jalview.git
7 years agoJAL-2544 unit tests for sort by feature score
gmungoc [Mon, 22 May 2017 13:39:57 +0000 (14:39 +0100)]
JAL-2544 unit tests for sort by feature score

7 years agoJAL-2544 check feature overlaps selection region
gmungoc [Mon, 22 May 2017 13:33:07 +0000 (14:33 +0100)]
JAL-2544 check feature overlaps selection region

7 years agoMerge remote-tracking branch 'origin/bug/JAL-2256' into develop
kiramt [Mon, 22 May 2017 10:57:47 +0000 (11:57 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2256' into develop

7 years agoJAL-2418 patch build - broken htsjdk import
Jim Procter [Mon, 22 May 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2418 patch build - broken htsjdk import

7 years agoJAL-2526 removed redundant call to Sequence.findPosition()
gmungoc [Fri, 19 May 2017 15:59:48 +0000 (16:59 +0100)]
JAL-2526 removed redundant call to Sequence.findPosition()

7 years agoMerge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop
Jim Procter [Thu, 18 May 2017 15:33:00 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop

7 years agoJAL-2388 return empty hidden columns for fully visible alignment view
Jim Procter [Thu, 18 May 2017 15:31:27 +0000 (16:31 +0100)]
JAL-2388 return empty hidden columns for fully visible alignment view

7 years agoJAL-2256 Corrected AllCols/Rows iterator behaviour for single element bug/JAL-2256
kiramt [Thu, 18 May 2017 13:09:21 +0000 (14:09 +0100)]
JAL-2256 Corrected AllCols/Rows iterator behaviour for single element

7 years agoJAL-2418 remove explicit test suite stats
Jim Procter [Thu, 18 May 2017 11:18:14 +0000 (12:18 +0100)]
JAL-2418 remove explicit test suite stats

7 years agoMerge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 17 May 2017 15:26:52 +0000 (16:26 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102

7 years agoMerge branch 'bug/JAL-2510amendFeatures' into develop
Jim Procter [Wed, 17 May 2017 15:10:15 +0000 (16:10 +0100)]
Merge branch 'bug/JAL-2510amendFeatures' into develop

7 years agoJAL-2447 add links to issues.jalview.org for experimental features
Jim Procter [Wed, 17 May 2017 14:50:14 +0000 (15:50 +0100)]
JAL-2447 add links to issues.jalview.org for experimental features

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 17 May 2017 14:41:04 +0000 (15:41 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2447 experimental section in ‘Whats New’
Jim Procter [Wed, 17 May 2017 14:39:43 +0000 (15:39 +0100)]
JAL-2447 experimental section in ‘Whats New’

7 years agoJAL-2447 JAL-2295 JAL-2296 documenting as experimental features
Jim Procter [Wed, 17 May 2017 14:39:17 +0000 (15:39 +0100)]
JAL-2447 JAL-2295 JAL-2296 documenting as experimental features

7 years agoMerge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 17 May 2017 13:46:38 +0000 (14:46 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102

7 years agoMerge branch 'features/JAL-2447experimentalFlag' into develop
Jim Procter [Wed, 17 May 2017 13:31:54 +0000 (14:31 +0100)]
Merge branch 'features/JAL-2447experimentalFlag' into develop

7 years agoJAL-2418 release notes
Jim Procter [Wed, 17 May 2017 13:28:08 +0000 (14:28 +0100)]
JAL-2418 release notes

7 years agoJAL-2504 use (and update) defaults for new feature only if not supplied
gmungoc [Wed, 17 May 2017 12:07:13 +0000 (13:07 +0100)]
JAL-2504 use (and update) defaults for new feature only if not supplied

7 years agoMerge branch 'develop' into bug/JAL-2510amendFeatures
gmungoc [Wed, 17 May 2017 07:59:07 +0000 (08:59 +0100)]
Merge branch 'develop' into bug/JAL-2510amendFeatures

Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties

7 years agoMerge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 16 May 2017 16:36:01 +0000 (17:36 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop

7 years agoJAL-2418 release notes
Jim Procter [Tue, 16 May 2017 16:27:35 +0000 (17:27 +0100)]
JAL-2418 release notes

7 years agoJAL-384 documentation on custom colours groovy examples
Jim Procter [Tue, 16 May 2017 15:51:31 +0000 (16:51 +0100)]
JAL-384 documentation on custom colours groovy examples

