gmungoc [Thu, 2 Nov 2017 14:47:10 +0000 (14:47 +0000)]
JAL-2808 feature filters held on FeatureRenderer, getColor(feature)
extracted
gmungoc [Thu, 2 Nov 2017 14:44:23 +0000 (14:44 +0000)]
JAL-2808 convenience method to get attribute as String
gmungoc [Thu, 2 Nov 2017 14:41:59 +0000 (14:41 +0000)]
JAL-2808 attribute filtering removed, extract method refactoring left in
gmungoc [Thu, 2 Nov 2017 14:41:31 +0000 (14:41 +0000)]
JAL-2808 reverted to develop (attribute filters removed)
gmungoc [Thu, 2 Nov 2017 14:36:04 +0000 (14:36 +0000)]
JAL-2808 toString modified, tests corrected
gmungoc [Tue, 31 Oct 2017 18:12:36 +0000 (18:12 +0000)]
Merge branch 'bug/JAL-2791selectVisibleFeatures' into
features/JAL-1793VCF
Conflicts:
src/jalview/controller/AlignViewController.java
gmungoc [Tue, 31 Oct 2017 18:09:19 +0000 (18:09 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Tue, 31 Oct 2017 16:23:19 +0000 (16:23 +0000)]
JAL-2791 select columns by _visible_ features
gmungoc [Tue, 31 Oct 2017 15:59:04 +0000 (15:59 +0000)]
JAL-2808 revised util.matcher package, 2 filter conditions per feature
type
gmungoc [Tue, 31 Oct 2017 15:24:27 +0000 (15:24 +0000)]
JAL-2792 test updated for 3 column table
gmungoc [Tue, 31 Oct 2017 08:58:11 +0000 (08:58 +0000)]
JAL-2808 reduce code with WindowAdapter
gmungoc [Mon, 30 Oct 2017 16:58:23 +0000 (16:58 +0000)]
JAL-2791 check feature visibility when selecting columns
gmungoc [Mon, 30 Oct 2017 16:57:24 +0000 (16:57 +0000)]
JAL-2808 add attribute filter options to graduate colour dialog
gmungoc [Mon, 30 Oct 2017 16:56:34 +0000 (16:56 +0000)]
JAL-2792 Javadoc updates
gmungoc [Mon, 30 Oct 2017 16:55:48 +0000 (16:55 +0000)]
JAL-2808 add attribute filter(s) to FeatureColour
gmungoc [Mon, 30 Oct 2017 16:54:55 +0000 (16:54 +0000)]
JAL-2808 remember attribute keys by feature type
gmungoc [Mon, 30 Oct 2017 16:51:40 +0000 (16:51 +0000)]
JAL-2808 classes to support filtering by attribute value
gmungoc [Fri, 27 Oct 2017 13:15:20 +0000 (14:15 +0100)]
JAL-2526 updated javadoc
gmungoc [Fri, 27 Oct 2017 11:20:28 +0000 (12:20 +0100)]
JAL-2754 renamed proguard.jar to include version number
gmungoc [Fri, 27 Oct 2017 11:18:53 +0000 (12:18 +0100)]
JAL-2754 updated proguard.jar to 5.3.3
gmungoc [Fri, 27 Oct 2017 09:52:56 +0000 (10:52 +0100)]
JAL-2792 include source in copy constructor; null pointer check
gmungoc [Fri, 27 Oct 2017 09:52:05 +0000 (10:52 +0100)]
JAL-2754 update to specify Java 1.8(+)
gmungoc [Fri, 27 Oct 2017 08:10:40 +0000 (09:10 +0100)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Fri, 27 Oct 2017 07:19:01 +0000 (08:19 +0100)]
JAL-2792 capture feature metadata and render in Feature Details
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
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 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 15:08:20 +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
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
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
git://source.jalview.org / jalview.git / log