Ben Soares [Mon, 9 Dec 2019 00:35:54 +0000 (00:35 +0000)]
JAL-3449 Now parsing install4j XML file to edit values. Should be safer
Ben Soares [Sun, 8 Dec 2019 21:09:10 +0000 (21:09 +0000)]
JAL-3449 Work in progress improving XML replacements by gradle
Ben Soares [Fri, 6 Dec 2019 17:42:49 +0000 (17:42 +0000)]
JAL-3394 disableSigning=true when DEV
Ben Soares [Fri, 6 Dec 2019 17:34:55 +0000 (17:34 +0000)]
JAL-3394 Changed most of the token replacement for adding compiler variables
Ben Soares [Fri, 6 Dec 2019 17:34:04 +0000 (17:34 +0000)]
JAL-3449 Added more versions to getdown splashscreen and fixed Jalview's Java Console installer version reporting
Ben Soares [Sat, 23 Nov 2019 10:17:20 +0000 (10:17 +0000)]
JAL-3420 multiple file extensions for the same mime-type now work in unix installer
Ben Soares [Fri, 22 Nov 2019 17:36:11 +0000 (17:36 +0000)]
JAL-3449 install4j version, install4j template version, getdown version now all being reported in Javliew console
Ben Soares [Fri, 22 Nov 2019 16:09:24 +0000 (16:09 +0000)]
JAL-3477 merging in 3477
Ben Soares [Fri, 22 Nov 2019 15:32:42 +0000 (15:32 +0000)]
JAL-3393 Improved background image for DMG finder window, and associated files for creating it
Ben Soares [Fri, 22 Nov 2019 15:29:39 +0000 (15:29 +0000)]
JAL-3449 adding an installer template version. Really an md5 and a commit hash
Ben Soares [Thu, 21 Nov 2019 20:45:21 +0000 (20:45 +0000)]
JAL-3449 added an install4j compiler var
Ben Soares [Thu, 21 Nov 2019 19:21:18 +0000 (19:21 +0000)]
JAL-3449 JAL-3394 merged on install4j8 template
Ben Soares [Thu, 21 Nov 2019 16:13:47 +0000 (16:13 +0000)]
Merge branch 'improvement/JAL-3393_DMG_Finder_window_improvements' into improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
Merging in JAL-3393, better Finder window for DMG
Ben Soares [Thu, 21 Nov 2019 12:56:38 +0000 (12:56 +0000)]
JAL-3449 Using .gitignore from Jalview-JS/develop
Ben Soares [Thu, 21 Nov 2019 12:54:35 +0000 (12:54 +0000)]
JAL-3449 Using tidied build.gradle and gradle.properties from Jalview-JS/develop
Ben Soares [Wed, 20 Nov 2019 13:11:07 +0000 (13:11 +0000)]
JAL-3477 A bit of refactoring for the better
Ben Soares [Wed, 20 Nov 2019 01:13:26 +0000 (01:13 +0000)]
JAL-3210 cache getdown config, remove jvmmem options for better defaults
Ben Soares [Tue, 19 Nov 2019 20:23:32 +0000 (20:23 +0000)]
JAL-3210 removing overly complicated logging. Settling for System.out.println and System.err.println for MemorySetting output
Ben Soares [Mon, 18 Nov 2019 16:55:51 +0000 (16:55 +0000)]
JAL-3477 New jvmmemmax config option in getdown and getdown config. Set to 32G cap.
Ben Soares [Mon, 18 Nov 2019 15:21:14 +0000 (15:21 +0000)]
JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute memory level
Jim Procter [Tue, 15 Oct 2019 15:11:07 +0000 (16:11 +0100)]
JAL-3407 update release date for Jalview 2.11.1
Jim Procter [Fri, 11 Oct 2019 10:00:30 +0000 (11:00 +0100)]
Merge branch 'develop' into documentation/JAL-3407_2.11.1_release
gmungoc [Thu, 26 Sep 2019 14:42:09 +0000 (15:42 +0100)]
JAL-2481 remove code duplication left by merge
gmungoc [Thu, 26 Sep 2019 13:59:23 +0000 (14:59 +0100)]
JAL-3441 action double-click in Feature Type column only
Ben Soares [Fri, 30 Aug 2019 13:32:54 +0000 (14:32 +0100)]
JAL-3394 JAL-3420 Temporary measure limits unix file extension to be the shortest one for each mime-type
Ben Soares [Thu, 29 Aug 2019 15:24:59 +0000 (16:24 +0100)]
JAL-3420 JAL-3424 Changed default JDK compile back to 1.8
Ben Soares [Thu, 29 Aug 2019 15:01:02 +0000 (16:01 +0100)]
JAL-3420 JAL-3394 Correct format of XML in added file extensions for install4j8. Also progress indicator for adding file associations (which can be slow). Still not entirely working, see comments in issue.
