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
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[]>
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
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
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
Jim Procter [Sun, 18 Jan 2015 11:27:30 +0000 (11:27 +0000)]
JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
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
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
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, 28 Dec 2014 10:34:27 +0000 (10:34 +0000)]
Merge branch 'features/JAL-1596ChimeraREST' into develop
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
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
Jim Procter [Mon, 15 Dec 2014 06:34:15 +0000 (06:34 +0000)]
JAL-1620 version bump and release notes
Jim Procter [Sun, 14 Dec 2014 21:36:17 +0000 (21:36 +0000)]
JAL-1617 test to verify Uniprot cross-references are available for EMBL records with Uniprot cross references, and that Jalview recovers the protein sequences
Mungo Carstairs [Sun, 14 Dec 2014 13:45:23 +0000 (13:45 +0000)]
JAL-1596 set HTTP 1.1 in HttpClient
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