jalview.git
4 years agoJAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or...
Ben Soares [Thu, 26 Mar 2020 17:13:40 +0000 (17:13 +0000)]
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

4 years agoJAL-3248 Added instructions for downloading and configuring as gradle project in...
Ben Soares [Wed, 25 Mar 2020 17:07:36 +0000 (17:07 +0000)]
JAL-3248 Added instructions for downloading and configuring as gradle project in Eclipse only, i.e. no command line tools needed

4 years agoJAL-3562 exclude testNG groups from a build via -PtestngExcludedGroups=Not-bamboo
Jim Procter [Fri, 20 Mar 2020 18:19:52 +0000 (18:19 +0000)]
JAL-3562 exclude testNG groups from a build via -PtestngExcludedGroups=Not-bamboo

4 years agoJAL-3407 JAL-3562 release notes
Jim Procter [Fri, 20 Mar 2020 18:01:57 +0000 (18:01 +0000)]
JAL-3407 JAL-3562 release notes

4 years agoJAL-3407 rejigging new features - simplify release note line for virtual features
Jim Procter [Fri, 20 Mar 2020 17:50:47 +0000 (17:50 +0000)]
JAL-3407 rejigging new features - simplify release note line for virtual features

4 years agoJAL-3407 reformat releases.html
Jim Procter [Fri, 20 Mar 2020 17:45:08 +0000 (17:45 +0000)]
JAL-3407 reformat releases.html

4 years agoJAL-3407 JAL-3549 javadoc
Jim Procter [Fri, 20 Mar 2020 17:27:01 +0000 (17:27 +0000)]
JAL-3407 JAL-3549 javadoc

4 years agoJAL-3407 - release notes for JAL-3547
Jim Procter [Fri, 20 Mar 2020 17:02:49 +0000 (17:02 +0000)]
JAL-3407 - release notes for JAL-3547

4 years agoJAL-3549 javadoc
Jim Procter [Fri, 20 Mar 2020 17:01:53 +0000 (17:01 +0000)]
JAL-3549 javadoc

4 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 19 Mar 2020 16:05:57 +0000 (16:05 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

4 years agoJAL-3541 increase maxheapsize for test worker process
Ben Soares [Thu, 19 Mar 2020 12:54:02 +0000 (12:54 +0000)]
JAL-3541 increase maxheapsize for test worker process

4 years agoJAL-3541 tidying build.gradle, delete cloverInstrDir re-added
Ben Soares [Thu, 19 Mar 2020 12:35:45 +0000 (12:35 +0000)]
JAL-3541 tidying build.gradle, delete cloverInstrDir re-added

4 years agoJAL-3305 don't propagate an empty SelectionGroup to complement view
gmungoc [Thu, 19 Mar 2020 12:29:46 +0000 (12:29 +0000)]
JAL-3305 don't propagate an empty SelectionGroup to complement view

4 years agoJAL-3541 put org.gradle.jvmargs explicitly into gradle.properties
Ben Soares [Thu, 19 Mar 2020 12:26:41 +0000 (12:26 +0000)]
JAL-3541 put org.gradle.jvmargs explicitly into gradle.properties

4 years agoJAL-3541 merged cleanClover with develop
Ben Soares [Wed, 18 Mar 2020 15:23:55 +0000 (15:23 +0000)]
JAL-3541 merged cleanClover with develop

4 years agoJAL-3541 perhaps a better clean for clover. fixed
Ben Soares [Wed, 18 Mar 2020 11:33:26 +0000 (11:33 +0000)]
JAL-3541 perhaps a better clean for clover. fixed

4 years agoJAL-3541 perhaps a better clean for clover
Ben Soares [Wed, 18 Mar 2020 11:21:37 +0000 (11:21 +0000)]
JAL-3541 perhaps a better clean for clover

4 years agoJAL-3541 rejigged clover tasks very mildly
Ben Soares [Tue, 17 Mar 2020 19:19:59 +0000 (19:19 +0000)]
JAL-3541 rejigged clover tasks very mildly

4 years agoRevert "JAL-3541 trying out previous cloverReport task"
Ben Soares [Tue, 17 Mar 2020 12:42:25 +0000 (12:42 +0000)]
Revert "JAL-3541 trying out previous cloverReport task"

This reverts commit dc70a1f7934471a4084c3f10e7bd630d72aa3bf3.