7 years agoJAL-384 - groovy scripts for conserved/unconserved colourscheme requests
Jim Procter [Tue, 16 May 2017 15:35:15 +0000 (16:35 +0100)]
JAL-384 - groovy scripts for conserved/unconserved colourscheme requests

7 years agoJAL-2418 release notes
Jim Procter [Tue, 16 May 2017 15:30:07 +0000 (16:30 +0100)]
JAL-2418 release notes

7 years agoJAL-2418 JAL-2316 added to new features
Jim Procter [Tue, 16 May 2017 13:54:17 +0000 (14:54 +0100)]
JAL-2418 JAL-2316 added to new features

7 years agoJAL-2316 tweaking docs and links in help
Jim Procter [Tue, 16 May 2017 13:30:04 +0000 (14:30 +0100)]
JAL-2316 tweaking docs and links in help

7 years agoJAL-2418 release 2.10.2 release notes template
Jim Procter [Tue, 16 May 2017 12:46:14 +0000 (13:46 +0100)]
JAL-2418 release 2.10.2 release notes template

7 years agoalternative patch for JAL-2339 readability in java-help
Jim Procter [Tue, 16 May 2017 12:45:29 +0000 (13:45 +0100)]
alternative patch for JAL-2339 readability in java-help

7 years agoJAL-2403 simplify instantiation / configuration of score model for view
gmungoc [Tue, 16 May 2017 12:40:27 +0000 (13:40 +0100)]
JAL-2403 simplify instantiation / configuration of score model for view

7 years agoJAL-2522 Missed fix to applet
kiramt [Tue, 16 May 2017 10:34:09 +0000 (11:34 +0100)]
JAL-2522 Missed fix to applet

7 years agoJAL-2388 Rationalised hashCode method in HiddenColumns
kiramt [Tue, 16 May 2017 09:37:48 +0000 (10:37 +0100)]
JAL-2388 Rationalised hashCode method in HiddenColumns

7 years agoMerge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
Jim Procter [Tue, 16 May 2017 08:48:31 +0000 (09:48 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

7 years agoJAL-2507 fix test: knockon from capitalisation on secondary structure from stockholm... bug/JAL-2507_rnasecstrstockholm
Jim Procter [Mon, 15 May 2017 18:23:56 +0000 (19:23 +0100)]
JAL-2507 fix test: knockon from capitalisation on secondary structure from stockholm file

7 years agoMerge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
Jim Procter [Mon, 15 May 2017 16:37:43 +0000 (17:37 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

7 years agoJAL-2311 disable and relocate Jared service tests to Network (prior to their removal)
Jim Procter [Mon, 15 May 2017 16:37:17 +0000 (17:37 +0100)]
JAL-2311 disable and relocate Jared service tests to Network (prior to their removal)

7 years agoJAL-2507 capitalisation for annotation lines generated from stockholm annotation
Jim Procter [Mon, 15 May 2017 16:26:53 +0000 (17:26 +0100)]
JAL-2507 capitalisation for annotation lines generated from stockholm annotation

7 years agoJAL-2507 case insensitive recognition of annotation type
Jim Procter [Mon, 15 May 2017 15:56:06 +0000 (16:56 +0100)]
JAL-2507 case insensitive recognition of annotation type

7 years agoJAL-2532 new feature types and colour changes from Amend Features
gmungoc [Mon, 15 May 2017 15:55:54 +0000 (16:55 +0100)]
JAL-2532 new feature types and colour changes from Amend Features
retained after Cancel in Feature Settings

7 years agoJAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testA...
Jim Procter [Mon, 15 May 2017 15:43:12 +0000 (16:43 +0100)]
JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testAlignmentEquivalent asserts

7 years agoJAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0...
Jim Procter [Mon, 15 May 2017 15:26:02 +0000 (16:26 +0100)]
JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 15 May 2017 14:50:28 +0000 (15:50 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

7 years agoJAL-2388 Add missed optimisation
kiramt [Mon, 15 May 2017 14:50:07 +0000 (15:50 +0100)]
JAL-2388 Add missed optimisation

7 years agoMerge branch 'features/JAL-2376_add-horizontal-bar' into develop
Jim Procter [Mon, 15 May 2017 11:14:20 +0000 (12:14 +0100)]
Merge branch 'features/JAL-2376_add-horizontal-bar' into develop

