Ben Soares [Thu, 31 Oct 2019 14:18:48 +0000 (14:18 +0000)]
JAL-3473 Checked value of def and min. Set def to min if lower than min.
Ben Soares [Thu, 31 Oct 2019 10:56:56 +0000 (10:56 +0000)]
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build
Ben Soares [Thu, 31 Oct 2019 10:55:34 +0000 (10:55 +0000)]
JAL-3210 unimportant error message
BobHanson [Wed, 30 Oct 2019 19:53:56 +0000 (14:53 -0500)]
JAL-3210 new transpiler fixes problem that it could have a null-pointer
exception for comparison to history, where, apparently,
IProject.getProject().getLocation() is null.
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)
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
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
gmungoc [Fri, 23 Aug 2019 14:38:29 +0000 (15:38 +0100)]
JAL-3141 correct cast of spinner value
gmungoc [Thu, 22 Aug 2019 15:06:05 +0000 (16:06 +0100)]
JAL-3187 case-insensitive codon variant calculation
gmungoc [Wed, 21 Aug 2019 16:01:52 +0000 (17:01 +0100)]
JAL-3187 minor code tidying, todo removal
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
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
Jim Procter [Thu, 4 Jul 2019 15:33:48 +0000 (16:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 4 Jul 2019 15:31:47 +0000 (16:31 +0100)]
JAL-3337 round-and-round the process source files again
Jim Procter [Thu, 4 Jul 2019 15:23:16 +0000 (16:23 +0100)]
JAL-3337 more includes and excludes
Jim Procter [Thu, 4 Jul 2019 14:52:05 +0000 (15:52 +0100)]
JAL-3337 remove the old lib directory !
Jim Procter [Thu, 4 Jul 2019 14:51:28 +0000 (15:51 +0100)]
JAL-3337 rejig the source distribution generation to process and replace tokens in source files
Jim Procter [Thu, 4 Jul 2019 14:36:07 +0000 (15:36 +0100)]
JAL-3111 replace year in header for help pages and put processed help in build/distributions
Ben Soares [Thu, 4 Jul 2019 13:43:47 +0000 (14:43 +0100)]
JAL-3225 try/catch for non-deprecated/deprecated property in sourceDist which is not available on older eclipses
Ben Soares [Thu, 4 Jul 2019 13:16:14 +0000 (14:16 +0100)]
JAL-3353 Change to build.gradle to use the file:// enabled getdown-launcher-local.jar for LOCAL and ARCHIVELOCAL builds only. Otherwise the getdown-launcher.jar (with no local file enabled) will be used
gmungoc [Thu, 4 Jul 2019 12:09:21 +0000 (13:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jul 2019 12:09:13 +0000 (13:09 +0100)]
JAL-3111 help pages minor corrections
Ben Soares [Thu, 4 Jul 2019 11:26:37 +0000 (12:26 +0100)]
JAL-3348 fixed an internal href in help to allow building
git://source.jalview.org / jalview.git / log