jalview.git
7 years agoMerge branch 'bug/JAL-2704gapColourFading' into documentation/JAL-2675_release2102b1
Jim Procter [Mon, 4 Sep 2017 11:10:09 +0000 (12:10 +0100)]
Merge branch 'bug/JAL-2704gapColourFading' into documentation/JAL-2675_release2102b1

7 years agoMerge branch 'releases/Release_2_10_2b1_Branch' of http://source.jalview.org/git...
Jim Procter [Mon, 4 Sep 2017 09:31:26 +0000 (10:31 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_2b1_Branch

7 years agoMerge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
Jim Procter [Mon, 4 Sep 2017 07:27:15 +0000 (08:27 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch

7 years agoJAL-2611 reinstated missed commit
kiramt [Mon, 4 Sep 2017 07:14:38 +0000 (08:14 +0100)]
JAL-2611 reinstated missed commit

7 years agoJAL-2675 release notes
Jim Procter [Sun, 3 Sep 2017 17:50:16 +0000 (18:50 +0100)]
JAL-2675 release notes

7 years agoMerge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 17:27:09 +0000 (18:27 +0100)]
Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1

7 years agoMerge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 17:06:24 +0000 (18:06 +0100)]
Merge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1

7 years agoJAL-2672 JAL-2665 release notes. Also note this merge does not resolve JAL-2673
Jim Procter [Sun, 3 Sep 2017 16:35:01 +0000 (17:35 +0100)]
JAL-2672 JAL-2665 release notes. Also note this merge does not resolve JAL-2673

7 years agoMerge branch 'bug/JAL-2665-2.10.2b' into documentation/JAL-2675_release2102b1 bug/JAL-2673_mergewithproblem
Jim Procter [Sun, 3 Sep 2017 16:12:49 +0000 (17:12 +0100)]
Merge branch 'bug/JAL-2665-2.10.2b' into documentation/JAL-2675_release2102b1

7 years agoJAL-2664 JAL-2527 signs for release
Jim Procter [Sun, 3 Sep 2017 14:29:56 +0000 (15:29 +0100)]
JAL-2664 JAL-2527 signs for release

7 years agoMerge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch
Jim Procter [Sun, 3 Sep 2017 12:37:54 +0000 (13:37 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2b1_Branch

7 years agoJAL-2588 overview tab docs, whats new and release notes
Jim Procter [Sun, 3 Sep 2017 12:35:45 +0000 (13:35 +0100)]
JAL-2588 overview tab docs, whats new and release notes

7 years agoJAL-2675 typo
Jim Procter [Sun, 3 Sep 2017 12:18:18 +0000 (13:18 +0100)]
JAL-2675 typo

7 years agoMerge branch 'feature/JAL-2527' into documentation/JAL-2675_release2102b1
Jim Procter [Sun, 3 Sep 2017 11:26:58 +0000 (12:26 +0100)]
Merge branch 'feature/JAL-2527' into documentation/JAL-2675_release2102b1

7 years agoJAL-2681 release notes
Jim Procter [Sun, 3 Sep 2017 10:55:42 +0000 (11:55 +0100)]
JAL-2681 release notes

7 years agoMerge branch 'features/JAL-2681_duplicatecrossrefs' into documentation/JAL-2675_relea...
Jim Procter [Sun, 3 Sep 2017 10:38:15 +0000 (11:38 +0100)]
Merge branch 'features/JAL-2681_duplicatecrossrefs' into documentation/JAL-2675_release2102b1

7 years agoJAL-2527 Additional test feature/JAL-2527
kiramt [Fri, 1 Sep 2017 06:37:10 +0000 (07:37 +0100)]
JAL-2527 Additional test

7 years agoJAL-2527 Unit test for group colouring
kiramt [Fri, 1 Sep 2017 06:22:55 +0000 (07:22 +0100)]
JAL-2527 Unit test for group colouring

7 years agoJAL-2527 Unit test
kiramt [Thu, 31 Aug 2017 13:27:50 +0000 (14:27 +0100)]
JAL-2527 Unit test

