Jim Procter [Mon, 15 Jun 2015 17:39:28 +0000 (18:39 +0100)]
JAL-1775 patch for regression from Anne Menard’s pseudo knot support JAL-1598
Jim Procter [Mon, 15 Jun 2015 16:06:51 +0000 (17:06 +0100)]
JAL-1775 patch regression bug when displayChar is null and secondaryStructure contains secondary structure info
Jim Procter [Mon, 15 Jun 2015 15:08:47 +0000 (16:08 +0100)]
fix for JAL-1775 (and reorganise imports)
Jim Procter [Mon, 15 Jun 2015 13:03:22 +0000 (14:03 +0100)]
JAL-1775 test demonstrating bug
Jim Procter [Mon, 15 Jun 2015 13:03:07 +0000 (14:03 +0100)]
JAL-1775 FileLoader javadoc
Jim Procter [Mon, 15 Jun 2015 13:02:37 +0000 (14:02 +0100)]
Jim Procter [Mon, 15 Jun 2015 12:37:44 +0000 (13:37 +0100)]
Merge branch 'develop' into bug/JAL-1775
gmungoc [Mon, 15 Jun 2015 11:19:54 +0000 (12:19 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 15 Jun 2015 11:18:55 +0000 (12:18 +0100)]
JAL-1778 deregister as a listener when panel closed
Jim Procter [Mon, 15 Jun 2015 10:42:52 +0000 (11:42 +0100)]
JAL-1775 fix broken test due to missing file (RF0031_unfolded).
tcofoegbu [Mon, 15 Jun 2015 10:39:23 +0000 (11:39 +0100)]
JAL-1641 clean up
tcofoegbu [Mon, 15 Jun 2015 10:29:46 +0000 (11:29 +0100)]
JAL-1641 docs for ComplexAlignFile interface
tcofoegbu [Mon, 15 Jun 2015 09:31:04 +0000 (10:31 +0100)]
clean up
tcofoegbu [Fri, 12 Jun 2015 16:52:28 +0000 (17:52 +0100)]
merge
tcofoegbu [Fri, 12 Jun 2015 16:50:02 +0000 (17:50 +0100)]
JAL-1627 removed extra spaces at end of tooltip
tcofoegbu [Fri, 12 Jun 2015 16:43:51 +0000 (17:43 +0100)]
JAL-1641 refactor
tcofoegbu [Wed, 10 Jun 2015 15:50:03 +0000 (16:50 +0100)]
updated build.xml
gmungoc [Wed, 10 Jun 2015 14:23:52 +0000 (15:23 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 10 Jun 2015 14:23:33 +0000 (15:23 +0100)]
Merge remote-tracking branch
'origin/schema/JAL-1764_structureViewAttribute' into develop
JAL-1764 save structure viewer type in project file
tcofoegbu [Wed, 10 Jun 2015 14:20:04 +0000 (15:20 +0100)]
merge
tcofoegbu [Wed, 10 Jun 2015 14:19:01 +0000 (15:19 +0100)]
JAL-1641 updated applet version
gmungoc [Wed, 10 Jun 2015 10:25:08 +0000 (11:25 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 10 Jun 2015 10:23:17 +0000 (11:23 +0100)]
JAL-1764 save Chimera/Jmol state as separate entries in project Jar
Jim Procter [Wed, 10 Jun 2015 10:19:17 +0000 (11:19 +0100)]
JAL-1764 add structure view type attribute to project schema
tcofoegbu [Tue, 9 Jun 2015 15:03:54 +0000 (16:03 +0100)]
merge commit
tcofoegbu [Tue, 9 Jun 2015 15:01:48 +0000 (16:01 +0100)]
JAL-1488 bug-fix for incorrect start/end position in flatfiles exported from alignments with hidden columns
gmungoc [Mon, 8 Jun 2015 14:05:35 +0000 (15:05 +0100)]
JAl-1421 fix method reflection argument (properly this time)
gmungoc [Mon, 8 Jun 2015 12:29:00 +0000 (13:29 +0100)]
JAL-1421 undid premature 'improvement' of method parameter to interface
tcofoegbu [Fri, 5 Jun 2015 16:12:41 +0000 (17:12 +0100)]
Merge branch 'bug/JAL-1760_restore-hidden-seqs' into develop
tcofoegbu [Fri, 5 Jun 2015 16:08:15 +0000 (17:08 +0100)]
JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability to retrieve hidden Seqs
gmungoc [Fri, 5 Jun 2015 15:26:15 +0000 (16:26 +0100)]
JAL-1752 structure highlight scoped to only its mapped sequences
gmungoc [Fri, 5 Jun 2015 14:51:07 +0000 (15:51 +0100)]
JAL-1588 error dialog if Chimera project opened on a m/c w/o Chimera
gmungoc [Fri, 5 Jun 2015 14:15:01 +0000 (15:15 +0100)]
JAL-1622 fix bug computing superposition + associated refactorings
gmungoc [Fri, 5 Jun 2015 14:09:25 +0000 (15:09 +0100)]
JAL-1746 return empty string rather than null in getStateInfo
