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
gmungoc [Wed, 26 Aug 2015 11:06:35 +0000 (12:06 +0100)]
JAL-1840 correct setting status bar for structure mouseover
gmungoc [Wed, 26 Aug 2015 11:03:45 +0000 (12:03 +0100)]
JAL-1759 added check for null (console 'history')
gmungoc [Wed, 26 Aug 2015 11:01:03 +0000 (12:01 +0100)]
Fix to use correct resource bundle entry
gmungoc [Wed, 26 Aug 2015 10:59:35 +0000 (11:59 +0100)]
JAL-1759 corrected syntax for 'atom picked' callback (toggles label
on/off in Jmol)
gmungoc [Tue, 25 Aug 2015 09:50:52 +0000 (10:50 +0100)]
JAL-1780 just a spelling change
gmungoc [Tue, 25 Aug 2015 09:42:45 +0000 (10:42 +0100)]
JAL-1674 more correct status bars in splitframe mouseover (applet)
gmungoc [Mon, 24 Aug 2015 12:05:32 +0000 (13:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 24 Aug 2015 12:05:09 +0000 (13:05 +0100)]
JAL-1759 removed trim() of Atom.resNumIns as not backwards compatible
with saved projects (generates duplicate annotations)
tcofoegbu [Mon, 24 Aug 2015 10:13:20 +0000 (11:13 +0100)]
JAL-1641 externalised save_as_biojs_html
tcofoegbu [Mon, 24 Aug 2015 10:06:31 +0000 (11:06 +0100)]
JAL-1835 corrected Embbed to Embed
tcofoegbu [Mon, 24 Aug 2015 08:39:26 +0000 (09:39 +0100)]
merge
tcofoegbu [Mon, 24 Aug 2015 08:36:56 +0000 (09:36 +0100)]
JAL-1834 removed quotes around truncated strings with ellipsis
gmungoc [Mon, 24 Aug 2015 08:25:22 +0000 (09:25 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 24 Aug 2015 08:25:01 +0000 (09:25 +0100)]
JAL-845 error message on syserr if supplied files don't map as cDNA and
protein
gmungoc [Mon, 24 Aug 2015 08:16:46 +0000 (09:16 +0100)]
remove mentions of non-functional RNAInteraction colourscheme
tcofoegbu [Fri, 21 Aug 2015 16:05:14 +0000 (17:05 +0100)]
JAL-1834 capped the tool-tip text at 500. once that is exceeded an ellipsis is added
tcofoegbu [Fri, 21 Aug 2015 13:59:19 +0000 (14:59 +0100)]
JAL-1834 disabled action buttons (Back / Ok / Cancel) when in 'Configure Displayed Columns' tab
tcofoegbu [Fri, 21 Aug 2015 10:27:19 +0000 (11:27 +0100)]
JAL-1443 bug fix for loading pasted alignments from clipboard via the file loader
tcofoegbu [Fri, 21 Aug 2015 09:50:35 +0000 (10:50 +0100)]
JAL-1831 updated json schema doc
tcofoegbu [Fri, 21 Aug 2015 09:47:43 +0000 (10:47 +0100)]
clean up
tcofoegbu [Fri, 21 Aug 2015 09:43:10 +0000 (10:43 +0100)]
JAL-1780 made the 'Select All' checkbox to be shown for all the setting panels
tcofoegbu [Fri, 21 Aug 2015 09:18:15 +0000 (10:18 +0100)]
JAL-1780 changed 'Check All' to 'Select All' and externalised all message labels in export settings window
tcofoegbu [Thu, 20 Aug 2015 14:00:13 +0000 (15:00 +0100)]
merge
tcofoegbu [Thu, 20 Aug 2015 12:58:10 +0000 (13:58 +0100)]
JAL-1833 revised implementation
gmungoc [Thu, 20 Aug 2015 08:42:44 +0000 (09:42 +0100)]
JAL-1833 added unit tests (some failing) for wrapToolitp
gmungoc [Wed, 19 Aug 2015 09:00:40 +0000 (10:00 +0100)]
JAL-1782 don't save TESTNG output summary to git
gmungoc [Wed, 19 Aug 2015 08:40:27 +0000 (09:40 +0100)]
JAL-1725 log to sysout when listener shuts down
gmungoc [Wed, 19 Aug 2015 08:39:26 +0000 (09:39 +0100)]
JAL-1742 suppress 'add chain' option for Jmol, pull up shared code for
Jmol/Chimera
tcofoegbu [Tue, 18 Aug 2015 15:17:28 +0000 (16:17 +0100)]
JAL-1861 bugfix to allow parsing of stockholm files with missing annotations
tcofoegbu [Tue, 18 Aug 2015 13:24:32 +0000 (14:24 +0100)]
JAL-1835 added UI for BioJSON embbeding preference
tcofoegbu [Tue, 18 Aug 2015 12:22:36 +0000 (13:22 +0100)]
JAL-1835 made BioJSON embedding to html exports configurable, and trapped import of html files without BioJSON
tcofoegbu [Tue, 18 Aug 2015 10:47:46 +0000 (11:47 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 18 Aug 2015 10:47:32 +0000 (11:47 +0100)]
JAL-1834 added tooltip to the PDB sequence fetcher and structure chooser summary tables
tcofoegbu [Tue, 18 Aug 2015 10:45:11 +0000 (11:45 +0100)]
JAL-1833 modified tooltip to force wraping of long texts without spaces
gmungoc [Mon, 17 Aug 2015 15:26:20 +0000 (16:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 17 Aug 2015 15:26:05 +0000 (16:26 +0100)]
JAL-1800 separated SearchResults.getCharacters() from toString()
gmungoc [Mon, 17 Aug 2015 15:23:29 +0000 (16:23 +0100)]