7 years agoJAL-2527 Fix typo
kiramt [Thu, 31 Aug 2017 11:06:41 +0000 (12:06 +0100)]
JAL-2527 Fix typo

7 years agoJAL-2527 Updated Spanish, adjusted UI so Spanish fits
kiramt [Thu, 31 Aug 2017 11:04:39 +0000 (12:04 +0100)]
JAL-2527 Updated Spanish, adjusted UI so Spanish fits

7 years agoJAL-2527 Updates following code review
kiramt [Thu, 31 Aug 2017 10:46:14 +0000 (11:46 +0100)]
JAL-2527 Updates following code review

7 years agoJAL-2704 unit test for Above PID gap colour, simplified findColour() bug/JAL-2704gapColourFading
gmungoc [Thu, 31 Aug 2017 07:47:05 +0000 (08:47 +0100)]
JAL-2704 unit test for Above PID gap colour, simplified findColour()

7 years agoJAL-2704 don't shade gap colour for PID/conservation
gmungoc [Wed, 30 Aug 2017 16:31:29 +0000 (17:31 +0100)]
JAL-2704 don't shade gap colour for PID/conservation

7 years agoJAL-2527 Code comments, tidy
kiramt [Wed, 30 Aug 2017 12:28:40 +0000 (13:28 +0100)]
JAL-2527 Code comments, tidy

7 years agoJAL-2527 Added default setting/resetting and first pass at Spanish
kiramt [Wed, 30 Aug 2017 12:22:47 +0000 (13:22 +0100)]
JAL-2527 Added default setting/resetting and first pass at Spanish

7 years agoJAL-2527 Wired up cached values to overview
kiramt [Wed, 30 Aug 2017 09:59:38 +0000 (10:59 +0100)]
JAL-2527 Wired up cached values to overview

7 years agoMerge remote-tracking branch 'origin/feature/2588' into feature/JAL-2527
kiramt [Wed, 30 Aug 2017 08:30:11 +0000 (09:30 +0100)]
Merge remote-tracking branch 'origin/feature/2588' into feature/JAL-2527

Conflicts:
src/jalview/renderer/OverviewRenderer.java

7 years agoMerge branch 'feature/JAL-2664' into feature/JAL-2527
kiramt [Wed, 30 Aug 2017 07:11:40 +0000 (08:11 +0100)]
Merge branch 'feature/JAL-2664' into feature/JAL-2527

7 years agoJAL-2664 Updates following review feature/JAL-2664
kiramt [Tue, 29 Aug 2017 15:27:40 +0000 (16:27 +0100)]
JAL-2664 Updates following review

7 years agoJAL-2527 Added overview prefs - don't get picked up by overview yet
kiramt [Tue, 29 Aug 2017 13:55:53 +0000 (14:55 +0100)]
JAL-2527 Added overview prefs - don't get picked up by overview yet

7 years agoJAL-2665 OOM checks just in case bug/JAL-2665-2.10.2b
kiramt [Tue, 29 Aug 2017 10:59:54 +0000 (11:59 +0100)]
JAL-2665 OOM checks just in case

7 years agoJAL-2665 Corrected to draw selections for wrapped printing
kiramt [Tue, 29 Aug 2017 08:28:29 +0000 (09:28 +0100)]
JAL-2665 Corrected to draw selections for wrapped printing

7 years agoJAL-2527 Started adding overview preferences
kiramt [Mon, 28 Aug 2017 15:38:03 +0000 (16:38 +0100)]
JAL-2527 Started adding overview preferences

7 years agoMerge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'
kiramt [Mon, 28 Aug 2017 11:15:35 +0000 (12:15 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'
into bug/JAL-2665-2.10.2b

Conflicts:
src/jalview/gui/SeqCanvas.java

7 years agoJAL-2665 Changes for review comments; printing with selgroup working bug/JAL-2665
kiramt [Mon, 28 Aug 2017 10:56:33 +0000 (11:56 +0100)]
JAL-2665 Changes for review comments; printing with selgroup working

