Jim Procter [Thu, 20 Jun 2019 15:11:07 +0000 (16:11 +0100)]
Merge branch 'develop' into bug/JAL-2934proportionalScrolling
Jalview Development Admin [Wed, 19 Jun 2019 12:42:49 +0000 (13:42 +0100)]
JAL-3111 codesign the uninstaller again
Ben Soares [Wed, 19 Jun 2019 11:51:21 +0000 (12:51 +0100)]
Merge branch 'merge/JAL-3310_and_JAL-3300' into develop
Ben Soares [Wed, 19 Jun 2019 11:50:36 +0000 (12:50 +0100)]
JAL-3321 Last pieces of the getdown-launcher.jar upgrade puzzle
Ben Soares [Wed, 19 Jun 2019 11:48:30 +0000 (12:48 +0100)]
JAL-3310 Removing i4jruntime.jar from dist. Not needed by Jalview
Jim Procter [Wed, 19 Jun 2019 10:13:34 +0000 (11:13 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 19 Jun 2019 10:12:47 +0000 (11:12 +0100)]
JAL-3111 release notes for JAL-3313
Jim Procter [Wed, 19 Jun 2019 10:09:20 +0000 (11:09 +0100)]
JAL-3111 formatting

Jim Procter [Wed, 19 Jun 2019 10:05:54 +0000 (11:05 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Wed, 19 Jun 2019 10:01:43 +0000 (11:01 +0100)]
JAL-3111 release notes for JAL-27830 JAL-2876 JAL-2567 and JAL-2256
Ben Soares [Wed, 19 Jun 2019 00:29:05 +0000 (01:29 +0100)]
JAL-3321 Corrected the badly configured getdown-launcher.jar for updating and updated build.gradle to make the right getdown.txt file
gmungoc [Tue, 18 Jun 2019 17:06:08 +0000 (18:06 +0100)]
JAL-3313 don't double count mapped codons
Jim Procter [Tue, 18 Jun 2019 16:49:23 +0000 (17:49 +0100)]
Merge branch 'bug/JAL-2830_editManglesDatasetSequence' into develop
Jim Procter [Tue, 18 Jun 2019 15:42:18 +0000 (16:42 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatasetSequence
Jim Procter [Tue, 18 Jun 2019 15:39:19 +0000 (16:39 +0100)]
Merge branch 'bug/JAL-2830_editManglesDatasetSequence' into documentation/JAL-3111_release_211
Jim Procter [Tue, 18 Jun 2019 15:38:10 +0000 (16:38 +0100)]
JAL-3111 JAL-2446 mentioned in context with NCList->intervalstoreJ lib
Jim Procter [Tue, 18 Jun 2019 15:31:43 +0000 (16:31 +0100)]
JAL-3111 JAL-2684 JAL-2360 JAL-2416 release notes
Ben Soares [Tue, 18 Jun 2019 15:31:20 +0000 (16:31 +0100)]
Merge branch 'develop' into merge/JAL-3310_and_JAL-3300
Jim Procter [Tue, 18 Jun 2019 15:08:39 +0000 (16:08 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Tue, 18 Jun 2019 15:08:11 +0000 (16:08 +0100)]
JAL-3286 JAL-3111 release notes
Jim Procter [Tue, 18 Jun 2019 15:05:46 +0000 (16:05 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Tue, 18 Jun 2019 14:44:53 +0000 (15:44 +0100)]
Merge branch 'bug/JAL-3286duplicatePdbQuery' into develop
Jim Procter [Tue, 18 Jun 2019 14:44:17 +0000 (15:44 +0100)]
JAL-3111 JAL-3003 documentation note
Jim Procter [Tue, 18 Jun 2019 13:56:41 +0000 (14:56 +0100)]
JAL-2296 JAL-2295 document in release notes post feature release in 2.10.4
Jim Procter [Tue, 18 Jun 2019 13:55:33 +0000 (14:55 +0100)]
JAL-3111 - new known issue JAL-3314
Jim Procter [Tue, 18 Jun 2019 13:54:47 +0000 (14:54 +0100)]
JAL-3111 release notes for JAL-3073 JAL-3042
Jim Procter [Tue, 18 Jun 2019 13:53:48 +0000 (14:53 +0100)]
JAL-3111 JAL-3080 documentation
