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
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
gmungoc [Fri, 30 Jan 2015 17:19:01 +0000 (17:19 +0000)]
JAL-845 linked protein/dna 'slave' further PoC functionality
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
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
gmungoc [Thu, 22 Jan 2015 15:50:54 +0000 (15:50 +0000)]
JAL-1619 refactoring / tests to support 'align linked dna as protein'
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
Jim Procter [Tue, 20 Jan 2015 14:31:36 +0000 (14:31 +0000)]
JAL-1304 revamped annotation file documentation structure to make it more usable
Charles Ofoegbu [Tue, 20 Jan 2015 12:17:37 +0000 (12:17 +0000)]
Merge branch 'features/JAL-1553_improvement-select-column-by-annotation-row-query-interface' into develop
Charles Ofoegbu [Tue, 20 Jan 2015 12:16:27 +0000 (12:16 +0000)]
JAL-1553 enhancement of column selection by annotation row to include the query filter interface and ability to perform further actions like hide/select on the filterd columns
gmungoc [Tue, 20 Jan 2015 09:46:30 +0000 (09:46 +0000)]
JAL-1619 test that reordering cDNA does not change translation results
gmungoc [Tue, 20 Jan 2015 09:11:43 +0000 (09:11 +0000)]
JAL-1619 tweaked for better reusability
gmungoc [Mon, 19 Jan 2015 17:18:20 +0000 (17:18 +0000)]
JAL-1619 refactored cDNA translation; modified codon comparison; tests
gmungoc [Mon, 19 Jan 2015 17:17:07 +0000 (17:17 +0000)]
JAL-1636 typed collections now in ResidueProperties
gmungoc [Mon, 19 Jan 2015 17:16:11 +0000 (17:16 +0000)]
JAL-1636 fix for mouseover of 'X' in translated protein
Jim Procter [Sun, 18 Jan 2015 15:45:29 +0000 (15:45 +0000)]
JAL-1372 i18n and tweaking set/unset representative sequence
Jim Procter [Sun, 18 Jan 2015 15:44:04 +0000 (15:44 +0000)]
JAL-1628 formatting
Jim Procter [Sun, 18 Jan 2015 15:43:17 +0000 (15:43 +0000)]
JAL-1628 employ new AnnotationFile reader method to allow the current view's ColumnSelection to be modified
Jim Procter [Sun, 18 Jan 2015 15:41:40 +0000 (15:41 +0000)]
JAL-1628 new entry point for reading annotation files that modify column visibility and implementation and test+data for VIEW_SETREF and HIDE_INSERTIONS
Jim Procter [Sun, 18 Jan 2015 15:38:57 +0000 (15:38 +0000)]
JAL-1628 formatting and javadoc
Jim Procter [Sun, 18 Jan 2015 15:36:14 +0000 (15:36 +0000)]
JAL-1628 method to hide insertions to current sequence selection
Jim Procter [Sun, 18 Jan 2015 15:32:30 +0000 (15:32 +0000)]
JAL-1628 wrappers for common checks on ColumnSelection
Jim Procter [Sun, 18 Jan 2015 15:29:57 +0000 (15:29 +0000)]
JAL-1628 ColumnSelection method to hide insertions for a given sequence
Jim Procter [Sun, 18 Jan 2015 15:21:00 +0000 (15:21 +0000)]
JAL-1628 new method to get a list of insertions in a SequenceI
Jim Procter [Sun, 18 Jan 2015 15:17:37 +0000 (15:17 +0000)]
always use interface rather than field access
gmungoc [Sun, 18 Jan 2015 11:58:13 +0000 (11:58 +0000)]
JAL-1619 refactoring wip
Jim Procter [Sun, 18 Jan 2015 11:27:30 +0000 (11:27 +0000)]
JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
gmungoc [Sat, 17 Jan 2015 06:51:37 +0000 (06:51 +0000)]
JAL-1619 further refactoring
gmungoc [Fri, 16 Jan 2015 15:09:06 +0000 (15:09 +0000)]
JAL-1619 refactoring in progress for Dna translation
gmungoc [Wed, 14 Jan 2015 16:36:34 +0000 (16:36 +0000)]
JAL-1619 AlignedCodonFrame in new alignment should references realigned
sequences
gmungoc [Wed, 14 Jan 2015 16:35:41 +0000 (16:35 +0000)]
JAL-1619 modified repaint after 'Align As' action
gmungoc [Wed, 14 Jan 2015 16:33:27 +0000 (16:33 +0000)]
JAL-1619 Javadoc
gmungoc [Wed, 14 Jan 2015 13:26:46 +0000 (13:26 +0000)]
JAL-1629 .jar option removed from Alignment File Save As dialog.