gmungoc [Fri, 5 Jun 2015 13:59:21 +0000 (14:59 +0100)]
JAL-1622 Chimera command timeout increased to 5 secs (+minor changes)
gmungoc [Fri, 5 Jun 2015 13:52:10 +0000 (14:52 +0100)]
JAL-1622 duplicate assignment removed (no functional change)
gmungoc [Fri, 5 Jun 2015 13:49:22 +0000 (14:49 +0100)]
JAL-1753 JAL-1596 asynchronous command to Chimera (with progress update)
gmungoc [Fri, 5 Jun 2015 13:43:00 +0000 (14:43 +0100)]
JAL-1622 code tidy only, no functional change
gmungoc [Fri, 5 Jun 2015 12:54:18 +0000 (13:54 +0100)]
JAL-1749 correcting snafu in last commit
gmungoc [Thu, 4 Jun 2015 15:29:40 +0000 (16:29 +0100)]
Clear status bar message when initialisation complete
gmungoc [Thu, 4 Jun 2015 15:09:30 +0000 (16:09 +0100)]
JAL-1750 small tidy of AlignSeq.printMapping (+Junit)
gmungoc [Thu, 4 Jun 2015 14:40:27 +0000 (15:40 +0100)]
JAL-1544 spelling in javadoc only
gmungoc [Thu, 4 Jun 2015 14:39:29 +0000 (15:39 +0100)]
JAL-1622 code tidy (+Junit) of collateForPdb()
gmungoc [Thu, 4 Jun 2015 14:07:41 +0000 (15:07 +0100)]
JAL-1747 close all windows on Quit (+small bug fix)
gmungoc [Thu, 4 Jun 2015 13:43:53 +0000 (14:43 +0100)]
toString method added to aid viewing in the debugger
gmungoc [Thu, 4 Jun 2015 13:43:12 +0000 (14:43 +0100)]
JAL-1270 testToString added
gmungoc [Thu, 4 Jun 2015 13:37:13 +0000 (14:37 +0100)]
JAL-1750 View Mapping scoped to that viewer's mappings only
gmungoc [Thu, 4 Jun 2015 13:08:04 +0000 (14:08 +0100)]
JAL-1743 new Chimera menu option to 'fit to window'
gmungoc [Thu, 4 Jun 2015 13:01:27 +0000 (14:01 +0100)]
JAL-1743 View Chain sub-menu now being populated
gmungoc [Thu, 4 Jun 2015 12:53:21 +0000 (13:53 +0100)]
JAL-1753 statusPanel added (for ProgressBar); 'Fit to Window' menu
option added
gmungoc [Thu, 4 Jun 2015 12:40:55 +0000 (13:40 +0100)]
JAL-1753 ChimeraViewFrame hosts its own ProgressBar
gmungoc [Thu, 4 Jun 2015 11:05:55 +0000 (12:05 +0100)]
JAL-1742 don't offer to align another chain to the same structure
gmungoc [Thu, 4 Jun 2015 10:51:47 +0000 (11:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jun 2015 10:51:28 +0000 (11:51 +0100)]
JAL-1757 match only first altloc CA in PDB structure for superposition
tcofoegbu [Thu, 4 Jun 2015 10:45:31 +0000 (11:45 +0100)]
JAL-1641 added some JSON libraries to appletlib
tcofoegbu [Thu, 4 Jun 2015 10:20:42 +0000 (11:20 +0100)]
clean up
tcofoegbu [Thu, 4 Jun 2015 10:12:03 +0000 (11:12 +0100)]
JAL-1756 fix failed test as a result of runing the BioJS updater from a new thread
gmungoc [Thu, 4 Jun 2015 10:07:28 +0000 (11:07 +0100)]
JAL-1421 generic collections in MCView package (+unit tests)
tcofoegbu [Thu, 4 Jun 2015 09:52:06 +0000 (10:52 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Thu, 4 Jun 2015 09:42:08 +0000 (10:42 +0100)]
JAL-1756 bug-fix
tcofoegbu [Thu, 4 Jun 2015 09:04:47 +0000 (10:04 +0100)]
JAL-1641 updated json schema to make it more generic in order to accomodate more dynamic parameters
tcofoegbu [Tue, 2 Jun 2015 16:59:23 +0000 (17:59 +0100)]
fixed bug in build.xml
tcofoegbu [Tue, 2 Jun 2015 15:51:56 +0000 (16:51 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 15:51:30 +0000 (16:51 +0100)]
JAL-1641 updated build.xml
tcofoegbu [Tue, 2 Jun 2015 14:54:44 +0000 (15:54 +0100)]
JAL-1641 updated examples/applets.html
tcofoegbu [Tue, 2 Jun 2015 14:12:45 +0000 (15:12 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 14:11:50 +0000 (15:11 +0100)]
JAL-1641 applet build fix
tcofoegbu [Mon, 1 Jun 2015 15:59:19 +0000 (16:59 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Mon, 1 Jun 2015 15:58:38 +0000 (16:58 +0100)]
JAL-1641 remove all refs/imports from gui package
