jalview.git
7 years agoJAL-2505 set SequenceFeature group in constructor
gmungoc [Tue, 16 May 2017 08:40:39 +0000 (09:40 +0100)]
JAL-2505 set SequenceFeature group in constructor

7 years agoMerge branch 'develop' into features/JAL-2446NCList
gmungoc [Mon, 15 May 2017 16:02:55 +0000 (17:02 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

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 'develop' into features/JAL-2446NCList
gmungoc [Mon, 15 May 2017 10:59:29 +0000 (11:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
src/jalview/gui/OverviewPanel.java

7 years agoJAL-2490 use findFeatures() for efficient feature overlap lookup
gmungoc [Mon, 15 May 2017 08:43:05 +0000 (09:43 +0100)]
JAL-2490 use findFeatures() for efficient feature overlap lookup

7 years agoJAL-2480 redundant code (from merge?) removed
gmungoc [Mon, 15 May 2017 07:46:56 +0000 (08:46 +0100)]
JAL-2480 redundant code (from merge?) removed

7 years agoJAL-2480 redundant code removed
gmungoc [Mon, 15 May 2017 07:45:17 +0000 (08:45 +0100)]
JAL-2480 redundant code removed

7 years agoJAL-2490 performant findFeaturesAtRes
gmungoc [Fri, 12 May 2017 15:59:19 +0000 (16:59 +0100)]
JAL-2490 performant findFeaturesAtRes

7 years agoJAL-2483 efficient lookup of feature types and groups - applet
gmungoc [Fri, 12 May 2017 15:29:07 +0000 (16:29 +0100)]
JAL-2483 efficient lookup of feature types and groups - applet

7 years agoJAL-2525 get sequence features for Ontology term(s), tidy feature sort
gmungoc [Fri, 12 May 2017 15:00:20 +0000 (16:00 +0100)]
JAL-2525 get sequence features for Ontology term(s), tidy feature sort
methods

7 years agoJAL-2480 more efficient contains check on add; tidied comparators
gmungoc [Fri, 12 May 2017 14:56:33 +0000 (15:56 +0100)]
JAL-2480 more efficient contains check on add; tidied comparators

7 years agoJAL-2480 java.util.RangeComparator renamed IntRangeComparator
gmungoc [Fri, 12 May 2017 14:53:29 +0000 (15:53 +0100)]
JAL-2480 java.util.RangeComparator renamed IntRangeComparator

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 agoJAL-2480 efficient test for features present on sequence
gmungoc [Fri, 12 May 2017 13:32:33 +0000 (14:32 +0100)]
JAL-2480 efficient test for features present on sequence

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 agoJAL-2480 renamed java.util.RangeComparator to IntRangeComparator
gmungoc [Fri, 12 May 2017 13:22:03 +0000 (14:22 +0100)]
JAL-2480 renamed java.util.RangeComparator to IntRangeComparator

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-2403 use preferred factory method to create score model
gmungoc [Tue, 9 May 2017 08:59:13 +0000 (09:59 +0100)]
JAL-2403 use preferred factory method to create score model

7 years agoJAL-2480 include sequenceFeatureStore in createDatasetSequence
gmungoc [Tue, 9 May 2017 08:52:14 +0000 (09:52 +0100)]
JAL-2480 include sequenceFeatureStore in createDatasetSequence

7 years agoJAL-2483 JAL-2481 fixed findAllFeatures to handle null group correctly
gmungoc [Tue, 9 May 2017 08:25:49 +0000 (09:25 +0100)]
JAL-2483 JAL-2481 fixed findAllFeatures to handle null group correctly

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-2505 use constructors to set (what will be) final fields in
gmungoc [Tue, 9 May 2017 07:46:21 +0000 (08:46 +0100)]
JAL-2505 use constructors to set (what will be) final fields in
SequenceFeature

7 years agoJAL-2505 set type,desc,begin,end,group,score in SequenceFeature
gmungoc [Mon, 8 May 2017 16:45:01 +0000 (17:45 +0100)]
JAL-2505 set type,desc,begin,end,group,score in SequenceFeature
constructor

7 years agoJAL-2505 refactored SequenceFeature construction so type,begin,end,group
gmungoc [Mon, 8 May 2017 16:38:18 +0000 (17:38 +0100)]
JAL-2505 refactored SequenceFeature construction so type,begin,end,group
are set in constructor

7 years agoMerge branch 'develop' into features/JAL-2446NCList
gmungoc [Mon, 8 May 2017 16:01:31 +0000 (17:01 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
src/jalview/appletgui/IdPanel.java
src/jalview/gui/FeatureRenderer.java

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 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 agoMerge branch 'develop' into features/JAL-2446NCList
gmungoc [Thu, 4 May 2017 11:34:21 +0000 (12:34 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

