Jim Procter [Thu, 12 Feb 2015 17:21:22 +0000 (17:21 +0000)]
Merge branch 'improvement/JAL-1350_makegroups_markedcolumns' into merge/JAL-845_JAL-1640
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 17:10:45 +0000 (17:10 +0000)]
JAL-1350 forgot to remove empty test
Jim Procter [Thu, 12 Feb 2015 17:05:17 +0000 (17:05 +0000)]
Merge branch 'improvement/JAL-1350_makegroups_markedcolumns' into merge/JAL-845_JAL-1640
Conflicts:
src/jalview/datamodel/SequenceGroup.java
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)
gmungoc [Thu, 12 Feb 2015 09:33:05 +0000 (09:33 +0000)]
Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into
features/JAL-845splitPaneMergeDevelop
Conflicts:
src/jalview/gui/Desktop.java
gmungoc [Wed, 11 Feb 2015 12:26:31 +0000 (12:26 +0000)]
JAL-845 handling eXpand/Gather split frame views
gmungoc [Wed, 11 Feb 2015 12:24:51 +0000 (12:24 +0000)]
JAL-1264 button labels (for panel currently not linked in menu)
Jim Procter [Wed, 11 Feb 2015 09:23:42 +0000 (09:23 +0000)]
JAL-1655 JAL-845 special support to set column width of protein panel 3*width of dna panel - probably should refactor logic to a SplitFrame.setStyle method call..
Jim Procter [Wed, 11 Feb 2015 09:19:55 +0000 (09:19 +0000)]
JAL-845 avoid OOBException when method is called with only one view
Jim Procter [Wed, 11 Feb 2015 09:16:45 +0000 (09:16 +0000)]
JAL-969 use AlignViewportI interface instance where ever possible in method signatures
Jim Procter [Wed, 11 Feb 2015 09:06:22 +0000 (09:06 +0000)]
JAL-1654 allow font to be specified without modifying column width
Jim Procter [Tue, 10 Feb 2015 17:11:11 +0000 (17:11 +0000)]
note about preserving/reinstating custom grid geometry for alignment (JAL-470) and for cDNA/protein JAL-845
Jim Procter [Tue, 10 Feb 2015 17:08:51 +0000 (17:08 +0000)]
JAL-1640 make font-size changes modify grid size again
Jim Procter [Tue, 10 Feb 2015 16:21:54 +0000 (16:21 +0000)]
JAL-845 - portability patch - workaround for lastToken failing for '\'
Jim Procter [Tue, 10 Feb 2015 15:57:41 +0000 (15:57 +0000)]
added comment to @gmungoc todo about referencing PDB entities in Javascript - also verified JAL-592 is now a bug again and can be reproduced :(
Jim Procter [Tue, 10 Feb 2015 15:35:48 +0000 (15:35 +0000)]
JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought
Jim Procter [Tue, 10 Feb 2015 14:57:50 +0000 (14:57 +0000)]
JAL-1382 slightly more efficient detection of non-gap entry in deleted region of sequence
Jim Procter [Tue, 10 Feb 2015 14:56:36 +0000 (14:56 +0000)]
JAL-1382 @mungo TODO done: use StringUtils for delete chars
Jim Procter [Tue, 10 Feb 2015 14:29:38 +0000 (14:29 +0000)]
JAL-966 @mungo TODO complete: List rather than bare int array
gmungoc [Tue, 10 Feb 2015 10:24:25 +0000 (10:24 +0000)]
JAL-1264 unit tests fixed (have to explicit set annotation sort order)
Jim Procter [Mon, 9 Feb 2015 16:06:40 +0000 (16:06 +0000)]
Merge branch 'features/JAL-845splitPaneMergeDevelop' into merge_JAL-845_JAL-1640
minimal conflicts where list accessors were used in methods where logic
also modified on Desktop
Conflicts:
.classpath
resources/lang/Messages.properties
src/jalview/api/AlignViewportI.java
src/jalview/gui/Desktop.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/TreeCanvas.java
src/jalview/viewmodel/AlignmentViewport.java
Jim Procter [Mon, 9 Feb 2015 15:30:40 +0000 (15:30 +0000)]
Merge branch 'develop' into JAL-1640_stylesettings
gmungoc [Mon, 9 Feb 2015 10:13:16 +0000 (10:13 +0000)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-845splitPaneMergeDevelop
Conflicts:
resources/lang/Messages.properties
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/Desktop.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/TreePanel.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/AWSThread.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java
gmungoc [Fri, 6 Feb 2015 14:12:19 +0000 (14:12 +0000)]
