Ben Soares [Wed, 30 Oct 2019 18:00:43 +0000 (18:00 +0000)]
JAL-3210 catch exception for eclipse
Ben Soares [Wed, 30 Oct 2019 17:13:34 +0000 (17:13 +0000)]
JAL-3210 _j2sclasslist.txt moved into swingjs
Ben Soares [Wed, 30 Oct 2019 17:10:47 +0000 (17:10 +0000)]
JAL-3210 Fixed jalviewjs dependencies. Changed linkCheck to tee output to .out file. Tidying jalviewjs paths.
Ben Soares [Wed, 30 Oct 2019 12:31:02 +0000 (12:31 +0000)]
JAL-3210 Fixed local.properties setting. Some tidying.
Ben Soares [Wed, 30 Oct 2019 01:52:21 +0000 (01:52 +0000)]
JAL-3210 firming up relative paths with jalviewDir. Some comments on possibility of using eclipse plugins differently
Ben Soares [Wed, 30 Oct 2019 01:02:58 +0000 (01:02 +0000)]
JAL-3210 Some tidying and now using swingjs/*
Ben Soares [Tue, 29 Oct 2019 23:28:16 +0000 (23:28 +0000)]
JAL-3210 Now add/override gradle.properties with local.properties
Ben Soares [Tue, 29 Oct 2019 19:51:51 +0000 (19:51 +0000)]
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build
Ben Soares [Tue, 29 Oct 2019 19:50:07 +0000 (19:50 +0000)]
JAL-3210 tidying j2s and swingjs
BobHanson [Tue, 29 Oct 2019 15:45:25 +0000 (10:45 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Tue, 29 Oct 2019 15:42:41 +0000 (10:42 -0500)]
JAL-3210 transpiler fix for package foo with path .../foo/.../foo
Ben Soares [Mon, 28 Oct 2019 14:16:00 +0000 (14:16 +0000)]
JAL-3210 Added eclipse instance info in j2s-transpile.out log.
Ben Soares [Fri, 25 Oct 2019 15:49:31 +0000 (16:49 +0100)]
JAL-3210 Tidied more build.gradle. Different j2s versions for different eclipse versions -- temporary. Only 2019-06 working.
Ben Soares [Fri, 25 Oct 2019 11:03:27 +0000 (12:03 +0100)]
JAL-3210 Using j2s plugins that work for 4.12. net.sf.j2s.core-3.2.4.08.jar not working yet
Ben Soares [Fri, 25 Oct 2019 09:04:30 +0000 (10:04 +0100)]
JAL-3210 Trying out new 3.2.4.08 j2s
Ben Soares [Thu, 24 Oct 2019 18:41:27 +0000 (19:41 +0100)]
JAL-3120 consistent paths/property interpolation in build.gradle. Test classes. Clean task corrections.
Ben Soares [Thu, 24 Oct 2019 09:46:29 +0000 (10:46 +0100)]
JAL-3210 Fixed cleaning tasks.
Ben Soares [Wed, 23 Oct 2019 22:16:30 +0000 (23:16 +0100)]
JAL-3210 changed .classpath in eclipse_files.zip
soares [Wed, 23 Oct 2019 20:14:31 +0000 (21:14 +0100)]
JAL-3210 some tidying
Ben Soares [Wed, 23 Oct 2019 19:17:10 +0000 (20:17 +0100)]
JAL-3210 Added .j2s creation task for Eclipse IDE
Ben Soares [Wed, 23 Oct 2019 19:01:18 +0000 (20:01 +0100)]
Merge branch 'Jalview-JS/develop_with_gradle_build' of https://source.jalview.org/git/jalview into Jalview-JS/develop_with_gradle_build
Ben Soares [Wed, 23 Oct 2019 19:00:44 +0000 (20:00 +0100)]
JAL-3210 renamed jar for consistency
soares [Wed, 23 Oct 2019 18:55:06 +0000 (19:55 +0100)]
JAL-3120 Emergency eclipse files in case you don't have gradle CLI
Ben Soares [Tue, 22 Oct 2019 16:38:56 +0000 (17:38 +0100)]
JAL-3210 Better integration with Eclipse as IDE. FIXED THE TEST JAR ATTRIBUTE, HOORAH
Ben Soares [Tue, 22 Oct 2019 10:35:15 +0000 (11:35 +0100)]
JAL-3210 small fix for jalviewjsBuildDir
Ben Soares [Tue, 22 Oct 2019 09:57:55 +0000 (10:57 +0100)]
JAL-3210 project name explicitly set. updated README_GRADLE_JALVIEWJS...md file. fixed eclipseRootDir detection for macos.
