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
gmungoc [Thu, 25 Apr 2019 09:05:34 +0000 (10:05 +0100)]
JAL-3010 adjusted tooltips
gmungoc [Thu, 25 Apr 2019 08:50:28 +0000 (09:50 +0100)]
JAL-3010 tidy logging and Javadoc, extract method to store synonyms
gmungoc [Wed, 24 Apr 2019 15:05:56 +0000 (16:05 +0100)]
JAL-3010 TEMPORARY patch for BioJava bug to save all synonyms
gmungoc [Wed, 24 Apr 2019 15:05:18 +0000 (16:05 +0100)]
JAL-3010 cache synonyms for Sequence Ontology terms
gmungoc [Mon, 22 Apr 2019 15:38:13 +0000 (16:38 +0100)]
JAL-3010 relocated ontology search method to OntologyBase
gmungoc [Mon, 22 Apr 2019 14:18:33 +0000 (15:18 +0100)]
JAL-3010 shorten Spanish text to fit space
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
gmungoc [Sat, 20 Apr 2019 07:47:11 +0000 (08:47 +0100)]
JAL-3010 unit test verify root SO terms are cached
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
gmungoc [Fri, 10 Nov 2017 13:45:50 +0000 (13:45 +0000)]
JAL-2791 tailored message if find fails on selection region
gmungoc [Sat, 20 Apr 2019 06:00:47 +0000 (07:00 +0100)]
JAL-3010 discover root parent SO terms at runtime
gmungoc [Fri, 19 Apr 2019 16:45:56 +0000 (17:45 +0100)]
JAL-3010 offer 'apply to all {parent SO term} features' where applicable
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
gmungoc [Thu, 18 Apr 2019 14:32:37 +0000 (15:32 +0100)]
JAL-1793 basic help text for VCF option
gmungoc [Thu, 18 Apr 2019 14:17:45 +0000 (15:17 +0100)]
JAL-3111 additional release notes
gmungoc [Thu, 18 Apr 2019 12:24:42 +0000 (13:24 +0100)]
JAL-3111 small simplification of table tags, valign top
gmungoc [Thu, 18 Apr 2019 12:08:26 +0000 (13:08 +0100)]
JAL-3111 release notes first pass complete
gmungoc [Thu, 18 Apr 2019 11:36:53 +0000 (12:36 +0100)]
JAL-2620 updated help page to mention alternative genetic code tables
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
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
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0
gmungoc [Wed, 3 Apr 2019 15:43:19 +0000 (16:43 +0100)]
JAL-3021 show Sequence Details with cursor at top
gmungoc [Tue, 2 Apr 2019 13:10:45 +0000 (14:10 +0100)]
JAL-3218 allow both Hide and Reveal in scale panel popup menu
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
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
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)
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
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:11 +0000 (17:34 +0000)]
JAL-3111 biojava dependencies
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
Jim Procter [Thu, 28 Mar 2019 17:20:04 +0000 (17:20 +0000)]
JAL-3111 fix jabaws dependency name in IA config
Jim Procter [Thu, 28 Mar 2019 16:59:51 +0000 (16:59 +0000)]
JAL-3111 intervalstore library on IA classpath
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
Jim Procter [Thu, 28 Mar 2019 15:55:08 +0000 (15:55 +0000)]
JAL-3111 typo in IA config
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
gmungoc [Thu, 28 Mar 2019 15:52:23 +0000 (15:52 +0000)]
JAL-1889 patch for failing isControDown test on build server
Jim Procter [Thu, 28 Mar 2019 15:40:20 +0000 (15:40 +0000)]
JAL-3111 update InstallAnywhere dependencies for changed libraries
gmungoc [Thu, 28 Mar 2019 07:56:40 +0000 (07:56 +0000)]
Merge branch 'feature/JAL-3181linkOrdering' into develop
gmungoc [Wed, 27 Mar 2019 17:06:12 +0000 (17:06 +0000)]
JAL-2620 improved error reporting on failure to load resource files
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change
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
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport
gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge
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
gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project
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
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file
gmungoc [Fri, 8 Mar 2019 11:55:15 +0000 (11:55 +0000)]
JAL-2903 typos fixed
gmungoc [Fri, 8 Mar 2019 11:26:52 +0000 (11:26 +0000)]
JAL-3075 update column selection on mouse up after scroll
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
gmungoc [Thu, 7 Mar 2019 15:08:15 +0000 (15:08 +0000)]
JAL-2250 default Apply Colour to All Groups selected
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).
gmungoc [Thu, 7 Mar 2019 12:57:28 +0000 (12:57 +0000)]
JAL-2717 JAL-2360 belated unit tests for ColourMenuHelper
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names
gmungoc [Thu, 7 Mar 2019 09:14:33 +0000 (09:14 +0000)]
Merge branch 'feature/JAL-3205symmetricCalc' into develop
gmungoc [Thu, 7 Mar 2019 08:43:44 +0000 (08:43 +0000)]
JAL-3035 removed spring libraries as only used for jdas
gmungoc [Wed, 6 Mar 2019 16:01:34 +0000 (16:01 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 16:01:12 +0000 (16:01 +0000)]
JAL-3035 restored erroneous deletion
gmungoc [Wed, 6 Mar 2019 15:50:20 +0000 (15:50 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 15:49:46 +0000 (15:49 +0000)]
JAL-3035 more das bits removed
gmungoc [Tue, 5 Mar 2019 17:57:54 +0000 (17:57 +0000)]
Merge branch 'bug/JAL-3201groupClustal' into develop
gmungoc [Tue, 5 Mar 2019 16:44:20 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into merge/JAL-2620
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
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
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
gmungoc [Tue, 5 Mar 2019 12:05:28 +0000 (12:05 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop
gmungoc [Tue, 5 Mar 2019 12:01:37 +0000 (12:01 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814
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
gmungoc [Tue, 5 Mar 2019 11:20:44 +0000 (11:20 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop
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
gmungoc [Tue, 5 Mar 2019 10:26:53 +0000 (10:26 +0000)]
JAL-3049 redo (part of) commit 92bc328
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
git://source.jalview.org / jalview.git / log