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
Jim Procter [Wed, 5 Aug 2015 17:04:15 +0000 (18:04 +0100)]
JAL-1821 patch for completeness - first model number is zero
tcofoegbu [Tue, 4 Aug 2015 17:05:42 +0000 (18:05 +0100)]
JAL-1816 fixed bug in identify file preventing it from identifying a Fasta file containing a right angle bracket in its annotation
tcofoegbu [Tue, 4 Aug 2015 15:16:48 +0000 (16:16 +0100)]
JAL-1821 updated implementation of launchStructureViewer method to use currently selected sequences instead of trying to collate them from the viewport (as suggested by Jim)
tcofoegbu [Tue, 4 Aug 2015 10:25:15 +0000 (11:25 +0100)]
updated the reference sequence column of cached structure summary table to hold the actual object
tcofoegbu [Tue, 4 Aug 2015 09:54:10 +0000 (10:54 +0100)]
JAL-1788 updated biojson docs
tcofoegbu [Tue, 4 Aug 2015 09:49:26 +0000 (10:49 +0100)]
JAL-1821 updated the reference sequence column of structure chooser summary table to hold the actual object
Jim Procter [Mon, 3 Aug 2015 15:48:54 +0000 (16:48 +0100)]
JAL-1821 JAL-1759 reinstate rotation speed configuration - parameter has some effect in 14.2
Jim Procter [Mon, 3 Aug 2015 14:45:49 +0000 (15:45 +0100)]
JAL-1821 JAL-1759 updated Jmol has different model behaviour - select model * to show all models. Need to check behaviour with multimodel files
Jim Procter [Mon, 3 Aug 2015 14:44:19 +0000 (15:44 +0100)]
JAL-1821 avoid race condition when multiple structures loaded in Jmol where getFiles() returns {null} and waitUntilLoad times out rather than performs superposition
tcofoegbu [Thu, 30 Jul 2015 10:32:27 +0000 (11:32 +0100)]
JAL-1443 modified exception notifications
tcofoegbu [Thu, 30 Jul 2015 10:18:43 +0000 (11:18 +0100)]
JAL-1710 filtered colons(:) from structure chooser query as it conflicts with solr queries and results in exceptions
tcofoegbu [Wed, 29 Jul 2015 13:44:58 +0000 (14:44 +0100)]
JAL-1821 discarded sequence name truncation in summary table
Jim Procter [Thu, 23 Jul 2015 18:03:21 +0000 (19:03 +0100)]
Merge branch 'features/JAL-1759jmolUpdate' into develop
updates from revisions due to JAL-1805
Jim Procter [Thu, 23 Jul 2015 17:52:39 +0000 (18:52 +0100)]
JAL-1759 formatting
Jim Procter [Thu, 23 Jul 2015 17:52:26 +0000 (18:52 +0100)]
JAL-1759 reinstate changes from
bdfde6ef989da0702cef90f03858f0f30e0bc83a
lost during merge.
Jim Procter [Thu, 23 Jul 2015 17:49:16 +0000 (18:49 +0100)]
JAL-1759 formatting
Jim Procter [Thu, 23 Jul 2015 16:19:57 +0000 (17:19 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 23 Jul 2015 12:15:59 +0000 (13:15 +0100)]
Merge branch 'task/JAL-1794_jettyExamplesServer' into develop
tcofoegbu [Thu, 23 Jul 2015 11:44:08 +0000 (12:44 +0100)]
Resolved merge conflict in EdtiCommandTest.java
tcofoegbu [Thu, 23 Jul 2015 11:40:24 +0000 (12:40 +0100)]
JAL-1805 modified test setup's so the are ran for groups which requires them
tcofoegbu [Thu, 23 Jul 2015 10:31:22 +0000 (11:31 +0100)]
JAL-1819 Test cases for Identify file
Jim Procter [Thu, 23 Jul 2015 10:30:56 +0000 (11:30 +0100)]
Merge branch 'bug/JAL-1819_isNaN' into develop
Jim Procter [Thu, 23 Jul 2015 10:27:57 +0000 (11:27 +0100)]
JAL-1819 commented out debugging message to stderr
Jim Procter [Thu, 23 Jul 2015 10:27:15 +0000 (11:27 +0100)]
JAL-1551 JAL-1819 formatting/imports
Jim Procter [Thu, 23 Jul 2015 10:26:11 +0000 (11:26 +0100)]
JAL-1819 use Float.isNaN() to check for NaNs!
Jim Procter [Wed, 22 Jul 2015 17:05:06 +0000 (18:05 +0100)]
JAL-1805 add group spec to the BeforeMethod setup - updated the TESTNG entry to show improvement.
Jim Procter [Wed, 22 Jul 2015 16:54:04 +0000 (17:54 +0100)]
JAL-1782 added summary test report for Release_2_9_Branch - Functional tests only
tcofoegbu [Wed, 22 Jul 2015 08:55:42 +0000 (09:55 +0100)]
JAL-1667 JAL-1668 JAL-1553 help docs update
tcofoegbu [Tue, 21 Jul 2015 17:02:03 +0000 (18:02 +0100)]
Merge
tcofoegbu [Tue, 21 Jul 2015 16:59:01 +0000 (17:59 +0100)]
JAL-1443 bugfix to prevent loading of unidentifiable gibberish data
Jim Procter [Tue, 21 Jul 2015 13:53:27 +0000 (14:53 +0100)]
Merge branch 'ismb/2015_demo' into develop
Jim Procter [Thu, 16 Jul 2015 15:19:39 +0000 (16:19 +0100)]
revision for JAL-1749 - ensure view 2D structure menu is removed when no structures are available
Jim Procter [Thu, 16 Jul 2015 15:18:19 +0000 (16:18 +0100)]
fix for JAL-1776 renamed popup menu entry
tcofoegbu [Wed, 15 Jul 2015 13:27:54 +0000 (14:27 +0100)]
updated version info in seqfetch.html
tcofoegbu [Wed, 15 Jul 2015 13:26:26 +0000 (14:26 +0100)]
JAL-1553 reviewed & updated docs
tcofoegbu [Wed, 15 Jul 2015 13:25:15 +0000 (14:25 +0100)]
JAL-1667 JAL-1668 updated reviewed and updated docs
git://source.jalview.org / jalview.git / log