Ben Soares [Wed, 28 Aug 2019 16:18:36 +0000 (17:18 +0100)]
JAL-3420 JAL-3394 Using install4j8 template with file associations. Attempts unix file associations but not working (only tested in Ubuntu) yet.
gmungoc [Fri, 23 Aug 2019 14:38:29 +0000 (15:38 +0100)]
JAL-3141 correct cast of spinner value
gmungoc [Thu, 22 Aug 2019 15:06:05 +0000 (16:06 +0100)]
JAL-3187 case-insensitive codon variant calculation
gmungoc [Wed, 21 Aug 2019 16:01:52 +0000 (17:01 +0100)]
JAL-3187 minor code tidying, todo removal
Jim Procter [Mon, 12 Aug 2019 15:35:36 +0000 (16:35 +0100)]
JAL-2987 release notes
Jim Procter [Mon, 12 Aug 2019 14:15:03 +0000 (15:15 +0100)]
JAL-3407 update RELEASE and cut new release notes in releaseHistory.html
Jim Procter [Mon, 12 Aug 2019 13:54:19 +0000 (14:54 +0100)]
JAL-3407 JAL-3406 update credits in Jalview 2.11.1
gmungoc [Fri, 9 Aug 2019 08:01:10 +0000 (09:01 +0100)]
JAL-3187 removal of variant feature (non-virtual) transfer to protein
gmungoc [Wed, 7 Aug 2019 09:25:09 +0000 (10:25 +0100)]
JAL-3187 (fudge) look in both alignments for stored mappings
gmungoc [Wed, 7 Aug 2019 08:42:01 +0000 (09:42 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
Ben Soares [Thu, 1 Aug 2019 15:08:00 +0000 (16:08 +0100)]
JAL-3393 New DS_Store with slightly bigger Finder window (in case of Path bar, Status bar, scroll bar) and definitely out-of-window .background folder
gmungoc [Wed, 31 Jul 2019 11:59:39 +0000 (12:59 +0100)]
JAL-3389 add .py to restored Chimera session filename so it opens!
gmungoc [Wed, 31 Jul 2019 08:10:11 +0000 (09:10 +0100)]
Merge branch 'bug/JAL-3388structureChooserSorting' into develop
gmungoc [Tue, 30 Jul 2019 17:45:21 +0000 (18:45 +0100)]
JAL-3198 more efficient Sequence.getDisplayId()
gmungoc [Tue, 30 Jul 2019 16:51:13 +0000 (17:51 +0100)]
JAL-3388 correct class for column 0 Ref Sequence
gmungoc [Mon, 29 Jul 2019 14:48:30 +0000 (15:48 +0100)]
JAL-3386 correct wrapped width calculation for headless image export
gmungoc [Mon, 29 Jul 2019 14:35:22 +0000 (15:35 +0100)]
JAL-3377 more reused of SeqCanvas.computeWrappedGeometry
gmungoc [Mon, 29 Jul 2019 10:44:06 +0000 (11:44 +0100)]
JAL-3377 add seq-annotations gap to cheight not to hgap
gmungoc [Mon, 29 Jul 2019 10:34:05 +0000 (11:34 +0100)]
JAL-3377 Javadoc added for getWrappedHeight()
gmungoc [Sun, 28 Jul 2019 10:05:32 +0000 (11:05 +0100)]
JAL-3377 corrected wrapped widths height for IdCanvas
gmungoc [Mon, 29 Jul 2019 10:20:44 +0000 (11:20 +0100)]
JAL-3377 include seq-annotation spacing in getWrappedHeight()
gmungoc [Fri, 26 Jul 2019 18:42:30 +0000 (20:42 +0200)]
Merge branch 'features/JAL-3375vcfValidation' into
feature/JAL-3187linkedFeatures
Conflicts:
src/jalview/io/vcf/VCFLoader.java
test/jalview/io/vcf/VCFLoaderTest.java
gmungoc [Fri, 26 Jul 2019 16:52:01 +0000 (18:52 +0200)]
JAL-1793 only decode specific special characters in VCF data
gmungoc [Fri, 26 Jul 2019 15:58:06 +0000 (17:58 +0200)]
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes
gmungoc [Fri, 26 Jul 2019 13:40:28 +0000 (15:40 +0200)]
