Jalview Development Admin [Thu, 13 Jun 2019 15:07:32 +0000 (16:07 +0100)]
Merge branch 'releases/Release_2_11_Branch' into develop
gmungoc [Thu, 13 Jun 2019 14:58:57 +0000 (15:58 +0100)]
JAL-3303 ignore deletions when computing peptide variants
Jim Procter [Thu, 13 Jun 2019 14:49:33 +0000 (15:49 +0100)]
Merge branch 'bug/JAL-3295_CMD_select_not_working_in_sequence_selection' into develop
gmungoc [Thu, 13 Jun 2019 11:13:34 +0000 (12:13 +0100)]
JAL-3143 recognise lnc_RNA as transcript
Ben Soares [Thu, 13 Jun 2019 09:10:11 +0000 (10:10 +0100)]
JAL-3295 Can now compile/run/debug in Eclipse with Java 1.8. Change JAVA_VERSION in gradle.properties
Ben Soares [Wed, 12 Jun 2019 16:16:35 +0000 (17:16 +0100)]
JAL-3295 Fixed CMD-select of sequences in alignment window
Ben Soares [Wed, 12 Jun 2019 14:58:04 +0000 (15:58 +0100)]
JAL-3299 Fixed gitHash and gitBranch definitions in build.gradle
gmungoc [Tue, 11 Jun 2019 18:29:56 +0000 (19:29 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Tue, 11 Jun 2019 18:28:59 +0000 (19:28 +0100)]
JAL-3143 also parse "phase" from JSON response if present
gmungoc [Tue, 11 Jun 2019 15:44:09 +0000 (16:44 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
Ben Soares [Tue, 11 Jun 2019 14:05:58 +0000 (15:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Tue, 11 Jun 2019 14:05:38 +0000 (15:05 +0100)]
JAL-3248 improved pandoc lookup. Now comma-separated value in pandoc_exe in gradle.properties
gmungoc [Tue, 11 Jun 2019 13:47:53 +0000 (14:47 +0100)]
JAL-3111 update release date placeholder
gmungoc [Tue, 11 Jun 2019 12:57:48 +0000 (13:57 +0100)]
JAL-3288 fixes for gain/lose focus
gmungoc [Tue, 11 Jun 2019 10:31:12 +0000 (11:31 +0100)]
JAL-3187 CDS has same dataset sequence as transcript
Ben Soares [Mon, 10 Jun 2019 14:15:29 +0000 (15:15 +0100)]
JAL-3248 quick fix for build.gradle when pandoc not available
Ben Soares [Mon, 10 Jun 2019 14:08:17 +0000 (15:08 +0100)]
JAL-3248 building.html now generated by pandoc 'brew install pandoc'
Ben Soares [Mon, 10 Jun 2019 13:39:20 +0000 (14:39 +0100)]
JAL-3248 added conversion of building.md to building.html to gradle task. Will happen before making jar if pandoc available
tva [Mon, 10 Jun 2019 10:54:37 +0000 (11:54 +0100)]
JAL-3297 pad gaps in alignment to ensure hmmalign runs
Ben Soares [Mon, 10 Jun 2019 10:46:01 +0000 (11:46 +0100)]
Merge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
Merging in develop
Ben Soares [Mon, 10 Jun 2019 10:41:48 +0000 (11:41 +0100)]
Merge branch 'task/JAL-3248_rewritten_building_md_instructions' of https://source.jalview.org/git/jalview into task/JAL-3248_rewritten_building_md_instructions
Ben Soares [Mon, 10 Jun 2019 10:38:40 +0000 (11:38 +0100)]
JAL-3248 Building from source documentation in markdown and converted to HTML
Ben Soares [Mon, 10 Jun 2019 10:38:40 +0000 (11:38 +0100)]
JAL-3248 Building from source documentation in markdown and converted to HTML
