jalview.git
5 years agoJAL-3010 updated SO data file to latest 3.1
gmungoc [Thu, 25 Apr 2019 09:11:47 +0000 (10:11 +0100)]
JAL-3010 updated SO data file to latest 3.1
https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so-simple.obo

5 years agoJAL-3010 adjusted tooltips
gmungoc [Thu, 25 Apr 2019 09:05:34 +0000 (10:05 +0100)]
JAL-3010 adjusted tooltips

5 years agoJAL-3010 tidy logging and Javadoc, extract method to store synonyms
gmungoc [Thu, 25 Apr 2019 08:50:28 +0000 (09:50 +0100)]
JAL-3010 tidy logging and Javadoc, extract method to store synonyms

5 years agoJAL-3010 TEMPORARY patch for BioJava bug to save all synonyms
gmungoc [Wed, 24 Apr 2019 15:05:56 +0000 (16:05 +0100)]
JAL-3010 TEMPORARY patch for BioJava bug to save all synonyms

5 years agoJAL-3010 cache synonyms for Sequence Ontology terms
gmungoc [Wed, 24 Apr 2019 15:05:18 +0000 (16:05 +0100)]
JAL-3010 cache synonyms for Sequence Ontology terms

5 years agoJAL-3010 relocated ontology search method to OntologyBase
gmungoc [Mon, 22 Apr 2019 15:38:13 +0000 (16:38 +0100)]
JAL-3010 relocated ontology search method to OntologyBase

5 years agoJAL-3010 shorten Spanish text to fit space
gmungoc [Mon, 22 Apr 2019 14:18:33 +0000 (15:18 +0100)]
JAL-3010 shorten Spanish text to fit space

5 years agoJAL-3010 choose feature types to apply changes to by parent SO term
gmungoc [Mon, 22 Apr 2019 14:13:52 +0000 (15:13 +0100)]
JAL-3010 choose feature types to apply changes to by parent SO term

5 years agoJAL-3010 unit test verify root SO terms are cached
gmungoc [Sat, 20 Apr 2019 07:47:11 +0000 (08:47 +0100)]
JAL-3010 unit test verify root SO terms are cached

5 years agoMerge branch 'develop' into features/JAL-3010ontologyFeatureSettings
gmungoc [Sat, 20 Apr 2019 07:40:22 +0000 (08:40 +0100)]
Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

Conflicts:
src/jalview/controller/AlignViewController.java

5 years agoJAL-2791 tailored message if find fails on selection region
gmungoc [Fri, 10 Nov 2017 13:45:50 +0000 (13:45 +0000)]
JAL-2791 tailored message if find fails on selection region

5 years agoJAL-3010 discover root parent SO terms at runtime
gmungoc [Sat, 20 Apr 2019 06:00:47 +0000 (07:00 +0100)]
JAL-3010 discover root parent SO terms at runtime

5 years agoJAL-3010 offer 'apply to all {parent SO term} features' where applicable
gmungoc [Fri, 19 Apr 2019 16:45:56 +0000 (17:45 +0100)]
JAL-3010 offer 'apply to all {parent SO term} features' where applicable

5 years agoMerge branch 'develop' into trialMerge
gmungoc [Fri, 19 Apr 2019 15:04:51 +0000 (16:04 +0100)]
Merge branch 'develop' into trialMerge

Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FeatureTypeSettings.java

5 years agoJAL-1793 basic help text for VCF option
gmungoc [Thu, 18 Apr 2019 14:32:37 +0000 (15:32 +0100)]
JAL-1793 basic help text for VCF option

5 years agoJAL-3111 additional release notes
gmungoc [Thu, 18 Apr 2019 14:17:45 +0000 (15:17 +0100)]
JAL-3111 additional release notes

5 years agoJAL-3111 small simplification of table tags, valign top
gmungoc [Thu, 18 Apr 2019 12:24:42 +0000 (13:24 +0100)]
JAL-3111 small simplification of table tags, valign top

5 years agoJAL-3111 release notes first pass complete
gmungoc [Thu, 18 Apr 2019 12:08:26 +0000 (13:08 +0100)]
JAL-3111 release notes first pass complete

5 years agoJAL-2620 updated help page to mention alternative genetic code tables
gmungoc [Thu, 18 Apr 2019 11:36:53 +0000 (12:36 +0100)]
JAL-2620 updated help page to mention alternative genetic code tables

5 years agoJAL-3193 dbSource always "ENSEMBL"
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"

5 years agoJAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs

5 years agoMerge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop

5 years agoJAL-3111 Jalview 2.11 what’s New and estimated release date
Jim Procter [Wed, 17 Apr 2019 14:32:36 +0000 (15:32 +0100)]
JAL-3111 Jalview 2.11 what’s New and estimated release date

5 years agoJAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation

5 years agoMerge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211

5 years agoMerge branch 'bug/JAL-3218scalePanelPopups' into develop
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop

5 years agoJAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher

5 years agoJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org

5 years agoJAL-3018 REST version updated to 10.0
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0

5 years agoJAL-3021 show Sequence Details with cursor at top
gmungoc [Wed, 3 Apr 2019 15:43:19 +0000 (16:43 +0100)]
JAL-3021 show Sequence Details with cursor at top

5 years agoJAL-3218 allow both Hide and Reveal in scale panel popup menu bug/JAL-3218scalePanelPopups
gmungoc [Tue, 2 Apr 2019 13:10:45 +0000 (14:10 +0100)]
JAL-3218 allow both Hide and Reveal in scale panel popup menu

5 years agoJAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Mar 2019 10:31:02 +0000 (10:31 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

5 years agoJAL-3140 intervalstore now v1.0 (public release)
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)

5 years agoJAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete
Jim Procter [Fri, 29 Mar 2019 09:54:49 +0000 (09:54 +0000)]
JAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete

5 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

5 years agoJAL-3111 biojava dependencies
Jim Procter [Thu, 28 Mar 2019 17:34:11 +0000 (17:34 +0000)]
JAL-3111 biojava dependencies

5 years agoJAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere
Jim Procter [Thu, 28 Mar 2019 17:20:31 +0000 (17:20 +0000)]
JAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere

5 years agoJAL-3111 fix jabaws dependency name in IA config
Jim Procter [Thu, 28 Mar 2019 17:20:04 +0000 (17:20 +0000)]
JAL-3111 fix jabaws dependency name in IA config

5 years agoJAL-3111 intervalstore library on IA classpath
Jim Procter [Thu, 28 Mar 2019 16:59:51 +0000 (16:59 +0000)]
JAL-3111 intervalstore library on IA classpath

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 28 Mar 2019 16:13:39 +0000 (16:13 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

5 years agoJAL-3111 typo in IA config
Jim Procter [Thu, 28 Mar 2019 15:55:08 +0000 (15:55 +0000)]
JAL-3111 typo in IA config

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 28 Mar 2019 15:52:34 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

5 years agoJAL-1889 patch for failing isControDown test on build server
gmungoc [Thu, 28 Mar 2019 15:52:23 +0000 (15:52 +0000)]
JAL-1889 patch for failing isControDown test on build server

5 years agoJAL-3111 update InstallAnywhere dependencies for changed libraries
Jim Procter [Thu, 28 Mar 2019 15:40:20 +0000 (15:40 +0000)]
JAL-3111 update InstallAnywhere dependencies for changed libraries

5 years agoMerge branch 'feature/JAL-3181linkOrdering' into develop
gmungoc [Thu, 28 Mar 2019 07:56:40 +0000 (07:56 +0000)]
Merge branch 'feature/JAL-3181linkOrdering' into develop

5 years agoJAL-2620 improved error reporting on failure to load resource files
gmungoc [Wed, 27 Mar 2019 17:06:12 +0000 (17:06 +0000)]
JAL-2620 improved error reporting on failure to load resource files

5 years agoJAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails

5 years agoJAL-3127 scripts updated for method signature change
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change

5 years agoJAL-1889 explicit recalc of geometry for scale left/right/above on/off bug/JAL-1889serverTestSuite
gmungoc [Sat, 23 Mar 2019 08:49:52 +0000 (08:49 +0000)]
JAL-1889 explicit recalc of geometry for scale left/right/above on/off

5 years agoJAL-1889 remove debug logging, add updateLayout()
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()

5 years agoJAL-1889 more debug logging
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging

5 years agoJAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging

5 years agoJAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()

5 years agoJAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file

5 years agoJAL-1889 correct props param, remove dasserver, output file paths
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths

5 years agoJAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations

5 years agoJAL-1889 diagnostics for failing test on server
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server

5 years agoJAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip

5 years agoJAL-3212 unit test and fix for Scale Panel bug
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug

5 years agoJAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views

5 years agoJAL-3203 Overview show hidden default false also in Preferences
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences

5 years agoJAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown

5 years agoMerge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

5 years agoJAL-3127 check for null viewport feature/JAL-3127_seqidChainshading
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport

5 years agoMerge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127

5 years agoJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!

5 years agoJAL-3127 fix faulty merge
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge

5 years agoMerge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 15:07:39 +0000 (15:07 +0000)]
Merge branch 'develop' into merge/JAL-3127

Conflicts:
src/jalview/viewmodel/AlignmentViewport.java

5 years agoMerge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop

5 years agoJAL-3201 restore group colours correctly from project feature/JAL-2250colourAllGroups
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project

5 years agoMerge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 11:37:58 +0000 (11:37 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

Conflicts:
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
test/jalview/io/Jalview2xmlTests.java

5 years agoJAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored

5 years agoMerge branch 'bug/JAL-3075' into develop
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop

5 years agoJAL-3193 defensive trim of URL read from properties file
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file

5 years agoJAL-2903 typos fixed
gmungoc [Fri, 8 Mar 2019 11:55:15 +0000 (11:55 +0000)]
JAL-2903 typos fixed