7 years agoJAL-2371 create a default ResidueShader when constructing the viewport
Jim Procter [Mon, 15 May 2017 11:07:39 +0000 (12:07 +0100)]
JAL-2371 create a default ResidueShader when constructing the viewport

7 years agoMerge branch 'features/JAL-2435splitScreenFont' into develop
Jim Procter [Fri, 12 May 2017 14:48:16 +0000 (15:48 +0100)]
Merge branch 'features/JAL-2435splitScreenFont' into develop

7 years agoJAL-2418 broken help ref
Jim Procter [Fri, 12 May 2017 14:47:10 +0000 (15:47 +0100)]
JAL-2418 broken help ref

7 years agoJAL-2435 documentation and what’s new
Jim Procter [Fri, 12 May 2017 14:46:27 +0000 (15:46 +0100)]
JAL-2435 documentation and what’s new

7 years agoJAL-2435 mention new checkbox in linked cDNA/Protein view documentation
Jim Procter [Fri, 12 May 2017 14:42:17 +0000 (15:42 +0100)]
JAL-2435 mention new checkbox in linked cDNA/Protein view documentation

7 years agoJAL-2435 mirror antiAlias setting between cDNA and Protein
Jim Procter [Fri, 12 May 2017 14:41:45 +0000 (15:41 +0100)]
JAL-2435 mirror antiAlias setting between cDNA and Protein

7 years agoMerge branch 'features/JAL-2388OverviewWindow' into develop
Jim Procter [Fri, 12 May 2017 14:09:45 +0000 (15:09 +0100)]
Merge branch 'features/JAL-2388OverviewWindow' into develop

7 years agoJAL-2388 mention overview popup in documentation
Jim Procter [Fri, 12 May 2017 14:01:17 +0000 (15:01 +0100)]
JAL-2388 mention overview popup in documentation

7 years agoJAL-2388 checkbox in overview popup for applet
Jim Procter [Fri, 12 May 2017 13:56:21 +0000 (14:56 +0100)]
JAL-2388 checkbox in overview popup for applet

7 years agoMerge branch 'features/JAL-2228_efficient_featurecounts' into develop
Jim Procter [Fri, 12 May 2017 13:29:46 +0000 (14:29 +0100)]
Merge branch 'features/JAL-2228_efficient_featurecounts' into develop

7 years agoJAL-2228 updated script in help docs, renamed docs, and added note about non-backward...
Jim Procter [Fri, 12 May 2017 13:29:28 +0000 (14:29 +0100)]
JAL-2228 updated script in help docs, renamed docs, and added note about non-backwards compatibility of feature counter script

7 years agoMerge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
Jim Procter [Thu, 11 May 2017 15:21:14 +0000 (16:21 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

7 years agoJAL-2509 JAL-2507 allow whitespace in GS annotation lines (removed old code for proce...
Jim Procter [Thu, 11 May 2017 15:20:29 +0000 (16:20 +0100)]
JAL-2509 JAL-2507 allow whitespace in GS annotation lines (removed old code for processing GS column annotation into features)

7 years agoJAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test...
Jim Procter [Thu, 11 May 2017 15:17:29 +0000 (16:17 +0100)]
JAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test coverage for Annotation equivalence asserts

7 years agoJAL-2507 test if an annotation is ‘whitespace’
Jim Procter [Thu, 11 May 2017 14:29:00 +0000 (15:29 +0100)]
JAL-2507 test if an annotation is ‘whitespace’

7 years agoJAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitespace annotation
Jim Procter [Thu, 11 May 2017 14:28:24 +0000 (15:28 +0100)]
JAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitespace annotation

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Wed, 10 May 2017 13:29:07 +0000 (14:29 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

7 years agoJAL-2522 Fix to cursor scrolling
kiramt [Wed, 10 May 2017 13:28:50 +0000 (14:28 +0100)]
JAL-2522 Fix to cursor scrolling

7 years agoJAL-2507 spit out tests for ‘{‘ WUSS io from ‘[‘ WUSS io (which may be causing proble...
Jim Procter [Tue, 9 May 2017 17:18:27 +0000 (18:18 +0100)]
JAL-2507 spit out tests for ‘{‘ WUSS io from ‘[‘ WUSS io (which may be causing problems via JAL-1863)

