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
gmungoc [Mon, 26 Jan 2015 16:42:56 +0000 (16:42 +0000)]
JAL-1588 restoring saved Chimera session(s)
Charles Ofoegbu [Fri, 23 Jan 2015 16:49:49 +0000 (16:49 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
gmungoc [Fri, 23 Jan 2015 16:49:19 +0000 (16:49 +0000)]
JAL-1588 first working (?) restore of Chimera session incl bindings
Charles Ofoegbu [Fri, 23 Jan 2015 16:47:20 +0000 (16:47 +0000)]
JAL-1553 added help documentation and updated AnnotationColumnChooser to exclude MigLayout as it is not supported in applets
Jim Procter [Fri, 23 Jan 2015 15:40:14 +0000 (15:40 +0000)]
Merge branch 'feature_29/JAL-1372_referenceseq' into develop
Jim Procter [Fri, 23 Jan 2015 15:33:06 +0000 (15:33 +0000)]
JAL-1541 changed assert to JUnit assert - test now fails for current version of BioJS export method
Jim Procter [Fri, 23 Jan 2015 15:32:05 +0000 (15:32 +0000)]
JAL-1551 formatting
Jim Procter [Fri, 23 Jan 2015 15:31:26 +0000 (15:31 +0000)]
JAL-1286 don't print an exception if a non-gzip stream is attempted to be opened as gzip
Jim Procter [Fri, 23 Jan 2015 15:17:26 +0000 (15:17 +0000)]
JAL-1551 crlf changes
Jim Procter [Fri, 23 Jan 2015 14:11:14 +0000 (14:11 +0000)]
JAL-969 hasHiddenRows is now an interface method
Jim Procter [Fri, 23 Jan 2015 14:10:20 +0000 (14:10 +0000)]
JAL-969 drop the hiddenColumns flag in favour of checking current state of columnSelection
Jim Procter [Fri, 23 Jan 2015 14:06:11 +0000 (14:06 +0000)]
Merge branch 'develop' into feature_29/JAL-1372_referenceseq
finessing between two branches where bugs are patched twice
Conflicts:
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/datamodel/ColumnSelection.java
Jim Procter [Fri, 23 Jan 2015 13:14:58 +0000 (13:14 +0000)]
JAL-1628 tweak signature of core annotation printer for outputting hidden columns and view names via VIEW_HIDECOLS and VIEW_DEF
Jim Procter [Fri, 23 Jan 2015 13:13:44 +0000 (13:13 +0000)]
JAL-1551 formatting/imports
Jim Procter [Fri, 23 Jan 2015 13:13:03 +0000 (13:13 +0000)]
JAL-1551 JAL-962 formatting and code change ripples from changing HiddenColumns & accessor from Vector to List<int[]>
Charles Ofoegbu [Fri, 23 Jan 2015 10:38:46 +0000 (10:38 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Fri, 23 Jan 2015 10:37:58 +0000 (10:37 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Charles Ofoegbu [Fri, 23 Jan 2015 10:37:09 +0000 (10:37 +0000)]
JAL-1553 fixed null pointer exception thrown in SeqCanvas and ScalePanel of jalview applet while attempting to redraw the panels when hidden columns no longer exists
Jim Procter [Fri, 23 Jan 2015 09:05:17 +0000 (09:05 +0000)]
JAL-1551 source code formatting
Jim Procter [Fri, 23 Jan 2015 09:04:27 +0000 (09:04 +0000)]
JAL-969 javadoc and mark interface overrides for clarity
Jim Procter [Fri, 23 Jan 2015 08:59:19 +0000 (08:59 +0000)]
JAL-1628 drop getShowAnnotation accessor in favour of isShowAnnotation in AlignViewportI and change method signature for printing annotation files to allow view (for column selection) and alignment object to be accessed
Charles Ofoegbu [Thu, 22 Jan 2015 18:34:45 +0000 (18:34 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Thu, 22 Jan 2015 18:33:43 +0000 (18:33 +0000)]
JAL-1553 added applet support for the select-column-by-annotation-row feature
Jim Procter [Thu, 22 Jan 2015 17:28:43 +0000 (17:28 +0000)]
JAL-1372 JAL-1169 documentation for new commands HIDE_INSERTIONS AND VIEW_SETREF
Jim Procter [Wed, 21 Jan 2015 15:04:37 +0000 (15:04 +0000)]
Merge branch 'develop' into feature_29/JAL-1372_referenceseq
Jim Procter [Wed, 21 Jan 2015 10:36:38 +0000 (10:36 +0000)]
tidy up class files that shouldn't be in repo
Charles Ofoegbu [Tue, 20 Jan 2015 17:28:21 +0000 (17:28 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Tue, 20 Jan 2015 17:27:26 +0000 (17:27 +0000)]
clean up
Charles Ofoegbu [Tue, 20 Jan 2015 17:25:35 +0000 (17:25 +0000)]
clean up
Charles Ofoegbu [Tue, 20 Jan 2015 17:22:45 +0000 (17:22 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Tue, 20 Jan 2015 17:20:40 +0000 (17:20 +0000)]
Further abstractions and clean up
Charles Ofoegbu [Tue, 20 Jan 2015 15:04:37 +0000 (15:04 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Tue, 20 Jan 2015 15:02:05 +0000 (15:02 +0000)]
basic house keeping
git://source.jalview.org / jalview.git / log