JAL-3375 format validate VCF Integer and Float fields
gmungoc [Thu, 25 Jul 2019 10:48:33 +0000 (12:48 +0200)]
JAL-3375 ignore '.' values for VCF data
gmungoc [Tue, 16 Jul 2019 16:13:19 +0000 (17:13 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Tue, 16 Jul 2019 10:23:35 +0000 (11:23 +0100)]
JAL-2987 tolerate null double values when formatting JTable
gmungoc [Wed, 10 Jul 2019 16:03:42 +0000 (17:03 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
Jim Procter [Wed, 10 Jul 2019 13:09:18 +0000 (14:09 +0100)]
JAL-3289 bamboo properties for ‘BUILD’ getdown channel - fix
Jim Procter [Wed, 10 Jul 2019 12:55:56 +0000 (13:55 +0100)]
JAL-3289 bamboo properties for ‘BUILD’ getdown channel
gmungoc [Mon, 8 Jul 2019 10:47:06 +0000 (11:47 +0100)]
JAL-3187 derived peptide variants tweaks and tests
gmungoc [Fri, 5 Jul 2019 10:44:14 +0000 (11:44 +0100)]
JAL-3187 initial refactoring towards peptide variant in tooltip
Ben Soares [Fri, 5 Jul 2019 09:43:30 +0000 (10:43 +0100)]
JAL-1544 fixed a html encoding of '<' (%lt; -> <) in commandline.html
gmungoc [Fri, 5 Jul 2019 09:09:12 +0000 (10:09 +0100)]
JAL-1793 apply URL decoding when saving VCF attribute values (%3D -> =)
Jim Procter [Thu, 4 Jul 2019 15:40:13 +0000 (16:40 +0100)]
JAL-3111 correct JVL appbase for 2.10.5 via getdown
Jim Procter [Thu, 4 Jul 2019 15:34:12 +0000 (16:34 +0100)]
Merge branch 'task/JAL-3337-rm-lib-update-sourceDist' into develop
Jim Procter [Thu, 4 Jul 2019 15:33:48 +0000 (16:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 4 Jul 2019 15:31:47 +0000 (16:31 +0100)]
JAL-3337 round-and-round the process source files again
Jim Procter [Thu, 4 Jul 2019 15:23:16 +0000 (16:23 +0100)]
JAL-3337 more includes and excludes
Jim Procter [Thu, 4 Jul 2019 14:52:05 +0000 (15:52 +0100)]
JAL-3337 remove the old lib directory !
Jim Procter [Thu, 4 Jul 2019 14:51:28 +0000 (15:51 +0100)]
JAL-3337 rejig the source distribution generation to process and replace tokens in source files
Jim Procter [Thu, 4 Jul 2019 14:36:07 +0000 (15:36 +0100)]
JAL-3111 replace year in header for help pages and put processed help in build/distributions
Ben Soares [Thu, 4 Jul 2019 13:43:47 +0000 (14:43 +0100)]
JAL-3225 try/catch for non-deprecated/deprecated property in sourceDist which is not available on older eclipses
Ben Soares [Thu, 4 Jul 2019 13:16:14 +0000 (14:16 +0100)]
JAL-3353 Change to build.gradle to use the file:// enabled getdown-launcher-local.jar for LOCAL and ARCHIVELOCAL builds only. Otherwise the getdown-launcher.jar (with no local file enabled) will be used
gmungoc [Thu, 4 Jul 2019 12:09:21 +0000 (13:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jul 2019 12:09:13 +0000 (13:09 +0100)]
JAL-3111 help pages minor corrections
Ben Soares [Thu, 4 Jul 2019 11:26:37 +0000 (12:26 +0100)]
JAL-3348 fixed an internal href in help to allow building
Ben Soares [Thu, 4 Jul 2019 11:25:43 +0000 (12:25 +0100)]
JAL-3337 adjusted building doc as sourceDist uses gradle 5.2 or above properties
Jim Procter [Thu, 4 Jul 2019 08:08:21 +0000 (09:08 +0100)]
