jalview.git
4 years agoJAL-3253 Platform reconciled with applet
BobHanson [Wed, 8 Apr 2020 15:08:58 +0000 (10:08 -0500)]
JAL-3253 Platform reconciled with applet

4 years agoJAL-3253 SwingJS upgrade including J11 transpiler 3.2.9.v1f
BobHanson [Wed, 8 Apr 2020 14:12:52 +0000 (09:12 -0500)]
JAL-3253 SwingJS upgrade including J11 transpiler 3.2.9.v1f

4 years agoJAL-3253 merge of new SwingJS api
BobHanson [Wed, 8 Apr 2020 14:12:11 +0000 (09:12 -0500)]
JAL-3253 merge of new SwingJS api

4 years agomerge from develop: the fixy bit merge/Jalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j
soares [Tue, 7 Apr 2020 19:39:05 +0000 (20:39 +0100)]
merge from develop: the fixy bit

4 years agomerge from develop: the rest of the changes
soares [Tue, 7 Apr 2020 19:14:19 +0000 (20:14 +0100)]
merge from develop: the rest of the changes

4 years agomerge from develop: Most of the changes
soares [Tue, 7 Apr 2020 16:55:50 +0000 (17:55 +0100)]
merge from develop: Most of the changes

4 years agoJAL-3589 (old Platform) fix for Jalvew-JS/develop only.
BobHanson [Tue, 7 Apr 2020 15:27:38 +0000 (10:27 -0500)]
JAL-3589 (old Platform) fix for Jalvew-JS/develop only.

4 years agoJAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility
gmungoc [Tue, 7 Apr 2020 13:30:47 +0000 (14:30 +0100)]
JAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility

4 years agoJAL-3577 improvement to non-release DMG background and source SVG. Updated docs on... task/JAL-3577_Jalview_Test_installers
Ben Soares [Tue, 7 Apr 2020 13:24:02 +0000 (14:24 +0100)]
JAL-3577 improvement to non-release DMG background and source SVG. Updated docs on image specification/creation.

4 years agoMerge branch 'task/JAL-3577_Jalview_Test_installers' into develop
Ben Soares [Tue, 7 Apr 2020 00:30:12 +0000 (01:30 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop

4 years agoJAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling
Ben Soares [Tue, 7 Apr 2020 00:29:33 +0000 (01:29 +0100)]
JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling

4 years agoJAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for...
Ben Soares [Mon, 6 Apr 2020 21:34:06 +0000 (22:34 +0100)]
JAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for RELEASE channel only and Examples folder in Jalview Programme Group in Windows.

4 years agoJAL-3407 redact java 8 incompatible type inference
Jim Procter [Mon, 6 Apr 2020 16:47:45 +0000 (17:47 +0100)]
JAL-3407 redact java 8 incompatible type inference

4 years agoJAL-3581 no hidden sequence marker if hidden markers not shown
gmungoc [Mon, 6 Apr 2020 14:58:33 +0000 (15:58 +0100)]
JAL-3581 no hidden sequence marker if hidden markers not shown

4 years agoJAL-3407 updated release date to Thursday 9th April, and release notes for JAL-3577...
Jim Procter [Mon, 6 Apr 2020 16:25:35 +0000 (17:25 +0100)]
JAL-3407 updated release date to Thursday 9th April, and release notes for JAL-3577 JAL-3581 JAL-3571

4 years agoJAL-3581 no hidden sequence marker if hidden markers not shown
gmungoc [Mon, 6 Apr 2020 14:58:33 +0000 (15:58 +0100)]
JAL-3581 no hidden sequence marker if hidden markers not shown

4 years agoJAL-3577 Moved application Categories for freedesktop menus into correct place in...
Ben Soares [Mon, 6 Apr 2020 14:49:30 +0000 (15:49 +0100)]
JAL-3577 Moved application Categories for freedesktop menus into correct place in install4j

4 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Mon, 6 Apr 2020 13:17:24 +0000 (14:17 +0100)]
Merge branch 'develop' into Jalview-JS/develop

Conflicts:
build.gradle
src/jalview/gui/SeqPanel.java
build.gradle and gradle.properties changes in develop ignored