Ben Soares [Fri, 7 Jun 2019 17:13:11 +0000 (18:13 +0100)]
JAL-3248 Almost completed building doc
gmungoc [Fri, 7 Jun 2019 16:08:28 +0000 (17:08 +0100)]
JAL-3187 save and restore flags for show complement features
gmungoc [Fri, 7 Jun 2019 16:08:01 +0000 (17:08 +0100)]
JAL-3187 change fields to local variables
gmungoc [Fri, 7 Jun 2019 15:22:03 +0000 (16:22 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Fri, 7 Jun 2019 14:31:59 +0000 (15:31 +0100)]
Merge branch 'bug/JAL-3288splitFrameMenusJava11' into develop
tva [Fri, 7 Jun 2019 14:23:34 +0000 (15:23 +0100)]
JAL-3291 issue fixed, passing tests added
Ben Soares [Fri, 7 Jun 2019 13:33:36 +0000 (14:33 +0100)]
JAL-3248 a bit more
gmungoc [Fri, 7 Jun 2019 12:42:24 +0000 (13:42 +0100)]
JAL-3187 Viewport schema attributes for showComplementFeatures[OnTop]
Conflicts:
src/jalview/xml/binding/jalview/AlcodonFrame.java
src/jalview/xml/binding/jalview/Annotation.java
src/jalview/xml/binding/jalview/AnnotationColourScheme.java
src/jalview/xml/binding/jalview/AnnotationElement.java
src/jalview/xml/binding/jalview/DoubleMatrix.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/Feature.java
src/jalview/xml/binding/jalview/FeatureMatcher.java
src/jalview/xml/binding/jalview/FeatureMatcherSet.java
src/jalview/xml/binding/jalview/FilterBy.java
src/jalview/xml/binding/jalview/JalviewModel.java
src/jalview/xml/binding/jalview/JalviewUserColours.java
src/jalview/xml/binding/jalview/MapListType.java
src/jalview/xml/binding/jalview/Mapping.java
src/jalview/xml/binding/jalview/NoValueColour.java
src/jalview/xml/binding/jalview/ObjectFactory.java
src/jalview/xml/binding/jalview/PcaDataType.java
src/jalview/xml/binding/jalview/Pdbentry.java
src/jalview/xml/binding/jalview/Sequence.java
src/jalview/xml/binding/jalview/SequenceSet.java
src/jalview/xml/binding/jalview/SequenceType.java
src/jalview/xml/binding/jalview/ThresholdType.java
src/jalview/xml/binding/jalview/VAMSAS.java
src/jalview/xml/binding/jalview/WebServiceParameterSet.java
src/jalview/xml/binding/jalview/package-info.java
gmungoc [Fri, 7 Jun 2019 13:03:58 +0000 (14:03 +0100)]
JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType
Conflicts:
src/jalview/xml/binding/jalview/AlcodonFrame.java
src/jalview/xml/binding/jalview/Annotation.java
src/jalview/xml/binding/jalview/AnnotationColourScheme.java
src/jalview/xml/binding/jalview/AnnotationElement.java
src/jalview/xml/binding/jalview/DoubleMatrix.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/Feature.java
src/jalview/xml/binding/jalview/FeatureMatcher.java
src/jalview/xml/binding/jalview/FeatureMatcherSet.java
src/jalview/xml/binding/jalview/FilterBy.java
src/jalview/xml/binding/jalview/JalviewModel.java
src/jalview/xml/binding/jalview/JalviewUserColours.java
src/jalview/xml/binding/jalview/MapListType.java
src/jalview/xml/binding/jalview/Mapping.java
src/jalview/xml/binding/jalview/NoValueColour.java
src/jalview/xml/binding/jalview/ObjectFactory.java
