kiramt [Wed, 15 Nov 2017 16:05:18 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Wed, 15 Nov 2017 13:23:00 +0000 (13:23 +0000)]
JAL-2811 Updated following review
kiramt [Wed, 15 Nov 2017 08:47:47 +0000 (08:47 +0000)]
JAL-2831 ported to applet
kiramt [Tue, 14 Nov 2017 19:36:53 +0000 (19:36 +0000)]
JAL-2831 tidies and tests
kiramt [Tue, 14 Nov 2017 16:03:47 +0000 (16:03 +0000)]
JAL-2831 tidy
kiramt [Tue, 14 Nov 2017 14:59:52 +0000 (14:59 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 14:56:37 +0000 (14:56 +0000)]
JAL-2811 Changed to overlay on via graphics context, not separate image
kiramt [Tue, 14 Nov 2017 14:10:30 +0000 (14:10 +0000)]
JAL-2811 Missed commit
kiramt [Tue, 14 Nov 2017 13:43:40 +0000 (13:43 +0000)]
JAL-2811 Made it work for hidden columns/seqs too
kiramt [Tue, 14 Nov 2017 12:11:21 +0000 (12:11 +0000)]
JAL-2831 Attempt at cursor fix for wrapped mode
kiramt [Tue, 14 Nov 2017 11:12:55 +0000 (11:12 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 10:33:33 +0000 (10:33 +0000)]
JAL-2831 deal with hidden cols and seqs in new cursor code
kiramt [Tue, 14 Nov 2017 10:15:46 +0000 (10:15 +0000)]
JAL-2831 Added move viewport event and set up cursor code to use it
kiramt [Tue, 14 Nov 2017 09:30:31 +0000 (09:30 +0000)]
Merge branch 'imp/JAL-2774' into bug/JAL-2831
kiramt [Mon, 13 Nov 2017 19:40:06 +0000 (19:40 +0000)]
JAL-2811 Tidy
kiramt [Mon, 13 Nov 2017 16:42:20 +0000 (16:42 +0000)]
JAl-2811 Working for wrapped panels too
kiramt [Mon, 13 Nov 2017 15:53:12 +0000 (15:53 +0000)]
JAL-2811 Add layer for cursor in SeqCanvas
gmungoc [Mon, 13 Nov 2017 12:02:43 +0000 (12:02 +0000)]
JAL-2679 example accession changed to
CAD01290
Jim Procter [Wed, 8 Nov 2017 17:02:42 +0000 (17:02 +0000)]
Merge branch 'bug/JAL-2742' into develop
Jim Procter [Wed, 8 Nov 2017 17:02:06 +0000 (17:02 +0000)]
Revert "JAL-2742 release notes - pending confirmation that there was impact to user"
-- no impact so won't include development detail in release notes.
This reverts commit
ba70dbddc08876d8d72bb303823f683b65bf13c7.