7 years agoJAL-2509 verify stockholm parser’s bracket regex is working for all WUSS notation
Jim Procter [Tue, 9 May 2017 16:58:52 +0000 (17:58 +0100)]
JAL-2509 verify stockholm parser’s bracket regex is working for all WUSS notation

7 years agoJAL-2509 extend set of brackets recognised by stockholm parser
Jim Procter [Tue, 9 May 2017 16:58:27 +0000 (17:58 +0100)]
JAL-2509 extend set of brackets recognised by stockholm parser

7 years agoJAL-2507 JAL-2509 extend test to cover round trip of full range of WUSS RNA secondary...
Jim Procter [Tue, 9 May 2017 16:57:20 +0000 (17:57 +0100)]
JAL-2507 JAL-2509 extend test to cover round trip of full range of WUSS RNA secondary structure

7 years agoJAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS line
Jim Procter [Tue, 9 May 2017 15:55:14 +0000 (16:55 +0100)]
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS line

7 years agoJAL-2507 output secondary structure regardless of presence of dataset sequence
Jim Procter [Tue, 9 May 2017 15:54:15 +0000 (16:54 +0100)]
JAL-2507 output secondary structure regardless of presence of dataset sequence

7 years agoJAL-2507 simplify round trip test via AppletFormatAdapter
Jim Procter [Tue, 9 May 2017 15:51:46 +0000 (16:51 +0100)]
JAL-2507 simplify round trip test via AppletFormatAdapter

7 years agoJAL-2507 test for alignment+rna annotation -> Stockholm -> roundtrip.
Jim Procter [Tue, 9 May 2017 14:15:54 +0000 (15:15 +0100)]
JAL-2507 test for alignment+rna annotation -> Stockholm -> roundtrip.

7 years agoJAL-1632 correct i18n and NPE
gmungoc [Tue, 9 May 2017 09:16:50 +0000 (10:16 +0100)]
JAL-1632 correct i18n and NPE

7 years agoJAL-2388 Added checkbox to toggle hidden columns menu & updated text
kiramt [Tue, 9 May 2017 08:09:55 +0000 (09:09 +0100)]
JAL-2388 Added checkbox to toggle hidden columns menu & updated text

7 years agoJAL-1933 Spanish tooltips for annotation
gmungoc [Mon, 8 May 2017 14:40:19 +0000 (15:40 +0100)]
JAL-1933 Spanish tooltips for annotation

7 years agoJAL-1632 i18n for warning messages
gmungoc [Mon, 8 May 2017 13:54:56 +0000 (14:54 +0100)]
JAL-1632 i18n for warning messages

7 years agoMerge remote-tracking branch 'origin/bug/JAL-2515' into develop
gmungoc [Mon, 8 May 2017 12:17:04 +0000 (13:17 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2515' into develop

7 years agoJAL-2515 Id panel in applet updated for NPE on urlProvider bug/JAL-2515
kiramt [Mon, 8 May 2017 08:23:31 +0000 (09:23 +0100)]
JAL-2515 Id panel in applet updated for NPE on urlProvider

7 years agoJAL-2512 And corresponding test bug/JAL-2512
kiramt [Mon, 8 May 2017 08:06:22 +0000 (09:06 +0100)]
JAL-2512 And corresponding test

7 years agoJAL-2512 And applet
kiramt [Mon, 8 May 2017 07:59:46 +0000 (08:59 +0100)]
JAL-2512 And applet

7 years agoJAL-2512 Fix to show non-gap positions in None colour scheme
kiramt [Mon, 8 May 2017 07:54:41 +0000 (08:54 +0100)]
JAL-2512 Fix to show non-gap positions in None colour scheme

7 years agoMerge branch 'develop' into features/JAL-2435splitScreenFont
gmungoc [Fri, 5 May 2017 15:21:02 +0000 (16:21 +0100)]
Merge branch 'develop' into features/JAL-2435splitScreenFont

7 years agoJAL-964 JAL-2510 update Feature Settings from Amend Features, warn if
gmungoc [Fri, 5 May 2017 15:14:36 +0000 (16:14 +0100)]
JAL-964 JAL-2510 update Feature Settings from Amend Features, warn if
hidden type or group

