gmungoc [Thu, 4 Jun 2020 16:22:29 +0000 (17:22 +0100)]
JAL-1191 reduce logging level for warnings
gmungoc [Thu, 4 Jun 2020 16:21:29 +0000 (17:21 +0100)]
JAL-3446 post-merge unit test fixes, formatting
BobHanson [Wed, 3 Jun 2020 21:30:49 +0000 (16:30 -0500)]
I see...
BobHanson [Wed, 3 Jun 2020 21:30:12 +0000 (16:30 -0500)]
adds link for __j2sflags.htm to template.html
BobHanson [Wed, 3 Jun 2020 21:26:41 +0000 (16:26 -0500)]
updated template.html
BobHanson [Wed, 3 Jun 2020 21:19:44 +0000 (16:19 -0500)]
_jvjmol.txt
BobHanson [Wed, 3 Jun 2020 20:54:57 +0000 (15:54 -0500)]
JAL-3664 support for new Locale(""), meaning "not actually a
ResourceBundle, just one file (MessageManager)
BobHanson [Wed, 3 Jun 2020 20:54:03 +0000 (15:54 -0500)]
JAL-3664 support for user.home, user.dir, user
BobHanson [Wed, 3 Jun 2020 20:47:30 +0000 (15:47 -0500)]
JAL-3446 adds SIFTs JAL-3625 SiftsClient
BobHanson [Wed, 3 Jun 2020 14:24:06 +0000 (09:24 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider missing for
RestClient; others are just cosmetic
BobHanson [Wed, 3 Jun 2020 13:12:37 +0000 (08:12 -0500)]
JAL-3446 AsyncSwingWorker upgrade
BobHanson [Wed, 3 Jun 2020 03:05:11 +0000 (22:05 -0500)]
JAL-3446 from JAL-3253 Discoverers
BobHanson [Wed, 3 Jun 2020 00:58:05 +0000 (19:58 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider
StructureSelectionManager and others
BobHanson [Wed, 3 Jun 2020 00:29:28 +0000 (19:29 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop
BobHanson [Tue, 2 Jun 2020 23:47:20 +0000 (18:47 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider 1/many
BobHanson [Tue, 2 Jun 2020 23:23:42 +0000 (18:23 -0500)]
JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.
- integrated changes from 0b573ed (gmungoc)
BobHanson [Tue, 2 Jun 2020 21:56:28 +0000 (16:56 -0500)]
JAL-3446 from JAL-3253-applet Jalview2XML integration (retains
GeneLocus; switches to invokeLater)
BobHanson [Tue, 2 Jun 2020 21:54:57 +0000 (16:54 -0500)]
JAL-3446 from JAL-3253-applet Desktop and Jws2Discoverer getInstance()
BobHanson [Tue, 2 Jun 2020 21:51:32 +0000 (16:51 -0500)]
JAL-3446 JAL-3401 from JAL-3253-applet AlignmentPanel.holdRepaint
BobHanson [Tue, 2 Jun 2020 21:06:05 +0000 (16:06 -0500)]
JAL-3446 from JAL-3253 AppletFormatAdapter not fixed
BobHanson [Tue, 2 Jun 2020 21:04:47 +0000 (16:04 -0500)]
Preferences/StructureViewer fix
BobHanson [Tue, 2 Jun 2020 18:22:59 +0000 (13:22 -0500)]
this was supposed to go on a separate branch. Didn't know I had to be
sure I was synchronized.