src/jalview/xml/binding/jalview/PcaDataType.java
src/jalview/xml/binding/jalview/Pdbentry.java
src/jalview/xml/binding/jalview/Sequence.java
src/jalview/xml/binding/jalview/SequenceSet.java
src/jalview/xml/binding/jalview/SequenceType.java
src/jalview/xml/binding/jalview/ThresholdType.java
src/jalview/xml/binding/jalview/VAMSAS.java
src/jalview/xml/binding/jalview/WebServiceParameterSet.java
src/jalview/xml/binding/jalview/package-info.java
gmungoc [Wed, 6 Feb 2019 15:27:49 +0000 (15:27 +0000)]
JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings
Ben Soares [Fri, 7 Jun 2019 11:20:33 +0000 (12:20 +0100)]
Merge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
merging in latest changes in develop
Ben Soares [Fri, 7 Jun 2019 11:18:59 +0000 (12:18 +0100)]
JAL-3225 removing slightly misleading rewrite of .classpath when synchronizing/building in gradle
tva [Fri, 7 Jun 2019 08:13:08 +0000 (09:13 +0100)]
JAL-3285 fix errors in tests introduced by merge
tva [Thu, 6 Jun 2019 16:00:19 +0000 (17:00 +0100)]
JAL-3285 build Jalview XML file for current version
tva [Thu, 6 Jun 2019 14:28:52 +0000 (15:28 +0100)]
JAL-3285 fix incorrect file paths on HMMAlign/Search results
Ben Soares [Thu, 6 Jun 2019 14:06:58 +0000 (15:06 +0100)]
JAL-3225 Classpath now made in eclipse.classpath.file.whenMerged and recognised by buildship :)
gmungoc [Thu, 6 Jun 2019 13:37:42 +0000 (14:37 +0100)]
Merge branch 'bug/JAL-3288splitFrameMenusJava11' into trialMerge
gmungoc [Thu, 6 Jun 2019 13:34:56 +0000 (14:34 +0100)]
JAL-3187 deletions (of Castor code) after merge from develop
gmungoc [Thu, 6 Jun 2019 13:33:40 +0000 (14:33 +0100)]
Merge branch 'develop' into trialMerge
Conflicts:
src/jalview/datamodel/features/SequenceFeatures.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/SeqPanel.java
src/jalview/project/Jalview2XML.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/io/Jalview2xmlTests.java
gmungoc [Thu, 6 Jun 2019 13:15:58 +0000 (14:15 +0100)]
JAL-3187 commit to enable merge from develop
tva [Thu, 6 Jun 2019 13:08:58 +0000 (14:08 +0100)]
JAL-3285 add Cygwin environment path fix for Windows
tva [Thu, 6 Jun 2019 09:20:33 +0000 (10:20 +0100)]
JAL-3285 code changes to HMMER colour schemes not included in merge
tva [Thu, 6 Jun 2019 08:13:18 +0000 (09:13 +0100)]
JAL-3285 fix FileLoader failing to load HMMER file
tva [Wed, 5 Jun 2019 15:32:43 +0000 (16:32 +0100)]
JAL-3285 method call change tin Information to match develop
tva [Wed, 5 Jun 2019 15:28:34 +0000 (16:28 +0100)]
JAL-3285 delete duplicate variables in AlignmentViewport from merge
tva [Wed, 5 Jun 2019 15:23:56 +0000 (16:23 +0100)]
JAL-3285 method call change to HMMBuild not included in merge
gmungoc [Wed, 5 Jun 2019 14:22:02 +0000 (15:22 +0100)]
JAL-3288 override JInternalFrame.setSelected() to avoid cancelling menus
tva [Wed, 5 Jun 2019 13:41:26 +0000 (14:41 +0100)]
JAL-3285 method call change in SeqPanel to match develop
