tcofoegbu [Fri, 17 Apr 2015 15:35:03 +0000 (16:35 +0100)]
Merge branch 'bug/JAL-1697_browse-local-structures' into Release_2_8_3_Branch
tcofoegbu [Fri, 17 Apr 2015 15:33:52 +0000 (16:33 +0100)]
JAL-1697 added ablity to select/view cached structures in the new structure chooser interface
tcofoegbu [Fri, 17 Apr 2015 09:39:13 +0000 (10:39 +0100)]
Merge branch 'bug/JAL-1698_Append-Structures' into Release_2_8_3_Branch
tcofoegbu [Fri, 17 Apr 2015 09:34:35 +0000 (10:34 +0100)]
JAL-1698 bug fix to enable addition of a single structure to an already launched structure viewer
gmungoc [Tue, 14 Apr 2015 19:56:29 +0000 (20:56 +0100)]
JAL-1693 generate multiple exon sequences for 1-many dna-protein
mappings
tcofoegbu [Tue, 14 Apr 2015 13:28:04 +0000 (14:28 +0100)]
Merge branch 'bug/Jal-1696_disable-pdb_id-field-settings' into Release_2_8_3_Branch
tcofoegbu [Tue, 14 Apr 2015 13:26:29 +0000 (14:26 +0100)]
JAL-1696 disabled editing of PDB Id field from settings
tcofoegbu [Tue, 14 Apr 2015 08:54:31 +0000 (09:54 +0100)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into Release_2_8_3_Branch
gmungoc [Mon, 13 Apr 2015 15:57:16 +0000 (16:57 +0100)]
JAL-1695 enableSplitFrame=true for applet example
gmungoc [Mon, 13 Apr 2015 15:36:31 +0000 (16:36 +0100)]
JAL-1690 adjusted wording
gmungoc [Mon, 13 Apr 2015 15:22:35 +0000 (16:22 +0100)]
JAL-1693 make exon alignment for get-xref splitframe (with CDS xref)
gmungoc [Mon, 13 Apr 2015 15:03:23 +0000 (16:03 +0100)]
JAL-1681 work around ConcurrentModificationException on startup
gmungoc [Mon, 13 Apr 2015 14:59:59 +0000 (15:59 +0100)]
JAL-1690 show 'scale protein' in protein _and_ dna menus; default true
gmungoc [Mon, 13 Apr 2015 14:58:02 +0000 (15:58 +0100)]
JAL-1695 new property ENABLE_SPLIT_FRAME
gmungoc [Mon, 13 Apr 2015 14:56:31 +0000 (15:56 +0100)]
JAL-1695 parameter controls whether SplitFrame is enabled
gmungoc [Wed, 8 Apr 2015 14:24:29 +0000 (15:24 +0100)]
JAL-1684 adjusting parameters for split frame applet example
gmungoc [Wed, 8 Apr 2015 14:23:17 +0000 (15:23 +0100)]
JAL-1690 scaleProteinAsCdna new applet parameter documented
gmungoc [Wed, 8 Apr 2015 14:22:08 +0000 (15:22 +0100)]
JAL-1270 protection against NullPointer when run as JUnit
gmungoc [Wed, 8 Apr 2015 14:21:23 +0000 (15:21 +0100)]
JAL-1691 applet SplitFrame scrolling; pull up of 5 fields to
AlignmentViewport
gmungoc [Wed, 8 Apr 2015 14:17:55 +0000 (15:17 +0100)]
JAL-1270 separated standalone tests out of Jws2ParamView, interactive
test marked @Ignore
gmungoc [Tue, 7 Apr 2015 08:18:49 +0000 (09:18 +0100)]
JAL-1270 test added
gmungoc [Tue, 7 Apr 2015 08:18:26 +0000 (09:18 +0100)]
JAL-1691 linked scrollling in split frame (Desktop)
gmungoc [Tue, 7 Apr 2015 08:17:00 +0000 (09:17 +0100)]
JAL-1691 defensive check for null
gmungoc [Thu, 2 Apr 2015 14:37:06 +0000 (15:37 +0100)]
JAL-1690 'scale protein as cDNA' options in Preferences, FontChooser
gmungoc [Wed, 1 Apr 2015 13:59:27 +0000 (14:59 +0100)]
JAL-845 fixed start/end range of a mapped SequenceGroup