5 years agoJAL-3075 update column selection on mouse up after scroll bug/JAL-3075
gmungoc [Fri, 8 Mar 2019 11:26:52 +0000 (11:26 +0000)]
JAL-3075 update column selection on mouse up after scroll

5 years agoMerge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180
gmungoc [Thu, 7 Mar 2019 16:12:25 +0000 (16:12 +0000)]
Merge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180

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

5 years agoJAL-2250 default Apply Colour to All Groups selected
gmungoc [Thu, 7 Mar 2019 15:08:15 +0000 (15:08 +0000)]
JAL-2250  default Apply Colour to All Groups selected

5 years agoJAL-3127 set ‘updateStructures’ flag for viewports associated with each tree to true...
Jim Procter [Thu, 7 Mar 2019 14:25:41 +0000 (14:25 +0000)]
JAL-3127 set ‘updateStructures’ flag for viewports associated with each tree to true when groups are deleted, rather then when we create new groups (which may not always be the case).

5 years agoJAL-2717 JAL-2360 belated unit tests for ColourMenuHelper
gmungoc [Thu, 7 Mar 2019 12:57:28 +0000 (12:57 +0000)]
JAL-2717 JAL-2360 belated unit tests for ColourMenuHelper

5 years agoJAL-2717 corrected i18n of colour scheme names
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names

5 years agoMerge branch 'feature/JAL-3205symmetricCalc' into develop
gmungoc [Thu, 7 Mar 2019 09:14:33 +0000 (09:14 +0000)]
Merge branch 'feature/JAL-3205symmetricCalc' into develop

5 years agoJAL-3035 removed spring libraries as only used for jdas
gmungoc [Thu, 7 Mar 2019 08:43:44 +0000 (08:43 +0000)]
JAL-3035 removed spring libraries as only used for jdas

5 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 16:01:34 +0000 (16:01 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

5 years agoJAL-3035 restored erroneous deletion tasks/JAL-3035_remove_dasobert_dependency
gmungoc [Wed, 6 Mar 2019 16:01:12 +0000 (16:01 +0000)]
JAL-3035 restored erroneous deletion

5 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 15:50:20 +0000 (15:50 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

5 years agoJAL-3035 more das bits removed
gmungoc [Wed, 6 Mar 2019 15:49:46 +0000 (15:49 +0000)]
JAL-3035 more das bits removed

5 years agoMerge branch 'bug/JAL-3201groupClustal' into develop
gmungoc [Tue, 5 Mar 2019 17:57:54 +0000 (17:57 +0000)]
Merge branch 'bug/JAL-3201groupClustal' into develop

5 years agoMerge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into...
gmungoc [Tue, 5 Mar 2019 16:44:20 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into merge/JAL-2620

5 years agoMerge branch 'bug/JAL-2621' into develop
gmungoc [Tue, 5 Mar 2019 15:22:40 +0000 (15:22 +0000)]
Merge branch 'bug/JAL-2621' into develop

Conflicts:
src/jalview/gui/OverviewPanel.java

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3141_Messages_discrepancy_fix' into...
gmungoc [Tue, 5 Mar 2019 15:07:51 +0000 (15:07 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3141_Messages_discrepancy_fix' into develop

5 years agoMerge remote-tracking branch 'origin/bug/JAL-2839findWithHidden' into merge/JAL-2839_2933
gmungoc [Tue, 5 Mar 2019 12:40:08 +0000 (12:40 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2839findWithHidden' into merge/JAL-2839_2933

5 years agoMerge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop
gmungoc [Tue, 5 Mar 2019 12:05:28 +0000 (12:05 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop

5 years agoMerge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814
gmungoc [Tue, 5 Mar 2019 12:01:37 +0000 (12:01 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814

5 years agoJAL-3141 Fixed inconsistent (changed) message labels in Messages_es.props and changed... bug/JAL-3141_Messages_discrepancy_fix
Ben Soares [Tue, 5 Mar 2019 11:44:27 +0000 (11:44 +0000)]
JAL-3141 Fixed inconsistent (changed) message labels in Messages_es.props and changed a label in props and code for consistency/avoid confusion

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop
gmungoc [Tue, 5 Mar 2019 11:20:44 +0000 (11:20 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop

5 years agoJAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration
gmungoc [Wed, 22 Aug 2018 10:31:04 +0000 (11:31 +0100)]
JAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration

Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/gui/FeatureSettings.java

5 years agoJAL-3049 redo (part of) commit 92bc328
gmungoc [Tue, 5 Mar 2019 10:26:53 +0000 (10:26 +0000)]
JAL-3049 redo (part of) commit 92bc328

5 years agoJAL-3054 small y-overlap of tooltip and cell leads the eye better
gmungoc [Fri, 6 Jul 2018 09:55:46 +0000 (10:55 +0100)]
JAL-3054 small y-overlap of tooltip and cell leads the eye better