Charles Ofoegbu [Wed, 14 Jan 2015 12:53:54 +0000 (12:53 +0000)]
Merge branch 'features/JAL-1553_select-columns-by-annotation' into develop
Charles Ofoegbu [Wed, 14 Jan 2015 11:21:57 +0000 (11:21 +0000)]
Modified AnnotationColumnChooser to maintain state of previous selection when current operation is canceled
Charles Ofoegbu [Tue, 13 Jan 2015 15:55:37 +0000 (15:55 +0000)]
Merge branch 'features/JAL-1553_select-columns-by-annotation' into develop
Charles Ofoegbu [Tue, 13 Jan 2015 15:21:45 +0000 (15:21 +0000)]
Refactored AnnotationColumnChoser and AnnotationColorChooser to apply the DRY principle
gmungoc [Mon, 12 Jan 2015 17:13:45 +0000 (17:13 +0000)]
JAL-1619 load/align cDNA for protein (wip)
Charles Ofoegbu [Sat, 10 Jan 2015 14:38:01 +0000 (14:38 +0000)]
JAL-1553 merge commit
Charles Ofoegbu [Sat, 10 Jan 2015 14:29:31 +0000 (14:29 +0000)]
JAL-1553 implementation of column selection by annotation and threshold queries
Jim Procter [Fri, 9 Jan 2015 17:12:04 +0000 (17:12 +0000)]
Merge branch 'JAL-1372_referenceseq' into feature_29/JAL-1372_referenceseq
merge forward to implement support for reference sequences in 2.9
Conflicts:
resources/lang/Messages.properties
src/jalview/appletgui/APopupMenu.java
src/jalview/datamodel/Alignment.java
src/jalview/gui/PopupMenu.java
Charles Ofoegbu [Fri, 9 Jan 2015 15:11:09 +0000 (15:11 +0000)]
Merge branch 'features/JAL-1605_html-svg-export' into develop
Jim Procter [Fri, 9 Jan 2015 11:11:18 +0000 (11:11 +0000)]
Merge branch 'JAL-1483_29dev' into develop
Jim Procter [Fri, 9 Jan 2015 11:10:51 +0000 (11:10 +0000)]
JAL-1483 formatting
Jim Procter [Fri, 9 Jan 2015 11:10:40 +0000 (11:10 +0000)]
JAL-1483 remember to look at base dataset sequence for updated sequence feaures
gmungoc [Fri, 9 Jan 2015 08:31:08 +0000 (08:31 +0000)]
JAL-1588 check Chimera session file still exists
gmungoc [Thu, 8 Jan 2015 15:05:31 +0000 (15:05 +0000)]
JAL-1588 part work save/restore of Chimera session
Jim Procter [Thu, 8 Jan 2015 14:48:33 +0000 (14:48 +0000)]
Merge branch 'JAL-1483_29dev' into develop
Jim Procter [Wed, 7 Jan 2015 23:08:47 +0000 (23:08 +0000)]
Merge branch 'develop' into JAL-1483_29dev
updated JAL-1483 with commits from 15th Dec-7th Jan 2015
Conflicts:
.classpath
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqPanel.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
Jim Procter [Wed, 7 Jan 2015 18:04:46 +0000 (18:04 +0000)]
JAL-1483 patches to make test case pass: hamming distance counts differences in presence across all features currently displayed on alignment
Jim Procter [Wed, 7 Jan 2015 18:02:10 +0000 (18:02 +0000)]
JAL-1483 basic test of sequence similarity score model (also gives the refactored sequence feature components a workout)
Jim Procter [Wed, 7 Jan 2015 17:57:43 +0000 (17:57 +0000)]
JAL-1483 source formatting
Jim Procter [Wed, 7 Jan 2015 17:56:40 +0000 (17:56 +0000)]
JAL-1483 refactor NJTree constructor to allow preconfigured scoremodel to be passed in with alignment view
Jim Procter [Wed, 7 Jan 2015 17:33:11 +0000 (17:33 +0000)]
JAL-1483 register feature similarity model
Jim Procter [Wed, 7 Jan 2015 17:32:20 +0000 (17:32 +0000)]
JAL-1483 null features not displayed
Jim Procter [Wed, 7 Jan 2015 17:31:34 +0000 (17:31 +0000)]
JAL-1483 check dataset for features if none found on local sequence
Jim Procter [Wed, 7 Jan 2015 17:30:34 +0000 (17:30 +0000)]
JAL-1483 organise imports
gmungoc [Wed, 7 Jan 2015 17:23:04 +0000 (17:23 +0000)]
JAL-845 TODO comment added
git://source.jalview.org / jalview.git / log