jalview.git
9 years agoJAL-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

9 years agoMerge branch 'improvement/JAL-1350_makegroups_markedcolumns' into merge/JAL-845_JAL...
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

9 years agoJAL-1350 pass the columnselection rather then selected sequence strings if column...
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.

9 years agoJAL-1350 cloned method and tested equivalence for using column selection to subdivide...
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

9 years agoJAL-1115 switch to lists in SequenceGroup
Jim Procter [Thu, 12 Feb 2015 16:47:49 +0000 (16:47 +0000)]
JAL-1115 switch to lists in SequenceGroup

9 years agoJAL-1115 typecast
Jim Procter [Thu, 12 Feb 2015 16:47:18 +0000 (16:47 +0000)]
JAL-1115 typecast

9 years agojavadoc
Jim Procter [Thu, 12 Feb 2015 16:46:57 +0000 (16:46 +0000)]
javadoc

9 years agoJAL-1115 List rather than vector for sequence groups (minimal additional synchronized...
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)

9 years agoMerge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into
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

9 years agoJAL-845 handling eXpand/Gather split frame views
gmungoc [Wed, 11 Feb 2015 12:26:31 +0000 (12:26 +0000)]
JAL-845 handling eXpand/Gather split frame views

9 years agoJAL-1264 button labels (for panel currently not linked in menu)
gmungoc [Wed, 11 Feb 2015 12:24:51 +0000 (12:24 +0000)]
JAL-1264 button labels (for panel currently not linked in menu)

9 years agoJAL-1655 JAL-845 special support to set column width of protein panel 3*width of...
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..

9 years agoJAL-845 avoid OOBException when method is called with only one view
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

9 years agoJAL-969 use AlignViewportI interface instance where ever possible in method signatures
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

9 years agoJAL-1654 allow font to be specified without modifying column width
Jim Procter [Wed, 11 Feb 2015 09:06:22 +0000 (09:06 +0000)]
JAL-1654 allow font to be specified without modifying column width

9 years agonote about preserving/reinstating custom grid geometry for alignment (JAL-470) and...
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

9 years agoJAL-1640 make font-size changes modify grid size again
Jim Procter [Tue, 10 Feb 2015 17:08:51 +0000 (17:08 +0000)]
JAL-1640 make font-size changes modify grid size again

9 years agoJAL-845 - portability patch - workaround for lastToken failing for '\'
Jim Procter [Tue, 10 Feb 2015 16:21:54 +0000 (16:21 +0000)]
JAL-845 - portability patch - workaround for lastToken failing for '\'

9 years agoadded comment to @gmungoc todo about referencing PDB entities in Javascript - also...
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 :(

9 years agoJAL-845 @mungoc TODO comments - addAlignment needs a bit more thought
Jim Procter [Tue, 10 Feb 2015 15:35:48 +0000 (15:35 +0000)]
JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought

9 years agoJAL-1382 slightly more efficient detection of non-gap entry in deleted region of...
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

9 years agoJAL-1382 @mungo TODO done: use StringUtils for delete chars
Jim Procter [Tue, 10 Feb 2015 14:56:36 +0000 (14:56 +0000)]
JAL-1382 @mungo TODO done: use StringUtils for delete chars

9 years agoJAL-966 @mungo TODO complete: List rather than bare int array
Jim Procter [Tue, 10 Feb 2015 14:29:38 +0000 (14:29 +0000)]
JAL-966 @mungo TODO complete: List rather than bare int array

9 years agoJAL-1264 unit tests fixed (have to explicit set annotation sort order)
gmungoc [Tue, 10 Feb 2015 10:24:25 +0000 (10:24 +0000)]
JAL-1264 unit tests fixed (have to explicit set annotation sort order)

9 years agoMerge branch 'features/JAL-845splitPaneMergeDevelop' into merge_JAL-845_JAL-1640
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

9 years agoMerge branch 'develop' into JAL-1640_stylesettings
Jim Procter [Mon, 9 Feb 2015 15:30:40 +0000 (15:30 +0000)]
Merge branch 'develop' into JAL-1640_stylesettings

