jalview.git
4 years agoMerge branch 'bug/JAL-3296changeStartInvalidateCursor' into develop
Jim Procter [Thu, 27 Feb 2020 15:08:49 +0000 (15:08 +0000)]
Merge branch 'bug/JAL-3296changeStartInvalidateCursor' into develop

4 years agoJAL-3477 jalview.jvmmemmax / jvmmemmax maximum value documentation
Jim Procter [Wed, 26 Feb 2020 16:58:58 +0000 (16:58 +0000)]
JAL-3477 jalview.jvmmemmax / jvmmemmax maximum value documentation

4 years agoMerge branch 'bug/JAL-3477_memory_max_allocation' into develop
Jim Procter [Wed, 26 Feb 2020 16:55:54 +0000 (16:55 +0000)]
Merge branch 'bug/JAL-3477_memory_max_allocation' into develop
replaced all libs with libs onbug/JAL-3477_memory_max_allocation, though these will still need to be rebuilt (but how !)

4 years agoJAL-3407 release notes for JAL-3449 JAL-3393 JAL-3420 JAL-3477 JAL-3447 JAL-3542
Jim Procter [Wed, 26 Feb 2020 16:21:57 +0000 (16:21 +0000)]
JAL-3407 release notes for  JAL-3449 JAL-3393 JAL-3420 JAL-3477 JAL-3447 JAL-3542

4 years agoMerge branch 'improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalvie...
Jim Procter [Wed, 26 Feb 2020 14:52:19 +0000 (14:52 +0000)]
Merge branch 'improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2' into develop

4 years agoJAL-3541 docs for enabling OpenClover coverage reports and adjustable build parameter...
Jim Procter [Wed, 26 Feb 2020 14:33:20 +0000 (14:33 +0000)]
JAL-3541 docs for enabling OpenClover coverage reports and adjustable build parameters for troubleshooting report generation.

4 years agoJAL-3541 removed clover report generation debug flag (utf-8 encoding enforcement...
Jim Procter [Wed, 26 Feb 2020 11:22:39 +0000 (11:22 +0000)]
JAL-3541 removed clover report generation debug flag (utf-8 encoding enforcement seems to have fixed parsing of jalview.gui.desktop source)

4 years agoJAL-3541 configurables for clover report generation (JVM heap, JVM args, and -v or...
Jim Procter [Wed, 26 Feb 2020 10:10:31 +0000 (10:10 +0000)]
JAL-3541 configurables for clover report generation (JVM heap, JVM args, and -v or -d for debugging)

4 years agoJAL-3541 track own jalview.gui.Desktop clover source parsing error
Jim Procter [Tue, 25 Feb 2020 18:22:19 +0000 (18:22 +0000)]
JAL-3541 track own jalview.gui.Desktop clover source parsing error

4 years agoJAL-3541 2g heap for clover xml and clover html - remove verbose on xml generation...
Jim Procter [Tue, 25 Feb 2020 18:02:01 +0000 (18:02 +0000)]
JAL-3541 2g heap for clover xml and clover html - remove verbose on xml generation (did't actually need it !)

4 years agoJAL-3541 add verbose and heap setting for HTML Report Generation
Jim Procter [Tue, 25 Feb 2020 17:44:10 +0000 (17:44 +0000)]
JAL-3541 add verbose and heap setting for HTML Report Generation

4 years agoJAL-3541 use javaExec to run clover tasks
Jim Procter [Tue, 25 Feb 2020 17:10:19 +0000 (17:10 +0000)]
JAL-3541 use javaExec to run clover tasks

4 years agoMerge branch 'bug/JAL-3536getCrossrefTwice' into develop
Jim Procter [Fri, 21 Feb 2020 17:18:34 +0000 (17:18 +0000)]
Merge branch 'bug/JAL-3536getCrossrefTwice' into develop

4 years agoJAL-3186 ensure transparency slider position is updated on revert
Jim Procter [Fri, 21 Feb 2020 15:12:18 +0000 (15:12 +0000)]
JAL-3186 ensure transparency slider position is updated on revert

4 years agoJAL-3186 avoid repainting twice in splitframe
Jim Procter [Fri, 21 Feb 2020 15:10:57 +0000 (15:10 +0000)]
JAL-3186 avoid repainting twice in splitframe

4 years agoMerge branch 'features/JAL-3187_uitweaks' into develop
Jim Procter [Fri, 21 Feb 2020 14:36:32 +0000 (14:36 +0000)]
Merge branch 'features/JAL-3187_uitweaks' into develop

