)]
JAL-2576 release notes
Jim Procter [Mon, 5 Jun 2017 19:44:23 +0000 (20:44 +0100)]
Merge branch 'bug/JAL-2576' into develop
Jim Procter [Mon, 5 Jun 2017 19:41:34 +0000 (20:41 +0100)]
Merge branch 'bug/JAL-2586' into develop
kiramt [Mon, 5 Jun 2017 13:19:58 +0000 (14:19 +0100)]
JAL-2586 Checkstyle flagged fix of unintended fall through
kiramt [Mon, 5 Jun 2017 06:51:49 +0000 (07:51 +0100)]
JAL-2571 Missed (alwaysRun=true) for @BeforeMethod
Jim Procter [Sun, 4 Jun 2017 15:12:13 +0000 (16:12 +0100)]
JAL-2228 java 1.7 compliance
git://source.jalview.org / jalview.git / log