4 years agoJAL-3541 trying out previous cloverReport task
Ben Soares [Tue, 17 Mar 2020 11:28:17 +0000 (11:28 +0000)]
JAL-3541 trying out previous cloverReport task

4 years agoJAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings...
Jim Procter [Mon, 16 Mar 2020 17:51:38 +0000 (17:51 +0000)]
JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings for linked cds/protein views

4 years agoJAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing...
Jim Procter [Mon, 16 Mar 2020 17:42:45 +0000 (17:42 +0000)]
JAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing selection affects the sort alignment by feature score/density

4 years agoJAL-3407 group together ‘virtual feature’ related features in release notes
Jim Procter [Mon, 16 Mar 2020 17:00:07 +0000 (17:00 +0000)]
JAL-3407 group together ‘virtual feature’ related features in release notes

4 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Mon, 16 Mar 2020 10:57:16 +0000 (10:57 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

4 years agoJAL-3394 updated version if install4j gradle plugin
Ben Soares [Thu, 12 Mar 2020 14:44:57 +0000 (14:44 +0000)]
JAL-3394 updated version if install4j gradle plugin

4 years agoJAL-3528 unit tests added for failed lookup, Javadoc
gmungoc [Mon, 9 Mar 2020 14:54:16 +0000 (14:54 +0000)]
JAL-3528 unit tests added for failed lookup, Javadoc

4 years agoJAL-3407 3549 in release notes
gmungoc [Mon, 9 Mar 2020 13:12:18 +0000 (13:12 +0000)]
JAL-3407 3549 in release notes

4 years agoJAL-3549 JAL-3305 no Sort By Score / Density if no features visible
gmungoc [Mon, 9 Mar 2020 13:06:05 +0000 (13:06 +0000)]
JAL-3549 JAL-3305 no Sort By Score / Density if no features visible

4 years agoJAL-3412 update layout whenever desired id width changes testbuild/JAL-3412_getIdWidth_test
gmungoc [Mon, 9 Mar 2020 10:26:59 +0000 (10:26 +0000)]
JAL-3412 update layout whenever desired id width changes

4 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 6 Mar 2020 16:06:20 +0000 (16:06 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

4 years agoJAL-3187 unit test for findComplementFeaturesAtResidue
gmungoc [Fri, 6 Mar 2020 16:06:13 +0000 (16:06 +0000)]
JAL-3187 unit test for findComplementFeaturesAtResidue

4 years agoJAL-3394 getdown jar files had not been re-compiled
Ben Soares [Fri, 6 Mar 2020 15:08:50 +0000 (15:08 +0000)]
JAL-3394 getdown jar files had not been re-compiled

4 years agoJAL-3407 added 3468 to release notes
gmungoc [Fri, 6 Mar 2020 14:09:20 +0000 (14:09 +0000)]
JAL-3407 added 3468 to release notes

4 years agoMerge branch 'feature/JAL-3468featureDescriptionEllipsis' into develop
gmungoc [Fri, 6 Mar 2020 14:01:25 +0000 (14:01 +0000)]
Merge branch 'feature/JAL-3468featureDescriptionEllipsis' into develop

4 years agoJAL-3468 i18n and additional unit tests feature/JAL-3468featureDescriptionEllipsis
gmungoc [Fri, 6 Mar 2020 13:59:36 +0000 (13:59 +0000)]
JAL-3468 i18n and additional unit tests

4 years agoJAL-3407 release note tweaks, added 3533 3538 3534 2764 3541
gmungoc [Fri, 6 Mar 2020 11:17:25 +0000 (11:17 +0000)]
JAL-3407 release note tweaks, added 3533 3538 3534 2764 3541

4 years agoMerge branch 'improvement/JAL-3543_dont_report_null_versions_in_java_console' into...
Jim Procter [Thu, 5 Mar 2020 12:31:13 +0000 (12:31 +0000)]
Merge branch 'improvement/JAL-3543_dont_report_null_versions_in_java_console' into develop