4 years agoJAL-3577 removed debugging
Ben Soares [Mon, 6 Apr 2020 12:32:30 +0000 (13:32 +0100)]
JAL-3577 removed debugging

4 years agoMerge branch 'task/JAL-3577_Jalview_Test_installers' into develop
Ben Soares [Mon, 6 Apr 2020 12:29:40 +0000 (13:29 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop

4 years agoJAL-3577 Added existing and new Application IDs for Windows. Fixed Desktop shortcut...
Ben Soares [Mon, 6 Apr 2020 12:27:56 +0000 (13:27 +0100)]
JAL-3577 Added existing and new Application IDs for Windows. Fixed Desktop shortcut and Menu entry.

4 years agoJAL-3579 no Feature Editor if features not shown
gmungoc [Mon, 6 Apr 2020 09:18:17 +0000 (10:18 +0100)]
JAL-3579 no Feature Editor if features not shown

4 years agoJAL-3577 Changed shortName to INTERNAL_ID
Ben Soares [Mon, 6 Apr 2020 08:20:35 +0000 (09:20 +0100)]
JAL-3577 Changed shortName to INTERNAL_ID

4 years agoJAL-3577 Changed Windows internal ID to a new value which is backward compatible...
Ben Soares [Sun, 5 Apr 2020 09:50:46 +0000 (10:50 +0100)]
JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'

4 years agoJAL-3577 Changed Windows internal ID to a new value which is backward compatible...
Ben Soares [Sun, 5 Apr 2020 09:50:12 +0000 (10:50 +0100)]
JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'

4 years agoJAL-3577 Added DS_Store for Test release to look like proper installer
Ben Soares [Sat, 4 Apr 2020 00:01:39 +0000 (01:01 +0100)]
JAL-3577 Added DS_Store for Test release to look like proper installer

4 years agoJAL-3577 Added a jalviewt scheme ONLY to TEST-RELEASE and TEST-LOCAL channels so...
Ben Soares [Fri, 3 Apr 2020 16:04:30 +0000 (17:04 +0100)]
JAL-3577 Added a jalviewt scheme ONLY to TEST-RELEASE and TEST-LOCAL channels so that a test jvl can be made to ONLY open in the Test installation

4 years agoJAL-3577 cleaned up old DMG files. Added NON-RELEASE DMG files. Changed how Jalview...
Ben Soares [Fri, 3 Apr 2020 15:44:56 +0000 (16:44 +0100)]
JAL-3577 cleaned up old DMG files. Added NON-RELEASE DMG files. Changed how Jalview name propogates through install4j -- now dynamically created depending on the CHANNEL

4 years agoJAL-3577 First attempt at new folder names
Ben Soares [Thu, 2 Apr 2020 23:41:49 +0000 (00:41 +0100)]
JAL-3577 First attempt at new folder names

4 years agoJAL-3572 Added getdown Implementation-Version to getdown jars META-INF/MANIFEST.MF
Ben Soares [Thu, 2 Apr 2020 13:55:22 +0000 (14:55 +0100)]
JAL-3572 Added getdown Implementation-Version to getdown jars META-INF/MANIFEST.MF

4 years agoMerge branch 'improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_f...
Ben Soares [Thu, 2 Apr 2020 11:42:30 +0000 (12:42 +0100)]
Merge branch 'improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file' into develop

4 years agoJAL-3438 Added spotless task to use the utils/eclipse/JalviewCodeStyle.xml to reforma...
soares [Wed, 1 Apr 2020 15:50:53 +0000 (16:50 +0100)]
JAL-3438 Added spotless task to use the utils/eclipse/JalviewCodeStyle.xml to reformat all .java source files

4 years agoJAL-3225 tasks to create extra desired settings for eclipse
soares [Wed, 1 Apr 2020 15:37:55 +0000 (16:37 +0100)]
JAL-3225 tasks to create extra desired settings for eclipse

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into...
soares [Wed, 1 Apr 2020 14:20:01 +0000 (15:20 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into Jalview-JS/develop

4 years agoMerge branch 'documentation/Release_2_11_1_Branch' into develop
Jim Procter [Tue, 31 Mar 2020 22:10:44 +0000 (23:10 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop

4 years agoJAL-3407 basic doc for releasing jalview - will be embellished as we go
Jim Procter [Tue, 31 Mar 2020 22:09:42 +0000 (23:09 +0100)]
JAL-3407 basic doc for releasing jalview - will be embellished as we go

4 years agoJAL-3407 updated release date to 2nd April, and first draft of release notes
Jim Procter [Tue, 31 Mar 2020 21:53:24 +0000 (22:53 +0100)]
JAL-3407 updated release date to 2nd April, and first draft of release notes

4 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Tue, 31 Mar 2020 13:42:09 +0000 (14:42 +0100)]
Merge branch 'develop' into Jalview-JS/develop

4 years agoJAL-1889 better (?) wait for Conservation thread
gmungoc [Tue, 31 Mar 2020 13:41:15 +0000 (14:41 +0100)]
JAL-1889 better (?) wait for Conservation thread

4 years agoJAL-3248 quick fix to not remove doc/building.html with a gradle clean
soares [Tue, 31 Mar 2020 11:14:43 +0000 (12:14 +0100)]
JAL-3248 quick fix to not remove doc/building.html with a gradle clean

4 years agoJAL-3210 JAL-3130 merge changes to JSON processing
gmungoc [Tue, 31 Mar 2020 10:16:02 +0000 (11:16 +0100)]
JAL-3210 JAL-3130 merge changes to JSON processing

4 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Tue, 31 Mar 2020 09:35:05 +0000 (10:35 +0100)]
Merge branch 'develop' into Jalview-JS/develop

4 years agoMerge branch 'documentation/Release_2_11_1_Branch' into develop
Jim Procter [Tue, 31 Mar 2020 09:25:54 +0000 (10:25 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
gmungoc [Mon, 30 Mar 2020 18:02:00 +0000 (19:02 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

4 years agoJAL-3393 Don't need PDF file using Illustrator. Replaced with SVG using Inkscape
soares [Mon, 30 Mar 2020 17:09:05 +0000 (18:09 +0100)]
JAL-3393 Don't need PDF file using Illustrator. Replaced with SVG using Inkscape

4 years agoJAL-3407 2.11.1.0 release date bump - maybe tomorrow - maybe the next day !
Jim Procter [Mon, 30 Mar 2020 17:03:30 +0000 (18:03 +0100)]
JAL-3407 2.11.1.0 release date bump - maybe tomorrow - maybe the next day !

4 years agoJAL-3407 JAL-3130 back out java 9+ syntax that breaks java 8 builds
Jim Procter [Mon, 30 Mar 2020 17:03:09 +0000 (18:03 +0100)]
JAL-3407 JAL-3130 back out java 9+ syntax that breaks java 8 builds

4 years agoJAL-3210 merged from develop: build.gradle and gradle.properties
soares [Mon, 30 Mar 2020 17:01:19 +0000 (18:01 +0100)]
JAL-3210 merged from develop: build.gradle and gradle.properties

4 years agoJAL-3210 debug logging commented out
gmungoc [Mon, 30 Mar 2020 14:22:11 +0000 (15:22 +0100)]
JAL-3210 debug logging commented out

4 years agoJAL-3210 test updated for changed signature of SequenceI.getDBRefs()
gmungoc [Mon, 30 Mar 2020 11:45:30 +0000 (12:45 +0100)]
JAL-3210 test updated for changed signature of SequenceI.getDBRefs()

4 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Mon, 30 Mar 2020 10:51:45 +0000 (11:51 +0100)]
Merge branch 'develop' into Jalview-JS/develop

Conflicts:
.gitignore
build.gradle
gradle.properties
src/jalview/gui/AlignFrame.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/JvSwingUtils.java
src/jalview/util/MessageManager.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/JvSwingUtilsTest.java
test/jalview/gui/PopupMenuTest.java
utils/eclipse/org.eclipse.jdt.core.jalview.prefs

4 years agoJAL-3225 updated essential files for eclipse project if buildship fails
soares [Fri, 27 Mar 2020 16:08:13 +0000 (16:08 +0000)]
JAL-3225 updated essential files for eclipse project if buildship fails