4 years agoMerge branch 'develop' into features/JAL-3187_uitweaks
Jim Procter [Fri, 21 Feb 2020 14:34:21 +0000 (14:34 +0000)]
Merge branch 'develop' into features/JAL-3187_uitweaks

4 years agoJAL-3187 nice to have enabling/disabling of apply/cancel when feature settings have... features/JAL-3187_uitweaks
Jim Procter [Thu, 20 Feb 2020 17:25:27 +0000 (17:25 +0000)]
JAL-3187 nice to have enabling/disabling of apply/cancel when feature settings have not yet been modified for a view

4 years agoJAL-3187 i18n
Jim Procter [Thu, 20 Feb 2020 17:24:37 +0000 (17:24 +0000)]
JAL-3187 i18n

4 years agoJAL-3187 use the recommended way of catching tab selection change events
Jim Procter [Thu, 20 Feb 2020 17:24:08 +0000 (17:24 +0000)]
JAL-3187 use the recommended way of catching tab selection change events

4 years agoJAL-3187 repaint complement after loading on features
gmungoc [Thu, 20 Feb 2020 16:20:08 +0000 (16:20 +0000)]
JAL-3187 repaint complement after loading on features

4 years agoJAL-3187 individual feature settings panel has revert/apply when embedded in a tab...
Jim Procter [Thu, 20 Feb 2020 14:11:06 +0000 (14:11 +0000)]
JAL-3187 individual feature settings panel has revert/apply when embedded in a tab, and split frame feature settings has an OK and Cancel.

4 years agoJAL-3187 i18n for titles in windows/tabs
Jim Procter [Wed, 19 Feb 2020 18:46:25 +0000 (18:46 +0000)]
JAL-3187 i18n for titles in windows/tabs

4 years agoJAL-3535 todo re titles for CDS and Protein views in the feature settings dialog...
Jim Procter [Wed, 19 Feb 2020 18:43:45 +0000 (18:43 +0000)]
JAL-3535 todo re titles for CDS and Protein views in the feature settings dialog pane

4 years agoJAL-3187 - tabbed pane is nulled when feature settings is closed but not featureSetti...
Jim Procter [Wed, 19 Feb 2020 18:43:05 +0000 (18:43 +0000)]
JAL-3187 - tabbed pane is nulled when feature settings is closed but not featureSettingsUI - check both are non-null or reconstruct

4 years agoMerge branch 'develop' into improvement/JAL-3449_add_install4j_installer_getdown_vers... improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
Ben Soares [Wed, 19 Feb 2020 16:40:09 +0000 (16:40 +0000)]
Merge branch 'develop' into improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2

4 years agoJAL-3289 Improved the name of the channel_launch.jvl file to channel_launch-CHANNELNA...
Ben Soares [Wed, 19 Feb 2020 16:37:47 +0000 (16:37 +0000)]
JAL-3289 Improved the name of the channel_launch.jvl file to channel_launch-CHANNELNAMEWITHPLANKEY.jvl

4 years agoJAL-3187 JAL-2764 close feature settings when parent align frame is closed (need...
Jim Procter [Wed, 19 Feb 2020 15:03:44 +0000 (15:03 +0000)]
JAL-3187 JAL-2764 close feature settings when parent align frame is closed (need to check feature settings is open before closing it :) )

4 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Wed, 19 Feb 2020 14:22:53 +0000 (14:22 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

4 years agoJAL-3337 Adding .settings/org.eclipse.jdt.core.jalview.prefs file needed for gradle...
Ben Soares [Wed, 19 Feb 2020 14:22:48 +0000 (14:22 +0000)]
JAL-3337 Adding .settings/org.eclipse.jdt.core.jalview.prefs file needed for gradle eclipse

4 years agoMerge branch 'patch/JAL-3538_fontantialiasingbydefault' into develop
Jim Procter [Wed, 19 Feb 2020 12:05:57 +0000 (12:05 +0000)]
Merge branch 'patch/JAL-3538_fontantialiasingbydefault' into develop

4 years agoJAL-3538 JAL-3407 release notes
Jim Procter [Wed, 19 Feb 2020 12:05:33 +0000 (12:05 +0000)]
JAL-3538 JAL-3407 release notes

4 years agoJAL-3407 release next week :D
Jim Procter [Wed, 19 Feb 2020 12:03:45 +0000 (12:03 +0000)]
JAL-3407 release next week :D

