jalview.git
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-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 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 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 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-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

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

9 years agoclean up
Charles Ofoegbu [Tue, 20 Jan 2015 17:27:26 +0000 (17:27 +0000)]
clean up

9 years agoclean up
Charles Ofoegbu [Tue, 20 Jan 2015 17:25:35 +0000 (17:25 +0000)]
clean up

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

9 years agoFurther abstractions and clean up
Charles Ofoegbu [Tue, 20 Jan 2015 17:20:40 +0000 (17:20 +0000)]
Further abstractions and clean up

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

9 years agobasic house keeping
Charles Ofoegbu [Tue, 20 Jan 2015 15:02:05 +0000 (15:02 +0000)]
basic house keeping

9 years agoJAL-1304 revamped annotation file documentation structure to make it more usable
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

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

9 years agoJAL-1553 enhancement of column selection by annotation row to include the query filte...
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

9 years agoJAL-1619 test that reordering cDNA does not change translation results
gmungoc [Tue, 20 Jan 2015 09:46:30 +0000 (09:46 +0000)]
JAL-1619 test that reordering cDNA does not change translation results

9 years agoJAL-1619 tweaked for better reusability
gmungoc [Tue, 20 Jan 2015 09:11:43 +0000 (09:11 +0000)]
JAL-1619 tweaked for better reusability

9 years agoJAL-1619 refactored cDNA translation; modified codon comparison; tests
gmungoc [Mon, 19 Jan 2015 17:18:20 +0000 (17:18 +0000)]
JAL-1619 refactored cDNA translation; modified codon comparison; tests

9 years agoJAL-1636 typed collections now in ResidueProperties
gmungoc [Mon, 19 Jan 2015 17:17:07 +0000 (17:17 +0000)]
JAL-1636 typed collections now in ResidueProperties

9 years agoJAL-1636 fix for mouseover of 'X' in translated protein
gmungoc [Mon, 19 Jan 2015 17:16:11 +0000 (17:16 +0000)]
JAL-1636 fix for mouseover of 'X' in translated protein

9 years agoJAL-1372 i18n and tweaking set/unset representative sequence
Jim Procter [Sun, 18 Jan 2015 15:45:29 +0000 (15:45 +0000)]
JAL-1372 i18n and tweaking set/unset representative sequence

9 years agoJAL-1628 formatting
Jim Procter [Sun, 18 Jan 2015 15:44:04 +0000 (15:44 +0000)]
JAL-1628 formatting

9 years agoJAL-1628 employ new AnnotationFile reader method to allow the current view's ColumnSe...
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

9 years agoJAL-1628 new entry point for reading annotation files that modify column visibility...
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

9 years agoJAL-1628 formatting and javadoc
Jim Procter [Sun, 18 Jan 2015 15:38:57 +0000 (15:38 +0000)]
JAL-1628 formatting and javadoc

9 years agoJAL-1628 method to hide insertions to current sequence selection
Jim Procter [Sun, 18 Jan 2015 15:36:14 +0000 (15:36 +0000)]
JAL-1628 method to hide insertions to current sequence selection

9 years agoJAL-1628 wrappers for common checks on ColumnSelection
Jim Procter [Sun, 18 Jan 2015 15:32:30 +0000 (15:32 +0000)]
JAL-1628 wrappers for common checks on ColumnSelection

9 years agoJAL-1628 ColumnSelection method to hide insertions for a given sequence
Jim Procter [Sun, 18 Jan 2015 15:29:57 +0000 (15:29 +0000)]
JAL-1628 ColumnSelection method to hide insertions for a given sequence

9 years agoJAL-1628 new method to get a list of insertions in a SequenceI
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

9 years agoalways use interface rather than field access
Jim Procter [Sun, 18 Jan 2015 15:17:37 +0000 (15:17 +0000)]
always use interface rather than field access

9 years agoJAL-1619 refactoring wip
gmungoc [Sun, 18 Jan 2015 11:58:13 +0000 (11:58 +0000)]
JAL-1619 refactoring wip

9 years agoJAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
Jim Procter [Sun, 18 Jan 2015 11:27:30 +0000 (11:27 +0000)]
JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence

9 years agoJAL-1619 further refactoring
gmungoc [Sat, 17 Jan 2015 06:51:37 +0000 (06:51 +0000)]
JAL-1619 further refactoring

9 years agoJAL-1619 refactoring in progress for Dna translation
gmungoc [Fri, 16 Jan 2015 15:09:06 +0000 (15:09 +0000)]
JAL-1619 refactoring in progress for Dna translation

9 years agoJAL-1619 AlignedCodonFrame in new alignment should references realigned
gmungoc [Wed, 14 Jan 2015 16:36:34 +0000 (16:36 +0000)]
JAL-1619 AlignedCodonFrame in new alignment should references realigned
sequences