4 years agoJAL-3225 updated essential files for eclipse project if buildship fails
soares [Fri, 27 Mar 2020 16:08:13 +0000 (16:08 +0000)]
JAL-3225 updated essential files for eclipse project if buildship fails

4 years agoJAL-3225 Also look for local.properties in file named ../${projectDir}_local.properti...
Ben Soares [Thu, 26 Mar 2020 20:22:52 +0000 (20:22 +0000)]
JAL-3225 Also look for local.properties in file named ../${projectDir}_local.properties. This allows multiple instances of the same project in Eclipse by changing the eclipse_project_name propert (and other local properties)

4 years agoJAL-3225 This one file needed for project if git clean -dfx run
soares [Thu, 26 Mar 2020 17:37:44 +0000 (17:37 +0000)]
JAL-3225 This one file needed for project if git clean -dfx run

4 years agoJAL-3225 This one file needed for project if git clean -dfx run
soares [Thu, 26 Mar 2020 17:37:44 +0000 (17:37 +0000)]
JAL-3225 This one file needed for project if git clean -dfx run

4 years agoJAL-3225 fix comparing Eclispe IDE j2s plugin and this branch j2s plugin
soares [Thu, 26 Mar 2020 17:32:52 +0000 (17:32 +0000)]
JAL-3225 fix comparing Eclispe IDE j2s plugin and this branch j2s plugin

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-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-3210 fix an undefined copyPlugin var and improved warning in Eclipse console...
soares [Wed, 25 Mar 2020 13:39:41 +0000 (13:39 +0000)]
JAL-3210 fix an undefined copyPlugin var and improved warning in Eclipse console when copying plugin

4 years agoJAL-3210 Fixed Eclipse IDE usage
soares [Wed, 25 Mar 2020 01:57:40 +0000 (01:57 +0000)]
JAL-3210 Fixed Eclipse IDE usage

4 years agoJAL-3210 New site-resources dir too
soares [Tue, 24 Mar 2020 17:00:32 +0000 (17:00 +0000)]
JAL-3210 New site-resources dir too

4 years agoJAL-3210 New version of swingjs and supporting .zip libraries. Swing-JS version 3...
soares [Tue, 24 Mar 2020 15:35:03 +0000 (15:35 +0000)]
JAL-3210 New version of swingjs and supporting .zip libraries. Swing-JS version 3.2.9.v1e

4 years agoJAL-3210 adjustment to build.gradle, gradle.properties to look for net.sf.j2s.core...
soares [Tue, 24 Mar 2020 15:32:14 +0000 (15:32 +0000)]
JAL-3210 adjustment to build.gradle, gradle.properties to look for net.sf.j2s.core-j11.jar

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 agoMerge commit '3fe5792cc63d53a5ace952bd68d3bb673c97f588' into improvement/JAL-3394_add... improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file
Ben Soares [Thu, 12 Mar 2020 21:30:03 +0000 (21:30 +0000)]
Merge commit '3fe5792cc63d53a5ace952bd68d3bb673c97f588' into improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file

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 agoMerge branch 'develop' into improvement/JAL-3394_added_categories_to_unix_shell_insta...
Ben Soares [Thu, 12 Mar 2020 13:49:51 +0000 (13:49 +0000)]
Merge branch 'develop' into improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file

Merging on develop

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-3227 slightly adapted download_jres.sh to make it easier to specify GNU tar on...
Ben Soares [Mon, 9 Mar 2020 12:11:13 +0000 (12:11 +0000)]
JAL-3227 slightly adapted download_jres.sh to make it easier to specify GNU tar on macos. 'TAR=gtar'

4 years agoJAL-3394 Made Categories line configurable/readable in gradle.properties as will...
Ben Soares [Mon, 9 Mar 2020 12:09:03 +0000 (12:09 +0000)]
JAL-3394 Made Categories line configurable/readable in gradle.properties as will be used more generically in future

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 agoJAL-3394 Added Categories=Science;Biology;Java; to unix shell installer .desktop...
Ben Soares [Fri, 6 Mar 2020 17:35:11 +0000 (17:35 +0000)]
JAL-3394 Added Categories=Science;Biology;Java; to unix shell installer .desktop file

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