Ben Soares [Tue, 12 Nov 2019 00:37:09 +0000 (00:37 +0000)]
JAL-3210 working in Eclipse improvements
Ben Soares [Mon, 11 Nov 2019 23:56:20 +0000 (23:56 +0000)]
JAL-3210 minor fix
Ben Soares [Mon, 11 Nov 2019 17:17:36 +0000 (17:17 +0000)]
JAL-3210 Better ustEclipse IDE/CLI refinements
Ben Soares [Mon, 11 Nov 2019 16:43:50 +0000 (16:43 +0000)]
JAL-3210 Better use of ext properties, no more globals, auto detect Eclipse IDE
Ben Soares [Mon, 11 Nov 2019 01:05:27 +0000 (01:05 +0000)]
Revert "JAL-3210 merging in Jalview-JS/develop"
This reverts commit
9499aed89323b8f53689d6428ffc9b32250eae6c, reversing
changes made to
fb616bbaa70ca0f8bbae7e076f3c403a737205a9.
Still not working right in Eclipse
Ben Soares [Mon, 11 Nov 2019 00:58:33 +0000 (00:58 +0000)]
JAL-3210 Moved local.properties override into ext, now picked up in Eclipse IDE
Ben Soares [Sun, 10 Nov 2019 16:33:56 +0000 (16:33 +0000)]
JAL-3210 merging in Jalview-JS/develop
Ben Soares [Sun, 10 Nov 2019 16:06:50 +0000 (16:06 +0000)]
JAL-3210 _jalview core published, added to jalviewjsTest.html
soares [Sat, 9 Nov 2019 16:43:22 +0000 (16:43 +0000)]
JAL-3210 working on dependencies for publishcoretemplate. tidying
soares [Sat, 9 Nov 2019 16:35:26 +0000 (16:35 +0000)]
JAL-3210 working on dependencies for publishcoretemplate. tidying
Ben Soares [Fri, 8 Nov 2019 17:18:05 +0000 (17:18 +0000)]
JAL-3210 PublishCoreTemplate task
Ben Soares [Fri, 8 Nov 2019 17:00:26 +0000 (17:00 +0000)]
JAL-3210 Add a local.properties ECLIPSE_IDE_DEVELOPER=true to prevent headless eclipse from running
Ben Soares [Fri, 8 Nov 2019 16:45:20 +0000 (16:45 +0000)]
JAL-3210 BuildAllCores dependencies carefully implemented so Eclipse does not call headless task
Ben Soares [Fri, 8 Nov 2019 10:20:19 +0000 (10:20 +0000)]
Revert "JAL-3210 work in progress on closures"
This reverts commit
581fcc0aab400bcdd52f5c0ec64f34a8fd5e786a.
Seems to have broken development in Eclipse IDE. Reverting.
Ben Soares [Fri, 8 Nov 2019 10:18:12 +0000 (10:18 +0000)]
Revert "JAL-3210 Added jalviewjsBuildAllClosures. Improved incrementality of jalviewjsSetEclipseWorkspace and jalviewjsProjectImport and hence jalviewjsTranspile :)"
This reverts commit
9fe5286cbcbbfdca0e9548e6ab1b6543871a8073.
Seems to have broken development in Eclipse IDE. Reverting.
Ben Soares [Fri, 8 Nov 2019 10:17:42 +0000 (10:17 +0000)]
Revert "JAL-3210 small tidies"
This reverts commit
ed512fe4ab6c8a61bbf2e3b9d2b09ea9746af78d.
Seems to have broken development in Eclipse IDE. Reverting.
Ben Soares [Fri, 8 Nov 2019 10:14:16 +0000 (10:14 +0000)]
JAL-3210 jmol, stevesoft and publish template tasks in progress
BobHanson [Thu, 7 Nov 2019 20:03:49 +0000 (14:03 -0600)]
SwingJS update adds java.awt.Taskbar (untested)
Ben Soares [Thu, 7 Nov 2019 16:52:40 +0000 (16:52 +0000)]
JAL-3210 small tidies
Ben Soares [Thu, 7 Nov 2019 15:36:48 +0000 (15:36 +0000)]
JAL-3210 Added jalviewjsBuildAllClosures. Improved incrementality of jalviewjsSetEclipseWorkspace and jalviewjsProjectImport and hence jalviewjsTranspile :)
soares [Wed, 6 Nov 2019 20:59:00 +0000 (20:59 +0000)]
JAL-3210 work in progress on closures
Ben Soares [Tue, 5 Nov 2019 23:50:35 +0000 (23:50 +0000)]
JAL-3274 .build_properties now copied to j2s in jalviewjs site
Ben Soares [Tue, 5 Nov 2019 21:44:27 +0000 (21:44 +0000)]
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build
BobHanson [Tue, 5 Nov 2019 18:38:46 +0000 (12:38 -0600)]
new transpiler - important!
fixes null pointer exception report for bad package declaration in a
Java file.
gmungoc [Tue, 5 Nov 2019 17:43:05 +0000 (17:43 +0000)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
soares [Tue, 5 Nov 2019 17:42:12 +0000 (17:42 +0000)]
Revert "JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle"
This reverts commit
aaa5f22a4544c3e72b5d29ef2f319e55af8e14f7.
gmungoc [Tue, 5 Nov 2019 17:20:59 +0000 (17:20 +0000)]
JAL-3210 JAL-3130 skip Taskbar in JalviewJS
gmungoc [Tue, 5 Nov 2019 17:19:01 +0000 (17:19 +0000)]
JAL-3210 reverted (ignore previous commit)
soares [Tue, 5 Nov 2019 17:12:14 +0000 (17:12 +0000)]
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build
gmungoc [Tue, 5 Nov 2019 17:09:20 +0000 (17:09 +0000)]
JAL-3210 JAL-3130 can't read java.specification.version in JalviewJS
gmungoc [Tue, 5 Nov 2019 17:07:33 +0000 (17:07 +0000)]
JAL-3120 JAL-3130 can't read "java.specification.version" in JalviewJS
gmungoc [Tue, 5 Nov 2019 16:46:11 +0000 (16:46 +0000)]
JAL-3210 JAL-3330 use SequenceOntologyLite in JalviewJS
soares [Tue, 5 Nov 2019 16:18:25 +0000 (16:18 +0000)]
JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle
gmungoc [Tue, 5 Nov 2019 16:02:14 +0000 (16:02 +0000)]
JAL-3210 JAL-3263 redo 'Mandarin' character for JS-develop pre-applet
Ben Soares [Mon, 4 Nov 2019 12:21:41 +0000 (12:21 +0000)]
JAL-3210 added a 'transfer' dir for unzip files to improve incremental site-building when using Eclipse as IDE
Ben Soares [Fri, 1 Nov 2019 15:21:35 +0000 (15:21 +0000)]
JAL-3474 removed all .cvsignore files stored in the repo
gmungoc [Fri, 1 Nov 2019 14:56:05 +0000 (14:56 +0000)]
JAL-3468 unit tests updated for changes
Ben Soares [Fri, 1 Nov 2019 00:57:00 +0000 (00:57 +0000)]
JAL-3210 Automatic buildship/eclipse update to site when making changes to code
Ben Soares [Thu, 31 Oct 2019 15:47:41 +0000 (15:47 +0000)]
JAL-3210 Added jdt prefs from applet branch. Made IDE tasks more visible
gmungoc [Thu, 31 Oct 2019 15:45:51 +0000 (15:45 +0000)]
JAL-3468 truncate feature description to 40 chars in tooltip/menu item
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)
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