BobHanson [Tue, 2 Jun 2020 18:19:25 +0000 (13:19 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Tue, 2 Jun 2020 17:28:18 +0000 (12:28 -0500)]
JAL-3446 JAL-3253 JAL-3445 BSML bbb XML format reader (preliminary)
Ben Soares [Tue, 2 Jun 2020 16:30:51 +0000 (17:30 +0100)]
JAL-3225 some fixes to build.gradle for working in Eclipse and not always changing doc/building.html
BobHanson [Tue, 2 Jun 2020 15:20:30 +0000 (10:20 -0500)]
JAL-3446 JAL-3253 Preferences
- unnecessary static initialization of StructureViewer
BobHanson [Tue, 2 Jun 2020 12:27:43 +0000 (07:27 -0500)]
JAL-3446 from JAL-3253-applet StockholmFile updated to 26b115b (gmungoc)
BobHanson [Tue, 2 Jun 2020 11:30:54 +0000 (06:30 -0500)]
helpful hints from Ben
gmungoc [Tue, 2 Jun 2020 10:19:16 +0000 (11:19 +0100)]
JAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)
gmungoc [Tue, 2 Jun 2020 10:00:36 +0000 (11:00 +0100)]
JAL-3446 fix broken test
BobHanson [Tue, 2 Jun 2020 03:32:31 +0000 (22:32 -0500)]
Bob's gitignore addition
/build-site.xml
/buildcore.xml
/j11lib/intervalstore-v1.0.jar
BobHanson [Tue, 2 Jun 2020 03:13:03 +0000 (22:13 -0500)]
JAL-3626 from JAL-3253-applet Jalview.java
adds JalviewLite interface; removes deprecated AppletContext interface
BobHanson [Tue, 2 Jun 2020 03:10:58 +0000 (22:10 -0500)]
JAL-3626 from JAL-3253-applet Cache applicationProperties made private
-- adds remove/setPropertyNoSave
BobHanson [Tue, 2 Jun 2020 00:34:02 +0000 (19:34 -0500)]
JAL-3626 from JAL-3253-applet Cache applicationProperties made private
-- adds remove/setPropertyNoSave
BobHanson [Tue, 2 Jun 2020 00:32:42 +0000 (19:32 -0500)]
JAL-3626 from JAL-3253-applet web page embedding
BobHanson [Mon, 1 Jun 2020 22:37:20 +0000 (17:37 -0500)]
JAL-3626 from JAL-3253-applet JalviewLite scrollTo capability
BobHanson [Mon, 1 Jun 2020 22:25:24 +0000 (17:25 -0500)]
JAL-3626 from JAL-3253-applet CalculationChooser
-- dissociated from panel for static access by JavaScript
BobHanson [Mon, 1 Jun 2020 22:18:07 +0000 (17:18 -0500)]
JAL-3626 from JAL-3253-applet StructureViewer/Chooser
-- disassociates viewer launch from chooser
-- for JavaScript interface
(sorry about JAL-3262 ref previously)
BobHanson [Mon, 1 Jun 2020 21:48:12 +0000 (16:48 -0500)]
JAL-3262 from JAL-3253-applet temp. Desktop instance hack
BobHanson [Mon, 1 Jun 2020 21:43:44 +0000 (16:43 -0500)]
JAL-3262 from JAL-3253-applet JalviewApp integration
BobHanson [Mon, 1 Jun 2020 21:41:54 +0000 (16:41 -0500)]
JAL-3262 from JAL-3253-applet JalviewApp integration
BobHanson [Mon, 1 Jun 2020 21:39:06 +0000 (16:39 -0500)]
JAL-3262 from JAL-3253-applet AppletParams + Cache.setPropertyNoSave
BobHanson [Mon, 1 Jun 2020 21:33:54 +0000 (16:33 -0500)]
JAL-3262 from JAL-3253-applet ArgsParser
BobHanson [Mon, 1 Jun 2020 21:29:54 +0000 (16:29 -0500)]
JAL-3262 from JAL-3253-applet Platform JS interface upgrade
BobHanson [Mon, 1 Jun 2020 21:29:10 +0000 (16:29 -0500)]
JAL-3262 from JAL-3253-applet Preferences final static String upgrade
BobHanson [Mon, 1 Jun 2020 21:20:28 +0000 (16:20 -0500)]
JAL-3262 from JAL-3523-applet JalviewApp and JalviewJSApi
- removes JaliewJSLite dependence
- removes AlignFrameI reference
BobHanson [Mon, 1 Jun 2020 21:14:33 +0000 (16:14 -0500)]
JAL-3262 from JAL3253-applet core_jvjmol.z.js static load
BobHanson [Mon, 1 Jun 2020 21:10:28 +0000 (16:10 -0500)]
JAL-3626 Regex optimization from JAL-3253-applet; also minor
StockholmFile for loop opt.