4 years agoJAL-3538 anti-aliasing enabled by default
Jim Procter [Wed, 19 Feb 2020 12:03:24 +0000 (12:03 +0000)]
JAL-3538 anti-aliasing enabled by default

4 years agoJAL-3449 helper task to perform getdown digest on any dir
Ben Soares [Wed, 19 Feb 2020 09:06:16 +0000 (09:06 +0000)]
JAL-3449 helper task to perform getdown digest on any dir

4 years agoJAL-3449 ensuring latest getdown jar files after merge
Ben Soares [Wed, 19 Feb 2020 09:05:43 +0000 (09:05 +0000)]
JAL-3449 ensuring latest getdown jar files after merge

4 years agoJAL-3449 merge from develop
Ben Soares [Tue, 18 Feb 2020 19:49:38 +0000 (19:49 +0000)]
JAL-3449 merge from develop

4 years agoJAl-3187 JAL-3535 JAL-3534 update open feature settings when a different view is...
Jim Procter [Tue, 18 Feb 2020 16:32:31 +0000 (16:32 +0000)]
JAl-3187 JAL-3535 JAL-3534 update open feature settings when a different view is selected or close when none shown

4 years agoJAL-3536 JAL-3187 don't create duplicate CDS-to-protein mappings bug/JAL-3536getCrossrefTwice
Mungo Carstairs [Tue, 18 Feb 2020 12:13:13 +0000 (12:13 +0000)]
JAL-3536 JAL-3187 don't create duplicate CDS-to-protein mappings

4 years agoJAL-3341 Increase number of lines looked at by test. Fixes two tests
Ben Soares [Wed, 29 Jan 2020 16:20:24 +0000 (16:20 +0000)]
JAL-3341 Increase number of lines looked at by test. Fixes two tests

4 years agoJAL-3289 Added option and documentation for a TEST-LOCAL channel to test OTA updates...
Ben Soares [Mon, 17 Feb 2020 16:47:16 +0000 (16:47 +0000)]
JAL-3289 Added option and documentation for a TEST-LOCAL channel to test OTA updates using local filesystem

4 years agoJAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property...
Ben Soares [Wed, 12 Feb 2020 12:18:27 +0000 (12:18 +0000)]
JAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property during building

4 years agoJAL-3252 download-jres.sh helper script for keeping JREs for all platforms up to...
Ben Soares [Mon, 17 Feb 2020 16:35:05 +0000 (16:35 +0000)]
JAL-3252 download-jres.sh helper script for keeping JREs for all platforms up to date changed to create .zip files for getdown OTA updates

4 years agoJAL-3536 failing test and test data
Jim Procter [Mon, 17 Feb 2020 16:08:40 +0000 (16:08 +0000)]
JAL-3536 failing test and test data

4 years agoJAL-3534 patch for simple case (Protein or Nucleotide, but not linked): transfer...
Jim Procter [Mon, 17 Feb 2020 15:27:15 +0000 (15:27 +0000)]
JAL-3534 patch for simple case (Protein or Nucleotide, but not linked): transfer feature settings dialog ref to exploded views, and preserve one of the feature settings dialogs refs when views are gathered again


4 years agoJAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency...
Ben Soares [Mon, 17 Feb 2020 14:49:18 +0000 (14:49 +0000)]
JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mentioning common-compress updated.

4 years agoJAL-3187 fix for JAL-3533 on CDS/Protein tabbed feature settings
Jim Procter [Mon, 17 Feb 2020 14:45:18 +0000 (14:45 +0000)]
JAL-3187 fix for JAL-3533 on CDS/Protein tabbed feature settings

4 years agoJAL-3187 JAL-3533 JAL-3535 set feature settings dialog title from view, and stash...
Jim Procter [Mon, 17 Feb 2020 14:41:43 +0000 (14:41 +0000)]
JAL-3187 JAL-3533 JAL-3535 set feature settings dialog title from view, and stash geometry for a feature settings dialog when closed, and re-use any existing geometry when dialog re-opened.

