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
Jim Procter [Wed, 7 Jan 2015 17:17:12 +0000 (17:17 +0000)]
JAL-1483 making type visible also adds it to registry
gmungoc [Wed, 7 Jan 2015 12:14:17 +0000 (12:14 +0000)]
JAL-1551 formatting applied
gmungoc [Wed, 7 Jan 2015 12:13:32 +0000 (12:13 +0000)]
JAL-1588 refactoring to StructureViewerBase and related
gmungoc [Tue, 6 Jan 2015 11:31:32 +0000 (11:31 +0000)]
JAL-1588 refactoring prior to 'save Chimera project'
gmungoc [Sun, 4 Jan 2015 17:33:20 +0000 (17:33 +0000)]
JAL-1619 first draft of 'linked protein and cDNA'
gmungoc [Sun, 28 Dec 2014 10:34:27 +0000 (10:34 +0000)]
Merge branch 'features/JAL-1596ChimeraREST' into develop
gmungoc [Sun, 28 Dec 2014 09:54:56 +0000 (09:54 +0000)]
JAL-845 first working linked edit protein -> cDNA
Charles Ofoegbu [Mon, 22 Dec 2014 16:38:45 +0000 (16:38 +0000)]
Patch to synchronize title svg and allignment svg scrolling
Jim Procter [Mon, 22 Dec 2014 16:16:17 +0000 (16:16 +0000)]
Merge: 497958b 68dcaa7
(fake synthesised by jbp)
Merge branch 'develop' into JAL-1483_29dev
Conflicts:
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/SeqPanel.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
gmungoc [Tue, 16 Dec 2014 11:21:54 +0000 (11:21 +0000)]
JAL-1328 System.exit() removed as it aborts an entire JUnit suite
gmungoc [Tue, 16 Dec 2014 10:47:48 +0000 (10:47 +0000)]
JAL-845 first simple unit tests added
gmungoc [Tue, 16 Dec 2014 10:46:46 +0000 (10:46 +0000)]
JAL-845 move main method to 'test' class (needs further work);
formatting
gmungoc [Tue, 16 Dec 2014 10:44:16 +0000 (10:44 +0000)]
JAL-1618 feature parsing bug (and formatting)
gmungoc [Tue, 16 Dec 2014 10:40:59 +0000 (10:40 +0000)]
JAL-1619 refactorings: Map, StringBuilder, Override
gmungoc [Tue, 16 Dec 2014 10:29:08 +0000 (10:29 +0000)]
JAL-845 formatting only (block parentheses)
gmungoc [Tue, 16 Dec 2014 10:27:23 +0000 (10:27 +0000)]
JAL-1619 don't copy hidden or RNA SS annotations to protein translation
Charles Ofoegbu [Mon, 15 Dec 2014 15:35:54 +0000 (15:35 +0000)]
update HtmlSvgOutput to ignore browser invocation when running in headless mode
Charles Ofoegbu [Mon, 15 Dec 2014 15:35:54 +0000 (15:35 +0000)]
update HtmlSvgOutput to ignore browser invocation when running in headless mode
Mungo Carstairs [Sun, 14 Dec 2014 13:45:23 +0000 (13:45 +0000)]
JAL-1596 set HTTP 1.1 in HttpClient
gmungoc [Fri, 12 Dec 2014 15:29:11 +0000 (15:29 +0000)]
JAL-845 don't translate hidden annotation (plus formatting)
gmungoc [Tue, 9 Dec 2014 12:21:20 +0000 (12:21 +0000)]
JAL-1616 loading of datasets from XML patched
gmungoc [Tue, 9 Dec 2014 12:21:20 +0000 (12:21 +0000)]
JAL-1616 loading of datasets from XML patched
Charles Ofoegbu [Mon, 8 Dec 2014 12:33:53 +0000 (12:33 +0000)]
merge commit
Charles Ofoegbu [Mon, 8 Dec 2014 11:47:36 +0000 (11:47 +0000)]
JAL-1613 hotfix for duplicated sequence after pairwise alignment
Charles Ofoegbu [Mon, 8 Dec 2014 11:47:36 +0000 (11:47 +0000)]
JAL-1613 hotfix for duplicated sequence after pairwise alignment
Charles Ofoegbu [Mon, 8 Dec 2014 09:45:44 +0000 (09:45 +0000)]
Added annotation export configuration for Html export option
Charles Ofoegbu [Fri, 5 Dec 2014 14:59:55 +0000 (14:59 +0000)]
Merge branch 'features/JAL-1605_html-svg-export' into develop
Charles Ofoegbu [Fri, 5 Dec 2014 14:58:00 +0000 (14:58 +0000)]
JAL-1605 added command line support for html export option
Charles Ofoegbu [Fri, 5 Dec 2014 13:29:17 +0000 (13:29 +0000)]
modified html css
Charles Ofoegbu [Fri, 5 Dec 2014 12:45:11 +0000 (12:45 +0000)]
JAL-1605 merge commit
Charles Ofoegbu [Fri, 5 Dec 2014 12:23:07 +0000 (12:23 +0000)]
Change the Html export to utilize svg
gmungoc [Fri, 5 Dec 2014 10:52:38 +0000 (10:52 +0000)]
JAL-1614 flag 'protein' removed
gmungoc [Fri, 5 Dec 2014 10:52:38 +0000 (10:52 +0000)]
JAL-1614 flag 'protein' removed
gmungoc [Fri, 5 Dec 2014 08:40:45 +0000 (08:40 +0000)]
JAL-1609 refactored colour by sequence command, now performs ok
gmungoc [Fri, 5 Dec 2014 08:38:37 +0000 (08:38 +0000)]
Merge branch 'Release_2_8_2_Branch' of local repository into features/JAL-1596ChimeraREST
gmungoc [Wed, 3 Dec 2014 15:05:54 +0000 (15:05 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
gmungoc [Wed, 3 Dec 2014 15:00:53 +0000 (15:00 +0000)]
JAL-1609 wip on Chimera colour by sequence
Jim Procter [Wed, 3 Dec 2014 12:02:49 +0000 (12:02 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
git://source.jalview.org / jalview.git / log