7 years agoJAL-2691 assert chains are recovered by AAStructureBindingModel bug/JAL-2691_nomultimermapping
Jim Procter [Sun, 27 Aug 2017 14:50:03 +0000 (15:50 +0100)]
JAL-2691 assert chains are recovered by AAStructureBindingModel

7 years agoJAL-2691 catchall if passed dataset sequences (tests only)
Jim Procter [Sun, 27 Aug 2017 14:49:02 +0000 (15:49 +0100)]
JAL-2691 catchall if passed dataset sequences (tests only)

7 years agoJAL-2693 TODO comments
Jim Procter [Sun, 27 Aug 2017 13:25:01 +0000 (14:25 +0100)]
JAL-2693 TODO comments

7 years agoJAL-2691 discover any existing chain mappings for a structure view
Jim Procter [Sun, 27 Aug 2017 13:23:06 +0000 (14:23 +0100)]
JAL-2691 discover any existing chain mappings for a structure view

7 years agoJAL-2691 cached view combo box value javadoc
Jim Procter [Sun, 27 Aug 2017 13:17:30 +0000 (14:17 +0100)]
JAL-2691 cached view combo box value javadoc

7 years agoJAL-2587 Removed annoying double repaint on hide insertions
kiramt [Fri, 25 Aug 2017 13:13:48 +0000 (14:13 +0100)]
JAL-2587 Removed annoying double repaint on hide insertions

7 years agoJAL-2587 Update overview progress bar while drawing rows too
kiramt [Fri, 25 Aug 2017 11:54:05 +0000 (12:54 +0100)]
JAL-2587 Update overview progress bar while drawing rows too

7 years agoJAL-2587 Progress bar sizing tweaks
kiramt [Fri, 25 Aug 2017 08:41:25 +0000 (09:41 +0100)]
JAL-2587 Progress bar sizing tweaks

7 years agoJAL-2587 Made progress bar display before overview calc starts
kiramt [Fri, 25 Aug 2017 07:03:52 +0000 (08:03 +0100)]
JAL-2587 Made progress bar display before overview calc starts

7 years agoJAL-2435 last lost commit e926a5d redone
gmungoc [Wed, 23 Aug 2017 13:42:32 +0000 (14:42 +0100)]
JAL-2435 last lost commit e926a5d redone

7 years agoJAL-1551 formatting
Jim Procter [Tue, 22 Aug 2017 21:42:11 +0000 (22:42 +0100)]
JAL-1551 formatting

7 years agoJAL-2681 cross-ref selection for targeted debugging
Jim Procter [Tue, 22 Aug 2017 21:13:07 +0000 (22:13 +0100)]
JAL-2681 cross-ref selection for targeted debugging

7 years agoJAL-2681 source formatting
Jim Procter [Tue, 22 Aug 2017 21:12:07 +0000 (22:12 +0100)]
JAL-2681 source formatting

7 years agoJAL-2681 canonicalise DB source before fetching to avoid fetching the same ref !
Jim Procter [Tue, 22 Aug 2017 21:10:27 +0000 (22:10 +0100)]
JAL-2681 canonicalise DB source before fetching to avoid fetching the same ref !

7 years agoJAL-2681 formatting
Jim Procter [Tue, 22 Aug 2017 21:09:44 +0000 (22:09 +0100)]
JAL-2681 formatting

7 years agoMerge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 21 Aug 2017 13:47:22 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into releases/Release_2_10_2_Branch

7 years agoJAL-2675 typo in what's new href
Jim Procter [Mon, 21 Aug 2017 13:46:45 +0000 (14:46 +0100)]
JAL-2675 typo in what's new href

7 years agoJAL-2588 don’t test char==gap until we know the shader won’t colour gaps itself feature/2588
Jim Procter [Mon, 21 Aug 2017 13:22:52 +0000 (14:22 +0100)]
JAL-2588 don’t test char==gap until we know the shader won’t colour gaps itself