BobHanson [Mon, 1 Jun 2020 19:22:56 +0000 (14:22 -0500)]
THIRDPARTYLIBS referred to intervalstore-v1.0 still
BobHanson [Mon, 1 Jun 2020 19:12:41 +0000 (14:12 -0500)]
corrects Platform.openURL
BobHanson [Mon, 1 Jun 2020 19:02:47 +0000 (14:02 -0500)]
JAL-3626 adding compatible Platform.java
BobHanson [Mon, 1 Jun 2020 17:40:31 +0000 (12:40 -0500)]
SwingJS update
BobHanson [Mon, 1 Jun 2020 17:38:02 +0000 (12:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Mon, 1 Jun 2020 17:32:19 +0000 (12:32 -0500)]
swingjs/api, javajs/async
soares [Mon, 1 Jun 2020 14:54:16 +0000 (15:54 +0100)]
JAL-3225 small fixes for building within Eclipse
soares [Thu, 28 May 2020 21:07:28 +0000 (22:07 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into Jalview-JS/develop
BobHanson [Thu, 28 May 2020 20:58:58 +0000 (15:58 -0500)]
JAL-3626 transpiler and SwingJS upgrade
BobHanson [Thu, 28 May 2020 20:58:09 +0000 (15:58 -0500)]
Varna fix for hashtable.remove(value) [unclear]
BobHanson [Thu, 28 May 2020 20:56:38 +0000 (15:56 -0500)]
JAL-3636 ColorUtils cleaner test for hex color
soares [Thu, 28 May 2020 16:24:09 +0000 (17:24 +0100)]
Merge branch 'develop' into Jalview-JS/develop
BobHanson [Thu, 28 May 2020 13:39:29 +0000 (08:39 -0500)]
Gitter comment 2020.05.28 Cache.log.err(msg) not appearing
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails
Ben Soares [Wed, 27 May 2020 16:37:12 +0000 (17:37 +0100)]
JAL-3541 ensure deletion of cloverReportDir
Ben Soares [Wed, 27 May 2020 15:53:40 +0000 (16:53 +0100)]
JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity
gmungoc [Tue, 26 May 2020 16:27:08 +0000 (17:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 May 2020 16:26:55 +0000 (17:26 +0100)]
JAL-1889 disable test failing on build server
soares [Tue, 26 May 2020 14:36:27 +0000 (15:36 +0100)]
Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop
soares [Tue, 26 May 2020 14:08:17 +0000 (15:08 +0100)]
JAL-3541 added a property/variable style comment to build.gradle
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails
gmungoc [Tue, 26 May 2020 12:38:55 +0000 (13:38 +0100)]
Merge branch 'feature/JAL-3624siftsInJS' into develop
soares [Mon, 25 May 2020 23:14:15 +0000 (00:14 +0100)]
JAL-3541 selectively merged build.gradle and gradle.properties
Jim Procter [Mon, 25 May 2020 13:33:39 +0000 (14:33 +0100)]
JAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE properties file, and exclusion of ‘examples’ from the windows installer.
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-3621 corrected sequence feature sort and test
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Mon, 18 May 2020 14:57:13 +0000 (15:57 +0100)]
JAL-3621 update to intervalstore v1.1
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
Ben Soares [Fri, 15 May 2020 00:03:57 +0000 (01:03 +0100)]
JAL-3541 Fixed report path for build artifacts
Ben Soares [Thu, 14 May 2020 20:11:47 +0000 (21:11 +0100)]
JAL-3541 Added mem setting and jvmArgs for cloverReporting
Ben Soares [Thu, 14 May 2020 14:53:00 +0000 (15:53 +0100)]
JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.
Ben Soares [Tue, 12 May 2020 22:05:58 +0000 (23:05 +0100)]
JAL-3541 Helpers for running tests, and other commands headlessly
Ben Soares [Tue, 12 May 2020 22:05:14 +0000 (23:05 +0100)]
JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.
gmungoc [Fri, 1 May 2020 11:36:58 +0000 (12:36 +0100)]
JAL-3613 check sequence overlap when matching search results
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
git://source.jalview.org / jalview.git / log