4 years agoJAL-3187 better semantics for feature settings closed event handler
Jim Procter [Mon, 17 Feb 2020 12:28:40 +0000 (12:28 +0000)]
JAL-3187 better semantics for feature settings closed event handler

4 years agoJAL-3394 A little streamlining and fixing of helper script
Ben Soares [Fri, 14 Feb 2020 17:09:08 +0000 (17:09 +0000)]
JAL-3394 A little streamlining and fixing of helper script

4 years agoJAL-3394 remove no longer used files
Ben Soares [Fri, 14 Feb 2020 17:08:18 +0000 (17:08 +0000)]
JAL-3394 remove no longer used files

4 years agoJAL-3187 alternative solution - gather feature settings for CDS/Protein as tabs in...
Jim Procter [Fri, 14 Feb 2020 09:22:52 +0000 (09:22 +0000)]
JAL-3187 alternative solution - gather feature settings for CDS/Protein as tabs in a window managed by SplitFrame

4 years agoJAL-1354 JAL-3528 fix bug from b594d516dac69eebcccdc743933880b00fb6d44c only try...
Jim Procter [Fri, 14 Feb 2020 09:18:55 +0000 (09:18 +0000)]
JAL-1354 JAL-3528 fix bug from b594d516dac69eebcccdc743933880b00fb6d44c only try to look up message via formatMessage once.

4 years agoJAL-3449 getdown resilience change to launcher classpath, includes the backup getdown...
Ben Soares [Thu, 13 Feb 2020 17:13:31 +0000 (17:13 +0000)]
JAL-3449 getdown resilience change to launcher classpath, includes the backup getdown-launcher.jar

4 years agoJAL-3227 helper shell scripts for setting up a build environment
Ben Soares [Thu, 13 Feb 2020 17:12:35 +0000 (17:12 +0000)]
JAL-3227 helper shell scripts for setting up a build environment

4 years agoJAL-3449 fix a getdownAppDir error introduced in previous commit 55f545014
Ben Soares [Thu, 13 Feb 2020 15:28:46 +0000 (15:28 +0000)]
JAL-3449 fix a getdownAppDir error introduced in previous commit 55f545014

4 years agoJAL-3449 More tidying of build.gradle for CHANNEL selection
Ben Soares [Thu, 13 Feb 2020 10:50:37 +0000 (10:50 +0000)]
JAL-3449 More tidying of build.gradle for CHANNEL selection

4 years agoJAL-3187 applet alignFrame needs new api method
Jim Procter [Wed, 12 Feb 2020 17:53:54 +0000 (17:53 +0000)]
JAL-3187 applet alignFrame needs new api method

4 years agoJAL-3187 first stab at ‘show CDS/Protein Settings’ for convenient switching between...
Jim Procter [Wed, 12 Feb 2020 17:36:44 +0000 (17:36 +0000)]
JAL-3187 first stab at ‘show CDS/Protein Settings’ for convenient switching between complementary feature settings

4 years agoJAL-3187 view controller UI api method to show feature settings UI

Jim Procter [Wed, 12 Feb 2020 17:10:07 +0000 (17:10 +0000)]
JAL-3187 view controller UI api method to show feature settings UI


4 years agoJAL-3187 convenience method on SplitContainerI to retrieve a complement’s alignFrame
Jim Procter [Wed, 12 Feb 2020 17:09:12 +0000 (17:09 +0000)]
JAL-3187 convenience method on SplitContainerI to retrieve a complement’s alignFrame

4 years agoJAL-1354 JAL-3528 report missing keys for MessageManager.format calls
Jim Procter [Wed, 12 Feb 2020 17:02:16 +0000 (17:02 +0000)]
JAL-1354 JAL-3528 report missing keys for MessageManager.format calls

4 years agoJAL-3407 release notes for JAL-3121
Jim Procter [Wed, 12 Feb 2020 16:00:51 +0000 (16:00 +0000)]
JAL-3407 release notes for JAL-3121

4 years agoJAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property...
Ben Soares [Wed, 12 Feb 2020 12:18:27 +0000 (12:18 +0000)]
JAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property during building

4 years agoJAL-3523 No longer change CWD of getdown when invoked by install4j launcher
Ben Soares [Wed, 12 Feb 2020 10:43:37 +0000 (10:43 +0000)]
JAL-3523 No longer change CWD of getdown when invoked by install4j launcher

4 years agoJAL-3407 release notes for JAL-3375
Jim Procter [Tue, 11 Feb 2020 16:52:21 +0000 (16:52 +0000)]
JAL-3407 release notes for JAL-3375

4 years agoJAL-3376 highlighted in what’s new
Jim Procter [Tue, 11 Feb 2020 12:14:10 +0000 (12:14 +0000)]
JAL-3376 highlighted in what’s new