4 years agoJAL-3468 small tidy
Ben Soares [Wed, 4 Mar 2020 11:05:01 +0000 (11:05 +0000)]
JAL-3468 small tidy

4 years agoJAL-3468 improvement to feature description truncation when <a> links in text
Ben Soares [Wed, 4 Mar 2020 11:02:18 +0000 (11:02 +0000)]
JAL-3468 improvement to feature description truncation when <a> links in text

4 years agoJAL-3468 Fixed tests and added test for max-length of feature set tooltip
Ben Soares [Wed, 4 Mar 2020 02:14:11 +0000 (02:14 +0000)]
JAL-3468 Fixed tests and added test for max-length of feature set tooltip

4 years agoJAL-3468 Obsessively fixed self-closing <br/> tags
Ben Soares [Wed, 4 Mar 2020 02:13:25 +0000 (02:13 +0000)]
JAL-3468 Obsessively fixed self-closing <br/> tags

4 years agoJAL-3468 Adapted methods to report how many features have been dropped from the toolt...
soares [Tue, 3 Mar 2020 20:40:03 +0000 (20:40 +0000)]
JAL-3468 Adapted methods to report how many features have been dropped from the tooltip, and add final note to tooltip. Backward compatible methods left in.

4 years agoMerge branch 'groovy/JAL-3547_conservationsequenceexport' into develop
Jim Procter [Tue, 3 Mar 2020 09:07:09 +0000 (09:07 +0000)]
Merge branch 'groovy/JAL-3547_conservationsequenceexport' into develop

4 years agoJAL-3547 groovy script to get the conservation sequence and output it as fasta
Jim Procter [Tue, 3 Mar 2020 09:06:16 +0000 (09:06 +0000)]
JAL-3547 groovy script to get the conservation sequence and output it as fasta

4 years agoJAL-3407 redact Java 8 incompatible '<>' with anonymous inner classes
Jim Procter [Mon, 2 Mar 2020 10:42:07 +0000 (10:42 +0000)]
JAL-3407 redact Java 8 incompatible '<>' with anonymous inner classes

4 years agoMerge branch 'bug/JAL-3412idWidthDiscrepancy' into develop
Jim Procter [Thu, 27 Feb 2020 17:27:41 +0000 (17:27 +0000)]
Merge branch 'bug/JAL-3412idWidthDiscrepancy' into develop

4 years agoJAL-3407 release notes for JAL-3412
Jim Procter [Thu, 27 Feb 2020 17:27:18 +0000 (17:27 +0000)]
JAL-3407 release notes for JAL-3412

4 years agoJAL-3412 patch for failing test
Jim Procter [Thu, 27 Feb 2020 17:15:24 +0000 (17:15 +0000)]
JAL-3412 patch for failing test

4 years agoJAL-3543 remove debugging output improvement/JAL-3543_dont_report_null_versions_in_java_console
Ben Soares [Thu, 27 Feb 2020 16:23:04 +0000 (16:23 +0000)]
JAL-3543 remove debugging output

4 years agoMerge branch 'develop' into improvement/JAL-3543_dont_report_null_versions_in_java_co...
Ben Soares [Thu, 27 Feb 2020 16:18:02 +0000 (16:18 +0000)]
Merge branch 'develop' into improvement/JAL-3543_dont_report_null_versions_in_java_console

Merging with develop

4 years agoJAL-3543 Conditional reporting of Install4j and Getdown versions if null
Ben Soares [Thu, 27 Feb 2020 16:09:30 +0000 (16:09 +0000)]
JAL-3543 Conditional reporting of Install4j and Getdown versions if null

4 years agoMerge branch 'bug/JAL-3412idWidthDiscrepancy' into develop bug/JAL-3412idWidthDiscrepancy
Jim Procter [Thu, 27 Feb 2020 15:56:49 +0000 (15:56 +0000)]
Merge branch 'bug/JAL-3412idWidthDiscrepancy' into develop

4 years agoJAL-3407 JAL-3296 release notes
Jim Procter [Thu, 27 Feb 2020 15:49:08 +0000 (15:49 +0000)]
JAL-3407 JAL-3296 release notes

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