JAL-1270 testIsMappable added
gmungoc [Mon, 17 Aug 2015 15:22:20 +0000 (16:22 +0100)]
JAL-1805 corrected javadoc only
tcofoegbu [Mon, 17 Aug 2015 14:23:51 +0000 (15:23 +0100)]
merge
tcofoegbu [Mon, 17 Aug 2015 14:23:01 +0000 (15:23 +0100)]
JAL-1832 improvement to enable result update only when displayed column configuration is updated
gmungoc [Mon, 17 Aug 2015 11:09:19 +0000 (12:09 +0100)]
JAL-1829 JAL-1830 refactoring for correct mapping (de-)registration
gmungoc [Mon, 17 Aug 2015 11:06:22 +0000 (12:06 +0100)]
JAL-1800 smarter matching when following mouseover of sequence
gmungoc [Mon, 17 Aug 2015 10:38:52 +0000 (11:38 +0100)]
JAL-1691 scan full width and depth of alignment for smoother scrolling
gmungoc [Mon, 17 Aug 2015 10:16:52 +0000 (11:16 +0100)]
JAL-1800 SearchResults.equals() to allow smarter mouseover of codons
gmungoc [Mon, 17 Aug 2015 10:05:19 +0000 (11:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 17 Aug 2015 10:04:56 +0000 (11:04 +0100)]
JAL-1551 updated to reflect changes to Eclipse preferences settings
gmungoc [Mon, 17 Aug 2015 09:35:13 +0000 (10:35 +0100)]
JAL-1551 properties sorted (unchanged) for ease of comparison with
org.eclipse.jdt.core.prefs
tcofoegbu [Mon, 17 Aug 2015 08:47:12 +0000 (09:47 +0100)]
JAL-1831 update all maxItems annotation to the max value for a 32-bit signed binary integer -
2147483674
tcofoegbu [Fri, 14 Aug 2015 15:40:53 +0000 (16:40 +0100)]
merge
tcofoegbu [Fri, 14 Aug 2015 15:37:13 +0000 (16:37 +0100)]
JAL-1831 added changes to allow auto-generation of BioJSON schema from src code
tcofoegbu [Thu, 13 Aug 2015 12:39:46 +0000 (13:39 +0100)]
JAL-1826 bug fix to select pdb sequence fetcher via enter key
tcofoegbu [Thu, 13 Aug 2015 09:46:49 +0000 (10:46 +0100)]
JAL-1641 added type to BioJSON sequence object and modified seqsHash to sequenceRefs in for the sequence group object
tcofoegbu [Tue, 11 Aug 2015 16:28:59 +0000 (17:28 +0100)]
JAL-1641 updated json help doc
tcofoegbu [Tue, 11 Aug 2015 13:10:05 +0000 (14:10 +0100)]
merge
tcofoegbu [Tue, 11 Aug 2015 13:07:59 +0000 (14:07 +0100)]
add ability to launch jalview from exported html + svg file. Abstracted Jalview build details so that jalview version can be obtained dynmaicaly from JSONFile class.
Jim Procter [Mon, 10 Aug 2015 14:51:01 +0000 (15:51 +0100)]
JAL-1645 updated final release date for version 2.9
Jim Procter [Mon, 10 Aug 2015 14:47:15 +0000 (15:47 +0100)]
Merge branch 'release/2_9_documentation' into develop
gmungoc [Mon, 10 Aug 2015 13:12:10 +0000 (14:12 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 10 Aug 2015 13:11:54 +0000 (14:11 +0100)]
JAL-1516 indent multiple annotation parameters on new lines
Jim Procter [Mon, 10 Aug 2015 10:16:05 +0000 (11:16 +0100)]
JAL-736 relocate group associated conservation symbols to alignment column position
Jim Procter [Mon, 10 Aug 2015 10:14:21 +0000 (11:14 +0100)]
JAL-736 source formatting
tcofoegbu [Mon, 10 Aug 2015 09:33:48 +0000 (10:33 +0100)]
JAL-1486 fixed flatfile output of visible region for consensus sequence
tcofoegbu [Fri, 7 Aug 2015 13:59:50 +0000 (14:59 +0100)]
JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry method in SequenceI to getAllPDBEntries as it returns a collection of all available PDBEntry
tcofoegbu [Thu, 6 Aug 2015 10:41:01 +0000 (11:41 +0100)]
merge
tcofoegbu [Thu, 6 Aug 2015 10:40:15 +0000 (11:40 +0100)]
JAL-1824 corrected copy'n'paste error introduced from JAL-1821 refactor which causes the IndexOutOfBoundException
Jim Procter [Wed, 5 Aug 2015 17:11:27 +0000 (18:11 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 5 Aug 2015 17:11:15 +0000 (18:11 +0100)]
JAL-1821 formatting
Jim Procter [Wed, 5 Aug 2015 17:10:56 +0000 (18:10 +0100)]
JAL-1821 launch the structure view in a separate thread to avoid blocking the UI
Jim Procter [Wed, 5 Aug 2015 17:09:59 +0000 (18:09 +0100)]
JAL-1822 create dataset sequences if they aren’t already created before checking for cDNA/protein mapping
note JAL-407 - should really search for copies of the nucleotides in the local dataset and merge rather than create new ones willynilly!
Jim Procter [Wed, 5 Aug 2015 17:05:08 +0000 (18:05 +0100)]
JAL-1821 JAL-1759 make sure we wait around until the current script has finished before starting superposition
git://source.jalview.org / jalview.git / log