Ben Soares [Thu, 14 Nov 2019 15:57:21 +0000 (15:57 +0000)]
JAL-3210 need this .gitignore addition for the new location of .build_properties
Ben Soares [Thu, 14 Nov 2019 15:55:35 +0000 (15:55 +0000)]
JAL-3210 .build_properties now created in /resources, which is found in Eclipse/buildship classpath. Does not affect jar build
Ben Soares [Thu, 14 Nov 2019 10:35:11 +0000 (10:35 +0000)]
JAL-3210 Auto copy j2s plugin to Eclipse IDE dropins dir. Off by default
Ben Soares [Wed, 13 Nov 2019 23:26:29 +0000 (23:26 +0000)]
JAL-3210 add more memory to javaexec running closure compiler
Ben Soares [Wed, 13 Nov 2019 22:52:42 +0000 (22:52 +0000)]
JAL-3210 task jalviewjsIDE_checkJ2sPlugin compares installed net.sf.j2s.core with version in eclipse being run
Ben Soares [Wed, 13 Nov 2019 17:10:31 +0000 (17:10 +0000)]
JAL-3210 Possibly fixed eclipse_workspace_location disappearances, again
Ben Soares [Wed, 13 Nov 2019 17:01:32 +0000 (17:01 +0000)]
JAL-3210 Improved dirs in build.gradle. Fixed _all core (added exclusions). Possibly fixed eclipse_workspace_location disappearances
soares [Tue, 12 Nov 2019 20:24:45 +0000 (20:24 +0000)]
JAL-3210 merge. j2sclasslist_jmol seems to be removed
soares [Tue, 12 Nov 2019 20:10:08 +0000 (20:10 +0000)]
JAL-3210 multiple core templates.
soares [Tue, 12 Nov 2019 18:08:59 +0000 (18:08 +0000)]
JAL-3210 multiple core templates. work in progress
soares [Tue, 12 Nov 2019 14:47:39 +0000 (14:47 +0000)]
JAL-3210 Test with coreall.z.js
gmungoc [Tue, 12 Nov 2019 08:46:32 +0000 (08:46 +0000)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
gmungoc [Tue, 12 Nov 2019 08:46:14 +0000 (08:46 +0000)]
JAL-3274 resource path correction, code tidying (constants etc)
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 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
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
git://source.jalview.org / jalview.git / log