gmungoc [Mon, 17 Jun 2019 15:59:08 +0000 (16:59 +0100)]
JAL-2792 JAL-3187 linked features (if shown) in Feature details submenu
gmungoc [Mon, 17 Jun 2019 12:18:44 +0000 (13:18 +0100)]
JAL-3187 update alignAs code and unit tests for 'shared dataset' case
gmungoc [Mon, 17 Jun 2019 12:18:12 +0000 (13:18 +0100)]
JAL-3187 update unit test - protein variants not now precomputed
gmungoc [Mon, 17 Jun 2019 12:17:20 +0000 (13:17 +0100)]
JAL-3187 add sequence to feature details table (and refactor PopupMenu)
gmungoc [Fri, 14 Jun 2019 10:54:50 +0000 (11:54 +0100)]
JAL-3302 transfer visible 'linked' features to Chimera
gmungoc [Thu, 13 Jun 2019 14:58:57 +0000 (15:58 +0100)]
JAL-3303 ignore deletions when computing peptide variants
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
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
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
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 [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
gmungoc [Wed, 5 Jun 2019 14:22:02 +0000 (15:22 +0100)]
JAL-3288 override JInternalFrame.setSelected() to avoid cancelling menus
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 12:42:37 +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
Ben Soares [Fri, 24 May 2019 01:24:18 +0000 (02:24 +0100)]
JAL-3141 Reworked a lot of BackupFiles to allow the Customise Checkbox
Ben Soares [Wed, 22 May 2019 11:18:01 +0000 (12:18 +0100)]
Merge branch 'bug/JAL-3141_backupfiles_prefs_widget_disable_bug' into merge/develop_backupfilefix/JAL-3141_remove_saveproject_and_fix_buglet
Merging three unmerged commits
gmungoc [Wed, 22 May 2019 08:41:41 +0000 (09:41 +0100)]
JAL-3111 help file spelling correction
Ben Soares [Tue, 21 May 2019 17:15:53 +0000 (18:15 +0100)]
JAL-3247 Launcher start improvements. RPM and DEB no longer packaged with getdown (due to difficulties)
gmungoc [Tue, 21 May 2019 16:45:40 +0000 (17:45 +0100)]
JAL-3273 small correction to expected result calculation
Ben Soares [Mon, 20 May 2019 22:03:23 +0000 (23:03 +0100)]
Merge branch 'task/JAL-3254_improved_max_memory_stack_setting' into task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge
Merging a number of fixes/improvements into one branch and then merge in develop
Ben Soares [Mon, 20 May 2019 15:33:04 +0000 (16:33 +0100)]
JAL-3247 Unix shell installer and tar archive corrected -- network and offline versions. RPM and DEB have had JRE dependencies added (not tested yet)
Ben Soares [Mon, 20 May 2019 14:15:19 +0000 (15:15 +0100)]
JAL-3254 Improved memory setting (allows mem for OS). Moved OperatingSystemMXBean stuff to separate class. Class duplicated in getdown for same Memory Per Centage calculation.
Jim Procter [Mon, 13 May 2019 15:53:08 +0000 (16:53 +0100)]
Merge branch 'task/JAL-3247_Install4j_improvements' into develop
Ben Soares [Mon, 13 May 2019 15:01:14 +0000 (16:01 +0100)]
Merge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into task/JAL-3247_Install4j_improvements
Ben Soares [Mon, 13 May 2019 14:51:15 +0000 (15:51 +0100)]
JAL-3247 nogradle option on this mac build/install helper script
Ben Soares [Mon, 13 May 2019 14:17:24 +0000 (15:17 +0100)]
JAL-3247 JAL-3254 JAL-3260 Fixed: JVL file jalview.apparg args. File association problem in Windows NETWORK installer.
Jim Procter [Fri, 10 May 2019 16:41:37 +0000 (17:41 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop
Ben Soares [Fri, 10 May 2019 16:39:24 +0000 (17:39 +0100)]
JAL-3246 JAL-3247 Reworked JVL files as getdown.txt config with limitations
Jim Procter [Fri, 10 May 2019 16:21:16 +0000 (17:21 +0100)]
Merge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into develop
Ben Soares [Thu, 9 May 2019 19:14:13 +0000 (20:14 +0100)]
JAL-3236 Added unixInstaller to install4jMediaTypes in gradle.properties
Jim Procter [Thu, 9 May 2019 16:19:45 +0000 (17:19 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop
Ben Soares [Thu, 9 May 2019 16:04:06 +0000 (17:04 +0100)]
JAL-3247 JAL-3254 Ensure .jvp and .jvl appear first in File Associations list (visible in Windows installer)
Ben Soares [Thu, 9 May 2019 16:03:12 +0000 (17:03 +0100)]
JAL-3247 JAL-3254 Fixed file association launch behaviour in getdown in Windows
Ben Soares [Wed, 8 May 2019 17:25:06 +0000 (18:25 +0100)]
JAL-3246 add -Pgetdown_local=true to use local files
Ben Soares [Wed, 8 May 2019 16:35:31 +0000 (17:35 +0100)]
JAL-3247 JAL-3254 changing default location of jalview/io/FileFormat.java relative to the util/install4j dir
Ben Soares [Wed, 8 May 2019 16:33:45 +0000 (17:33 +0100)]
JAL-3247 JAL-3254 Getdown now opening any files thrown at it by a file-association double-click
Ben Soares [Wed, 8 May 2019 16:18:22 +0000 (17:18 +0100)]
JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info.plist and install4j installer
Ben Soares [Wed, 8 May 2019 16:17:05 +0000 (17:17 +0100)]
JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info.plist and install4j installer
Ben Soares [Wed, 8 May 2019 12:43:33 +0000 (13:43 +0100)]
JAL-3247 Script to produce auto file association files for mac and windows installer, and changes in build.gradle to read in the produced, and edited, auto files
Ben Soares [Wed, 8 May 2019 10:57:57 +0000 (11:57 +0100)]
JAL-3247 Note in launcher.log when using a JVL file
Ben Soares [Tue, 7 May 2019 23:05:44 +0000 (00:05 +0100)]
JAL-3247 Changed JVL file to be a props file, with appbase=... required for the new appbase URL
Ben Soares [Tue, 7 May 2019 21:49:38 +0000 (22:49 +0100)]
JAL-3247 Script to automatically install Jalview from the .dmg to /Applications
Ben Soares [Tue, 7 May 2019 19:17:48 +0000 (20:17 +0100)]
JAL-3247 Auto generated file associations from jalview/io/FileFormat.java
Ben Soares [Mon, 6 May 2019 23:38:52 +0000 (00:38 +0100)]
JAL-3247 Allowing 'file' protocol URL with empty domain in a .jvl file
Ben Soares [Mon, 6 May 2019 16:06:29 +0000 (17:06 +0100)]
JAL-3247 Code changes to getdown. Double click open of .jvp files in Windows and macOS, and .jvl new appbase file working in macOS.
Ben Soares [Mon, 6 May 2019 13:54:23 +0000 (14:54 +0100)]
JAL-3247 improvements
Ben Soares [Mon, 6 May 2019 12:56:31 +0000 (13:56 +0100)]
JAL-3247 Some getdown image file changes/tidying
gmungoc [Mon, 6 May 2019 08:49:45 +0000 (09:49 +0100)]
JAL-3240 known issue for release notes
git://source.jalview.org / jalview.git / log