7 years agoMerge remote-tracking branch
kiramt [Fri, 5 May 2017 11:05:50 +0000 (12:05 +0100)]
Merge remote-tracking branch
'origin/features/JAL-2388hiddencolumnschanges' into
features/JAL-2388OverviewWindow

Conflicts:
resources/lang/Messages.properties

7 years agoMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
kiramt [Fri, 5 May 2017 09:50:22 +0000 (10:50 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges

Conflicts:
src/jalview/appletgui/TreePanel.java
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/TreePanel.java

7 years agoMerge remote-tracking branch 'origin/develop' into
kiramt [Fri, 5 May 2017 09:35:48 +0000 (10:35 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges

Conflicts:
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/io/AnnotationFile.java

7 years agoJAL-2506 allow graduated colour as default in new Sequence Feature
gmungoc [Thu, 4 May 2017 16:08:59 +0000 (17:08 +0100)]
JAL-2506 allow graduated colour as default in new Sequence Feature
dialog

7 years agoJAL-2510 ensure modified feature type is displayed
gmungoc [Thu, 4 May 2017 15:13:06 +0000 (16:13 +0100)]
JAL-2510 ensure modified feature type is displayed

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 May 2017 14:56:42 +0000 (15:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

7 years agoJAL-2504 allow feature type to be specified for Create Features dialog
gmungoc [Thu, 4 May 2017 14:56:32 +0000 (15:56 +0100)]
JAL-2504 allow feature type to be specified for Create Features dialog

7 years agoMerge branch 'develop' into features/JAL-2228_efficient_featurecounts
Jim Procter [Thu, 4 May 2017 14:00:58 +0000 (15:00 +0100)]
Merge branch 'develop' into features/JAL-2228_efficient_featurecounts

7 years agoMerge branch 'bug/JAL-2507_rnasecstrstockholmoutput' into develop
Jim Procter [Thu, 4 May 2017 13:10:44 +0000 (14:10 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholmoutput' into develop

7 years agoMerge branch 'features/JAL-2503_filteronquantitativeannotation' into develop
Jim Procter [Thu, 4 May 2017 13:10:03 +0000 (14:10 +0100)]
Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop

7 years agoMerge branch 'features/JAL-2393customMatrices' into develop
Jim Procter [Thu, 4 May 2017 13:09:44 +0000 (14:09 +0100)]
Merge branch 'features/JAL-2393customMatrices' into develop

7 years agoJAL-1656 make RNAML->Stockholm round trip test pass by ignoring differences in second...
Jim Procter [Thu, 4 May 2017 13:04:36 +0000 (14:04 +0100)]
JAL-1656 make RNAML->Stockholm round trip test pass by ignoring differences in secondary structure annotation visibility

7 years agoJAL-2507 JAL-2509 allow differences in visibility of annotation rows to be ignored...
Jim Procter [Thu, 4 May 2017 13:03:42 +0000 (14:03 +0100)]
JAL-2507 JAL-2509 allow differences in visibility of annotation rows to be ignored when comparing round-tripped alignments

7 years agoJAL-2507 JAL-2509 new assert to compare secondary structure in two annotation rows
Jim Procter [Thu, 4 May 2017 13:02:24 +0000 (14:02 +0100)]
JAL-2507 JAL-2509 new assert to compare secondary structure in two annotation rows

7 years agofix for JAL-2509 - don’t replace all bracket types with ()
Jim Procter [Thu, 4 May 2017 12:56:11 +0000 (13:56 +0100)]
fix for JAL-2509 - don’t replace all bracket types with ()

7 years agofix for JAL-2507 - resolve stockholm per residue annotation type by annotation label...
Jim Procter [Thu, 4 May 2017 10:37:19 +0000 (11:37 +0100)]
fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label or 'isRNA' RNA secondary structure annotation flag

7 years agoMerge branch 'features/JAL-2473_set-minimium-dimensions' into develop
tcofoegbu [Thu, 4 May 2017 10:06:37 +0000 (11:06 +0100)]
Merge branch 'features/JAL-2473_set-minimium-dimensions' into develop

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...
tcofoegbu [Thu, 4 May 2017 10:03:14 +0000 (11:03 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2473_set-minimium-dimensions

7 years agoMerge branch 'features/JAL-2503_filteronquantitativeannotation' into develop
Jim Procter [Thu, 4 May 2017 08:53:10 +0000 (09:53 +0100)]
Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop