gmungoc [Thu, 26 Oct 2017 13:32:13 +0000 (14:32 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
Conflicts:
src/jalview/util/MappingUtils.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/util/MappingUtilsTest.java
gmungoc [Thu, 26 Oct 2017 10:56:27 +0000 (11:56 +0100)]
JAL-2792 html table for Feature Details report
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 15:08:20 +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
gmungoc [Wed, 25 Oct 2017 14:37:53 +0000 (15:37 +0100)]
JAL-2743 fall back to parsing description if chromosome lookup fails;
code formatting
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
gmungoc [Tue, 24 Oct 2017 16:03:40 +0000 (17:03 +0100)]
JAL-2743 slightly fancier species/assembly matching for VCF/sequence
gmungoc [Tue, 24 Oct 2017 16:02:58 +0000 (17:02 +0100)]
JAL-2738 tidy Javadoc, remove debug logging
gmungoc [Tue, 24 Oct 2017 16:01:49 +0000 (17:01 +0100)]
JAL-2743 look up species and gene loci for Ensembl gene
Jim Procter [Tue, 24 Oct 2017 15:58:27 +0000 (16:58 +0100)]
JAL-2542 release notes
gmungoc [Tue, 24 Oct 2017 12:56:10 +0000 (13:56 +0100)]
JAL-1739 Javadoc updated for Lambda expression parser functions
gmungoc [Tue, 24 Oct 2017 12:45:15 +0000 (13:45 +0100)]
Merge branch 'develop' into features/JAL-1793VCF; lambda Function for
EnsemblLookup parsing
Conflicts:
src/jalview/ext/ensembl/EnsemblInfo.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblRestClient.java
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
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
gmungoc [Fri, 20 Oct 2017 09:22:26 +0000 (10:22 +0100)]
JAL-2755 update caller for method rename!
gmungoc [Fri, 20 Oct 2017 07:44:17 +0000 (08:44 +0100)]
JAL-2609 fully erase scale above, tidy code change
gmungoc [Thu, 19 Oct 2017 15:45:56 +0000 (16:45 +0100)]
JAL-2609 adjustments for test findings
gmungoc [Thu, 19 Oct 2017 14:02:45 +0000 (15:02 +0100)]
JAL-2755 find gene loci for fetched xrefs where possible
gmungoc [Thu, 19 Oct 2017 14:01:56 +0000 (15:01 +0100)]
JAL-2755 put chromosomal dbref first in report
gmungoc [Thu, 19 Oct 2017 14:01:16 +0000 (15:01 +0100)]
JAL-2755 add lookup of cds/cdna gene loci
gmungoc [Thu, 19 Oct 2017 14:00:34 +0000 (15:00 +0100)]
JAL-2755 add species lookup
gmungoc [Thu, 19 Oct 2017 13:57:12 +0000 (14:57 +0100)]
JAL-2755 add missing Javadoc
gmungoc [Thu, 19 Oct 2017 13:56:13 +0000 (14:56 +0100)]
JAL-2755 rename EnsemblInfo as EnsemblData, add 'true' EnsemblInfo
kiramt [Thu, 19 Oct 2017 13:14:59 +0000 (14:14 +0100)]
Merge branch 'develop' into bug/JAL-2609attemptedmerge
Jim Procter [Wed, 18 Oct 2017 16:17:30 +0000 (17:17 +0100)]
JAL-2779 switch order for updating the current alignment frame reference in response to gain/lost focus events
Jim Procter [Wed, 18 Oct 2017 16:16:01 +0000 (17:16 +0100)]
JAL-2779 remove dead code
Jim Procter [Wed, 18 Oct 2017 16:14:46 +0000 (17:14 +0100)]
JAL-2779 hook in our own AquaInternalFrameManager when on OSX
Jim Procter [Wed, 18 Oct 2017 16:14:07 +0000 (17:14 +0100)]
JAL-2779 JAL-1551 source formatting
Jim Procter [Wed, 18 Oct 2017 16:12:51 +0000 (17:12 +0100)]
JAL-2779 patch so closing most recent frame doesn’t transfer focus to oldest frame on the stack
Jim Procter [Wed, 18 Oct 2017 16:08:11 +0000 (17:08 +0100)]
