Jim Procter [Thu, 24 Nov 2016 16:16:27 +0000 (16:16 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into releases/Release_2_10_Branch
Jim Procter [Thu, 24 Nov 2016 16:16:13 +0000 (16:16 +0000)]
JAL-2325 exclude .class and .* files (install anywhere build files) from source distribution
Jim Procter [Thu, 24 Nov 2016 15:49:07 +0000 (15:49 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into releases/Release_2_10_Branch
Jim Procter [Thu, 24 Nov 2016 15:48:30 +0000 (15:48 +0000)]
JAL-2325 applied BSD license for chimera/StrucViz2 code
Jim Procter [Thu, 24 Nov 2016 15:35:39 +0000 (15:35 +0000)]
JAL-2325 apply license to new source files
Jim Procter [Thu, 24 Nov 2016 15:35:17 +0000 (15:35 +0000)]
JAL-2325 update release date to next Tuesday
Jim Procter [Thu, 24 Nov 2016 10:10:19 +0000 (10:10 +0000)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Thu, 24 Nov 2016 10:06:03 +0000 (10:06 +0000)]
JAL-2325 tidy up release notes
Jim Procter [Wed, 23 Nov 2016 18:51:01 +0000 (18:51 +0000)]
JAL-2325 remove 2.10.0 what’s new
Jim Procter [Wed, 23 Nov 2016 18:50:49 +0000 (18:50 +0000)]
JAL-2325 latest release to 2.10
Jim Procter [Wed, 23 Nov 2016 17:44:50 +0000 (17:44 +0000)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 23 Nov 2016 17:44:12 +0000 (17:44 +0000)]
JAL-1738 Ctrl/Cmd/Alt modifiers and mention that B and Alt-B by default add columns to selection
Jim Procter [Wed, 23 Nov 2016 17:43:24 +0000 (17:43 +0000)]
JAL-1738 hint about using the task switching key combination to quickly mark highlighted regions in Jalview from selections in Chimera.
Jim Procter [Wed, 23 Nov 2016 17:41:56 +0000 (17:41 +0000)]
JAL-1738 mention Ctrl/Cmd/Alt modifiers and mention that B by default adds columns to selection
Jim Procter [Wed, 23 Nov 2016 17:40:59 +0000 (17:40 +0000)]
JAL-1738 mention Ctrl or Cmd for toggle behaviour in tooltip
Jim Procter [Wed, 23 Nov 2016 17:14:12 +0000 (17:14 +0000)]
JAL-2325 updated what’s new for 2.10.1
Jim Procter [Wed, 23 Nov 2016 17:13:59 +0000 (17:13 +0000)]
JAL-2325 reword ‘tame tooltip’ JAL-1723 release note
Jim Procter [Wed, 23 Nov 2016 17:13:15 +0000 (17:13 +0000)]
JAL-2325 rejig authors and add Kira
Jim Procter [Wed, 23 Nov 2016 15:36:39 +0000 (15:36 +0000)]
JAL-2282 JAL-2325 added link to help text from release notes
Jim Procter [Wed, 23 Nov 2016 15:36:31 +0000 (15:36 +0000)]
JAL-2325 updated what’s new for 2.10.1
Jim Procter [Wed, 23 Nov 2016 15:22:50 +0000 (15:22 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 23 Nov 2016 15:22:44 +0000 (15:22 +0000)]
JAL-2282 revised docs about warning message.
gmungoc [Wed, 23 Nov 2016 15:07:31 +0000 (15:07 +0000)]
JAL-1738 Spanish versions added
Jim Procter [Wed, 23 Nov 2016 14:37:08 +0000 (14:37 +0000)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 23 Nov 2016 14:36:43 +0000 (14:36 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 14:36:17 +0000 (14:36 +0000)]
JAL-2325 JAL-2332 release notes
Jim Procter [Wed, 23 Nov 2016 14:16:01 +0000 (14:16 +0000)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Wed, 23 Nov 2016 14:02:29 +0000 (14:02 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 14:02:19 +0000 (14:02 +0000)]
Merge branch 'bug/JAL-2323disulfideOverview' into develop
Jim Procter [Wed, 23 Nov 2016 13:43:14 +0000 (13:43 +0000)]
JAL-2325 moved disulphide/contact bug fixes (JAL-2323,JAL-2333,JAL-2335,JAL-2327) to ‘General’ section of release notes
Jim Procter [Wed, 23 Nov 2016 12:25:32 +0000 (12:25 +0000)]
JAL-2325 release notes formatting
Jim Procter [Wed, 23 Nov 2016 12:24:43 +0000 (12:24 +0000)]
JAL-2325 release notes
Jim Procter [Wed, 23 Nov 2016 11:45:33 +0000 (11:45 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 11:44:40 +0000 (11:44 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 23 Nov 2016 11:43:42 +0000 (11:43 +0000)]
JAL-2325 release notes
Jim Procter [Tue, 22 Nov 2016 18:21:34 +0000 (18:21 +0000)]
JAL-2197 changed tooltip for Jnet annotation rows to “Jpred Output”