7 years agoJAL-2588 field on overview colour finder for default gap colour
Jim Procter [Mon, 21 Aug 2017 13:21:58 +0000 (14:21 +0100)]
JAL-2588 field on overview colour finder for default gap colour

7 years agoJAL-2588 JAL-2603 JAL-2610 release notes and docs
Jim Procter [Fri, 18 Aug 2017 15:34:03 +0000 (16:34 +0100)]
JAL-2588 JAL-2603 JAL-2610 release notes and docs

7 years agoMerge branch 'feature/2588' into merge/develop_feature/2588_JAL-2588
Jim Procter [Fri, 18 Aug 2017 14:38:20 +0000 (15:38 +0100)]
Merge branch 'feature/2588' into merge/develop_feature/2588_JAL-2588

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:17:50 +0000 (14:17 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2675 bump version for branch to 2.10.2b1
Jim Procter [Fri, 18 Aug 2017 13:15:40 +0000 (14:15 +0100)]
JAL-2675 bump version for branch to 2.10.2b1

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Fri, 18 Aug 2017 13:14:17 +0000 (14:14 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-1551 formatting
Jim Procter [Fri, 18 Aug 2017 13:13:28 +0000 (14:13 +0100)]
JAL-1551 formatting

7 years agoJAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest...
Jim Procter [Fri, 18 Aug 2017 13:08:03 +0000 (14:08 +0100)]
JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.

7 years agoMerge remote-tracking branch 'origin/develop' into feature/JAL-2664
kiramt [Fri, 18 Aug 2017 10:53:23 +0000 (11:53 +0100)]
Merge remote-tracking branch 'origin/develop' into feature/JAL-2664

7 years agoJAL-2664 Adjusted colour of hidden cols/seqs
kiramt [Fri, 18 Aug 2017 10:44:18 +0000 (11:44 +0100)]
JAL-2664 Adjusted colour of hidden cols/seqs

7 years agoJAL-2664 Correct colouring for rows
kiramt [Fri, 18 Aug 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2664 Correct colouring for rows

7 years agoMerge remote-tracking branch 'origin/develop' into bug/JAL-2665
kiramt [Fri, 18 Aug 2017 08:19:58 +0000 (09:19 +0100)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2665

7 years agoJAL-2665 Comments
kiramt [Fri, 18 Aug 2017 08:13:57 +0000 (09:13 +0100)]
JAL-2665 Comments

7 years agoJAL-2665 Refactoring (and side-effect fix for JAL-2672)
kiramt [Fri, 18 Aug 2017 08:03:44 +0000 (09:03 +0100)]
JAL-2665 Refactoring (and side-effect fix for JAL-2672)

7 years agoJAL-2665 tidies
kiramt [Fri, 18 Aug 2017 06:50:05 +0000 (07:50 +0100)]
JAL-2665 tidies

7 years agoJAL-2665 Code tidies
kiramt [Thu, 17 Aug 2017 15:49:49 +0000 (16:49 +0100)]
JAL-2665 Code tidies

7 years agoJAL-2665 Fixed wrapped mode group over >1 panel; and hidden cols
kiramt [Thu, 17 Aug 2017 14:16:28 +0000 (15:16 +0100)]
JAL-2665 Fixed wrapped mode group over >1 panel; and hidden cols

7 years agoJAL-2418 ahem - correct year for what's new releases/Release_2_10_2_Branch
Jim Procter [Thu, 17 Aug 2017 12:07:53 +0000 (13:07 +0100)]
JAL-2418 ahem - correct year for what's new

7 years agoJAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to...
Jim Procter [Thu, 17 Aug 2017 11:37:50 +0000 (12:37 +0100)]
JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9

7 years agoJAL-2418 JAL-2116 make sure java 8,7 vm args are also listed
Jim Procter [Thu, 17 Aug 2017 10:41:33 +0000 (11:41 +0100)]
JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed

7 years agoJAL-2665 partial fix for selection running over 2 wrapped panels
kiramt [Thu, 17 Aug 2017 10:23:51 +0000 (11:23 +0100)]
JAL-2665 partial fix for selection running over 2 wrapped panels