9 years agoMerge remote-tracking branch 'origin/develop' into
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

9 years agoJAL-845 further code/tests/refactoring
gmungoc [Fri, 6 Feb 2015 14:12:19 +0000 (14:12 +0000)]
JAL-845 further code/tests/refactoring

9 years agoMerge branch 'bug/JAL-1643_File-chooser-improvement' into develop
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

9 years agoJAL-1640 new menu allowing view settings to be transferred from any other view on...
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

9 years agoJAL-1640 Desktop.getAlignmentPanel and Desktop.getViewports can now take a null argum...
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

9 years agoJAL-1551 formatting
Jim Procter [Fri, 6 Feb 2015 10:50:51 +0000 (10:50 +0000)]
JAL-1551 formatting

9 years agoJAL-1640 more properties moved to style bean and rationalisation of layout update...
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

9 years agoJAL-1551 formatting
Jim Procter [Fri, 6 Feb 2015 10:44:04 +0000 (10:44 +0000)]
JAL-1551 formatting

9 years agoJAL-1640 JAL-966 is for boolean getter on AlignViewportI
Jim Procter [Fri, 6 Feb 2015 10:37:52 +0000 (10:37 +0000)]
JAL-1640 JAL-966 is for boolean getter on AlignViewportI

9 years agomerge commit
Charles Ofoegbu [Thu, 5 Feb 2015 17:10:39 +0000 (17:10 +0000)]
merge commit

9 years agoJAL-1643 jarred up the quaqua native libraries and added nativelib
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

9 years agoJAL-1643 added quaqua filechooser and jni libraries to the InstallAnywhere distribution
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

9 years agoJAL-1643 correct version of quaqua (8) plus THIRDPARTYLIB details
Jim Procter [Thu, 5 Feb 2015 10:23:39 +0000 (10:23 +0000)]
JAL-1643 correct version of quaqua (8) plus THIRDPARTYLIB details

9 years agoJAL-1643 renamed quaqua library to add version number
Jim Procter [Thu, 5 Feb 2015 10:19:07 +0000 (10:19 +0000)]
JAL-1643 renamed quaqua library to add version number

9 years agoJAL-1643 modified jalviewFileChooser to retain default behaviour on other non-mac...
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

9 years agoJAL-1643 Modified JalviewFileChooser to have a more native laf on mac
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

9 years agocomment only
gmungoc [Tue, 3 Feb 2015 16:51:27 +0000 (16:51 +0000)]
comment only

9 years agoJAL-845 column mapping speed-up
gmungoc [Tue, 3 Feb 2015 16:51:16 +0000 (16:51 +0000)]
JAL-845 column mapping speed-up

9 years agoJAL-845 SplitFrame key bindings delegation to AlignFrame menu actions
gmungoc [Tue, 3 Feb 2015 16:50:22 +0000 (16:50 +0000)]
JAL-845 SplitFrame key bindings delegation to AlignFrame menu actions

9 years agoJAL-845 preparation for awareness of AlignFrame in SplitFrame for save
gmungoc [Tue, 3 Feb 2015 16:49:47 +0000 (16:49 +0000)]
JAL-845 preparation for awareness of AlignFrame in SplitFrame for save

9 years agoJAL-845 redundant 'map to self' removed from buildSearchResults
gmungoc [Tue, 3 Feb 2015 11:13:53 +0000 (11:13 +0000)]
JAL-845 redundant 'map to self' removed from buildSearchResults

9 years agoComments added
gmungoc [Tue, 3 Feb 2015 11:13:19 +0000 (11:13 +0000)]
Comments added

9 years agoJAL-845 code/refactoring/tests related to linking DNA and protein
gmungoc [Tue, 3 Feb 2015 10:53:56 +0000 (10:53 +0000)]
JAL-845 code/refactoring/tests related to linking DNA and protein

9 years agoMerge branch 'bug/JAL-1644_Finder-logic-improvement' into develop
Charles Ofoegbu [Mon, 2 Feb 2015 20:35:48 +0000 (20:35 +0000)]
Merge branch 'bug/JAL-1644_Finder-logic-improvement' into develop