Jim Procter [Wed, 8 Nov 2017 16:57:14 +0000 (16:57 +0000)]
JAL-2225 release note
Jim Procter [Wed, 8 Nov 2017 16:52:03 +0000 (16:52 +0000)]
Merge branch 'bug/JAL-2225mapMultipleChains' into develop
Jim Procter [Wed, 8 Nov 2017 15:21:13 +0000 (15:21 +0000)]
Merge branch 'develop' into bug/JAL-2225mapMultipleChains
Jim Procter [Tue, 7 Nov 2017 17:33:07 +0000 (17:33 +0000)]
JAL-2698 14 Nov 2017 release date for 2.10.3
Jim Procter [Tue, 7 Nov 2017 17:27:46 +0000 (17:27 +0000)]
JAL-2775 release notes
Jim Procter [Tue, 7 Nov 2017 17:25:51 +0000 (17:25 +0000)]
Merge branch 'imp/JAL-2775' into develop
kiramt [Tue, 7 Nov 2017 17:13:20 +0000 (17:13 +0000)]
JAL-2774 Added javadoc for new event parameters
kiramt [Tue, 7 Nov 2017 17:09:30 +0000 (17:09 +0000)]
JAL-2774 Fix fastpaint of wrapped alignment
Jim Procter [Mon, 6 Nov 2017 16:41:28 +0000 (16:41 +0000)]
JAL-2756 release notes
Jim Procter [Mon, 6 Nov 2017 16:34:05 +0000 (16:34 +0000)]
Merge branch 'bug/JAL-2756sequenceidmessage' into develop
Jim Procter [Fri, 3 Nov 2017 15:57:47 +0000 (15:57 +0000)]
Merge branch 'documentation/JAL-2698_release2103' into develop
Jim Procter [Fri, 3 Nov 2017 15:56:12 +0000 (15:56 +0000)]
JAL-2818 modified README for launching jalview from source build
kiramt [Wed, 1 Nov 2017 11:21:47 +0000 (11:21 +0000)]
Merge branch 'develop' into imp/JAL-2775
kiramt [Tue, 31 Oct 2017 15:05:01 +0000 (15:05 +0000)]
JAL-2774 Fix repaint artefacts
kiramt [Tue, 31 Oct 2017 14:24:54 +0000 (14:24 +0000)]
JAL-2774 Fixed merge issues
kiramt [Tue, 31 Oct 2017 13:59:31 +0000 (13:59 +0000)]
Merge remote-tracking branch 'origin/develop' into imp/JAL-2774
Conflicts:
src/jalview/gui/SeqCanvas.java
kiramt [Tue, 31 Oct 2017 10:00:52 +0000 (10:00 +0000)]
JAL-2756 update for new EBI https link
gmungoc [Fri, 27 Oct 2017 13:15:20 +0000 (14:15 +0100)]
JAL-2526 updated javadoc
Jim Procter [Thu, 26 Oct 2017 16:45:43 +0000 (17:45 +0100)]
JAL-2698 update version and cut release branch
Jim Procter [Thu, 26 Oct 2017 16:31:40 +0000 (17:31 +0100)]
JAL-2546 release notes
Jim Procter [Thu, 26 Oct 2017 16:18:57 +0000 (17:18 +0100)]
JAL-2488 patch causes of NPE during testStoreAndRecoverExpandedviews Jalview2xml tests.
Jim Procter [Thu, 26 Oct 2017 15:26:06 +0000 (16:26 +0100)]
Merge branch 'feature/JAL-2488finalize' into develop
Jim Procter [Thu, 26 Oct 2017 15:20:14 +0000 (16:20 +0100)]
JAL-2036 2.10.3 release notes
Jim Procter [Thu, 26 Oct 2017 14:47:32 +0000 (15:47 +0100)]
JAL-2793 cancelling font changed dialog didn't call ap.fontChanged() to reset layout
Jim Procter [Thu, 26 Oct 2017 13:41:34 +0000 (14:41 +0100)]
JAL-2548 release notes
Jim Procter [Thu, 26 Oct 2017 10:51:35 +0000 (11:51 +0100)]
Merge branch 'bug/JAL-2776toggleGroupColour' into develop
Jim Procter [Thu, 26 Oct 2017 10:50:03 +0000 (11:50 +0100)]
JAL-2684 JAL-2685 release notes
Jim Procter [Thu, 26 Oct 2017 10:40:25 +0000 (11:40 +0100)]
JAL-2685 tidy up html doc
Jim Procter [Thu, 26 Oct 2017 10:14:38 +0000 (11:14 +0100)]
Merge branch 'features/JAL-2685pairwiseSeqLimits' into develop
Jim Procter [Thu, 26 Oct 2017 09:57:13 +0000 (10:57 +0100)]
JAL-2392 test asserts for progressbar creation on the Swing GUI thread.
