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 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
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
kiramt [Mon, 16 Oct 2017 13:31:39 +0000 (14:31 +0100)]
JAL-2775 added repaint clipping
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 14:37:55 +0000 (15:37 +0100)]
JAL-2225 updates for review comments, Checkstyle
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
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
kiramt [Tue, 10 Oct 2017 13:30:43 +0000 (14:30 +0100)]
JAL-2690attemptedmerge seems to work
Jim Procter [Tue, 10 Oct 2017 13:02:37 +0000 (14:02 +0100)]
JAL-2392 wrap public progress bar methods as InvokeLater events. Guess we need to do some thorough testing here !
Jim Procter [Tue, 10 Oct 2017 13:01:46 +0000 (14:01 +0100)]
JAL-2392 formatting
Jim Procter [Tue, 10 Oct 2017 11:50:03 +0000 (12:50 +0100)]
Merge branch 'codereviews/JAL-1990_IProgressIndicator_jalview.structure' into patch/JAL-1990_JAL-2392_deadlockssm
updated for 2.10.3. Still need to remove jalview.gui.IProgressBar imports from non-swing packages (appletgui, structures, etc)
Jim Procter [Tue, 10 Oct 2017 11:11:02 +0000 (12:11 +0100)]
JAL-2523 release notes
Jim Procter [Tue, 10 Oct 2017 11:08:51 +0000 (12:08 +0100)]
Merge branch 'features/JAL-2523httpRetries' into develop
kiramt [Tue, 10 Oct 2017 10:59:51 +0000 (11:59 +0100)]
JAL-2690attemptedmerge partial merge
gmungoc [Mon, 9 Oct 2017 15:03:22 +0000 (16:03 +0100)]
JAL-2480 use interface type for sequenceFeatureStore
gmungoc [Mon, 9 Oct 2017 14:31:13 +0000 (15:31 +0100)]
JAL-2523 basic sleep and retry (3 times) on 429 response code with
Retry-After
gmungoc [Mon, 9 Oct 2017 14:24:10 +0000 (15:24 +0100)]
JAL-2523 convenience method to get model organisms
Jim Procter [Mon, 9 Oct 2017 13:47:00 +0000 (14:47 +0100)]
Merge branch 'patch/JAL-2446_mergeconflictmissed' into develop
Jim Procter [Mon, 9 Oct 2017 13:46:24 +0000 (14:46 +0100)]
JAL-2446 remove duplicate code from pulled up method.
Jim Procter [Fri, 6 Oct 2017 16:02:42 +0000 (17:02 +0100)]
Merge branch 'patch/JAL-2116_java9_antjnlpfix' into develop
Jim Procter [Fri, 6 Oct 2017 16:01:38 +0000 (17:01 +0100)]
JAL-2116 fix jnlp file post-processing so java 9 module path and java version added correctly
Jim Procter [Fri, 6 Oct 2017 15:01:54 +0000 (16:01 +0100)]
JAL-2758 flag and tests for omitting uniprot accession prefix from sequence names
Jim Procter [Thu, 5 Oct 2017 17:59:09 +0000 (18:59 +0100)]
JAL-2757 reset textbox after a non HTTP 200 response
gmungoc [Wed, 4 Oct 2017 12:55:17 +0000 (13:55 +0100)]
JAL-2523 start of refactoring...