JAL-2779 original version of AquaInternalFrame Manager
Jim Procter [Wed, 18 Oct 2017 14:28:30 +0000 (15:28 +0100)]
JAL-2782 remark about possible exception due to unsafe regex
Jim Procter [Wed, 18 Oct 2017 13:25:37 +0000 (14:25 +0100)]
JAL-2777 JAL-2773 release notes
Jim Procter [Wed, 18 Oct 2017 13:22:57 +0000 (14:22 +0100)]
Merge branch 'bugs/JAL-2777_whitespaceChain' into develop
Jim Procter [Wed, 18 Oct 2017 13:20:00 +0000 (14:20 +0100)]
JAL-2777 remove duplicate code outside conditional from rebase artefact
Jim Procter [Tue, 17 Oct 2017 13:46:09 +0000 (14:46 +0100)]
JAL-2777 release notes
Jim Procter [Tue, 17 Oct 2017 13:43:20 +0000 (14:43 +0100)]
Merge branch 'features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview' into develop
Jim Procter [Tue, 17 Oct 2017 13:42:56 +0000 (14:42 +0100)]
JAL-2773 renamed flags for clarity
Jim Procter [Mon, 16 Oct 2017 14:04:57 +0000 (15:04 +0100)]
JAL-2777 patch for whitespace chain
Jim Procter [Mon, 16 Oct 2017 14:03:40 +0000 (15:03 +0100)]
JAL-2777 test for the whitespace chain
Jim Procter [Mon, 16 Oct 2017 13:35:17 +0000 (14:35 +0100)]
JAL-2481 patch to fix findFeatureColour for end-of-sequence test
Jim Procter [Mon, 16 Oct 2017 13:34:20 +0000 (14:34 +0100)]
JAL-2481 test correct behaviour of findFeatureColour for final residue in sequence
Jim Procter [Fri, 13 Oct 2017 16:27:57 +0000 (17:27 +0100)]
JAL-2777 noticed exception raised on construction of feature settings because transparency slider 'setMax' triggers a repaint
Jim Procter [Thu, 12 Oct 2017 16:40:50 +0000 (17:40 +0100)]
JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first pass at limiting updates of structure to just those that are necessary.
gmungoc [Wed, 11 Oct 2017 17:46:16 +0000 (18:46 +0100)]
JAL-2609 tests updated for revised label width
gmungoc [Wed, 11 Oct 2017 15:17:13 +0000 (16:17 +0100)]
JAL-2772 check array bounds for sequence access
gmungoc [Wed, 11 Oct 2017 14:01:16 +0000 (15:01 +0100)]
JAL-2609 tidy label width code, some checkstyle warnings
gmungoc [Wed, 11 Oct 2017 12:41:13 +0000 (13:41 +0100)]
Merge branch 'bug/JAL-2742' into develop
gmungoc [Wed, 11 Oct 2017 12:39:34 +0000 (13:39 +0100)]
JAL-2742 set HiddenColumns null for no hidden coluns test to match
Jalview usage
Jim Procter [Wed, 11 Oct 2017 11:46:33 +0000 (12:46 +0100)]
JAL-2757 release notes
gmungoc [Wed, 11 Oct 2017 11:12:54 +0000 (12:12 +0100)]
Merge branch 'bug/JAL-2757_uniprotftsbadquery' into develop
gmungoc [Wed, 11 Oct 2017 11:12:11 +0000 (12:12 +0100)]
JAL-2757 fix PDB also; suppress stack trace and compiler warnings
kiramt [Wed, 11 Oct 2017 11:11:03 +0000 (12:11 +0100)]
JAL-2742 test updates following review
kiramt [Wed, 11 Oct 2017 11:08:25 +0000 (12:08 +0100)]
JAL-2742 minor test updates following review
gmungoc [Wed, 11 Oct 2017 07:59:54 +0000 (08:59 +0100)]
JAL-2738 javadoc correction
kiramt [Wed, 11 Oct 2017 07:20:21 +0000 (08:20 +0100)]
JAL-2742 removed unused getViewAsCigars
kiramt [Tue, 10 Oct 2017 13:38:30 +0000 (14:38 +0100)]
JAL-2609attemptedmerge tidy
kiramt [Tue, 10 Oct 2017 13:34:50 +0000 (14:34 +0100)]
Merge remote-tracking branch 'origin/features/JAL-2609fastPaintWrapped'
into bug/JAL-2690attemptedmerge
Conflicts:
src/jalview/gui/SeqCanvas.java
git://source.jalview.org / jalview.git / log