jalview.git
5 years agoJAL-3111 JAL-3080 documentation
Jim Procter [Tue, 18 Jun 2019 13:53:48 +0000 (14:53 +0100)]
JAL-3111 JAL-3080 documentation

5 years agoJAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations missing SHIFT
Ben Soares [Tue, 18 Jun 2019 11:49:32 +0000 (12:49 +0100)]
JAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations missing SHIFT

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
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

5 years agoMerge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Mon, 17 Jun 2019 12:53:52 +0000 (13:53 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop

5 years agoJAL-3111 rejigged release notes again
Jim Procter [Mon, 17 Jun 2019 12:46:54 +0000 (13:46 +0100)]
JAL-3111 rejigged release notes again

5 years agoJAL-2975,JAL-2647,JAL-1767,JAL-2965, JAL-3111 updated PCA viewer documentation
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

5 years agoMerge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Fri, 14 Jun 2019 15:58:47 +0000 (16:58 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop

5 years agoJAL-3111 release date now 20th June. more release note work..
Jim Procter [Fri, 14 Jun 2019 15:57:50 +0000 (16:57 +0100)]
JAL-3111 release date now 20th June. more release note work..

5 years agoJAL-3111 report build type and commit in stdout from command line and in About/Splash...
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

5 years agoJAL-3299 JAL-3280 javadoc on BuildDetails bean
Jim Procter [Fri, 14 Jun 2019 15:44:30 +0000 (16:44 +0100)]
JAL-3299 JAL-3280 javadoc on BuildDetails bean

5 years agoJAL-3111 report time when Jalview was built (consider making this a conditional)
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)

5 years agoMerge branch 'releases/Release_2_11_Branch' into develop
Jalview Development Admin [Thu, 13 Jun 2019 15:07:32 +0000 (16:07 +0100)]
Merge branch 'releases/Release_2_11_Branch' into develop

5 years agoMerge branch 'bug/JAL-3295_CMD_select_not_working_in_sequence_selection' 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

5 years agoJAL-3143 recognise lnc_RNA as transcript
gmungoc [Thu, 13 Jun 2019 11:13:34 +0000 (12:13 +0100)]
JAL-3143 recognise lnc_RNA as transcript

5 years agoJAL-3295 Can now compile/run/debug in Eclipse with Java 1.8. Change JAVA_VERSION...
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

5 years agoJAL-3295 Fixed CMD-select of sequences in alignment window
Ben Soares [Wed, 12 Jun 2019 16:16:35 +0000 (17:16 +0100)]
JAL-3295 Fixed CMD-select of sequences in alignment window

5 years agoJAL-3299 Fixed gitHash and gitBranch definitions in build.gradle
Ben Soares [Wed, 12 Jun 2019 14:58:04 +0000 (15:58 +0100)]
JAL-3299 Fixed gitHash and gitBranch definitions in build.gradle

5 years agoJAL-3143 also parse "phase" from JSON response if present
gmungoc [Tue, 11 Jun 2019 18:28:59 +0000 (19:28 +0100)]
JAL-3143 also parse "phase" from JSON response if present

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
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

5 years agoJAL-3248 improved pandoc lookup. Now comma-separated value in pandoc_exe in gradle...
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

5 years agoJAL-3111 update release date placeholder
gmungoc [Tue, 11 Jun 2019 13:47:53 +0000 (14:47 +0100)]
JAL-3111 update release date placeholder

5 years agoJAL-3288 fixes for gain/lose focus
gmungoc [Tue, 11 Jun 2019 12:57:48 +0000 (13:57 +0100)]
JAL-3288 fixes for gain/lose focus

5 years agoJAL-3248 quick fix for build.gradle when pandoc not available
Ben Soares [Mon, 10 Jun 2019 14:15:29 +0000 (15:15 +0100)]
JAL-3248 quick fix for build.gradle when pandoc not available

5 years agoJAL-3248 building.html now generated by pandoc 'brew install pandoc'
Ben Soares [Mon, 10 Jun 2019 14:08:17 +0000 (15:08 +0100)]
JAL-3248 building.html now generated by pandoc 'brew install pandoc'

5 years agoJAL-3248 added conversion of building.md to building.html to gradle task. Will happen...
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

5 years agoMerge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
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

5 years agoMerge branch 'task/JAL-3248_rewritten_building_md_instructions' of https://source...
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

5 years agoJAL-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

5 years agoJAL-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

5 years agoJAL-3248 Almost completed building doc
Ben Soares [Fri, 7 Jun 2019 17:13:11 +0000 (18:13 +0100)]
JAL-3248 Almost completed building doc

5 years agoMerge branch 'bug/JAL-3288splitFrameMenusJava11' into develop
gmungoc [Fri, 7 Jun 2019 14:31:59 +0000 (15:31 +0100)]
Merge branch 'bug/JAL-3288splitFrameMenusJava11' into develop