Ben Soares [Tue, 18 Jun 2019 11:52:40 +0000 (12:52 +0100)]
JAL-3310 tidying unecessary files from getdown src tree
Ben Soares [Tue, 18 Jun 2019 11:49:32 +0000 (12:49 +0100)]
JAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations missing SHIFT
Ben Soares [Tue, 18 Jun 2019 09:52:27 +0000 (10:52 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Tue, 18 Jun 2019 07:43:24 +0000 (08:43 +0100)]
Merge branch 'develop' into merge/JAL-3310_and_JAL-3300
Merging in develop in preparation to merge back
Ben Soares [Mon, 17 Jun 2019 19:15:00 +0000 (20:15 +0100)]
JAL-3310 JAL-3300 two getdown fixes merged
Ben Soares [Mon, 17 Jun 2019 11:08:59 +0000 (12:08 +0100)]
JAL-3310 Remove install4j from getdown-launcher.jar. Separate and catch call to install4j's StartupNotification.Listener.
Jim Procter [Mon, 17 Jun 2019 12:53:52 +0000 (13:53 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Mon, 17 Jun 2019 12:46:54 +0000 (13:46 +0100)]
JAL-3111 rejigged release notes again
Jim Procter [Mon, 17 Jun 2019 12:46:28 +0000 (13:46 +0100)]
JAL-2975,JAL-2647,JAL-1767,JAL-2965, JAL-3111 updated PCA viewer documentation
Ben Soares [Fri, 14 Jun 2019 16:33:47 +0000 (17:33 +0100)]
JAL-3295 pre-merged code with JAL-3295 branch which will go onto develop
Ben Soares [Fri, 14 Jun 2019 16:31:28 +0000 (17:31 +0100)]
JAL-3278 A system.out.println turned into a cache.log.error
Ben Soares [Fri, 14 Jun 2019 16:25:36 +0000 (17:25 +0100)]
JAL-3300 instant Splash screen on getdown
Ben Soares [Fri, 14 Jun 2019 16:23:07 +0000 (17:23 +0100)]
JAL-3130 added a bit of gradle support for compiling in Java 12 and potentially 13
Jim Procter [Fri, 14 Jun 2019 15:58:47 +0000 (16:58 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Fri, 14 Jun 2019 15:57:50 +0000 (16:57 +0100)]
JAL-3111 release date now 20th June. more release note work..
Jim Procter [Fri, 14 Jun 2019 15:48:19 +0000 (16:48 +0100)]
JAL-3111 report build type and commit in stdout from command line and in About/Splash screen
Jim Procter [Fri, 14 Jun 2019 15:44:30 +0000 (16:44 +0100)]
JAL-3299 JAL-3280 javadoc on BuildDetails bean
Jim Procter [Fri, 14 Jun 2019 15:43:21 +0000 (16:43 +0100)]
JAL-3111 report time when Jalview was built (consider making this a conditional)
Jalview Development Admin [Thu, 13 Jun 2019 15:07:32 +0000 (16:07 +0100)]
Merge branch 'releases/Release_2_11_Branch' into develop
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 18:28:59 +0000 (19:28 +0100)]
JAL-3143 also parse "phase" from JSON response if present
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
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
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 14:31:59 +0000 (15:31 +0100)]
Merge branch 'bug/JAL-3288splitFrameMenusJava11' into develop
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
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 [Wed, 5 Jun 2019 14:22:02 +0000 (15:22 +0100)]
JAL-3288 override JInternalFrame.setSelected() to avoid cancelling menus
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
git://source.jalview.org / jalview.git / log