Jim Procter [Mon, 18 May 2020 14:26:30 +0000 (15:26 +0100)]
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112
resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/api/AlignViewportI.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/WsJobParameters.java
src/jalview/io/AlignmentFileReaderI.java
src/jalview/io/FileLoader.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/jws2/Jws2Discoverer.java
test/jalview/analysis/AAFrequencyTest.java
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java
gmungoc [Mon, 18 May 2020 10:01:29 +0000 (11:01 +0100)]
JAL-3529 test updated for revised signature of getDBRefs()
gmungoc [Mon, 18 May 2020 09:59:52 +0000 (10:59 +0100)]
Merge branch 'Jalview-JS/develop' into develop
Conflicts:
build.gradle
src/jalview/gui/PopupMenu.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error
gmungoc [Fri, 1 May 2020 11:36:58 +0000 (12:36 +0100)]
JAL-3613 check sequence overlap when matching search results
Jim Procter [Thu, 23 Apr 2020 17:54:49 +0000 (18:54 +0100)]
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha
update for 2.11.1 release
Jim Procter [Thu, 23 Apr 2020 17:41:45 +0000 (18:41 +0100)]
Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalview_212_alpha
soares [Wed, 22 Apr 2020 19:58:55 +0000 (20:58 +0100)]
JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used
Jim Procter [Tue, 21 Apr 2020 23:07:21 +0000 (00:07 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 23:06:07 +0000 (00:06 +0100)]
JAL-3407 add GPL license to Jalview source files
Jim Procter [Tue, 21 Apr 2020 23:03:25 +0000 (00:03 +0100)]
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera
Jim Procter [Tue, 21 Apr 2020 20:19:16 +0000 (21:19 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 20:18:56 +0000 (21:18 +0100)]
JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0
Jim Procter [Tue, 21 Apr 2020 17:23:46 +0000 (18:23 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 17:23:11 +0000 (18:23 +0100)]
JAL-3574 JAL-3407 release notes
Jim Procter [Tue, 21 Apr 2020 17:06:17 +0000 (18:06 +0100)]
Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release
Jim Procter [Tue, 21 Apr 2020 17:03:45 +0000 (18:03 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 16:39:33 +0000 (17:39 +0100)]
JAL-3407 add and document ComputePeptideVariants.groovy
Ben Soares [Tue, 21 Apr 2020 14:37:32 +0000 (15:37 +0100)]
JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time
Jim Procter [Tue, 21 Apr 2020 13:16:17 +0000 (14:16 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 21 Apr 2020 13:10:22 +0000 (14:10 +0100)]
JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April
gmungoc [Tue, 21 Apr 2020 13:03:35 +0000 (14:03 +0100)]
JAL-3210 try adding setup method to unit test failing on server...
gmungoc [Tue, 21 Apr 2020 11:34:13 +0000 (12:34 +0100)]
JAL-1889 corrected wait for consensus to be calculated
Ben Soares [Tue, 21 Apr 2020 11:07:53 +0000 (12:07 +0100)]
JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list
Jim Procter [Tue, 21 Apr 2020 10:58:30 +0000 (11:58 +0100)]
Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop
Jim Procter [Tue, 21 Apr 2020 10:48:44 +0000 (11:48 +0100)]
JAL-367 code tidy
Jim Procter [Tue, 21 Apr 2020 10:48:35 +0000 (11:48 +0100)]
JAL-3567 translated rather than imputed peptide
gmungoc [Tue, 21 Apr 2020 09:59:19 +0000 (10:59 +0100)]
JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies
Ben Soares [Tue, 21 Apr 2020 00:11:04 +0000 (01:11 +0100)]
JAL-3602 Added configuration for enforced use of UTF-8 for creating the
core js files and also in the closure-compiler.
gmungoc [Fri, 17 Apr 2020 13:00:10 +0000 (14:00 +0100)]
JAL-3567 unit tests for linked feature tooltips
BobHanson [Fri, 17 Apr 2020 00:19:45 +0000 (19:19 -0500)]
added .gitignore paths
I need these until I fully grasp the ways that gradle works.
BobHanson [Thu, 16 Apr 2020 19:08:11 +0000 (14:08 -0500)]
JAL-3587 Load Project bug
Fixed 2019.01.24 in Applet branch.
commit
db8caac49ea663fbc2b8b78f7eb2e6ae893f40da
didn't have a JAL number. My mistake.
gmungoc [Thu, 16 Apr 2020 17:43:21 +0000 (18:43 +0100)]
JAL-3567 adjust layout of linked feature report, unit test
gmungoc [Thu, 16 Apr 2020 16:37:46 +0000 (17:37 +0100)]
JAL-3567 added 'imputed by Jalview' to protein consequence in report
gmungoc [Thu, 16 Apr 2020 15:11:23 +0000 (16:11 +0100)]
JAL-3567 report mapped location for virtual features in tooltip etc
Jim Procter [Tue, 14 Apr 2020 15:38:39 +0000 (16:38 +0100)]
JAL-3407 JAL-3529 release notes
Jim Procter [Tue, 14 Apr 2020 15:33:50 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into develop
Jim Procter [Tue, 14 Apr 2020 15:33:22 +0000 (16:33 +0100)]
JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>
Jim Procter [Tue, 14 Apr 2020 12:50:54 +0000 (13:50 +0100)]
JAL-3597 improved Memory test suite by detecting base memory usage rather than assuming it is constant for each release.
