kjvdheide [Wed, 11 Oct 2017 20:31:57 +0000 (21:31 +0100)]
forester as submodule with InternalFrame + start of distance conversion
kjvdheide [Wed, 11 Oct 2017 19:28:38 +0000 (20:28 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Wed, 11 Oct 2017 14:03:33 +0000 (15:03 +0100)]
just a comment
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
kjvdheide [Wed, 11 Oct 2017 09:52:52 +0000 (10:52 +0100)]
Added tree building (without distances yet)
kiramt [Wed, 11 Oct 2017 07:20:21 +0000 (08:20 +0100)]
JAL-2742 removed unused getViewAsCigars
kjvdheide [Tue, 10 Oct 2017 12:42:09 +0000 (13:42 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 10 Oct 2017 12:41:44 +0000 (13:41 +0100)]
Start of programmatically creating Aptx trees
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
kjvdheide [Mon, 9 Oct 2017 22:22:24 +0000 (23:22 +0100)]
fixed incorrect panel title
kjvdheide [Mon, 9 Oct 2017 21:39:54 +0000 (22:39 +0100)]
Start of creating tree nodes for Aptx
kjvdheide [Mon, 9 Oct 2017 11:38:30 +0000 (12:38 +0100)]
Fully separated tree GUI from calculation
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.
kjvdheide [Sat, 7 Oct 2017 22:10:32 +0000 (23:10 +0100)]
Renaming
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
kjvdheide [Fri, 6 Oct 2017 15:33:17 +0000 (16:33 +0100)]
Start of creating the objects Archaeopteryx needs
Jim Procter [Thu, 5 Oct 2017 17:59:09 +0000 (18:59 +0100)]
JAL-2757 reset textbox after a non HTTP 200 response
kjvdheide [Thu, 5 Oct 2017 11:47:13 +0000 (12:47 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Thu, 5 Oct 2017 11:37:16 +0000 (12:37 +0100)]
Blank interfaces added
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
kjvdheide [Tue, 3 Oct 2017 12:22:41 +0000 (13:22 +0100)]
Proper copyright dating added
kjvdheide [Tue, 3 Oct 2017 12:18:10 +0000 (13:18 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Tue, 3 Oct 2017 12:17:52 +0000 (13:17 +0100)]
Kept copyright test to just the new classes
kjvdheide [Tue, 3 Oct 2017 12:06:18 +0000 (13:06 +0100)]
Copyright test
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
kjvdheide [Fri, 29 Sep 2017 15:56:49 +0000 (16:56 +0100)]
Begin separation of GUI and tree calculation logic
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
kjvdheide [Fri, 29 Sep 2017 14:31:59 +0000 (15:31 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
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
kjvanderheide [Wed, 27 Sep 2017 11:01:50 +0000 (12:01 +0100)]
proof of concept for passing tree data to archaeopteryx
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 [Wed, 20 Sep 2017 10:28:01 +0000 (11:28 +0100)]
JAL-2662 Adjustments to hidden columns benchmark
kiramt [Tue, 19 Sep 2017 14:26:56 +0000 (15:26 +0100)]
JAL-2662 Updated README
kiramt [Tue, 19 Sep 2017 14:23:59 +0000 (15:23 +0100)]
JAL-2737 Checkstyle error fixes
kiramt [Tue, 19 Sep 2017 14:10:19 +0000 (15:10 +0100)]
JAL-2622 Tidied up gitignore, added to README
kiramt [Tue, 19 Sep 2017 14:05:01 +0000 (15:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Tue, 19 Sep 2017 14:03:14 +0000 (15:03 +0100)]
Merge remote-tracking branch 'origin/task/JAL-2662' into develop
gmungoc [Mon, 18 Sep 2017 09:44:25 +0000 (10:44 +0100)]
Merge remote-tracking branch 'origin/patch/JAL-2732' into develop
gmungoc [Mon, 18 Sep 2017 08:26:43 +0000 (09:26 +0100)]
JAL-2728 fine tuned initial split of split frame view
Jim Procter [Fri, 15 Sep 2017 15:37:47 +0000 (16:37 +0100)]
Merge branch 'documentation/JAL-2698_release2103' into develop
Jim Procter [Fri, 15 Sep 2017 15:37:31 +0000 (16:37 +0100)]
JAL-2698 new releases.html entry, whatsNew.html and first signoff : JAL-2728
Jim Procter [Fri, 15 Sep 2017 15:21:22 +0000 (16:21 +0100)]
Merge branch 'bug/JAL-2728splitFrameDivision' into develop
Jim Procter [Fri, 15 Sep 2017 15:05:12 +0000 (16:05 +0100)]
JAL-1625 ensure we don’t regress on JAL-20 - we always use the DefaultDesktopManager on Windows
Jim Procter [Fri, 15 Sep 2017 15:04:06 +0000 (16:04 +0100)]
JAL-1625 javadoc
Jim Procter [Fri, 15 Sep 2017 14:45:46 +0000 (15:45 +0100)]
JAL-2733 redraw after changing the memory status display setting
Jim Procter [Fri, 15 Sep 2017 14:43:46 +0000 (15:43 +0100)]
JAL-1625 JAL-1900 preserve the original DesktopManager instance provided by platform rather than create our own, so iconify works correctly (should mean we also get iconify working in Linux too)
Jim Procter [Fri, 15 Sep 2017 14:42:50 +0000 (15:42 +0100)]
JAL-1900 JAL-1625 back out OSX specific double buffer disabling (seems to do nothing)
Jim Procter [Fri, 15 Sep 2017 14:23:58 +0000 (15:23 +0100)]
JAL-1551 standard code formatting
Jim Procter [Fri, 15 Sep 2017 14:23:15 +0000 (15:23 +0100)]
JAL-2732 force a redraw after resize/drag to clear any outlines
gmungoc [Fri, 15 Sep 2017 14:03:34 +0000 (15:03 +0100)]
JAL-2728 use right denominator for min/max ratio calculations
gmungoc [Fri, 15 Sep 2017 13:49:05 +0000 (14:49 +0100)]
JAL-2728 limit divider to ensure seqs visible (wip!)
gmungoc [Fri, 15 Sep 2017 10:00:46 +0000 (11:00 +0100)]
JAL-741 add tooltip to feature group checkbox
gmungoc [Tue, 12 Sep 2017 13:54:15 +0000 (14:54 +0100)]
Merge branch 'bug/JAL-2721fastPaintNPE' into develop
Jim Procter [Thu, 7 Sep 2017 13:19:03 +0000 (14:19 +0100)]
Merge branch 'releases/Release_2_10_2b1_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_2b1_Branch
Jim Procter [Thu, 7 Sep 2017 13:18:36 +0000 (14:18 +0100)]
Merge branch 'bug/JAL-2511idAlignment' into develop
Jim Procter [Thu, 7 Sep 2017 13:17:07 +0000 (14:17 +0100)]
JAL-2511 release notes for 2.10.2b1
Jim Procter [Thu, 7 Sep 2017 13:17:07 +0000 (14:17 +0100)]
JAL-2511 release notes for 2.10.2b1
gmungoc [Thu, 7 Sep 2017 10:06:34 +0000 (11:06 +0100)]
JAL-2511 invalidate scale panel holder on font change to update layout
gmungoc [Thu, 7 Sep 2017 10:06:34 +0000 (11:06 +0100)]
JAL-2511 invalidate scale panel holder on font change to update layout
git://source.jalview.org / jalview.git / log