Jim Procter [Tue, 3 Oct 2017 14:25:34 +0000 (15:25 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' into develop
Conflicts:
help/html/releases.html
help/html/whatsNew.html
src/jalview/ws/dbsources/Uniprot.java
gmungoc [Mon, 2 Oct 2017 14:41:02 +0000 (15:41 +0100)]
JAL-2525 lookup transcript features by Ontology
Jim Procter [Sun, 1 Oct 2017 11:43:41 +0000 (12:43 +0100)]
Merge branch 'documentation/JAL-2751patch2102b2' into releases/Release_2_10_2b1_Branch
Jim Procter [Sun, 1 Oct 2017 11:42:32 +0000 (12:42 +0100)]
JAL-2751 what's new for 2.10.2b2 patch
Jim Procter [Sun, 1 Oct 2017 11:40:53 +0000 (12:40 +0100)]
JAL-2751 patch release notes
Jim Procter [Sat, 30 Sep 2017 10:26:15 +0000 (11:26 +0100)]
JAL-2751 bump version and new releases entry
Jim Procter [Fri, 29 Sep 2017 16:00:57 +0000 (17:00 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 15:48:58 +0000 (16:48 +0100)]
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher
Jim Procter [Fri, 29 Sep 2017 15:48:21 +0000 (16:48 +0100)]
JAL-2745 patch tests for https
Jim Procter [Fri, 29 Sep 2017 15:47:59 +0000 (16:47 +0100)]
JAL-2748 formatting
Jim Procter [Fri, 29 Sep 2017 15:47:48 +0000 (16:47 +0100)]
JAL-2745 JAL-2748 direct download of XML from uniprot.org
patch for 2.10.2b1 branch
Jim Procter [Fri, 29 Sep 2017 15:48:58 +0000 (16:48 +0100)]
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher
Jim Procter [Fri, 29 Sep 2017 15:48:21 +0000 (16:48 +0100)]
JAL-2745 patch tests for https
Jim Procter [Fri, 29 Sep 2017 15:47:59 +0000 (16:47 +0100)]
JAL-2748 formatting
Jim Procter [Fri, 29 Sep 2017 15:47:48 +0000 (16:47 +0100)]
JAL-2745 JAL-2748 direct download of XML from uniprot.org
Jim Procter [Fri, 29 Sep 2017 10:51:41 +0000 (11:51 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 10:49:49 +0000 (11:49 +0100)]
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
EBI ftp confirmed to remain accesible via HTTP
This reverts commit
c7f663521cb82b94d832015010fa488d3dc7ff58.
Jim Procter [Fri, 29 Sep 2017 10:49:49 +0000 (11:49 +0100)]
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
EBI ftp confirmed to remain accesible via HTTP
This reverts commit
c7f663521cb82b94d832015010fa488d3dc7ff58.
Jim Procter [Fri, 29 Sep 2017 07:20:59 +0000 (08:20 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 07:18:53 +0000 (08:18 +0100)]
JAL-2745 update default EBI-eye search URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:18:30 +0000 (08:18 +0100)]
JAL-2745 update SIFTS FTP URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:18:53 +0000 (08:18 +0100)]
JAL-2745 update default EBI-eye search URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:18:30 +0000 (08:18 +0100)]
JAL-2745 update SIFTS FTP URL to HTTPS
Jim Procter [Fri, 29 Sep 2017 07:03:39 +0000 (08:03 +0100)]
Merge branch 'feature/JAL-2745ebiHttps' into develop
Jim Procter [Fri, 29 Sep 2017 06:58:32 +0000 (07:58 +0100)]
JAL-2745 stderr rather than stdout for unexpected HTTP response
Jim Procter [Fri, 29 Sep 2017 06:58:32 +0000 (07:58 +0100)]
JAL-2745 stderr rather than stdout for unexpected HTTP response
gmungoc [Thu, 28 Sep 2017 15:51:30 +0000 (16:51 +0100)]
JAL-2745 update www.ebi.ac.uk to https
gmungoc [Thu, 28 Sep 2017 15:51:30 +0000 (16:51 +0100)]
JAL-2745 update www.ebi.ac.uk to https
gmungoc [Thu, 28 Sep 2017 12:12:28 +0000 (13:12 +0100)]
JAL-2036 set menus after fully loading AlignFrame
kiramt [Tue, 26 Sep 2017 18:37:20 +0000 (19:37 +0100)]
JAL-2742 uncomment test
kiramt [Tue, 26 Sep 2017 18:33:07 +0000 (19:33 +0100)]
JAL-2742 fixed
kiramt [Tue, 26 Sep 2017 15:35:23 +0000 (16:35 +0100)]
JAL-2742 CigarArray constructor unit test
gmungoc [Mon, 25 Sep 2017 13:44:56 +0000 (14:44 +0100)]
JAL-2525 return no features if none matches ontology term!
kiramt [Fri, 22 Sep 2017 13:09:52 +0000 (14:09 +0100)]
JAL-2739 Fix ported to 2.10.3
git://source.jalview.org / jalview.git / log