9 years agoJAL-1644 added null check for sequence description field
Charles Ofoegbu [Mon, 2 Feb 2015 20:34:32 +0000 (20:34 +0000)]
JAL-1644 added null check for sequence description field

9 years agoJAL-1640 setStyle method and associated tests (required a sameStyle method to be...
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)

9 years agoJAL-966 allow access to viewport interface from alignPanel
Jim Procter [Mon, 2 Feb 2015 18:14:44 +0000 (18:14 +0000)]
JAL-966 allow access to viewport interface from alignPanel

9 years agoJAL-1640 getters and setters for viewStyleI - note the caller needs to trigger view...
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

9 years agoJAL-1640 copy constructor test and implementation by reflection
Jim Procter [Mon, 2 Feb 2015 17:40:41 +0000 (17:40 +0000)]
JAL-1640 copy constructor test and implementation by reflection

9 years agoJAL-715 tweaks for SRBS description string parsing
Jim Procter [Mon, 2 Feb 2015 16:43:10 +0000 (16:43 +0000)]
JAL-715 tweaks for SRBS description string parsing

9 years agoJAL-1161 JAL-1606 note about awt/swing dependency in interface
Jim Procter [Mon, 2 Feb 2015 16:42:13 +0000 (16:42 +0000)]
JAL-1161 JAL-1606 note about awt/swing dependency in interface

9 years agoMerge commit
Charles Ofoegbu [Mon, 2 Feb 2015 15:49:53 +0000 (15:49 +0000)]
Merge commit

9 years agoJAL-1644 revised Finder's implementation to use a flag to enalbe searching an alignme...
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

9 years agoJAL-1640 JAL-1551 formatting/imports/remove dead code
Jim Procter [Mon, 2 Feb 2015 11:56:54 +0000 (11:56 +0000)]
JAL-1640 JAL-1551 formatting/imports/remove dead code

9 years agoJAL-1640 updates to use get/setter on viewportI: efficiencies - temp variables create...
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)

9 years agoJAL-1640 separated style operations into a new ViewStyle databean (implements jalview...
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)

9 years agoMerge branch 'bug/JAL-1644_Finder-logic-improvement' into develop
Charles Ofoegbu [Mon, 2 Feb 2015 10:32:14 +0000 (10:32 +0000)]
Merge branch 'bug/JAL-1644_Finder-logic-improvement' into develop

9 years agoJAL-1644 improvment of finder logic to include the sequence description field
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

9 years agoJAL-845 linked protein/dna 'slave' further PoC functionality features/JAL-845linkedProteinDnaEditing
gmungoc [Fri, 30 Jan 2015 17:19:01 +0000 (17:19 +0000)]
JAL-845 linked protein/dna 'slave' further PoC functionality

9 years agoJAL-1565 automatically mark query sequence as the sequence reference and hide any...
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

9 years ago JAL-674 patch to make Mapping.compareTransferredToRefPDBAnnot test
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

9 years agoJAL-674 JAL-1270 added settings to ensure temperature and secondary
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

9 years agoJAL-1588 new class renamed
gmungoc [Tue, 27 Jan 2015 08:58:12 +0000 (08:58 +0000)]
JAL-1588 new class renamed

9 years agoMerge branch 'features/JAL-1588saveChimeraSession' into develop
gmungoc [Mon, 26 Jan 2015 16:45:29 +0000 (16:45 +0000)]
Merge branch 'features/JAL-1588saveChimeraSession' into develop

9 years agoJAL-1588 restoring saved Chimera session(s)
gmungoc [Mon, 26 Jan 2015 16:42:56 +0000 (16:42 +0000)]
JAL-1588 restoring saved Chimera session(s)

9 years agoMerge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query...
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

9 years agoJAL-1588 first working (?) restore of Chimera session incl bindings
gmungoc [Fri, 23 Jan 2015 16:49:19 +0000 (16:49 +0000)]
JAL-1588 first working (?) restore of Chimera session incl bindings