tcofoegbu [Tue, 22 Nov 2016 17:21:16 +0000 (17:21 +0000)]
Merge branch 'bug/JAL-2277_refactorPrintUnwrapped' into develop
Jim Procter [Tue, 22 Nov 2016 17:14:38 +0000 (17:14 +0000)]
Merge branch 'features/JAL-2177_update_jmol_to_14.6.4_2016.10.26' into develop
Jim Procter [Tue, 22 Nov 2016 17:10:08 +0000 (17:10 +0000)]
JAL-2325 update release date for 2.10.1
Jim Procter [Tue, 22 Nov 2016 17:07:36 +0000 (17:07 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101
gmungoc [Tue, 22 Nov 2016 16:41:36 +0000 (16:41 +0000)]
JAL-2337 fix: only adjust once for scroll offset
gmungoc [Tue, 22 Nov 2016 15:52:32 +0000 (15:52 +0000)]
JAL-1919 JAL-2177 handle empty pdbentries list correctly
Jim Procter [Tue, 22 Nov 2016 13:34:17 +0000 (13:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 22 Nov 2016 12:48:30 +0000 (12:48 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 22 Nov 2016 12:48:20 +0000 (12:48 +0000)]
JAL-2322 added runnable interface to HTMLOutput class, abstracted anonymous threads in child classes to the overriding run methods, and then other minor housekeeping
Jim Procter [Tue, 22 Nov 2016 12:45:31 +0000 (12:45 +0000)]
Merge branch 'features/JAL-1738_JAL-345_selectionfromhighlight' into develop
Jim Procter [Tue, 22 Nov 2016 12:42:25 +0000 (12:42 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 22 Nov 2016 12:41:33 +0000 (12:41 +0000)]
JAL-1738 JAL-345 changed keystroke to ‘B’ (with modifiers) and added documentation
gmungoc [Tue, 22 Nov 2016 12:22:46 +0000 (12:22 +0000)]
JAL-2277 refactored AlignmentPanel.printUnwrapped to simplify
tcofoegbu [Mon, 21 Nov 2016 17:47:27 +0000 (17:47 +0000)]
JAL-2277 bug fix for mis-alligned graphics output for scrolled annotations
Jim Procter [Mon, 21 Nov 2016 17:05:56 +0000 (17:05 +0000)]
JAL-2325 JAL-2118 2.10.0 patch in release note
Jim Procter [Mon, 21 Nov 2016 16:31:45 +0000 (16:31 +0000)]
JAL-2335 patched FeatureRendererModel.findFeaturesAtRes to honour isContactFeature
Jim Procter [Mon, 21 Nov 2016 16:22:19 +0000 (16:22 +0000)]
JAL-2335 failing test for FeatureRendererModel.findFeaturesAt and contact features
Jim Procter [Mon, 21 Nov 2016 15:40:46 +0000 (15:40 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 15:40:08 +0000 (15:40 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101
Jim Procter [Mon, 21 Nov 2016 15:39:39 +0000 (15:39 +0000)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Mon, 21 Nov 2016 13:24:10 +0000 (13:24 +0000)]
JAL-2284 documentation for the new command-line option
Jim Procter [Mon, 21 Nov 2016 13:09:37 +0000 (13:09 +0000)]
JAL-2325 post-document JAL-2284 released in 2.10.0
Jim Procter [Mon, 21 Nov 2016 13:04:13 +0000 (13:04 +0000)]
JAL-2325 release notes for JAL-2317
tcofoegbu [Mon, 21 Nov 2016 13:03:50 +0000 (13:03 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 21 Nov 2016 13:03:40 +0000 (13:03 +0000)]
JAL-2332 bugfix to enable structure chooser opening for hen lysozyme
gmungoc [Mon, 21 Nov 2016 11:58:49 +0000 (11:58 +0000)]
JAL-2333 test beefed up with gaps
Jim Procter [Mon, 21 Nov 2016 11:44:00 +0000 (11:44 +0000)]
JAL-1888 JAL-2325 release 2.9.0b1 notes updated post-release
gmungoc [Mon, 21 Nov 2016 11:35:44 +0000 (11:35 +0000)]
JAL-2333 corrected select columns with 'contact' feature
Jim Procter [Mon, 21 Nov 2016 11:29:16 +0000 (11:29 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 11:28:01 +0000 (11:28 +0000)]
JAL-1723 release notes and note in documentation about abbreviation of tooltip
Jim Procter [Mon, 21 Nov 2016 11:14:06 +0000 (11:14 +0000)]
JAL-2325 update release 2.10.0 release notes for JAL-1932
gmungoc [Mon, 21 Nov 2016 11:02:04 +0000 (11:02 +0000)]
Merge branch 'develop' into bug/JAL-2323disulfideOverview
Conflicts:
src/jalview/io/SequenceAnnotationReport.java
Jim Procter [Fri, 18 Nov 2016 16:31:52 +0000 (16:31 +0000)]
Merge branch 'bug/JAL-98consensusMemory' into develop
gmungoc [Fri, 18 Nov 2016 08:55:47 +0000 (08:55 +0000)]
JAL-98 with the two types missing from last commit Profiles[I] !