gmungoc [Wed, 1 Apr 2015 13:57:24 +0000 (14:57 +0100)]
JAL-1264 reinstate Show annotations menu item
gmungoc [Mon, 30 Mar 2015 14:18:25 +0000 (15:18 +0100)]
JAL-1264 remove broken applet build dependencies
gmungoc [Mon, 30 Mar 2015 09:57:40 +0000 (10:57 +0100)]
JAL-1270 fall back on compbio if no localhost:8080/jabaws
gmungoc [Mon, 30 Mar 2015 09:05:22 +0000 (10:05 +0100)]
JAL-1596 refactoring to allow unit tests to start and shut down Chimera
gmungoc [Mon, 30 Mar 2015 09:01:02 +0000 (10:01 +0100)]
JAL-1270 Cache.logger initialisation added
tcofoegbu [Fri, 27 Mar 2015 13:23:42 +0000 (13:23 +0000)]
Merge branch 'merge/JAL-1667_PDBe_Search_API' into Release_2_8_3_Branch
tcofoegbu [Fri, 27 Mar 2015 13:22:09 +0000 (13:22 +0000)]
JAL-1667 updated the collection type for searchSummaryFields and structureSummaryFields preferences
tcofoegbu [Fri, 27 Mar 2015 11:43:50 +0000 (11:43 +0000)]
Merge branch 'merge/JAL-1667_PDBe_Search_API' into Release_2_8_3_Branch
tcofoegbu [Fri, 27 Mar 2015 11:37:34 +0000 (11:37 +0000)]
merge commit
tcofoegbu [Thu, 26 Mar 2015 15:15:39 +0000 (15:15 +0000)]
JAL-1667 updated parseJsonExceptionString method in PDBRestClient.java and its equivalent test case in PDBRestClientTest.java
tcofoegbu [Thu, 26 Mar 2015 12:49:15 +0000 (12:49 +0000)]
Updated BioJsHTMLOutputTest asserts to include error messages for failed Assertions
tcofoegbu [Thu, 26 Mar 2015 12:25:43 +0000 (12:25 +0000)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into Release_2_8_3_Branch
tcofoegbu [Thu, 26 Mar 2015 12:25:12 +0000 (12:25 +0000)]
Modified BioJsHTMLOutputTest to test specific json object values rather than comparing the raw json string values which are not usually ordered
gmungoc [Thu, 26 Mar 2015 11:14:54 +0000 (11:14 +0000)]
Merge develop to Release_2_8_3_Branch
gmungoc [Thu, 26 Mar 2015 09:57:03 +0000 (09:57 +0000)]
JAL-1688 compiler warnings removed
gmungoc [Thu, 26 Mar 2015 09:52:09 +0000 (09:52 +0000)]
JAL-1665 getSequenceFeatures; Desktop.getAlignFrames camel-cased
gmungoc [Wed, 25 Mar 2015 14:06:58 +0000 (14:06 +0000)]
JAL-1270 System.exit(0) changed to fail() so as not to abort test suite
tcofoegbu [Wed, 25 Mar 2015 10:27:43 +0000 (10:27 +0000)]
JAL-1667 clean up commented codes in PopupMenu.java and StructureChooser.java
tcofoegbu [Wed, 25 Mar 2015 09:39:53 +0000 (09:39 +0000)]
JAL-1668 Tab for summary config, auto refresh after config and table column sorting
tcofoegbu [Thu, 19 Mar 2015 14:50:29 +0000 (14:50 +0000)]
JAL-1668 finally clean up
Charles Ofoegbu [Wed, 18 Mar 2015 17:05:03 +0000 (17:05 +0000)]
JAL-1668 house keeping
Charles Ofoegbu [Wed, 18 Mar 2015 10:58:26 +0000 (10:58 +0000)]
JAL-1668 added PDBDocFieldPreference for configuring rest response summary fields
Charles Ofoegbu [Mon, 16 Mar 2015 17:31:16 +0000 (17:31 +0000)]
JAL-1668 added validation for manual entry of pdb structures
Charles Ofoegbu [Sun, 15 Mar 2015 15:10:40 +0000 (15:10 +0000)]
JAL-1667 updated test and internationalization messages
