Jim Procter [Thu, 8 Jan 2015 14:48:33 +0000 (14:48 +0000)]
Merge branch 'JAL-1483_29dev' into develop
Jim Procter [Wed, 7 Jan 2015 23:08:47 +0000 (23:08 +0000)]
Merge branch 'develop' into JAL-1483_29dev
updated JAL-1483 with commits from 15th Dec-7th Jan 2015
Conflicts:
.classpath
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqPanel.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
Jim Procter [Wed, 7 Jan 2015 18:04:46 +0000 (18:04 +0000)]
JAL-1483 patches to make test case pass: hamming distance counts differences in presence across all features currently displayed on alignment
Jim Procter [Wed, 7 Jan 2015 18:02:10 +0000 (18:02 +0000)]
JAL-1483 basic test of sequence similarity score model (also gives the refactored sequence feature components a workout)
Jim Procter [Wed, 7 Jan 2015 17:57:43 +0000 (17:57 +0000)]
JAL-1483 source formatting
Jim Procter [Wed, 7 Jan 2015 17:56:40 +0000 (17:56 +0000)]
JAL-1483 refactor NJTree constructor to allow preconfigured scoremodel to be passed in with alignment view
Jim Procter [Wed, 7 Jan 2015 17:33:11 +0000 (17:33 +0000)]
JAL-1483 register feature similarity model
Jim Procter [Wed, 7 Jan 2015 17:32:20 +0000 (17:32 +0000)]
JAL-1483 null features not displayed
Jim Procter [Wed, 7 Jan 2015 17:31:34 +0000 (17:31 +0000)]
JAL-1483 check dataset for features if none found on local sequence
Jim Procter [Wed, 7 Jan 2015 17:30:34 +0000 (17:30 +0000)]
JAL-1483 organise imports
Jim Procter [Wed, 7 Jan 2015 17:17:12 +0000 (17:17 +0000)]
JAL-1483 making type visible also adds it to registry
gmungoc [Sun, 28 Dec 2014 10:34:27 +0000 (10:34 +0000)]
Merge branch 'features/JAL-1596ChimeraREST' into develop
Charles Ofoegbu [Mon, 22 Dec 2014 16:38:45 +0000 (16:38 +0000)]
Patch to synchronize title svg and allignment svg scrolling
Jim Procter [Mon, 22 Dec 2014 16:16:17 +0000 (16:16 +0000)]
Merge: 497958b 68dcaa7
(fake synthesised by jbp)
Merge branch 'develop' into JAL-1483_29dev
Conflicts:
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqPanel.java
Charles Ofoegbu [Mon, 15 Dec 2014 15:35:54 +0000 (15:35 +0000)]
update HtmlSvgOutput to ignore browser invocation when running in headless mode
Mungo Carstairs [Sun, 14 Dec 2014 13:45:23 +0000 (13:45 +0000)]
JAL-1596 set HTTP 1.1 in HttpClient
gmungoc [Tue, 9 Dec 2014 12:21:20 +0000 (12:21 +0000)]
JAL-1616 loading of datasets from XML patched
Charles Ofoegbu [Mon, 8 Dec 2014 12:33:53 +0000 (12:33 +0000)]
merge commit
Charles Ofoegbu [Mon, 8 Dec 2014 11:47:36 +0000 (11:47 +0000)]
JAL-1613 hotfix for duplicated sequence after pairwise alignment
Charles Ofoegbu [Mon, 8 Dec 2014 09:45:44 +0000 (09:45 +0000)]
Added annotation export configuration for Html export option
Charles Ofoegbu [Fri, 5 Dec 2014 14:59:55 +0000 (14:59 +0000)]
Merge branch 'features/JAL-1605_html-svg-export' into develop
Charles Ofoegbu [Fri, 5 Dec 2014 14:58:00 +0000 (14:58 +0000)]
JAL-1605 added command line support for html export option
Charles Ofoegbu [Fri, 5 Dec 2014 13:29:17 +0000 (13:29 +0000)]
modified html css
Charles Ofoegbu [Fri, 5 Dec 2014 12:45:11 +0000 (12:45 +0000)]
JAL-1605 merge commit
Charles Ofoegbu [Fri, 5 Dec 2014 12:23:07 +0000 (12:23 +0000)]
Change the Html export to utilize svg
gmungoc [Fri, 5 Dec 2014 10:52:38 +0000 (10:52 +0000)]
JAL-1614 flag 'protein' removed
gmungoc [Fri, 5 Dec 2014 10:52:38 +0000 (10:52 +0000)]
JAL-1614 flag 'protein' removed
gmungoc [Fri, 5 Dec 2014 08:40:45 +0000 (08:40 +0000)]
JAL-1609 refactored colour by sequence command, now performs ok
gmungoc [Fri, 5 Dec 2014 08:38:37 +0000 (08:38 +0000)]
Merge branch 'Release_2_8_2_Branch' of local repository into features/JAL-1596ChimeraREST
gmungoc [Wed, 3 Dec 2014 15:05:54 +0000 (15:05 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
gmungoc [Wed, 3 Dec 2014 15:00:53 +0000 (15:00 +0000)]
JAL-1609 wip on Chimera colour by sequence
Jim Procter [Wed, 3 Dec 2014 12:02:49 +0000 (12:02 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 12:02:18 +0000 (12:02 +0000)]
JAL-1517 update applet authors list
Jim Procter [Wed, 3 Dec 2014 09:21:29 +0000 (09:21 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 09:20:54 +0000 (09:20 +0000)]
JAL-1517 disable desktop 'take snapshot' menu item for release
Jim Procter [Wed, 3 Dec 2014 08:16:21 +0000 (08:16 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 08:16:02 +0000 (08:16 +0000)]
JAL-1517 dropped jnlp file in help documentation in favour of link to Jalview launchApp service
Jim Procter [Wed, 3 Dec 2014 07:48:02 +0000 (07:48 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Wed, 3 Dec 2014 07:47:33 +0000 (07:47 +0000)]
JAL-1517 updated library licensing info
Jim Procter [Wed, 3 Dec 2014 07:39:56 +0000 (07:39 +0000)]
JAL-1517 release notes
Jim Procter [Tue, 2 Dec 2014 18:02:19 +0000 (18:02 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 18:02:00 +0000 (18:02 +0000)]
JAL-1517 typo
Jim Procter [Tue, 2 Dec 2014 16:53:17 +0000 (16:53 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 16:53:02 +0000 (16:53 +0000)]
JAL-1517 TOC items must be on one line for help2Website
Jim Procter [Tue, 2 Dec 2014 16:24:16 +0000 (16:24 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 16:23:52 +0000 (16:23 +0000)]
JAL-1602 tweak VM inclusion options
Jim Procter [Tue, 2 Dec 2014 13:22:20 +0000 (13:22 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 13:21:49 +0000 (13:21 +0000)]
JAL-1517 documentation for 2.8.2 release
Jim Procter [Tue, 2 Dec 2014 11:43:22 +0000 (11:43 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 11:43:00 +0000 (11:43 +0000)]
JAL-1602 typo in jsonsimple jar
Jim Procter [Tue, 2 Dec 2014 10:22:40 +0000 (10:22 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 10:22:21 +0000 (10:22 +0000)]
JAL-1602 add missing jars to install
Jim Procter [Mon, 1 Dec 2014 23:56:13 +0000 (23:56 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 23:55:44 +0000 (23:55 +0000)]
JAL-1602 upgrade to InstallAnywhere 2014 J17 runtimes
Jim Procter [Mon, 1 Dec 2014 21:49:16 +0000 (21:49 +0000)]
JAL-1199 JAL-1569 incremental patch allow non-standard annotation to be output
Jim Procter [Mon, 1 Dec 2014 21:47:37 +0000 (21:47 +0000)]
JAL-1517 updating author list
Jim Procter [Mon, 1 Dec 2014 21:47:13 +0000 (21:47 +0000)]
JAL-1517 updating authors list
Jim Procter [Mon, 1 Dec 2014 16:55:02 +0000 (16:55 +0000)]
JAL-795 hack to ignore black colour in annotation element.
Jim Procter [Mon, 1 Dec 2014 16:43:02 +0000 (16:43 +0000)]
JAL-1601 ignore the JABA Jpred client in Jalview 2.8.2 release
gmungoc [Mon, 1 Dec 2014 16:17:20 +0000 (16:17 +0000)]
JAL-429 Phylip added to help page
gmungoc [Mon, 1 Dec 2014 16:14:50 +0000 (16:14 +0000)]
JAL-1544 typos/formatting in help (and Phylip added)
Jim Procter [Mon, 1 Dec 2014 15:40:00 +0000 (15:40 +0000)]
Merge branch 'bug/JAL-1610refAnnotationsInViews' into develop
Jim Procter [Mon, 1 Dec 2014 15:39:42 +0000 (15:39 +0000)]
Merge branch 'bug/JAL-1610refAnnotationsInViews' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 15:38:26 +0000 (15:38 +0000)]
file for JAL-1268 jalview.io.Jalview2xmlTests.testTCoffeeScores
Jim Procter [Fri, 28 Nov 2014 16:01:47 +0000 (16:01 +0000)]
Merge branch 'JAL-1517_release282' into develop
Jim Procter [Fri, 28 Nov 2014 16:01:37 +0000 (16:01 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Fri, 28 Nov 2014 16:01:03 +0000 (16:01 +0000)]
JAL-1517 first stab at release notes... lots of documentation to go!
gmungoc [Fri, 28 Nov 2014 15:48:48 +0000 (15:48 +0000)]
JAL-1610 check reference annotations against alignment, not sequence
Jim Procter [Fri, 28 Nov 2014 14:58:00 +0000 (14:58 +0000)]
JAL-1522 output installation type to stdout
Jim Procter [Fri, 28 Nov 2014 14:47:37 +0000 (14:47 +0000)]
JAL-1522 remove build/deployment details imported from user preferences file
Jim Procter [Fri, 28 Nov 2014 14:46:41 +0000 (14:46 +0000)]
JAL-1517 formatting
Jim Procter [Fri, 28 Nov 2014 14:46:04 +0000 (14:46 +0000)]
JAL-1611 revise log level to reduce verbosity
Jim Procter [Fri, 28 Nov 2014 14:20:23 +0000 (14:20 +0000)]
JAL-1583 javadoc and fix constructor signature
Jim Procter [Fri, 28 Nov 2014 14:07:39 +0000 (14:07 +0000)]
JAL-1342 document argument to specify preferred JABA server
Jim Procter [Fri, 28 Nov 2014 14:06:08 +0000 (14:06 +0000)]
JAL-1604 formatting
Jim Procter [Fri, 28 Nov 2014 14:05:42 +0000 (14:05 +0000)]
JAL-1604 revised wording and internationalised dialog
Jim Procter [Fri, 28 Nov 2014 14:04:16 +0000 (14:04 +0000)]
JAL-1583 back out original fix and simply check MSAWSThread.hasValidInput flag before displaying job window and starting the web service job thread.
Jim Procter [Fri, 28 Nov 2014 14:01:27 +0000 (14:01 +0000)]
JAL-1583 formatting
Jim Procter [Fri, 28 Nov 2014 14:01:15 +0000 (14:01 +0000)]
JAL-1583 new validInput flag set according to validity of all MSA jobs prepared for submission
Jim Procter [Fri, 28 Nov 2014 13:58:51 +0000 (13:58 +0000)]
JAL-1583 refactored addInternalFrame to allow webservice job frame to be added but not automatically made visible
Jim Procter [Fri, 28 Nov 2014 13:55:05 +0000 (13:55 +0000)]
JAL-1517 formatting/tidy
gmungoc [Fri, 28 Nov 2014 12:19:58 +0000 (12:19 +0000)]
JAL-1596 first REST interface coded
Jim Procter [Tue, 25 Nov 2014 11:24:43 +0000 (11:24 +0000)]
JAL-1517 svg==scalable :)
Jim Procter [Thu, 27 Nov 2014 16:02:21 +0000 (16:02 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 16:02:07 +0000 (16:02 +0000)]
Merge branch 'patchJAL-674_offset' into develop
Jim Procter [Thu, 27 Nov 2014 15:59:39 +0000 (15:59 +0000)]
JAL-674 add sequence associated annotation rows to flanking alignment
Jim Procter [Thu, 27 Nov 2014 15:58:51 +0000 (15:58 +0000)]
JAL-1177 JAL-905 cannot recover sequences from dataset if dataset is currently being recovered
Jim Procter [Thu, 27 Nov 2014 14:56:35 +0000 (14:56 +0000)]
JAL-674 avoid writing \0 for chain code
Jim Procter [Thu, 27 Nov 2014 14:39:56 +0000 (14:39 +0000)]
Merge branch 'patchJAL-674_offset' into develop
Jim Procter [Thu, 27 Nov 2014 14:39:32 +0000 (14:39 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 14:32:52 +0000 (14:32 +0000)]
JAL-674 patch to fix bug with showing reference annotation for legacy jalview example file v2.7
Jim Procter [Thu, 27 Nov 2014 14:32:08 +0000 (14:32 +0000)]
JAL-674 formatting
Jim Procter [Thu, 27 Nov 2014 14:31:20 +0000 (14:31 +0000)]
JAL-674 unused variable
Jim Procter [Thu, 27 Nov 2014 14:31:05 +0000 (14:31 +0000)]
JAL-674 bug in test
gmungoc [Thu, 27 Nov 2014 11:56:25 +0000 (11:56 +0000)]
JAL-1603 if Chimera selected in Preferences, warn if not installed/found
gmungoc [Thu, 27 Nov 2014 11:53:50 +0000 (11:53 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 10:37:06 +0000 (10:37 +0000)]
JAL-674 test that PDB annotation created when importing a legacy jalview example file is mapped to the correct place as the manually created version (temperature factor in exampleFile_2_7.jar
Jim Procter [Thu, 27 Nov 2014 10:35:58 +0000 (10:35 +0000)]
JAL-674 patch NPE bug when test run in isolation
Jim Procter [Thu, 27 Nov 2014 10:35:23 +0000 (10:35 +0000)]
JAL-674 fix test properties path and add properties file
Jim Procter [Thu, 27 Nov 2014 10:31:31 +0000 (10:31 +0000)]
JAL-674 JAL-966 new method to retrieve all views
git://source.jalview.org / jalview.git / log