Jim Procter [Wed, 25 Oct 2017 16:24:27 +0000 (17:24 +0100)]
JAL-2617 release notes
Jim Procter [Wed, 25 Oct 2017 16:23:03 +0000 (17:23 +0100)]
Merge branch 'bug/JAL-2617mappedStopCodon' into develop
Jim Procter [Wed, 25 Oct 2017 15:45:05 +0000 (16:45 +0100)]
JAL-2636 release notes
Jim Procter [Wed, 25 Oct 2017 15:37:57 +0000 (16:37 +0100)]
JAL-2667 release notes
Jim Procter [Wed, 25 Oct 2017 15:33:01 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2667mouseWheelWrapped' into develop
Jim Procter [Wed, 25 Oct 2017 15:29:24 +0000 (16:29 +0100)]
JAL-2742 release notes - pending confirmation that there was impact to user
Jim Procter [Wed, 25 Oct 2017 15:08:20 +0000 (16:08 +0100)]
JAL-2727 release notes
Jim Procter [Wed, 25 Oct 2017 15:06:31 +0000 (16:06 +0100)]
JAL-2727 add not to Test failed message recommending re-running manually as per Mungo’s recommendation in comments
Jim Procter [Wed, 25 Oct 2017 14:53:29 +0000 (15:53 +0100)]
Merge branch 'bug/JAL-2727closeAllFreeMemory' into develop
Jim Procter [Wed, 25 Oct 2017 14:38:06 +0000 (15:38 +0100)]
JAL-2732 JAL-1900 JAL-1625 release notes
Jim Procter [Wed, 25 Oct 2017 14:37:16 +0000 (15:37 +0100)]
Merge branch 'bugs/JAL-2779_osx_dialogsequencingbroke' into develop
Jim Procter [Wed, 25 Oct 2017 14:36:42 +0000 (15:36 +0100)]
JAL-2779 remove empty block and if statement
Jim Procter [Wed, 25 Oct 2017 14:25:26 +0000 (15:25 +0100)]
JAL-2790 JAL-2392 release notes
Jim Procter [Wed, 25 Oct 2017 14:17:55 +0000 (15:17 +0100)]
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into develop
Jim Procter [Wed, 25 Oct 2017 14:14:17 +0000 (15:14 +0100)]
JAL-2790 provide a cancel button for JABAWS and AACon jobs
Jim Procter [Wed, 25 Oct 2017 13:58:11 +0000 (14:58 +0100)]
JAL-2392 auto boxing rather than explicit Long as key
Jim Procter [Tue, 24 Oct 2017 16:55:12 +0000 (17:55 +0100)]
JAL-2495 release notes
gmungoc [Fri, 28 Apr 2017 14:55:32 +0000 (15:55 +0100)]
JAL-2495 highlight all mapped sequences from structure pick
Jim Procter [Tue, 24 Oct 2017 16:50:01 +0000 (17:50 +0100)]
JAL-2643 JAL-2524 release notes
Jim Procter [Tue, 24 Oct 2017 16:44:27 +0000 (17:44 +0100)]
JAL-2524 release notes
Jim Procter [Tue, 24 Oct 2017 16:42:16 +0000 (17:42 +0100)]
JAL-2733 JAL-2658 release notes
Jim Procter [Tue, 24 Oct 2017 16:33:08 +0000 (17:33 +0100)]
JAL-1980 release notes (retrodoc for 2.10.0)
Jim Procter [Tue, 24 Oct 2017 16:24:52 +0000 (17:24 +0100)]
JAL-2687 JAL-2608 release notes
Jim Procter [Tue, 24 Oct 2017 16:09:42 +0000 (17:09 +0100)]
Merge branch 'features/JAL-2608closeOverview' into develop
Jim Procter [Tue, 24 Oct 2017 15:58:27 +0000 (16:58 +0100)]
JAL-2542 release notes
gmungoc [Tue, 24 Oct 2017 10:28:56 +0000 (11:28 +0100)]
JAL-2788 corrected merge error in propertyChange
gmungoc [Tue, 24 Oct 2017 08:31:38 +0000 (09:31 +0100)]