Jim Procter [Mon, 9 Mar 2015 12:52:11 +0000 (12:52 +0000)]
Merge branch 'features/JAL-1565_jpred4' into Release_2_8_3_Branch
Jim Procter [Mon, 9 Mar 2015 12:51:46 +0000 (12:51 +0000)]
JAL-1565 loading a concise file causes insertions to be automatically hidden in desktop
Charles Ofoegbu [Fri, 6 Mar 2015 19:17:14 +0000 (19:17 +0000)]
JAL-1668 added filtering and sorting capabilites
Jim Procter [Fri, 6 Mar 2015 15:29:03 +0000 (15:29 +0000)]
JAL-1683 bump version for r2.8.3 branch
Jim Procter [Fri, 6 Mar 2015 15:26:45 +0000 (15:26 +0000)]
JAL-1683 replace year/version strings with tokens in source
Jim Procter [Fri, 6 Mar 2015 15:13:51 +0000 (15:13 +0000)]
reassign features already created/documented for 2.9 to 2.8.3 JAL-1682
Jim Procter [Fri, 6 Mar 2015 14:44:39 +0000 (14:44 +0000)]
Jim Procter [Fri, 6 Mar 2015 14:42:01 +0000 (14:42 +0000)]
Charles Ofoegbu [Fri, 6 Mar 2015 08:59:38 +0000 (08:59 +0000)]
JAL-1667 refactoring to support JAL-1668
Jim Procter [Thu, 5 Mar 2015 15:48:04 +0000 (15:48 +0000)]
JAL-1678 fix replace token for launchApp in a buildwq
Jim Procter [Thu, 5 Mar 2015 15:05:31 +0000 (15:05 +0000)]
JAL-1678 fix replace token for launchApp in a buildwq
Jim Procter [Thu, 5 Mar 2015 14:36:18 +0000 (14:36 +0000)]
JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this in the future
Jim Procter [Thu, 5 Mar 2015 14:26:38 +0000 (14:26 +0000)]
JAL-1678 add version parameter to example files in publish phase
Jim Procter [Thu, 5 Mar 2015 14:22:21 +0000 (14:22 +0000)]
JAL-1678 add version parameter to example files in publish phase
Jim Procter [Thu, 5 Mar 2015 13:28:35 +0000 (13:28 +0000)]
Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop
Jim Procter [Thu, 5 Mar 2015 13:28:00 +0000 (13:28 +0000)]
JAL-1643 add quaqua libs as OSX specific resources
Charles Ofoegbu [Wed, 4 Mar 2015 20:49:30 +0000 (20:49 +0000)]
JAL-1668 First version JAL-1668
Charles Ofoegbu [Mon, 2 Mar 2015 17:33:27 +0000 (17:33 +0000)]
house keeping
Jim Procter [Fri, 27 Feb 2015 17:01:25 +0000 (17:01 +0000)]
Merge branch 'bug/addcustomlaunchdesktopparams' into develop
Jim Procter [Fri, 27 Feb 2015 17:01:08 +0000 (17:01 +0000)]
JAL-1678 - patch to make sure we only compare positions of the last / or ?
Jim Procter [Fri, 27 Feb 2015 16:58:45 +0000 (16:58 +0000)]
fix for JAL-1678
Charles Ofoegbu [Thu, 26 Feb 2015 18:20:38 +0000 (18:20 +0000)]
JAL-1667 PDBe Search Interface implementation
gmungoc [Thu, 19 Feb 2015 13:14:06 +0000 (13:14 +0000)]
JAL-1665 refactored Sequence.getSequenceFeatures
Jim Procter [Thu, 12 Feb 2015 17:20:51 +0000 (17:20 +0000)]
JAL-1350 added to 2.9 release notes
Jim Procter [Thu, 12 Feb 2015 17:16:04 +0000 (17:16 +0000)]
JAL-1350 document changed behaviour
Jim Procter [Thu, 12 Feb 2015 17:10:45 +0000 (17:10 +0000)]
JAL-1350 forgot to remove empty test
Jim Procter [Thu, 12 Feb 2015 16:50:31 +0000 (16:50 +0000)]
JAL-1350 pass the columnselection rather then selected sequence strings if column-selection exists.