tva [Wed, 5 Jun 2019 13:38:31 +0000 (14:38 +0100)]
JAL-3285 change method declaration in AAFrequency to match develop
tva [Wed, 5 Jun 2019 13:34:14 +0000 (14:34 +0100)]
JAL-3285 changed method call on AnnotationRenderer to match definition
tva [Wed, 5 Jun 2019 13:33:02 +0000 (14:33 +0100)]
JAL-3285 code changes to Jalview2XML not included in merge
tva [Wed, 5 Jun 2019 13:14:25 +0000 (14:14 +0100)]
JAL-3285 add unmerged code to AlignmentAnnotation
tva [Wed, 5 Jun 2019 13:09:06 +0000 (14:09 +0100)]
JAL-3285 method call name change to SeqPanel not included in merge
tva [Wed, 5 Jun 2019 13:07:47 +0000 (14:07 +0100)]
JAL-3285 method call name change in OverviewPanel not included during
merge
tva [Wed, 5 Jun 2019 13:06:22 +0000 (14:06 +0100)]
JAL-3285 small method call name change to AnnotationLabels
tva [Wed, 5 Jun 2019 13:04:52 +0000 (14:04 +0100)]
JAL-3285 add unmerged code to SequenceGroup
tva [Wed, 5 Jun 2019 12:40:26 +0000 (13:40 +0100)]
JAL-3285 small method call name change missed in ConsensusThread commit
tva [Wed, 5 Jun 2019 12:38:44 +0000 (13:38 +0100)]
JAL-3285 small code changes to ConsensusThread not included in merge
tva [Wed, 5 Jun 2019 12:35:10 +0000 (13:35 +0100)]
JAL-3285 small code changes to AnnotationRenderer not included in merge
tva [Wed, 5 Jun 2019 12:32:15 +0000 (13:32 +0100)]
JAL-3285 code changes to AnnotationLabels not included in the merge
tva [Wed, 5 Jun 2019 12:27:32 +0000 (13:27 +0100)]
JAL-3285 add unmerged features to AlignViewportI
tva [Wed, 5 Jun 2019 12:24:28 +0000 (13:24 +0100)]
JAL-3285 add unmerged features to AlignViewport
tva [Wed, 5 Jun 2019 12:22:13 +0000 (13:22 +0100)]
JAL-3285 add unmerged features into AlignmentViewport
tva [Wed, 5 Jun 2019 11:06:31 +0000 (12:06 +0100)]
JAL-3285 add methods and small changes to StockholmFile left out by git
Jim Procter [Tue, 4 Jun 2019 17:22:21 +0000 (18:22 +0100)]
Merge branch 'develop' into developtomchmmer
JAL-3285 merged 2.11 develop into the features/mchmmer branch
- need to fix code for migration from Castor to JAXB
- need to check Stockholm file IO and tests
Good luck !
gmungoc [Tue, 4 Jun 2019 15:50:05 +0000 (16:50 +0100)]
JAL-2386 avoid duplicate pdbids in free text query
Ben Soares [Tue, 4 Jun 2019 15:30:10 +0000 (16:30 +0100)]
JAL-3287 correct local file URI for appbase and getdownDigest in Windows
Ben Soares [Tue, 4 Jun 2019 14:38:46 +0000 (15:38 +0100)]
JAL-3287 adjustment to HelpLinksChecker
Ben Soares [Tue, 4 Jun 2019 14:28:13 +0000 (15:28 +0100)]
JAL-3287 adjustment to HelpLinksChecker to run in Windows and improvement to build.gradle
Ben Soares [Tue, 4 Jun 2019 08:16:53 +0000 (09:16 +0100)]
JAL-3248 small edits
Ben Soares [Fri, 31 May 2019 14:44:07 +0000 (15:44 +0100)]
JAL-3247 Adjusted Uninstall Old Jalview.app to just run the old uninstaller if it finds it, aded '(optional)' to the link name in the DMG. It will need re-signing. Edited VCFReader to allow java 1.8 compiling.