Merge branch 'task/JAL-3348_document_cli_memory_settings_when_launching_jalview' into develop
Jim Procter [Thu, 4 Jul 2019 08:05:12 +0000 (09:05 +0100)]
JAL-3111 JAL-3348 JVL file documentation
Jim Procter [Thu, 4 Jul 2019 07:36:42 +0000 (08:36 +0100)]
JAL-3348 revised bsoares memory settings documentation and updated docs for launching jalview from command line
Ben Soares [Thu, 4 Jul 2019 00:04:51 +0000 (01:04 +0100)]
Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching_jalview
merging in develop
Ben Soares [Wed, 3 Jul 2019 23:59:39 +0000 (00:59 +0100)]
JAL-3348 memory.html documentation finished for 2.11.0
Ben Soares [Wed, 3 Jul 2019 22:42:35 +0000 (23:42 +0100)]
JAL-3348 jvmmempc in jvl file now works in linux
Ben Soares [Wed, 3 Jul 2019 22:14:41 +0000 (23:14 +0100)]
JAL-3348 jvmmempc multiple values shouldn't be merged
Jim Procter [Wed, 3 Jul 2019 19:58:37 +0000 (20:58 +0100)]
JAL-3111 tidy up lists/indentation for release notes
Jim Procter [Wed, 3 Jul 2019 17:36:25 +0000 (18:36 +0100)]
JAL-3111 Java 11 only and 'onwards'
Jim Procter [Wed, 3 Jul 2019 17:35:15 +0000 (18:35 +0100)]
JAL-3111 more whatsNew tweaks
Jim Procter [Wed, 3 Jul 2019 17:06:46 +0000 (18:06 +0100)]
Merge branch 'task/JAL-3337_gradle_tasks_sourceDist_and_help2Website' into develop
Jim Procter [Wed, 3 Jul 2019 17:05:14 +0000 (18:05 +0100)]
JAL-3111 more whats new
Ben Soares [Wed, 3 Jul 2019 16:24:57 +0000 (17:24 +0100)]
JAL-3348 start of new memory setting text
Ben Soares [Wed, 3 Jul 2019 16:06:55 +0000 (17:06 +0100)]
JAL-3348 jvmmempc allowed in jvl file
Ben Soares [Wed, 3 Jul 2019 15:24:54 +0000 (16:24 +0100)]
Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching_jalview
merging in develop
Jim Procter [Wed, 3 Jul 2019 12:58:20 +0000 (13:58 +0100)]
Merge branch 'documentation/JAL-2843_featureFiltersFormat' into develop
Ben Soares [Wed, 3 Jul 2019 00:36:50 +0000 (01:36 +0100)]
JAL-3348 prepping getdown to pass JVM command line args
Jim Procter [Tue, 2 Jul 2019 22:35:18 +0000 (23:35 +0100)]
JAL-3111 updated what’s new… still more to come !
Jim Procter [Tue, 2 Jul 2019 22:34:46 +0000 (23:34 +0100)]
JAL-3111 updated privacy statement to remove mention of JNLP version checker JAL-3280
Jim Procter [Tue, 2 Jul 2019 22:30:52 +0000 (23:30 +0100)]
JAL-3111 JAL-3150 revised Jalview archive documentation and noted instructions about converting Jalview project files pre Jalview 2.1.
Jim Procter [Tue, 2 Jul 2019 22:20:04 +0000 (23:20 +0100)]
JAL-3111 JAL-3348 removed pre 2.11 instructions on setting Jalview’s memory settings. Needs information about configuring proportion of memory allocated.
Jim Procter [Tue, 2 Jul 2019 22:18:13 +0000 (23:18 +0100)]
JAL-3111 JAL-3280 hide the version check preference option in ‘Connections’ tab
Jim Procter [Tue, 2 Jul 2019 22:11:00 +0000 (23:11 +0100)]
JAL-3111 tidied up preferences dialog documentation
Jim Procter [Tue, 2 Jul 2019 20:21:09 +0000 (21:21 +0100)]
JAL-3111 fix broken helpTOC link
git://source.jalview.org / jalview.git / log