5 years agoJAL-3248 a bit more
Ben Soares [Fri, 7 Jun 2019 13:33:36 +0000 (14:33 +0100)]
JAL-3248 a bit more

5 years agoJAL-3187 Viewport schema attributes for showComplementFeatures[OnTop]
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

5 years agoJAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType
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

5 years agoJAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings
gmungoc [Wed, 6 Feb 2019 15:27:49 +0000 (15:27 +0000)]
JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

5 years agoMerge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
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

5 years agoJAL-3225 removing slightly misleading rewrite of .classpath when synchronizing/buildi...
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

5 years agoJAL-3225 Classpath now made in eclipse.classpath.file.whenMerged and recognised by...
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 :)

5 years agoJAL-3288 override JInternalFrame.setSelected() to avoid cancelling menus bug/JAL-3288splitFrameMenusJava11
gmungoc [Wed, 5 Jun 2019 14:22:02 +0000 (15:22 +0100)]
JAL-3288 override JInternalFrame.setSelected() to avoid cancelling menus

5 years agoJAL-3287 correct local file URI for appbase and getdownDigest in Windows
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

5 years agoJAL-3287 adjustment to HelpLinksChecker
Ben Soares [Tue, 4 Jun 2019 14:38:46 +0000 (15:38 +0100)]
JAL-3287 adjustment to HelpLinksChecker

5 years agoJAL-3287 adjustment to HelpLinksChecker to run in Windows and improvement to build...
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

5 years agoJAL-3248 small edits
Ben Soares [Tue, 4 Jun 2019 08:16:53 +0000 (09:16 +0100)]
JAL-3248 small edits

5 years agoJAL-3247 Adjusted Uninstall Old Jalview.app to just run the old uninstaller if it...
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.

5 years agoJAL-3248 extra tl;dr
Ben Soares [Fri, 31 May 2019 12:22:25 +0000 (13:22 +0100)]
JAL-3248 extra tl;dr

5 years agoJAL-3248 Essential tl;dr :)
Ben Soares [Thu, 30 May 2019 17:53:09 +0000 (18:53 +0100)]
JAL-3248 Essential tl;dr :)

5 years agoMerge branch 'develop' into task/JAL-3248_rewritten_building_md_instructions
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

5 years agoJAL-2738 error logging if no ##reference found
gmungoc [Wed, 29 May 2019 15:17:10 +0000 (16:17 +0100)]
JAL-2738 error logging if no ##reference found

5 years agoJAL-2738 accept .csi, default to GRCh37:homo_sapiens if no ##reference
gmungoc [Wed, 29 May 2019 15:13:10 +0000 (16:13 +0100)]
JAL-2738 accept .csi, default to GRCh37:homo_sapiens if no ##reference

5 years agoJAL-3277 Fixed getdown splashscreen. For unknown reasons getdown thought it had both...
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.

5 years agoJAL-1988 Some TEST code accidentally left in now removed -- was affecting some saved...
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

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jalview Development Admin [Tue, 28 May 2019 12:43:21 +0000 (13:43 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoJAL-3247 sign the AppleScript uninstaller
Jalview Development Admin [Tue, 28 May 2019 12:42:37 +0000 (13:42 +0100)]
JAL-3247 sign the AppleScript uninstaller

5 years agoJAL-3141 deleted TODO comment in Messages_es
Ben Soares [Tue, 28 May 2019 11:18:24 +0000 (12:18 +0100)]
JAL-3141 deleted TODO comment in Messages_es

5 years agoMerge branch 'develop' into task/JAL-3141_JAL-3247_merge
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

5 years agoJAL-3248 saving
Ben Soares [Tue, 28 May 2019 09:50:32 +0000 (10:50 +0100)]
JAL-3248 saving

5 years agoJAL-3141 Added HashMap types for Java 1.8 compatibility
Ben Soares [Mon, 27 May 2019 15:26:45 +0000 (16:26 +0100)]
JAL-3141 Added HashMap types for Java 1.8 compatibility

5 years agoMerge branch 'task/JAL-3141_Customise_checkbox' into task/JAL-3141_JAL-3247_merge
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

5 years agoJAL-3141 Object array cast missing
Ben Soares [Mon, 27 May 2019 15:18:09 +0000 (16:18 +0100)]
JAL-3141 Object array cast missing

5 years agoMerge branch 'task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge' into task/JAL-3141_JAL...
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

5 years agoMerge branch 'develop' into task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge
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

5 years agoJAL-3247 Added AppleScript based App to run old Jalview uninstaller if present
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

5 years agoJAL-3141 Generified the JvUtils.buildComboWithTooltips to an Object and adjusted...
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.