gmungoc [Thu, 17 Nov 2016 16:08:59 +0000 (16:08 +0000)]
JAL-2323 revert to thread-safe iteration over array field
gmungoc [Thu, 17 Nov 2016 16:01:43 +0000 (16:01 +0000)]
JAL-98 ProfilesI container for profiles for columns
gmungoc [Thu, 17 Nov 2016 11:50:44 +0000 (11:50 +0000)]
JAL-98 javadoc, third party acknowledgements (and very small code
change)
gmungoc [Thu, 17 Nov 2016 11:05:43 +0000 (11:05 +0000)]
JAL-2327 disulfide bond abstracted to SequenceFeature.isContactFeature
gmungoc [Thu, 17 Nov 2016 11:02:34 +0000 (11:02 +0000)]
JAL-2327 add isContactFeature
Jim Procter [Wed, 16 Nov 2016 17:12:43 +0000 (17:12 +0000)]
Merge branch 'features/JAL-1723_sequenceReport' into develop
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/io/SequenceAnnotationReport.java
reconciled refactored report/ellipsis code with refactored URLLink code for generating dynamic links with ACCESSION_ID tokens
Jim Procter [Wed, 16 Nov 2016 16:10:15 +0000 (16:10 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 16 Nov 2016 16:07:22 +0000 (16:07 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 16 Nov 2016 16:06:38 +0000 (16:06 +0000)]
JAL-2325 release notes for 2.10.1 - pass one
kiramt [Wed, 16 Nov 2016 15:55:37 +0000 (15:55 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Wed, 16 Nov 2016 15:54:05 +0000 (15:54 +0000)]
JAL-2282 Updated docs with information about when warning is shown
gmungoc [Wed, 16 Nov 2016 15:45:13 +0000 (15:45 +0000)]
JAL-2323 render disulfide bond correctly on overview and structure
tcofoegbu [Wed, 16 Nov 2016 14:38:42 +0000 (14:38 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 16 Nov 2016 14:38:32 +0000 (14:38 +0000)]
JAL-2322 JAL-2309 replaced references to isheadless variable with method call to isHeadless() in HTMLOutput class
Jim Procter [Wed, 16 Nov 2016 14:35:07 +0000 (14:35 +0000)]
JAL-2318 revised documentation for above PID Threshold
gmungoc [Wed, 16 Nov 2016 12:34:30 +0000 (12:34 +0000)]
JAL-2324 fix and tests for comparison of Float.NaN scores
gmungoc [Wed, 16 Nov 2016 12:27:31 +0000 (12:27 +0000)]
JAL-2319 corrected reporting of SIFTS mapping
Jim Procter [Wed, 16 Nov 2016 11:20:26 +0000 (11:20 +0000)]
JAL-2177 remove signature from desktop library Jmol jar
tcofoegbu [Mon, 14 Nov 2016 19:47:59 +0000 (19:47 +0000)]
JAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS msa exports
tcofoegbu [Fri, 11 Nov 2016 17:23:24 +0000 (17:23 +0000)]
JAL-2277 Refactored out duplicated method - printUnwrapped() in HtmlSvgOutput, externalised facebox script, and made other minor housekeepings
Jim Procter [Fri, 11 Nov 2016 15:28:21 +0000 (15:28 +0000)]
JAL-2177 remove Jmol project signature from jar so it can be resigned
tcofoegbu [Thu, 10 Nov 2016 16:11:36 +0000 (16:11 +0000)]
Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop
tcofoegbu [Thu, 10 Nov 2016 15:57:41 +0000 (15:57 +0000)]
Merge branch 'develop' into bug/JAL-2317_jmol_chimera-chain-factorisation
tcofoegbu [Thu, 10 Nov 2016 15:55:51 +0000 (15:55 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 10 Nov 2016 15:45:33 +0000 (15:45 +0000)]
JAL-2317 Fixed Chimera command for hiding/showing distinct chains
tcofoegbu [Thu, 10 Nov 2016 11:56:51 +0000 (11:56 +0000)]
Bugfix to enable accurate chain extraction/association with models loaded in Chimera, refactored and factorised some duplicated codes with Jmol viewer implementation.
gmungoc [Tue, 8 Nov 2016 15:53:55 +0000 (15:53 +0000)]
JAL-2301 corrected search example to match AA properties mentioned
gmungoc [Tue, 8 Nov 2016 15:47:30 +0000 (15:47 +0000)]
JAL-2301 made T hydrophobic as per the cited conservation method
gmungoc [Tue, 8 Nov 2016 15:16:26 +0000 (15:16 +0000)]
JAL-1961 added link to GFF3 format as well as GFF2
kiramt [Tue, 8 Nov 2016 14:18:48 +0000 (14:18 +0000)]
JAL-2309 Made test timeout slightly longer
git://source.jalview.org / jalview.git / log