Jim Procter [Tue, 17 Mar 2015 15:56:05 +0000 (15:56 +0000)]
JAL-1617 toString for DBRefEntry
Jim Procter [Mon, 9 Mar 2015 12:54:38 +0000 (12:54 +0000)]
Merge branch 'features/JAL-1565_jpred4' into develop
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
Jim Procter [Fri, 6 Mar 2015 15:43:05 +0000 (15:43 +0000)]
Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop
Jim Procter [Fri, 6 Mar 2015 15:40:33 +0000 (15:40 +0000)]
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
JAL-1645 bring JAL-845 feature branch up to date ready for develop merge
Conflicts:
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
test/jalview/analysis/DnaTranslation.java
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)]
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
gmungoc [Thu, 5 Mar 2015 13:50:58 +0000 (13:50 +0000)]
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
Conflicts:
src/jalview/datamodel/SequenceGroup.java
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
gmungoc [Thu, 5 Mar 2015 12:47:39 +0000 (12:47 +0000)]
JAL-845 minor tidy / tests / javadoc tweaks
gmungoc [Thu, 5 Mar 2015 10:38:43 +0000 (10:38 +0000)]
JAL-1270 tests added
gmungoc [Wed, 4 Mar 2015 13:37:13 +0000 (13:37 +0000)]
JAL-845 bug fixes correcting linked editing
gmungoc [Tue, 3 Mar 2015 15:55:46 +0000 (15:55 +0000)]
JAL-845 refactor / typo fix
gmungoc [Tue, 3 Mar 2015 10:35:19 +0000 (10:35 +0000)]
JAL-845 implement alignment of protein to match cDNA alignment
gmungoc [Tue, 3 Mar 2015 10:34:01 +0000 (10:34 +0000)]
JAL-1452 nucleotide/protein default colour; JAL-845 SplitFrame refactor
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
gmungoc [Fri, 27 Feb 2015 14:45:09 +0000 (14:45 +0000)]
JAL-1452 distinct colour preferences for nucleotide and protein
gmungoc [Fri, 27 Feb 2015 14:43:36 +0000 (14:43 +0000)]
JAL-845 SplitFrame for "show product" and after aligning from SplitFrame
gmungoc [Wed, 25 Feb 2015 10:42:13 +0000 (10:42 +0000)]
JAL-1677 commenting use of AlignViewport.gatherViewsHere
gmungoc [Tue, 24 Feb 2015 16:37:55 +0000 (16:37 +0000)]
JAL-1677 Castor source changes
gmungoc [Tue, 24 Feb 2015 16:29:21 +0000 (16:29 +0000)]
JAL-845 set top and bottom seq id widths the same
gmungoc [Tue, 24 Feb 2015 16:10:16 +0000 (16:10 +0000)]
JAL-1677 save/restore SplitFrame to Jalview project
gmungoc [Mon, 23 Feb 2015 15:48:13 +0000 (15:48 +0000)]
JAL-845 repaint of complementary selection (applet)
gmungoc [Mon, 23 Feb 2015 12:15:30 +0000 (12:15 +0000)]
JAL-1619 split frame now offered in applet 'input from textbox'
gmungoc [Fri, 20 Feb 2015 17:22:19 +0000 (17:22 +0000)]
JAL-1673 additional test (and trim of PDB resnum value)
gmungoc [Fri, 20 Feb 2015 17:19:21 +0000 (17:19 +0000)]
JAL-1675 correct highlighting in Chimera for mouseover of sequence
gmungoc [Fri, 20 Feb 2015 11:53:18 +0000 (11:53 +0000)]
JAL-1665 create dataset sequences in applet
gmungoc [Fri, 20 Feb 2015 11:51:56 +0000 (11:51 +0000)]
JAL-1674 update both status bars when mousing over linked sequences
gmungoc [Thu, 19 Feb 2015 10:31:38 +0000 (10:31 +0000)]
JAL-845 applet colour by tree; translate as cDNA; pull up history list
gmungoc [Fri, 13 Feb 2015 17:10:22 +0000 (17:10 +0000)]
JAL-845 first rough applet SplitFrame (add parameter file2)
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)
gmungoc [Thu, 12 Feb 2015 11:04:45 +0000 (11:04 +0000)]
JAL-1633 set file format on 'translate cDNA'
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
git://source.jalview.org / jalview.git / log