5 years agoJAL-3141 test file in test folder not examples
gmungoc [Mon, 27 May 2019 08:16:25 +0000 (09:16 +0100)]
JAL-3141 test file in test folder not examples

5 years agoJAL-3141 One more error log fix
Ben Soares [Sat, 25 May 2019 13:44:00 +0000 (14:44 +0100)]
JAL-3141 One more error log fix

5 years agoJAL-3141 Added tooltips on Schemes dropdown and Customise checkbox
Ben Soares [Sat, 25 May 2019 13:40:48 +0000 (14:40 +0100)]
JAL-3141 Added tooltips on Schemes dropdown and Customise checkbox

5 years agoJAL-3141 Fixes recommended from gmc's test
Ben Soares [Fri, 24 May 2019 16:35:41 +0000 (17:35 +0100)]
JAL-3141 Fixes recommended from gmc's test

5 years agoJAL-1988 Spanish typo corrección
gmungoc [Fri, 24 May 2019 13:31:57 +0000 (14:31 +0100)]
JAL-1988 Spanish typo corrección

5 years agoJAL-3141 Fixed vertical size of the example filenames box\! Yay\!
Ben Soares [Fri, 24 May 2019 11:32:43 +0000 (12:32 +0100)]
JAL-3141 Fixed vertical size of the example filenames box\! Yay\!

5 years agoJAL-3141 Fixed tests
Ben Soares [Fri, 24 May 2019 09:05:10 +0000 (10:05 +0100)]
JAL-3141 Fixed tests

5 years agoJAL-3141 Reworked a lot of BackupFiles to allow the Customise Checkbox
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

5 years agoMerge branch 'bug/JAL-3141_backupfiles_prefs_widget_disable_bug' into merge/develop_b...
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

5 years agoJAL-3111 help file spelling correction
gmungoc [Wed, 22 May 2019 08:41:41 +0000 (09:41 +0100)]
JAL-3111  help file spelling correction

5 years agoJAL-3247 Launcher start improvements. RPM and DEB no longer packaged with getdown...
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)

5 years agoJAL-3273 small correction to expected result calculation
gmungoc [Tue, 21 May 2019 16:45:40 +0000 (17:45 +0100)]
JAL-3273 small correction to expected result calculation

5 years agoMerge branch 'task/JAL-3254_improved_max_memory_stack_setting' into task/JAL-3247_JAL...
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

5 years agoJAL-3247 Unix shell installer and tar archive corrected -- network and offline versio...
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)

5 years agoJAL-3254 Improved memory setting (allows mem for OS). Moved OperatingSystemMXBean...
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.

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Mon, 13 May 2019 15:53:22 +0000 (16:53 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoMerge branch 'task/JAL-3247_Install4j_improvements' into develop
Jim Procter [Mon, 13 May 2019 15:53:08 +0000 (16:53 +0100)]
Merge branch 'task/JAL-3247_Install4j_improvements' into develop

5 years agoMerge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into task/JAL...
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

5 years agoJAL-3247 nogradle option on this mac build/install helper script
Ben Soares [Mon, 13 May 2019 14:51:15 +0000 (15:51 +0100)]
JAL-3247 nogradle option on this mac build/install helper script

5 years agoJAL-3247 JAL-3254 JAL-3260 Fixed: JVL file jalview.apparg args. File association...
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.

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Fri, 10 May 2019 16:42:30 +0000 (17:42 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoMerge branch 'task/JAL-3246_local_getdown_files' into develop
Jim Procter [Fri, 10 May 2019 16:41:37 +0000 (17:41 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop

5 years agoJAL-3246 JAL-3247 Reworked JVL files as getdown.txt config with limitations
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

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Fri, 10 May 2019 16:21:28 +0000 (17:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoMerge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into develop
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

5 years agoJAL-3236 Added unixInstaller to install4jMediaTypes in gradle.properties
Ben Soares [Thu, 9 May 2019 19:14:13 +0000 (20:14 +0100)]
JAL-3236 Added unixInstaller to install4jMediaTypes in gradle.properties

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Thu, 9 May 2019 16:21:17 +0000 (17:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoMerge branch 'task/JAL-3246_local_getdown_files' into develop
Jim Procter [Thu, 9 May 2019 16:19:45 +0000 (17:19 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop

5 years agoJAL-3247 JAL-3254 Ensure .jvp and .jvl appear first in File Associations list (visibl...
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)

5 years agoJAL-3247 JAL-3254 Fixed file association launch behaviour in getdown in Windows
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

5 years agoJAL-3246 add -Pgetdown_local=true to use local files
Ben Soares [Wed, 8 May 2019 17:25:06 +0000 (18:25 +0100)]
JAL-3246 add -Pgetdown_local=true to use local files

5 years agoJAL-3247 JAL-3254 changing default location of jalview/io/FileFormat.java relative...
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

5 years agoJAL-3247 JAL-3254 Getdown now opening any files thrown at it by a file-association...
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

5 years agoJAL-3247 JAL-3254 Automatically creating correct file association inserts for Info...
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

5 years agoJAL-3247 JAL-3254 Automatically creating correct file association inserts for Info...
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

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Wed, 8 May 2019 15:43:00 +0000 (16:43 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoJAL-3247 Script to produce auto file association files for mac and windows 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