7 years agoJAL-2505 delete and readd amended sequence feature
gmungoc [Thu, 4 May 2017 11:33:00 +0000 (12:33 +0100)]
JAL-2505 delete and readd amended sequence feature

7 years agoJAL-2480 JAL-2505 guard against duplicating links
gmungoc [Thu, 4 May 2017 11:31:36 +0000 (12:31 +0100)]
JAL-2480 JAL-2505 guard against duplicating links

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

7 years agoMerge branch 'features/JAL-2393customMatrices' into develop
Jim Procter [Thu, 4 May 2017 08:52:21 +0000 (09:52 +0100)]
Merge branch 'features/JAL-2393customMatrices' into develop

7 years agoJAL-2393 JAL-2416 refresh the score model menu when updating gui enabled/disabled... features/JAL-2393customMatrices
Jim Procter [Wed, 3 May 2017 16:48:11 +0000 (17:48 +0100)]
JAL-2393 JAL-2416 refresh the score model menu when updating gui enabled/disabled settings

7 years agoJAL-2503 show threshold slider for quantitative annotation rows
Jim Procter [Wed, 3 May 2017 16:43:55 +0000 (17:43 +0100)]
JAL-2503 show threshold slider for quantitative annotation rows

7 years agoJAL-2503 AlignmentAnnotation.isQuantitative() test
Jim Procter [Wed, 3 May 2017 16:35:47 +0000 (17:35 +0100)]
JAL-2503 AlignmentAnnotation.isQuantitative() test

7 years agoMerge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 3 May 2017 15:51:23 +0000 (16:51 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

7 years agoJAL-2246 basic sanity test of fetching example accessions
gmungoc [Wed, 3 May 2017 14:51:36 +0000 (15:51 +0100)]
JAL-2246 basic sanity test of fetching example accessions

7 years agoMerge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 3 May 2017 13:55:32 +0000 (14:55 +0100)]
Merge branch 'develop' into features/JAL-2446NCList

7 years agoMerge branch 'features/JAL-2432_annotbypercent' into develop
Jim Procter [Wed, 3 May 2017 11:17:56 +0000 (12:17 +0100)]
Merge branch 'features/JAL-2432_annotbypercent' into develop

7 years agoJAL-1933 JAL-2501 i18n for all auto calculated descriptions features/JAL-2432_annotbypercent
Jim Procter [Wed, 3 May 2017 11:15:34 +0000 (12:15 +0100)]
JAL-1933 JAL-2501 i18n for all auto calculated descriptions

7 years agoJAL-1933 show occupancy in tooltip for row
Jim Procter [Wed, 3 May 2017 10:56:47 +0000 (11:56 +0100)]
JAL-1933 show occupancy in tooltip for row

7 years agoJAL-2246 test a Uniprot fetch
gmungoc [Wed, 3 May 2017 10:52:24 +0000 (11:52 +0100)]
JAL-2246 test a Uniprot fetch

7 years agoJAL-2432 honour percentage checkbox when entering values in text box
Jim Procter [Wed, 3 May 2017 10:47:16 +0000 (11:47 +0100)]
JAL-2432 honour percentage checkbox when entering values in text box

7 years agoJAL-2432 applet: only enable percent checkbox when threshold is active
Jim Procter [Wed, 3 May 2017 10:46:23 +0000 (11:46 +0100)]
JAL-2432 applet: only enable percent checkbox when threshold is active

7 years agoJAL-2432 percentage checkbox follows threshold value field
Jim Procter [Wed, 3 May 2017 10:40:04 +0000 (11:40 +0100)]
JAL-2432 percentage checkbox follows threshold value field

7 years agoJAL-2105 Ensembl REST now at 5.0
gmungoc [Wed, 3 May 2017 09:46:10 +0000 (10:46 +0100)]
JAL-2105 Ensembl REST now at 5.0

7 years agoJAL-2485 JAL-2246 test Uniprot FTS summary
gmungoc [Wed, 3 May 2017 09:43:52 +0000 (10:43 +0100)]
JAL-2485 JAL-2246 test Uniprot FTS summary

7 years agoJAL-2432 recover state for ‘display percentage’ checkbox
Jim Procter [Wed, 3 May 2017 08:47:26 +0000 (09:47 +0100)]
JAL-2432 recover state for ‘display percentage’ checkbox

7 years agoJAL-2432 simplify code
Jim Procter [Wed, 3 May 2017 08:46:32 +0000 (09:46 +0100)]
JAL-2432 simplify code

7 years agoJAL-1632 validate CalculationChooser when selection or alignment changes
Jim Procter [Tue, 2 May 2017 16:59:01 +0000 (17:59 +0100)]
JAL-1632 validate CalculationChooser when selection or alignment changes