Jim Procter [Mon, 7 Sep 2015 12:06:06 +0000 (13:06 +0100)]
JAL-1522 make installation default 'applet' for the applet
Jim Procter [Mon, 7 Sep 2015 10:10:42 +0000 (11:10 +0100)]
JAL-1701 added links to example files. will probably remove them later
Jim Procter [Sun, 6 Sep 2015 16:43:04 +0000 (17:43 +0100)]
JAL-1655 transfer setting option only displayed in development version of Jalview
Jim Procter [Sun, 6 Sep 2015 16:31:21 +0000 (17:31 +0100)]
JAL-1368 JAL-1863 JAL-1304 reformatting and revision of wording, clarify RNA secondary structure example
Jim Procter [Sun, 6 Sep 2015 16:17:49 +0000 (17:17 +0100)]
JAL-1368 JAL-1628 revise documentation in line with code for VIEW_SETREF, VIEW_HIDECOLS, and VIEW_HIDE_INSERTIONS.
Jim Procter [Sun, 6 Sep 2015 13:47:57 +0000 (14:47 +0100)]
JAL-1645 JAL-1355 UI/i18n: added missing messages, moved ‘…’ into action messages for actions needing more user input, title caps for menu entries and dialog titles
Jim Procter [Sat, 5 Sep 2015 17:43:21 +0000 (18:43 +0100)]
JAL-1871 JAL-1553 don’t modify selection/view colour scheme again after OK is pressed.
Jim Procter [Sat, 5 Sep 2015 17:40:05 +0000 (18:40 +0100)]
JAL-1871 choose a new RNA Helices palette when annotation colouring is updated
Jim Procter [Sat, 5 Sep 2015 17:38:57 +0000 (18:38 +0100)]
JAL-1871 don’t change the palette every time an edit occurs
Jim Procter [Sat, 5 Sep 2015 17:37:17 +0000 (18:37 +0100)]
JAL-1871 reinstate random generation of palette when applying RNA Helices colouring
Jim Procter [Thu, 9 Jul 2015 16:21:22 +0000 (17:21 +0100)]
JAL-1869 make per-sequence RNA helix colours each time Colour By Annotation is opened
Jim Procter [Sat, 5 Sep 2015 11:34:23 +0000 (12:34 +0100)]
Merge branch 'bugfix/JAL-841_JAL-1081' into develop
Jim Procter [Sat, 5 Sep 2015 11:17:53 +0000 (12:17 +0100)]
JAL-1805 move misassigned test from Functional to Network
Jim Procter [Sat, 5 Sep 2015 09:24:36 +0000 (10:24 +0100)]
JAL-1233 tidy up and use same RNA helix colours in colour by annotation and RNA helix colouring
Jim Procter [Sat, 5 Sep 2015 09:21:45 +0000 (10:21 +0100)]
JAL-1081 JAL-891 don’t overwrite global colour scheme with base pair consensus
Jim Procter [Sat, 5 Sep 2015 09:13:54 +0000 (10:13 +0100)]
JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structure annotation employed for structure consensus and colour by helices
Jim Procter [Fri, 4 Sep 2015 16:31:52 +0000 (17:31 +0100)]
JAL-1847 Merge branch 'thiago' into develop
Jim Procter [Fri, 4 Sep 2015 16:31:35 +0000 (17:31 +0100)]
JAL-1847 added AUTOSUPERIMPOSE property which can be used to disable automatic superposition when loading multiple structures
tcofoegbu [Fri, 4 Sep 2015 16:24:16 +0000 (17:24 +0100)]
JAL-793 added ability to visualise raw BioJSON in the exported HTML using facebox
gmungoc [Fri, 4 Sep 2015 15:43:17 +0000 (16:43 +0100)]
JAL-1859 jmolFindTarget not JmolFindTarget
gmungoc [Fri, 4 Sep 2015 15:03:38 +0000 (16:03 +0100)]
JAL-1859 embedded Jmol applet example updated for Jmol 14.2 javascript
Jim Procter [Thu, 3 Sep 2015 21:19:34 +0000 (22:19 +0100)]
JAL-1863 allow RNA secondary structure rows exported by Jalview to be imported again
Jim Procter [Thu, 3 Sep 2015 21:00:18 +0000 (22:00 +0100)]
JAL-961 efficiency TODO: decouple overview updates from sequence colour broadcasts
Jim Procter [Thu, 3 Sep 2015 20:35:49 +0000 (21:35 +0100)]
JAL-1680 JAL-1576 JAL-1233 all conservation and consensus calculation triggers and applying colour schemes to subgroups are refactored to viewport model
Jim Procter [Thu, 3 Sep 2015 20:30:29 +0000 (21:30 +0100)]
JAL-1576 fix: trigger broadcast of colour change with paintAlignment(true)
Jim Procter [Thu, 3 Sep 2015 20:28:32 +0000 (21:28 +0100)]
JAL-961 TODO use workers for calculations supporting colour schemes
Jim Procter [Thu, 3 Sep 2015 20:23:42 +0000 (21:23 +0100)]
JAL-1551 source tidy
Jim Procter [Thu, 3 Sep 2015 20:21:08 +0000 (21:21 +0100)]
JAL-1550 JAL-1551 formatting
Jim Procter [Thu, 3 Sep 2015 20:20:13 +0000 (21:20 +0100)]
JAL-1233 JAL-1576 copy constructor to propagate helix colours and applyTo implementation to clone colour scheme to subgroups
tcofoegbu [Thu, 3 Sep 2015 15:11:24 +0000 (16:11 +0100)]
house keeping
tcofoegbu [Thu, 3 Sep 2015 14:01:03 +0000 (15:01 +0100)]
merge
tcofoegbu [Thu, 3 Sep 2015 14:00:34 +0000 (15:00 +0100)]
JAL-1861 disable the action buttons for 1500 millisec when the ok button is clicked
gmungoc [Thu, 3 Sep 2015 13:36:50 +0000 (14:36 +0100)]
JAL-1859 removed unneeded dependency on package not in Jmol applet lib
gmungoc [Thu, 3 Sep 2015 10:37:28 +0000 (11:37 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 3 Sep 2015 10:37:16 +0000 (11:37 +0100)]
JAL-1690 scaleProteinAsCdna new optional attribute on Viewport in
project file
tcofoegbu [Thu, 3 Sep 2015 10:33:47 +0000 (11:33 +0100)]
merge
tcofoegbu [Thu, 3 Sep 2015 10:27:46 +0000 (11:27 +0100)]
JAL-793 use default custom export settings for html exports
gmungoc [Thu, 3 Sep 2015 09:22:15 +0000 (10:22 +0100)]
JAL-1828 lookup table to convert MSE to MET when parsing PDB data
gmungoc [Thu, 3 Sep 2015 09:21:01 +0000 (10:21 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Wed, 2 Sep 2015 18:55:13 +0000 (19:55 +0100)]
JAL-1835 updated documentation in preferences
tcofoegbu [Wed, 2 Sep 2015 16:45:24 +0000 (17:45 +0100)]
JAL-1740 migrated BioJSMSAViewer git repo to https://github.com/jalview/exporter-templates/tree/master/biojs
tcofoegbu [Wed, 2 Sep 2015 15:50:52 +0000 (16:50 +0100)]
merge
tcofoegbu [Wed, 2 Sep 2015 15:48:07 +0000 (16:48 +0100)]
JAL-1805 JAL-1700 house keeping
tcofoegbu [Wed, 2 Sep 2015 15:44:25 +0000 (16:44 +0100)]
JAL-1739 reverted BioJSON schema to use one main version for the whole schema and remove every other versioning for different fragments of the schema
gmungoc [Wed, 2 Sep 2015 15:34:56 +0000 (16:34 +0100)]
JAL-1544 spelling
gmungoc [Wed, 2 Sep 2015 15:34:24 +0000 (16:34 +0100)]
JAL-1355 User error text externalised to message bundle
gmungoc [Wed, 2 Sep 2015 15:31:43 +0000 (16:31 +0100)]
JAL-1768 set initial 'enabled' state for id width label as well
gmungoc [Wed, 2 Sep 2015 15:27:56 +0000 (16:27 +0100)]
JAL-1264 test made i18n robust
gmungoc [Wed, 2 Sep 2015 15:21:55 +0000 (16:21 +0100)]
JAL-1768 enable fixed width output when auto-width _not_ enabled
gmungoc [Wed, 2 Sep 2015 14:55:17 +0000 (15:55 +0100)]
JAL-1843 fixed input/add from textbox; added @Override to Desktop
gmungoc [Wed, 2 Sep 2015 12:40:32 +0000 (13:40 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Wed, 2 Sep 2015 12:15:52 +0000 (13:15 +0100)]
merge
tcofoegbu [Wed, 2 Sep 2015 12:14:00 +0000 (13:14 +0100)]
JAL-1805 JAL-1782 added a draft documentation for TestNG to jalview doc directory
Jim Procter [Wed, 2 Sep 2015 11:40:14 +0000 (12:40 +0100)]
JAL-1853 add test to list for ant task
gmungoc [Wed, 2 Sep 2015 11:10:01 +0000 (12:10 +0100)]
JAL-1619 additions, standardised menu item symbols
gmungoc [Wed, 2 Sep 2015 11:08:47 +0000 (12:08 +0100)]
JAL-1681 mention of cDNA consensus added
Jim Procter [Wed, 2 Sep 2015 10:59:53 +0000 (11:59 +0100)]
JAL-535 todo: refactor logic to desktop controller class
Jim Procter [Wed, 2 Sep 2015 10:58:05 +0000 (11:58 +0100)]
JAL-1772 non-functional test added. not doing any more work for 2.9 release
gmungoc [Wed, 2 Sep 2015 10:11:32 +0000 (11:11 +0100)]
JAL-1673 new test to verify transferRESNUMFeatures()
gmungoc [Wed, 2 Sep 2015 08:27:10 +0000 (09:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Tue, 1 Sep 2015 16:40:17 +0000 (17:40 +0100)]
Merge branch 'bug/JAL-1853_gapchar_output' into develop
Jim Procter [Tue, 1 Sep 2015 16:39:15 +0000 (17:39 +0100)]
JAL-1853 add test to Functional group
Jim Procter [Tue, 1 Sep 2015 16:20:13 +0000 (17:20 +0100)]
JAL-1853 make getVisibleSeqs more memory efficient by clipping sequences as the sequence vector is populated
Jim Procter [Tue, 1 Sep 2015 16:19:38 +0000 (17:19 +0100)]
JAL-1853 refactor clip routine from getSequenceStrings
Jim Procter [Tue, 1 Sep 2015 16:15:21 +0000 (17:15 +0100)]
patch for JAL-1853 - use given gap character to reconstruct alignment
Jim Procter [Tue, 1 Sep 2015 16:10:01 +0000 (17:10 +0100)]
JAL-1853 test origin of gapChar bug in AlignView method
gmungoc [Tue, 1 Sep 2015 15:39:16 +0000 (16:39 +0100)]
JAL-1693 split frame opened for get xrefs, translate as cDNA
Jim Procter [Tue, 1 Sep 2015 15:36:09 +0000 (16:36 +0100)]
JAL-1853 test demonstrating bug
gmungoc [Tue, 1 Sep 2015 12:47:37 +0000 (13:47 +0100)]
JAL-1672 additional assertions added
gmungoc [Tue, 1 Sep 2015 12:47:05 +0000 (13:47 +0100)]
JAL-1355 user error message text externalised
tcofoegbu [Tue, 1 Sep 2015 11:37:59 +0000 (12:37 +0100)]
JAL-1668 house keeping
tcofoegbu [Mon, 31 Aug 2015 17:36:39 +0000 (18:36 +0100)]
merge
tcofoegbu [Mon, 31 Aug 2015 17:35:40 +0000 (18:35 +0100)]
JAL-1700 updated error handling with suggested improvements after Jim's testing
gmungoc [Fri, 28 Aug 2015 15:31:33 +0000 (16:31 +0100)]
JAL-1836 temporary workaround for negative resNumIns in PDB file
gmungoc [Thu, 27 Aug 2015 15:50:06 +0000 (16:50 +0100)]
JAL-1270 comments added regarding required remote service
gmungoc [Thu, 27 Aug 2015 15:49:00 +0000 (16:49 +0100)]
JAL-1759 updated unit test for removal of trim on Atom.resNumIns
gmungoc [Thu, 27 Aug 2015 15:33:19 +0000 (16:33 +0100)]
JAL-1830 tests relocated to AlignViewportTest after refactoring
gmungoc [Thu, 27 Aug 2015 15:31:58 +0000 (16:31 +0100)]
JAL-1627 updated expected tooltip text in unit test
gmungoc [Thu, 27 Aug 2015 15:30:54 +0000 (16:30 +0100)]
JAL-1830 unit tests for removing (or not) mappings on close frame
gmungoc [Thu, 27 Aug 2015 14:26:58 +0000 (15:26 +0100)]
JAL-1830 refactored so no jalview.gui references from jalview.structure
gmungoc [Thu, 27 Aug 2015 14:24:34 +0000 (15:24 +0100)]
JAL-845 compacting duplicated code
gmungoc [Thu, 27 Aug 2015 14:22:17 +0000 (15:22 +0100)]
JAL-1611 debug sysout suppressed
gmungoc [Thu, 27 Aug 2015 13:56:41 +0000 (14:56 +0100)]
JAL-1544 message label corrected
gmungoc [Thu, 27 Aug 2015 11:34:07 +0000 (12:34 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 27 Aug 2015 11:33:55 +0000 (12:33 +0100)]
JAL-1701 help page for Split Frame view linked in
Jim Procter [Thu, 27 Aug 2015 11:23:17 +0000 (12:23 +0100)]
JAL-1844 adding more missing jars - jersey, other json stuff, jsr311 and also jetty (for JAL-1575 JAL-1725)
gmungoc [Thu, 27 Aug 2015 11:00:37 +0000 (12:00 +0100)]
JAL-1544 'Jalview' consistently capitalised
gmungoc [Thu, 27 Aug 2015 10:59:03 +0000 (11:59 +0100)]
JAL-892 JAL-1764 Varna and Chimera also saved to project file
gmungoc [Thu, 27 Aug 2015 10:55:55 +0000 (11:55 +0100)]
JAL-892 saved to project; external help link updated
gmungoc [Thu, 27 Aug 2015 10:53:37 +0000 (11:53 +0100)]
JAL-1727 added EBI mirror of DAS registry
gmungoc [Thu, 27 Aug 2015 10:51:30 +0000 (11:51 +0100)]
JAL-1596 JAL-1725 JAL-1588 updates for selection in Chimera, save to
Project, Windows Firewall
gmungoc [Thu, 27 Aug 2015 10:45:47 +0000 (11:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 27 Aug 2015 10:45:36 +0000 (11:45 +0100)]
JAL-1725 restrict Jalview's Jetty server to localhost
Jim Procter [Thu, 27 Aug 2015 10:44:05 +0000 (11:44 +0100)]
fix for JAL-1844 add jersey-core,json,client-1.19 to install anywhere config
gmungoc [Wed, 26 Aug 2015 14:40:12 +0000 (15:40 +0100)]
JAL-1830 dropped reference counts for mappings, instead remove mapping
when no alignment holds a reference to it
gmungoc [Wed, 26 Aug 2015 14:30:50 +0000 (15:30 +0100)]
JAL-1596 check for null pointer (thread running after viewer closed)
gmungoc [Wed, 26 Aug 2015 14:26:46 +0000 (15:26 +0100)]
JAL-1270 test separated out of JalviewChimeraView
gmungoc [Wed, 26 Aug 2015 14:25:54 +0000 (15:25 +0100)]
JAL-1270 corrected path to test properties file
gmungoc [Wed, 26 Aug 2015 14:25:21 +0000 (15:25 +0100)]
JAL-1270 separated Jmol and Chimera tests to avoid concurrency problems
gmungoc [Wed, 26 Aug 2015 13:51:52 +0000 (14:51 +0100)]
JAL-1759 updated unit test for removal of trim of Atom.resNumIns
git://source.jalview.org / jalview.git / log