4 years agoJAL-3407 - JAL-3376 JAL-3377 release notes
Jim Procter [Tue, 11 Feb 2020 12:13:41 +0000 (12:13 +0000)]
JAL-3407 - JAL-3376 JAL-3377 release notes

4 years agoJAL-3407 start of whats new for 2.11.1.0
Jim Procter [Tue, 11 Feb 2020 12:13:05 +0000 (12:13 +0000)]
JAL-3407 start of whats new for 2.11.1.0

4 years agoJAL-3376 documentation for standard attributes for variants from VCF
Jim Procter [Tue, 11 Feb 2020 12:11:37 +0000 (12:11 +0000)]
JAL-3376 documentation for standard attributes for variants from VCF

4 years agoJAL-3407 release notes (JAL-3386 signoff, new-knowns JAL-3523 JAL-3525)
Jim Procter [Tue, 11 Feb 2020 10:38:31 +0000 (10:38 +0000)]
JAL-3407 release notes (JAL-3386 signoff, new-knowns JAL-3523 JAL-3525)

4 years agoJAL-3407 JAL-3508 move to 2.11.1.0 point release versioning and signed off JAL-3510...
Jim Procter [Mon, 10 Feb 2020 17:08:05 +0000 (17:08 +0000)]
JAL-3407 JAL-3508 move to 2.11.1.0 point release versioning and signed off JAL-3510 JAL-3513 JAL-3388 JAL-3389 JAL-3441 JAL-3473 JAL-3406

4 years agoJAL-3179 Version fix for taskTree gradle task in gradle 6
Ben Soares [Sat, 8 Feb 2020 18:06:51 +0000 (18:06 +0000)]
JAL-3179 Version fix for taskTree gradle task in gradle 6

4 years agoMerge branch 'task/JAL-3510-update-clover-to-4.4.1' into develop
Jim Procter [Mon, 3 Feb 2020 16:42:42 +0000 (16:42 +0000)]
Merge branch 'task/JAL-3510-update-clover-to-4.4.1' into develop
fix JAL-3513 and fixes/resolves JAL-3510

4 years agoJAL-3510 JAL-3153 clover instrumentation for tests task/JAL-3510-update-clover-to-4.4.1
Jim Procter [Mon, 3 Feb 2020 16:24:59 +0000 (16:24 +0000)]
JAL-3510 JAL-3153 clover instrumentation for tests

4 years agoJAL-3447 MSI installer for windows
Ben Soares [Fri, 31 Jan 2020 16:11:54 +0000 (16:11 +0000)]
JAL-3447 MSI installer for windows

4 years agoJAL-3510 bump clover version in gradle build dependencies
Jim Procter [Thu, 30 Jan 2020 08:44:47 +0000 (08:44 +0000)]
JAL-3510 bump clover version in gradle build dependencies

4 years agoJAL-3341 Increase number of lines looked at by test. Fixes two tests
Ben Soares [Wed, 29 Jan 2020 16:20:24 +0000 (16:20 +0000)]
JAL-3341 Increase number of lines looked at by test. Fixes two tests

4 years agoJAL-3341 debug for failing unit test bug/JAL-3341unitTestFails
gmungoc [Tue, 28 Jan 2020 15:18:12 +0000 (15:18 +0000)]
JAL-3341 debug for failing unit test

4 years agoMerge branch 'feature/JAL-3121gffAttributeMap' into develop
gmungoc [Tue, 28 Jan 2020 12:30:07 +0000 (12:30 +0000)]
Merge branch 'feature/JAL-3121gffAttributeMap' into develop

4 years agoJAL-3187 one more obsolete method removed
gmungoc [Thu, 22 Aug 2019 08:06:23 +0000 (09:06 +0100)]
JAL-3187 one more obsolete method removed

4 years agoJAL-3394 Removed libjli.dylib symbolic link from embedded macOS JRE, works in 8 and...
Ben Soares [Fri, 24 Jan 2020 17:11:10 +0000 (17:11 +0000)]
JAL-3394 Removed libjli.dylib symbolic link from embedded macOS JRE, works in 8 and 11. Preparation for non-linked Uninstall.app in DMG

4 years agoJAL-3394 Variable-ise output folders -- will work better with sub-project/modularised...
Ben Soares [Fri, 24 Jan 2020 10:54:00 +0000 (10:54 +0000)]
JAL-3394 Variable-ise output folders -- will work better with sub-project/modularised gradle build