9 years agoJAL-1619 modified repaint after 'Align As' action
gmungoc [Wed, 14 Jan 2015 16:35:41 +0000 (16:35 +0000)]
JAL-1619 modified repaint after 'Align As' action

9 years agoJAL-1619 Javadoc
gmungoc [Wed, 14 Jan 2015 16:33:27 +0000 (16:33 +0000)]
JAL-1619 Javadoc

9 years agoJAL-1629 .jar option removed from Alignment File Save As dialog.
gmungoc [Wed, 14 Jan 2015 13:26:46 +0000 (13:26 +0000)]
JAL-1629 .jar option removed from Alignment File Save As dialog.

9 years agoMerge branch 'features/JAL-1553_select-columns-by-annotation' into develop
Charles Ofoegbu [Wed, 14 Jan 2015 12:53:54 +0000 (12:53 +0000)]
Merge branch 'features/JAL-1553_select-columns-by-annotation' into develop

9 years agoModified AnnotationColumnChooser to maintain state of previous selection when current... features/JAL-1553_select-columns-by-annotation
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

9 years agoMerge branch 'features/JAL-1553_select-columns-by-annotation' into develop
Charles Ofoegbu [Tue, 13 Jan 2015 15:55:37 +0000 (15:55 +0000)]
Merge branch 'features/JAL-1553_select-columns-by-annotation' into develop

9 years agoRefactored AnnotationColumnChoser and AnnotationColorChooser to apply the DRY principle
Charles Ofoegbu [Tue, 13 Jan 2015 15:21:45 +0000 (15:21 +0000)]
Refactored AnnotationColumnChoser and AnnotationColorChooser to apply the DRY principle

9 years agoJAL-1619 load/align cDNA for protein (wip)
gmungoc [Mon, 12 Jan 2015 17:13:45 +0000 (17:13 +0000)]
JAL-1619 load/align cDNA for protein (wip)

9 years agoJAL-1553 merge commit
Charles Ofoegbu [Sat, 10 Jan 2015 14:38:01 +0000 (14:38 +0000)]
JAL-1553 merge commit

9 years agoJAL-1553 implementation of column selection by annotation and threshold queries
Charles Ofoegbu [Sat, 10 Jan 2015 14:29:31 +0000 (14:29 +0000)]
JAL-1553 implementation of column selection by annotation and threshold queries

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

9 years agoMerge branch 'features/JAL-1605_html-svg-export' into develop
Charles Ofoegbu [Fri, 9 Jan 2015 15:11:09 +0000 (15:11 +0000)]
Merge branch 'features/JAL-1605_html-svg-export' into develop

9 years agoMerge branch 'JAL-1483_29dev' into develop
Jim Procter [Fri, 9 Jan 2015 11:11:18 +0000 (11:11 +0000)]
Merge branch 'JAL-1483_29dev' into develop

9 years agoJAL-1483 formatting
Jim Procter [Fri, 9 Jan 2015 11:10:51 +0000 (11:10 +0000)]
JAL-1483 formatting

9 years agoJAL-1483 remember to look at base dataset sequence for updated sequence feaures
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

9 years agoJAL-1588 check Chimera session file still exists
gmungoc [Fri, 9 Jan 2015 08:31:08 +0000 (08:31 +0000)]
JAL-1588 check Chimera session file still exists

9 years agoJAL-1588 part work save/restore of Chimera session
gmungoc [Thu, 8 Jan 2015 15:05:31 +0000 (15:05 +0000)]
JAL-1588 part work save/restore of Chimera session

9 years agoMerge branch 'JAL-1483_29dev' into develop
Jim Procter [Thu, 8 Jan 2015 14:48:33 +0000 (14:48 +0000)]
Merge branch 'JAL-1483_29dev' into develop

9 years agoMerge branch 'develop' into JAL-1483_29dev
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

9 years agoJAL-1483 patches to make test case pass: hamming distance counts differences in prese...
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

9 years agoJAL-1483 basic test of sequence similarity score model (also gives the refactored...
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)

9 years agoJAL-1483 source formatting
Jim Procter [Wed, 7 Jan 2015 17:57:43 +0000 (17:57 +0000)]
JAL-1483 source formatting

9 years agoJAL-1483 refactor NJTree constructor to allow preconfigured scoremodel to be passed...
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

9 years agoJAL-1483 register feature similarity model
Jim Procter [Wed, 7 Jan 2015 17:33:11 +0000 (17:33 +0000)]
JAL-1483 register feature similarity model

9 years agoJAL-1483 null features not displayed
Jim Procter [Wed, 7 Jan 2015 17:32:20 +0000 (17:32 +0000)]
JAL-1483 null features not displayed