tcofoegbu [Mon, 1 Jun 2015 14:23:16 +0000 (15:23 +0100)]
Merge branch 'bug/JAL-1703_hint_select_by_annot' into develop
tcofoegbu [Mon, 1 Jun 2015 14:19:06 +0000 (15:19 +0100)]
JAL-1703 added tooltip hints to components of the Select by Annotation UI
tcofoegbu [Mon, 1 Jun 2015 10:15:34 +0000 (11:15 +0100)]
Merge branch 'bug/JAL-1734_misleading-progress-bar' into develop
tcofoegbu [Mon, 1 Jun 2015 10:15:04 +0000 (11:15 +0100)]
JAL-1734 updated progress bar messages
tcofoegbu [Fri, 29 May 2015 15:41:21 +0000 (16:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 29 May 2015 15:41:10 +0000 (16:41 +0100)]
JAL-1748 house keeping
gmungoc [Fri, 29 May 2015 13:56:48 +0000 (14:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 13:56:36 +0000 (14:56 +0100)]
JAL-1753 declare field with interface type; check for null dereference
Jim Procter [Fri, 29 May 2015 13:23:34 +0000 (14:23 +0100)]
Merge branch 'JAL-1755_npe_groupconsensus' into develop
Jim Procter [Fri, 29 May 2015 13:22:38 +0000 (14:22 +0100)]
JAL-1755 fix for NPE when setting up temporary variables
gmungoc [Fri, 29 May 2015 13:07:56 +0000 (14:07 +0100)]
JAL-1753 Junit for new class
gmungoc [Fri, 29 May 2015 11:06:20 +0000 (12:06 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 11:01:09 +0000 (12:01 +0100)]
JAL-1753 duplicated code refactored to new class ProgressBar
tcofoegbu [Fri, 29 May 2015 10:22:37 +0000 (11:22 +0100)]
Merge branch 'bug/JAL-1748_extend-pdb-query-opt' into develop
tcofoegbu [Fri, 29 May 2015 10:21:04 +0000 (11:21 +0100)]
JAL-1748 and employ preprocessing routine when return action event is triggered
tcofoegbu [Fri, 29 May 2015 08:53:50 +0000 (09:53 +0100)]
validate PDB selections on mouse release event
tcofoegbu [Thu, 28 May 2015 15:47:25 +0000 (16:47 +0100)]
JAL-1700 made PDB service error mechanism more user friendly
tcofoegbu [Thu, 28 May 2015 10:46:35 +0000 (11:46 +0100)]
Merge branch 'bug/JAL-1751_make-table-uneditable' into develop
tcofoegbu [Thu, 28 May 2015 10:45:50 +0000 (11:45 +0100)]
JAL-1751 provided method to overide isCellEditable for the PDB response table model
tcofoegbu [Thu, 28 May 2015 10:05:00 +0000 (11:05 +0100)]
Merge branch 'bug/JAL-1749_reinstate-rna-viewing' into develop
tcofoegbu [Thu, 28 May 2015 10:03:04 +0000 (11:03 +0100)]
JAL-1749 reinstated the ability to view RNA structures
tcofoegbu [Thu, 28 May 2015 08:20:33 +0000 (09:20 +0100)]
JAL-1740 minor house keeping
tcofoegbu [Wed, 27 May 2015 17:01:16 +0000 (18:01 +0100)]
Removed redundant classes and dependencies pulled in from last merge of features/JAL-1740_Decoup-BioJS branch
tcofoegbu [Wed, 27 May 2015 16:55:38 +0000 (17:55 +0100)]
Merge branch 'features/JAL-1740_Decoup-BioJS' into develop
tcofoegbu [Wed, 27 May 2015 16:49:47 +0000 (17:49 +0100)]
JAL-1740 updated synch codes to use a git repo rather than FTP
tcofoegbu [Tue, 26 May 2015 11:44:16 +0000 (12:44 +0100)]
JAL-1627 bug fix to remove wierd space in Sequence Features/Sequence Group tooltip on windows
tcofoegbu [Mon, 25 May 2015 15:04:22 +0000 (16:04 +0100)]
build fix
tcofoegbu [Fri, 22 May 2015 16:03:32 +0000 (17:03 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 16:02:55 +0000 (17:02 +0100)]
JAL-1745, JAL-1717 improvement to ensure cached PDB entries are unique within a sequence. Also only truly downloaded files should be shown in the cache view
tcofoegbu [Fri, 22 May 2015 11:09:58 +0000 (12:09 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 11:09:09 +0000 (12:09 +0100)]
JAL-1745 improvement to retreive already downloaded pdb structure file from cache
git://source.jalview.org / jalview.git / log