Ben Soares [Fri, 31 May 2019 12:22:25 +0000 (13:22 +0100)]
JAL-3248 extra tl;dr
Ben Soares [Thu, 30 May 2019 17:53:09 +0000 (18:53 +0100)]
JAL-3248 Essential tl;dr :)
Ben Soares [Thu, 30 May 2019 15:55:54 +0000 (16:55 +0100)]
Merge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
Merging in develop
gmungoc [Wed, 29 May 2019 15:17:10 +0000 (16:17 +0100)]
JAL-2738 error logging if no ##reference found
gmungoc [Wed, 29 May 2019 15:13:10 +0000 (16:13 +0100)]
JAL-2738 accept .csi, default to GRCh37:homo_sapiens if no ##reference
Ben Soares [Tue, 28 May 2019 23:28:58 +0000 (00:28 +0100)]
JAL-3277 Fixed getdown splashscreen. For unknown reasons getdown thought it had both ui.background_image and ui.rotating_background and so defaulted to using ui.rotating_background even though this was not provided. Changed it to default to ui.background_image.
Ben Soares [Tue, 28 May 2019 15:25:49 +0000 (16:25 +0100)]
JAL-1988 Some TEST code accidentally left in now removed -- was affecting some saved alignment files such as stk
Jalview Development Admin [Tue, 28 May 2019 12:43:21 +0000 (13:43 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch
Jalview Development Admin [Tue, 28 May 2019 12:42:37 +0000 (13:42 +0100)]
JAL-3247 sign the AppleScript uninstaller
Ben Soares [Tue, 28 May 2019 11:18:24 +0000 (12:18 +0100)]
JAL-3141 deleted TODO comment in Messages_es
Ben Soares [Tue, 28 May 2019 11:14:51 +0000 (12:14 +0100)]
Merge branch 'develop' into task/JAL-3141_JAL-3247_merge
updating merge
Ben Soares [Tue, 28 May 2019 09:50:32 +0000 (10:50 +0100)]
JAL-3248 saving
Ben Soares [Mon, 27 May 2019 15:26:45 +0000 (16:26 +0100)]
JAL-3141 Added HashMap types for Java 1.8 compatibility
Ben Soares [Mon, 27 May 2019 15:18:37 +0000 (16:18 +0100)]
Merge branch 'task/JAL-3141_Customise_checkbox' into task/JAL-3141_JAL-3247_merge
Ben Soares [Mon, 27 May 2019 15:18:09 +0000 (16:18 +0100)]
JAL-3141 Object array cast missing
Ben Soares [Mon, 27 May 2019 15:06:02 +0000 (16:06 +0100)]
Merge branch 'task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge' into task/JAL-3141_JAL-3247_merge
merge attempt
Ben Soares [Mon, 27 May 2019 14:50:52 +0000 (15:50 +0100)]
Merge branch 'develop' into task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge
Merging in develop
Ben Soares [Mon, 27 May 2019 14:50:37 +0000 (15:50 +0100)]
JAL-3247 Added AppleScript based App to run old Jalview uninstaller if present
Ben Soares [Mon, 27 May 2019 09:01:12 +0000 (10:01 +0100)]
JAL-3141 Generified the JvUtils.buildComboWithTooltips to an Object and adjusted other code in FeatureTypeSettings. Added one more tooltip.
gmungoc [Mon, 27 May 2019 08:16:25 +0000 (09:16 +0100)]
JAL-3141 test file in test folder not examples
Ben Soares [Sat, 25 May 2019 13:44:00 +0000 (14:44 +0100)]
JAL-3141 One more error log fix
Ben Soares [Sat, 25 May 2019 13:40:48 +0000 (14:40 +0100)]
JAL-3141 Added tooltips on Schemes dropdown and Customise checkbox
Ben Soares [Fri, 24 May 2019 16:35:41 +0000 (17:35 +0100)]
JAL-3141 Fixes recommended from gmc's test
gmungoc [Fri, 24 May 2019 13:31:57 +0000 (14:31 +0100)]
JAL-1988 Spanish typo corrección
Ben Soares [Fri, 24 May 2019 11:32:43 +0000 (12:32 +0100)]
JAL-3141 Fixed vertical size of the example filenames box\! Yay\!
Ben Soares [Fri, 24 May 2019 09:05:10 +0000 (10:05 +0100)]
JAL-3141 Fixed tests
git://source.jalview.org / jalview.git / log