Ben Soares [Mon, 21 Oct 2019 23:36:55 +0000 (00:36 +0100)]
JAL-3210 added absolute path for transpile log
Ben Soares [Mon, 21 Oct 2019 23:23:46 +0000 (00:23 +0100)]
JAL-3210 Improved/fixed the tempdir creation/storage for eclipse workspace
soares [Mon, 21 Oct 2019 20:16:37 +0000 (21:16 +0100)]
JAL-3210 Different j2s plugin for different versions of eclipse. Not great, but good for now
soares [Mon, 21 Oct 2019 18:51:32 +0000 (19:51 +0100)]
JAL-3210 Changed eclipse workspace dir to be a system temp dir [held in build/jalviewjs/eclipse_workspace_location] that persists until a gradle clean
Ben Soares [Thu, 17 Oct 2019 10:36:30 +0000 (11:36 +0100)]
JAL-3210 changed classes for net.sf.j2s.core
Ben Soares [Thu, 17 Oct 2019 00:33:38 +0000 (01:33 +0100)]
JAL-3210 Added site transfer dir. New net.sf.j2s.core.jar ONLY WORKS WITH ECLIPSE 2019-09+
Ben Soares [Wed, 16 Oct 2019 10:36:22 +0000 (11:36 +0100)]
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build
Merging in Jalview-JS/develop (should be no changes -- just checking)
Jim Procter [Tue, 15 Oct 2019 15:11:07 +0000 (16:11 +0100)]
JAL-3407 update release date for Jalview 2.11.1
soares [Tue, 15 Oct 2019 13:18:50 +0000 (14:18 +0100)]
JAL-3210 Added README_GRADLE_JALVIEWJS-2019-10-15.md
Ben Soares [Fri, 11 Oct 2019 16:23:25 +0000 (17:23 +0100)]
JAL-3210 Just about working transpilation. Some work needed for new Java 11 classes
Jim Procter [Fri, 11 Oct 2019 10:00:30 +0000 (11:00 +0100)]
Merge branch 'develop' into documentation/JAL-3407_2.11.1_release
Ben Soares [Thu, 10 Oct 2019 14:29:49 +0000 (15:29 +0100)]
JAL-3210 Two fixed tests (previously not compiling)
Ben Soares [Thu, 10 Oct 2019 14:24:02 +0000 (15:24 +0100)]
JAL-3210 Moving j2s components around
Ben Soares [Thu, 10 Oct 2019 14:29:49 +0000 (15:29 +0100)]
JAL-3210 Two fixed tests (previously not compiling)
Ben Soares [Thu, 10 Oct 2019 14:28:23 +0000 (15:28 +0100)]
Revert "JAL-3210 Moving j2s components around"
This reverts commit
ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.
Ben Soares [Thu, 10 Oct 2019 14:24:02 +0000 (15:24 +0100)]
JAL-3210 Moving j2s components around
Ben Soares [Tue, 8 Oct 2019 16:26:28 +0000 (17:26 +0100)]
JAL-3210 replacing j11lib/Jmol-14.29.17-no_netscape.jar with unsigned version. Temporary fix
Ben Soares [Tue, 8 Oct 2019 16:00:49 +0000 (17:00 +0100)]
JAL-3210 removed netscape.javascript objects from Jmol-14.29.17.jar to avoid blocking Java 11 clash with jdk.jsobject Java 11 module
Ben Soares [Tue, 8 Oct 2019 15:59:29 +0000 (16:59 +0100)]
JAL-3210 removed eclipse project, classpath and core settings files from branch. Now generate these (once only) with 'gradle eclipse'.
gmungoc [Tue, 8 Oct 2019 09:49:13 +0000 (10:49 +0100)]
Merge branch 'develop' into Jalview-JS/develop
Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/PopupMenu.java
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 16:26:53 +0000 (17:26 +0100)]
JAL-3121 slightly cleaner parsing of, and unit test for, map attributes
gmungoc [Thu, 22 Aug 2019 15:06:36 +0000 (16:06 +0100)]
Merge branch 'develop' into feature/JAL-3121gffAttributeMap
gmungoc [Thu, 22 Aug 2019 15:06:05 +0000 (16:06 +0100)]
JAL-3187 case-insensitive codon variant calculation
gmungoc [Thu, 22 Aug 2019 14:48:38 +0000 (15:48 +0100)]
JAL-3121 round trip GFF attributes including map-valued attributes
gmungoc [Thu, 22 Aug 2019 08:06:23 +0000 (09:06 +0100)]
JAL-3187 one more obsolete method removed
gmungoc [Wed, 21 Aug 2019 16:01:52 +0000 (17:01 +0100)]
JAL-3187 minor code tidying, todo removal
gmungoc [Mon, 19 Aug 2019 14:43:07 +0000 (15:43 +0100)]
JAL-3412 calculateIdWidth - more consistency, constants, tests
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 10:47:26 +0000 (11:47 +0100)]
JAL-3144 better error message if no database selected
gmungoc [Tue, 16 Jul 2019 10:27:05 +0000 (11:27 +0100)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Tue, 16 Jul 2019 10:23:35 +0000 (11:23 +0100)]
JAL-2987 tolerate null double values when formatting JTable
gmungoc [Tue, 16 Jul 2019 08:20:15 +0000 (09:20 +0100)]
JAL-3210 updated jmol jar in j8lib, j11lib
gmungoc [Tue, 16 Jul 2019 07:28:04 +0000 (08:28 +0100)]
JAL-3210 MCview now mc_view
gmungoc [Tue, 16 Jul 2019 07:14:32 +0000 (08:14 +0100)]
JAL-3210 Merge branch 'develop' into trialMerge
Conflicts:
.classpath
.project
.settings/org.eclipse.jdt.core.prefs
.settings/org.eclipse.jdt.ui.prefs
build.xml
resources/lang/Messages_es.properties
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/jalview/analysis/AAFrequency.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureTypeSettings.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/BackupFiles.java
src/jalview/io/FileLoader.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/util/ImageMaker.java
src/jalview/util/Platform.java
src/jalview/ws/SequenceFetcher.java
gmungoc [Mon, 15 Jul 2019 12:18:29 +0000 (13:18 +0100)]
Update to match develop to allow merge
gmungoc [Mon, 15 Jul 2019 12:17:09 +0000 (13:17 +0100)]
Update to latest to enable merge
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