7 years agoJAL-2665 Correct position of selection switching from wrap to normal
kiramt [Thu, 17 Aug 2017 08:02:34 +0000 (09:02 +0100)]
JAL-2665 Correct position of selection switching from wrap to normal

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 22:24:25 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 22:24:13 +0000 (23:24 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 formatting
Jim Procter [Wed, 16 Aug 2017 22:23:59 +0000 (23:23 +0100)]
JAL-2418 formatting

7 years agoJAL-2418 occupancy row in What’s New
Jim Procter [Wed, 16 Aug 2017 22:23:53 +0000 (23:23 +0100)]
JAL-2418 occupancy row in What’s New

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 21:37:37 +0000 (22:37 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoJAL-2418 add GPL to main sources
Jim Procter [Wed, 16 Aug 2017 21:30:21 +0000 (22:30 +0100)]
JAL-2418 add GPL to main sources

7 years agoJAL-2418 source formatting
Jim Procter [Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)]
JAL-2418 source formatting

7 years agoMerge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 20:52:55 +0000 (21:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 20:52:36 +0000 (21:52 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 mirror fonts option doc tweak
Jim Procter [Wed, 16 Aug 2017 20:52:07 +0000 (21:52 +0100)]
JAL-2418 mirror fonts option doc tweak

7 years agoJAL-2665 Working with hidden columns
kiramt [Wed, 16 Aug 2017 19:53:45 +0000 (20:53 +0100)]
JAL-2665 Working with hidden columns

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 19:17:43 +0000 (20:17 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 whats new for 2.10.2
Jim Procter [Wed, 16 Aug 2017 19:17:03 +0000 (20:17 +0100)]
JAL-2418 whats new for 2.10.2

7 years agoJAL-2418 reclassify some issues to features/bugs resolved
Jim Procter [Wed, 16 Aug 2017 19:16:52 +0000 (20:16 +0100)]
JAL-2418 reclassify some issues to features/bugs resolved

7 years agoJAL-2418 typos in release notes
Jim Procter [Wed, 16 Aug 2017 18:23:33 +0000 (19:23 +0100)]
JAL-2418 typos in release notes

7 years agoJAL-2418 check groovy script one-liners for restoring legacy score model behaviour
Jim Procter [Wed, 16 Aug 2017 18:16:08 +0000 (19:16 +0100)]
JAL-2418 check groovy script one-liners for restoring legacy score model behaviour

7 years agoJAL-2665 Added hidden columns group selection - almost working
kiramt [Wed, 16 Aug 2017 15:34:32 +0000 (16:34 +0100)]
JAL-2665 Added hidden columns group selection - almost working

7 years agoJAL-2665 Selecting on wrapped alignments
kiramt [Wed, 16 Aug 2017 14:51:55 +0000 (15:51 +0100)]
JAL-2665 Selecting on wrapped alignments

7 years agoJAL-2556 start to account for wrapped alignments
kiramt [Wed, 16 Aug 2017 13:25:03 +0000 (14:25 +0100)]
JAL-2556 start to account for wrapped alignments

7 years agoJAL-2665 Tidy
kiramt [Wed, 16 Aug 2017 12:28:13 +0000 (13:28 +0100)]
JAL-2665 Tidy

7 years agoJAL-2665 fix resize
kiramt [Wed, 16 Aug 2017 11:20:16 +0000 (12:20 +0100)]
JAL-2665 fix resize

7 years agoJAL-2556 Code tidy
kiramt [Wed, 16 Aug 2017 10:40:54 +0000 (11:40 +0100)]
JAL-2556 Code tidy

7 years agoJAL-2556 Resolved group update on colouring and escape
kiramt [Wed, 16 Aug 2017 10:21:55 +0000 (11:21 +0100)]
JAL-2556 Resolved group update on colouring and escape

7 years agoJAL-2665 Added sequence group update event.
kiramt [Wed, 16 Aug 2017 10:09:39 +0000 (11:09 +0100)]
JAL-2665 Added sequence group update event.