Jim Procter [Tue, 14 Apr 2020 12:21:38 +0000 (13:21 +0100)]
JAL-3407 release date set to 16th April, known issue report for JAL-3574
Jim Procter [Tue, 14 Apr 2020 11:25:20 +0000 (12:25 +0100)]
Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop
gmungoc [Tue, 14 Apr 2020 08:26:14 +0000 (09:26 +0100)]
JAL-3583 remove debug logging, Javadoc added
gmungoc [Mon, 13 Apr 2020 15:42:42 +0000 (16:42 +0100)]
JAL-3574 test coverage corners
gmungoc [Mon, 13 Apr 2020 11:45:38 +0000 (12:45 +0100)]
JAL-3574 Matcher with integer/long value pattern (e.g. VCF POS locus)
gmungoc [Sun, 12 Apr 2020 14:43:21 +0000 (15:43 +0100)]
JAL-3596 change redacted
gmungoc [Sun, 12 Apr 2020 12:24:24 +0000 (13:24 +0100)]
JAL-3596 don't draw text over features if Show Text is unselected
gmungoc [Sun, 12 Apr 2020 11:51:12 +0000 (12:51 +0100)]
JAL-3583 consistent last[Formatted]Tooltip, show once only per residue
BobHanson [Thu, 9 Apr 2020 18:07:31 +0000 (13:07 -0500)]
JAL-3587 save and reload project file fix
Ben Soares [Thu, 9 Apr 2020 13:32:03 +0000 (14:32 +0100)]
JAL-3588 Remove Examples folder in windows Program Group for all CHANNEL values
Jim Procter [Thu, 9 Apr 2020 11:04:07 +0000 (12:04 +0100)]
JAL-3577 automatically configure JALVIEW_VERSION for builds using jalview.version property in RELEASE file
BobHanson [Wed, 8 Apr 2020 14:12:52 +0000 (09:12 -0500)]
JAL-3253 SwingJS upgrade including J11 transpiler 3.2.9.v1f
BobHanson [Wed, 8 Apr 2020 14:12:11 +0000 (09:12 -0500)]
JAL-3253 merge of new SwingJS api
soares [Tue, 7 Apr 2020 19:39:05 +0000 (20:39 +0100)]
merge from develop: the fixy bit
soares [Tue, 7 Apr 2020 19:14:19 +0000 (20:14 +0100)]
merge from develop: the rest of the changes
soares [Tue, 7 Apr 2020 16:55:50 +0000 (17:55 +0100)]
merge from develop: Most of the changes
BobHanson [Tue, 7 Apr 2020 15:27:38 +0000 (10:27 -0500)]
JAL-3589 (old Platform) fix for Jalvew-JS/develop only.
gmungoc [Tue, 7 Apr 2020 13:30:47 +0000 (14:30 +0100)]
JAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility
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.
Ben Soares [Tue, 7 Apr 2020 00:30:12 +0000 (01:30 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop
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
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.
Jim Procter [Mon, 6 Apr 2020 16:47:45 +0000 (17:47 +0100)]
JAL-3407 redact java 8 incompatible type inference
gmungoc [Mon, 6 Apr 2020 14:58:33 +0000 (15:58 +0100)]
JAL-3581 no hidden sequence marker if hidden markers not shown
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
gmungoc [Mon, 6 Apr 2020 14:58:33 +0000 (15:58 +0100)]
JAL-3581 no hidden sequence marker if hidden markers not shown
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
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
Ben Soares [Mon, 6 Apr 2020 12:32:30 +0000 (13:32 +0100)]
JAL-3577 removed debugging
Ben Soares [Mon, 6 Apr 2020 12:29:40 +0000 (13:29 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop
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.
gmungoc [Mon, 6 Apr 2020 09:18:17 +0000 (10:18 +0100)]
JAL-3579 no Feature Editor if features not shown
Ben Soares [Mon, 6 Apr 2020 08:20:35 +0000 (09:20 +0100)]
JAL-3577 Changed shortName to INTERNAL_ID
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'
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'
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
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
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
Ben Soares [Thu, 2 Apr 2020 23:41:49 +0000 (00:41 +0100)]
JAL-3577 First attempt at new folder names
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
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
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
soares [Wed, 1 Apr 2020 15:37:55 +0000 (16:37 +0100)]
JAL-3225 tasks to create extra desired settings for eclipse
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
Jim Procter [Tue, 31 Mar 2020 22:10:44 +0000 (23:10 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop
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
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
gmungoc [Tue, 31 Mar 2020 13:42:09 +0000 (14:42 +0100)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Tue, 31 Mar 2020 13:41:15 +0000 (14:41 +0100)]
JAL-1889 better (?) wait for Conservation thread
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
gmungoc [Tue, 31 Mar 2020 10:16:02 +0000 (11:16 +0100)]
JAL-3210 JAL-3130 merge changes to JSON processing
gmungoc [Tue, 31 Mar 2020 09:35:05 +0000 (10:35 +0100)]
Merge branch 'develop' into Jalview-JS/develop
Jim Procter [Tue, 31 Mar 2020 09:25:54 +0000 (10:25 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop
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
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
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 !
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
soares [Mon, 30 Mar 2020 17:01:19 +0000 (18:01 +0100)]
JAL-3210 merged from develop: build.gradle and gradle.properties
gmungoc [Mon, 30 Mar 2020 14:22:11 +0000 (15:22 +0100)]
JAL-3210 debug logging commented out
gmungoc [Mon, 30 Mar 2020 11:45:30 +0000 (12:45 +0100)]
JAL-3210 test updated for changed signature of SequenceI.getDBRefs()
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
git://source.jalview.org / jalview.git / log