JAL-845 further code/tests/refactoring
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
Jim Procter [Fri, 6 Feb 2015 10:54:31 +0000 (10:54 +0000)]
JAL-1640 new menu allowing view settings to be transferred from any other view on the desktop
Jim Procter [Fri, 6 Feb 2015 10:52:08 +0000 (10:52 +0000)]
JAL-1640 Desktop.getAlignmentPanel and Desktop.getViewports can now take a null argument to get all alignment panels or viewports in the Desktop
Jim Procter [Fri, 6 Feb 2015 10:50:51 +0000 (10:50 +0000)]
JAL-1551 formatting
Jim Procter [Fri, 6 Feb 2015 10:50:05 +0000 (10:50 +0000)]
JAL-1640 more properties moved to style bean and rationalisation of layout update logic (wrap/non-wrap,idwidth,etc) to smaller number of methods
Jim Procter [Fri, 6 Feb 2015 10:44:04 +0000 (10:44 +0000)]
JAL-1551 formatting
Jim Procter [Fri, 6 Feb 2015 10:37:52 +0000 (10:37 +0000)]
JAL-1640 JAL-966 is for boolean getter on AlignViewportI
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
gmungoc [Tue, 3 Feb 2015 16:51:27 +0000 (16:51 +0000)]
comment only
gmungoc [Tue, 3 Feb 2015 16:51:16 +0000 (16:51 +0000)]
JAL-845 column mapping speed-up
gmungoc [Tue, 3 Feb 2015 16:50:22 +0000 (16:50 +0000)]
JAL-845 SplitFrame key bindings delegation to AlignFrame menu actions
gmungoc [Tue, 3 Feb 2015 16:49:47 +0000 (16:49 +0000)]
JAL-845 preparation for awareness of AlignFrame in SplitFrame for save
gmungoc [Tue, 3 Feb 2015 11:13:53 +0000 (11:13 +0000)]
JAL-845 redundant 'map to self' removed from buildSearchResults
gmungoc [Tue, 3 Feb 2015 11:13:19 +0000 (11:13 +0000)]
Comments added
gmungoc [Tue, 3 Feb 2015 10:53:56 +0000 (10:53 +0000)]
JAL-845 code/refactoring/tests related to linking DNA and protein
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
Jim Procter [Mon, 2 Feb 2015 18:16:44 +0000 (18:16 +0000)]
JAL-1640 setStyle method and associated tests (required a sameStyle method to be added to interface to test ViewStyleI equivalence)
Jim Procter [Mon, 2 Feb 2015 18:14:44 +0000 (18:14 +0000)]
JAL-966 allow access to viewport interface from alignPanel
Jim Procter [Mon, 2 Feb 2015 17:41:46 +0000 (17:41 +0000)]
JAL-1640 getters and setters for viewStyleI - note the caller needs to trigger view repaints themselves after setting the ViewStyleI for a view
Jim Procter [Mon, 2 Feb 2015 17:40:41 +0000 (17:40 +0000)]
JAL-1640 copy constructor test and implementation by reflection
Jim Procter [Mon, 2 Feb 2015 16:43:10 +0000 (16:43 +0000)]
JAL-715 tweaks for SRBS description string parsing
Jim Procter [Mon, 2 Feb 2015 16:42:13 +0000 (16:42 +0000)]
JAL-1161 JAL-1606 note about awt/swing dependency in interface
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
Jim Procter [Mon, 2 Feb 2015 11:56:54 +0000 (11:56 +0000)]
JAL-1640 JAL-1551 formatting/imports/remove dead code
Jim Procter [Mon, 2 Feb 2015 11:54:50 +0000 (11:54 +0000)]
JAL-1640 updates to use get/setter on viewportI: efficiencies - temp variables created for redraw loops and temp fields created where redraw involves multiple methods (methods made private where possible to avoid temp field being out of sync)
Jim Procter [Mon, 2 Feb 2015 11:16:32 +0000 (11:16 +0000)]
JAL-1640 separated style operations into a new ViewStyle databean (implements jalview.api.ViewStyleI)
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
gmungoc [Fri, 30 Jan 2015 17:19:01 +0000 (17:19 +0000)]
JAL-845 linked protein/dna 'slave' further PoC functionality
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
gmungoc [Fri, 23 Jan 2015 13:28:53 +0000 (13:28 +0000)]
JAL-1619 javadoc/tidy
gmungoc [Fri, 23 Jan 2015 13:27:10 +0000 (13:27 +0000)]
JAL-1635 show warning if less than 3 columns selected for translation
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[]>
gmungoc [Fri, 23 Jan 2015 11:27:47 +0000 (11:27 +0000)]
Random DNA generator tarted up
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
git://source.jalview.org / jalview.git / log