9 years agoJAL-1553 added help documentation and updated AnnotationColumnChooser to exclude... features/JAL-1553_improvement-select-column-by-annotation-row-query-interface
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

9 years agoMerge branch 'feature_29/JAL-1372_referenceseq' into develop
Jim Procter [Fri, 23 Jan 2015 15:40:14 +0000 (15:40 +0000)]
Merge branch 'feature_29/JAL-1372_referenceseq' into develop

9 years agoJAL-1541 changed assert to JUnit assert - test now fails for current version of BioJS...
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

9 years agoJAL-1551 formatting
Jim Procter [Fri, 23 Jan 2015 15:32:05 +0000 (15:32 +0000)]
JAL-1551 formatting

9 years agoJAL-1286 don't print an exception if a non-gzip stream is attempted to be opened...
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

9 years agoJAL-1551 crlf changes
Jim Procter [Fri, 23 Jan 2015 15:17:26 +0000 (15:17 +0000)]
JAL-1551 crlf changes

9 years agoJAL-969 hasHiddenRows is now an interface method
Jim Procter [Fri, 23 Jan 2015 14:11:14 +0000 (14:11 +0000)]
JAL-969 hasHiddenRows is now an interface method

9 years agoJAL-969 drop the hiddenColumns flag in favour of checking current state of columnSele...
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

9 years agoMerge branch 'develop' into feature_29/JAL-1372_referenceseq
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

9 years agoJAL-1619 javadoc/tidy
gmungoc [Fri, 23 Jan 2015 13:28:53 +0000 (13:28 +0000)]
JAL-1619 javadoc/tidy

9 years agoJAL-1635 show warning if less than 3 columns selected for translation
gmungoc [Fri, 23 Jan 2015 13:27:10 +0000 (13:27 +0000)]
JAL-1635 show warning if less than 3 columns selected for translation

9 years agoJAL-1628 tweak signature of core annotation printer for outputting hidden columns...
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

9 years agoJAL-1551 formatting/imports
Jim Procter [Fri, 23 Jan 2015 13:13:44 +0000 (13:13 +0000)]
JAL-1551 formatting/imports

9 years agoJAL-1551 JAL-962 formatting and code change ripples from changing HiddenColumns ...
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[]>

9 years agoRandom DNA generator tarted up
gmungoc [Fri, 23 Jan 2015 11:27:47 +0000 (11:27 +0000)]
Random DNA generator tarted up

9 years agoMerge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query...
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

9 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview 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

9 years agoJAL-1553 fixed null pointer exception thrown in SeqCanvas and ScalePanel of jalview...
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

9 years agoJAL-1551 source code formatting
Jim Procter [Fri, 23 Jan 2015 09:05:17 +0000 (09:05 +0000)]
JAL-1551 source code formatting

9 years agoJAL-969 javadoc and mark interface overrides for clarity
Jim Procter [Fri, 23 Jan 2015 09:04:27 +0000 (09:04 +0000)]
JAL-969 javadoc and mark interface overrides for clarity

9 years agoJAL-1628 drop getShowAnnotation accessor in favour of isShowAnnotation in AlignViewpo...
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

9 years agoMerge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query...
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

9 years agoJAL-1553 added applet support for the select-column-by-annotation-row feature
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

9 years agoJAL-1372 JAL-1169 documentation for new commands HIDE_INSERTIONS AND VIEW_SETREF
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

9 years agoJAL-1619 refactoring / tests to support 'align linked dna as protein'
gmungoc [Thu, 22 Jan 2015 15:50:54 +0000 (15:50 +0000)]
JAL-1619 refactoring / tests to support 'align linked dna as protein'

9 years agoMerge branch 'develop' into feature_29/JAL-1372_referenceseq
Jim Procter [Wed, 21 Jan 2015 15:04:37 +0000 (15:04 +0000)]
Merge branch 'develop' into feature_29/JAL-1372_referenceseq

9 years agotidy up class files that shouldn't be in repo
Jim Procter [Wed, 21 Jan 2015 10:36:38 +0000 (10:36 +0000)]
tidy up class files that shouldn't be in repo