Jim Procter [Thu, 12 Feb 2015 16:49:32 +0000 (16:49 +0000)]
JAL-1350 cloned method and tested equivalence for using column selection to subdivide groups
Jim Procter [Thu, 12 Feb 2015 16:47:49 +0000 (16:47 +0000)]
JAL-1115 switch to lists in SequenceGroup
Jim Procter [Thu, 12 Feb 2015 16:47:18 +0000 (16:47 +0000)]
JAL-1115 typecast
Jim Procter [Thu, 12 Feb 2015 16:46:57 +0000 (16:46 +0000)]
javadoc
Jim Procter [Thu, 12 Feb 2015 16:46:44 +0000 (16:46 +0000)]
JAL-1115 List rather than vector for sequence groups (minimal additional synchronized clauses added)
Jim Procter [Fri, 6 Feb 2015 10:59:33 +0000 (10:59 +0000)]
Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop
Conflicts:
.classpath
Charles Ofoegbu [Thu, 5 Feb 2015 17:10:39 +0000 (17:10 +0000)]
merge commit
Jim Procter [Thu, 5 Feb 2015 10:51:18 +0000 (10:51 +0000)]
JAL-1643 jarred up the quaqua native libraries and added nativelib
resource tags for Mac OS X
Jim Procter [Thu, 5 Feb 2015 10:33:04 +0000 (10:33 +0000)]
JAL-1643 added quaqua filechooser and jni libraries to the InstallAnywhere distribution
Jim Procter [Thu, 5 Feb 2015 10:23:39 +0000 (10:23 +0000)]
JAL-1643 correct version of quaqua (8) plus THIRDPARTYLIB details
Jim Procter [Thu, 5 Feb 2015 10:19:07 +0000 (10:19 +0000)]
JAL-1643 renamed quaqua library to add version number
Charles Ofoegbu [Wed, 4 Feb 2015 06:04:47 +0000 (06:04 +0000)]
JAL-1643 modified jalviewFileChooser to retain default behaviour on other non-mac platforms
Charles Ofoegbu [Wed, 4 Feb 2015 05:39:03 +0000 (05:39 +0000)]
JAL-1643 Modified JalviewFileChooser to have a more native laf on mac
Charles Ofoegbu [Mon, 2 Feb 2015 20:35:48 +0000 (20:35 +0000)]
Merge branch 'bug/JAL-1644_Finder-logic-improvement' into develop
Charles Ofoegbu [Mon, 2 Feb 2015 20:34:32 +0000 (20:34 +0000)]
JAL-1644 added null check for sequence description field
Charles Ofoegbu [Mon, 2 Feb 2015 15:49:53 +0000 (15:49 +0000)]
Merge commit
Charles Ofoegbu [Mon, 2 Feb 2015 15:45:32 +0000 (15:45 +0000)]
JAL-1644 revised Finder's implementation to use a flag to enalbe searching an alignment's sequences description field
Charles Ofoegbu [Mon, 2 Feb 2015 10:32:14 +0000 (10:32 +0000)]
Merge branch 'bug/JAL-1644_Finder-logic-improvement' into develop
Charles Ofoegbu [Mon, 2 Feb 2015 10:30:13 +0000 (10:30 +0000)]
JAL-1644 improvment of finder logic to include the sequence description field
Jim Procter [Wed, 28 Jan 2015 15:29:32 +0000 (15:29 +0000)]
JAL-1565 automatically mark query sequence as the sequence reference and hide any insertions to it
Jim Procter [Wed, 28 Jan 2015 11:13:47 +0000 (11:13 +0000)]
JAL-674 patch to make Mapping.compareTransferredToRefPDBAnnot test
pass
otherwise addAll throws an index not found exception with
inspos==-1
Jim Procter [Tue, 27 Jan 2015 17:18:05 +0000 (17:18 +0000)]
JAL-674 JAL-1270 added settings to ensure temperature and secondary
structure are propagated and finer grain checks on presence of annotation
gmungoc [Tue, 27 Jan 2015 08:58:12 +0000 (08:58 +0000)]
JAL-1588 new class renamed
gmungoc [Mon, 26 Jan 2015 16:45:29 +0000 (16:45 +0000)]
Merge branch 'features/JAL-1588saveChimeraSession' into develop
git://source.jalview.org / jalview.git / log