JAL-2787 set start/end seq explicitly for test
Jim Procter [Mon, 23 Oct 2017 16:17:09 +0000 (17:17 +0100)]
Merge branch 'bug/JAL-2609attemptedmerge' into develop
Jim Procter [Mon, 23 Oct 2017 16:15:51 +0000 (17:15 +0100)]
JAL-2609 remove unused AlignPanel.fastPaint flag and broken conditional preventing repaints on vertical scroll
Jim Procter [Mon, 23 Oct 2017 15:37:29 +0000 (16:37 +0100)]
Merge branch 'bug/JAL-2609attemptedmerge' into develop
Jim Procter [Mon, 23 Oct 2017 15:36:14 +0000 (16:36 +0100)]
JAL-2768 release notes
Jim Procter [Mon, 23 Oct 2017 15:27:46 +0000 (16:27 +0100)]
JAL-2739 release notes
Jim Procter [Mon, 23 Oct 2017 15:20:54 +0000 (16:20 +0100)]
Merge branch 'bug/JAL-2739' into develop
Jim Procter [Mon, 23 Oct 2017 15:09:23 +0000 (16:09 +0100)]
JAL-2682 release notes
Jim Procter [Mon, 23 Oct 2017 14:59:30 +0000 (15:59 +0100)]
Merge branch 'bug/JAL-2682parseId' into develop
gmungoc [Mon, 23 Oct 2017 14:48:11 +0000 (15:48 +0100)]
JAL-2776 repaint everything on toggle group colour
Jim Procter [Mon, 23 Oct 2017 14:33:12 +0000 (15:33 +0100)]
JAL-2253 release notes
Jim Procter [Mon, 23 Oct 2017 14:00:38 +0000 (15:00 +0100)]
Merge branch 'bug/JAL-2253' into develop
JAL-2253 resolve diffrences between patches post-code review and diverging develop
gmungoc [Mon, 23 Oct 2017 10:25:42 +0000 (11:25 +0100)]
JAL-1854 keep fallthrough but with comment to suppress error
gmungoc [Mon, 23 Oct 2017 09:58:44 +0000 (10:58 +0100)]
JAL-1854 remove fallthrough of switch case (Checkstyle error)
gmungoc [Mon, 23 Oct 2017 09:57:54 +0000 (10:57 +0100)]
JAL-2737 JAL-1854 corrected package suppressions, updated import
controls
Jim Procter [Fri, 20 Oct 2017 16:03:19 +0000 (17:03 +0100)]
JAL-2779 keep a reference to original Aqua manager so we can iconise/deiconise windows still
Jim Procter [Fri, 20 Oct 2017 14:48:16 +0000 (15:48 +0100)]
JAL-2779 remove OSX platform specific import (not needed anyway it seems ?)
Jim Procter [Fri, 20 Oct 2017 14:28:47 +0000 (15:28 +0100)]
Merge branch 'patch/JAL-547_pid_groovyscript' into develop
Jim Procter [Fri, 20 Oct 2017 14:28:08 +0000 (15:28 +0100)]
JAL-547 fix NPE when no selection available
Jim Procter [Fri, 20 Oct 2017 14:25:49 +0000 (15:25 +0100)]
JAL-547 only generate matrix for current selection if available. better comments.
Jim Procter [Fri, 20 Oct 2017 14:12:49 +0000 (15:12 +0100)]
JAL-547 PID script in release notes
Jim Procter [Fri, 20 Oct 2017 14:10:56 +0000 (15:10 +0100)]
Merge branch 'patch/JAL-547_pid_groovyscript' into develop
Jim Procter [Fri, 20 Oct 2017 14:09:29 +0000 (15:09 +0100)]
JAL-547 updated the PID script for 2.10.x series score model architecture
gmungoc [Fri, 20 Oct 2017 13:05:40 +0000 (14:05 +0100)]
JAL-2253 pull up constant, additional unit test
git://source.jalview.org / jalview.git / log