4 years agoJAL=3121 more data format validation/tests, help text tweak feature/JAL-3121gffAttributeMap
gmungoc [Fri, 24 Jan 2020 10:41:11 +0000 (10:41 +0000)]
JAL=3121 more data format validation/tests, help text tweak

4 years agoJAL-3130 removed a debug message from build.gradle
Ben Soares [Thu, 23 Jan 2020 19:46:51 +0000 (19:46 +0000)]
JAL-3130 removed a debug message from build.gradle

4 years agoJAL-3121 update help page for GFF column 9 nested attributes
gmungoc [Thu, 23 Jan 2020 17:19:03 +0000 (17:19 +0000)]
JAL-3121 update help page for GFF column 9 nested attributes

4 years agoJAL-3130 Improved locations of AdoptOpenJDK JRE downloads \(locally and on build...
Ben Soares [Thu, 23 Jan 2020 17:05:23 +0000 (17:05 +0000)]
JAL-3130 Improved locations of AdoptOpenJDK JRE downloads \(locally and on build server\) and helper script download_jres.sh to update them using AdoptOpenJDK API.

4 years agoJAL-3121 'attributes map' in GFF3 without special 'jvmap_' token
gmungoc [Thu, 23 Jan 2020 16:22:39 +0000 (16:22 +0000)]
JAL-3121 'attributes map' in GFF3 without special 'jvmap_' token

4 years agoJAL-3252 Don't add java_location until we've got a working mechanism
Ben Soares [Fri, 17 Jan 2020 17:19:54 +0000 (17:19 +0000)]
JAL-3252 Don't add java_location until we've got a working mechanism

4 years agoJAL-3447 Minor improvement on file association creation
Ben Soares [Fri, 17 Jan 2020 17:09:52 +0000 (17:09 +0000)]
JAL-3447 Minor improvement on file association creation

4 years agoMerge branch 'improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalvie...
Jim Procter [Thu, 16 Jan 2020 14:58:54 +0000 (14:58 +0000)]
Merge branch 'improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2' into develop

4 years agoJAL-3474 release notes
Jim Procter [Thu, 16 Jan 2020 14:38:45 +0000 (14:38 +0000)]
JAL-3474 release notes

4 years agoMerge branch 'improvement/JAL-3474_lots_of_.cvsignore_files' into develop
Jim Procter [Thu, 16 Jan 2020 14:30:31 +0000 (14:30 +0000)]
Merge branch 'improvement/JAL-3474_lots_of_.cvsignore_files' into develop

4 years agoJAL-3477 getdown jars. This commit can be left out if it conflicts. bug/JAL-3477_memory_max_allocation
Ben Soares [Fri, 10 Jan 2020 12:41:32 +0000 (12:41 +0000)]
JAL-3477 getdown jars. This commit can be left out if it conflicts.

4 years agoJAL-3477 updated getdown's jalview.bin.MemorySetting
Ben Soares [Fri, 10 Jan 2020 12:40:28 +0000 (12:40 +0000)]
JAL-3477 updated getdown's jalview.bin.MemorySetting

4 years agoJAL-3477 Javadoc, addition of -jvmmempc and -jvmmemmax args detection and some small...
Ben Soares [Fri, 10 Jan 2020 12:39:26 +0000 (12:39 +0000)]
JAL-3477 Javadoc, addition of -jvmmempc and -jvmmemmax args detection and some small tidying in jalview.bin.Launcher  based on CR-JAL-189, small tidy in jalview.bin.MemorySetting

4 years agoJAL-3477 getdown jars. This commit can be left out if it conflicts.
Ben Soares [Thu, 9 Jan 2020 16:56:59 +0000 (16:56 +0000)]
JAL-3477 getdown jars. This commit can be left out if it conflicts.

4 years agoJAL-3477 Newer jalview.bin.MemorySetting jalview.bin.GetMemory source files for getdown
Ben Soares [Thu, 9 Jan 2020 16:55:10 +0000 (16:55 +0000)]
JAL-3477 Newer jalview.bin.MemorySetting jalview.bin.GetMemory source files for getdown

4 years agoJAL-3477 Refactoring based on CR-JAL-189
Ben Soares [Thu, 9 Jan 2020 16:53:09 +0000 (16:53 +0000)]
JAL-3477 Refactoring based on CR-JAL-189

4 years agoJAL-3477 getdown jars. This commit can be left out if it conflicts.
Ben Soares [Thu, 9 Jan 2020 16:12:48 +0000 (16:12 +0000)]
JAL-3477 getdown jars. This commit can be left out if it conflicts.