hansonr [Tue, 21 Aug 2018 18:30:37 +0000 (13:30 -0500)]
JAL-3026 Boolean upgrade to Java 8
hansonr [Tue, 21 Aug 2018 18:21:16 +0000 (13:21 -0500)]
JAL-3026 GD#137 Boolean upgrade requires build-site.xml only
hansonr [Tue, 21 Aug 2018 18:21:16 +0000 (13:21 -0500)]
JAL-3026 GD#137 Boolean upgrade requires build-site.xml only
hansonr [Tue, 21 Aug 2018 17:15:55 +0000 (12:15 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 21 Aug 2018 17:15:08 +0000 (12:15 -0500)]
JAL-3027 GD#140 checkbox/radio text alignment not coded in
JSRadioButtonUI - requires build-site.xml
gmungoc [Tue, 21 Aug 2018 13:59:50 +0000 (14:59 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Tue, 21 Aug 2018 13:59:38 +0000 (14:59 +0100)]
JAL-3032 MCview package renamed mc_view in test classes
hansonr [Tue, 21 Aug 2018 13:00:09 +0000 (08:00 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 21 Aug 2018 12:59:38 +0000 (07:59 -0500)]
JAL-3026 fixes Jmol going into debug mode
much faster PDB file processing if it doesn't print every line as it
goes!
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names
hansonr [Tue, 21 Aug 2018 12:14:33 +0000 (07:14 -0500)]
JAL-3026 fixes ?j2strace=xxx message, user.home, error msg in
ItentifiersUrlProvider
gmungoc [Tue, 21 Aug 2018 11:16:50 +0000 (12:16 +0100)]
JAL-3032 JAL-3084 test class for JS layout bug(s)
hansonr [Tue, 21 Aug 2018 05:00:16 +0000 (00:00 -0500)]
JAL-3026 JSONObject: removing annotation sensing
hansonr [Tue, 21 Aug 2018 04:33:09 +0000 (23:33 -0500)]
swingjs.JSSAXParser working for Jalview
hansonr [Tue, 21 Aug 2018 02:12:36 +0000 (21:12 -0500)]
JAL-3026 JmolData running; new run time and transpiler.
Run build-site.xml and possibly do a clean build.
hansonr [Tue, 21 Aug 2018 02:10:41 +0000 (21:10 -0500)]
mc_view references were MCview
hansonr [Tue, 21 Aug 2018 02:09:25 +0000 (21:09 -0500)]
JAL-3026 MCview -> mc_view
SwingJS requires standard package and class capitalization;
_ added to avoid PC capitalization issue
hansonr [Mon, 20 Aug 2018 15:24:19 +0000 (10:24 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 20 Aug 2018 15:23:49 +0000 (10:23 -0500)]
JAL-3026 j2sClazz.js fixes
// BH 8/20/2018 3.2.2.04 adds character.isJavaIdentifierPart$C and
several Character...$I equivalents
// BH 8/19/2018 3.2.2.04 fixes Enum .name being .$name
// BH 8/16/2018 3.2.2.04 fixes Character.toTitleCase$C,
[Integer,Long,Short,Byte].toString(i,radix)
gmungoc [Mon, 20 Aug 2018 12:52:46 +0000 (13:52 +0100)]
JAL-3032 Feature Settings menu item always enabled (restored)
gmungoc [Mon, 20 Aug 2018 10:52:01 +0000 (11:52 +0100)]
JAL-3032 variant of Sequence Details panel for JalviewJS
gmungoc [Mon, 20 Aug 2018 09:57:09 +0000 (10:57 +0100)]
JAL-3084 force EPS output to "Text" for JalviewJS
gmungoc [Mon, 20 Aug 2018 09:32:14 +0000 (10:32 +0100)]
JAL-3084 hide startup file, Chimera, HTML/SVG, Web Services options/tab
in JalviewJS
hansonr [Mon, 20 Aug 2018 05:39:18 +0000 (00:39 -0500)]
Adds org.json (along with "org.json.simple") for
jalview.io.JSONFile.java
hansonr [Mon, 20 Aug 2018 04:23:06 +0000 (23:23 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 20 Aug 2018 04:22:24 +0000 (23:22 -0500)]
fixes for anonymous classes; preliminary Jmol classes
Problem: anonymous classes that reference superclass finals may not
escape them properly with $. (drag-drop of PDB file)
Jmol classes into libjs, but not working yet, since we need to now
distinguish between JavaScript/AWT for application and JavaScript/noAWT
for standard JSmol applet
gmungoc [Fri, 17 Aug 2018 13:57:49 +0000 (14:57 +0100)]
JAL-3048 remove obsolete way of handling dialogs in JalviewJS
gmungoc [Fri, 17 Aug 2018 13:57:12 +0000 (14:57 +0100)]
JAL-3048 adapt 'input from URL' dialog for JalviewJS
gmungoc [Fri, 17 Aug 2018 10:38:33 +0000 (11:38 +0100)]
JAL-3038 unit test updates for JalviewJS workaround hack
gmungoc [Thu, 16 Aug 2018 14:07:35 +0000 (15:07 +0100)]
JAL-3038 workaround to replace editable combobox with text field in JS
hansonr [Thu, 16 Aug 2018 13:13:45 +0000 (08:13 -0500)]
JAL-3026 Character.toUpperCase
hansonr [Thu, 16 Aug 2018 12:55:30 +0000 (07:55 -0500)]
JAL-3026 SwingJS-site.zip fix
gmungoc [Thu, 16 Aug 2018 09:08:49 +0000 (10:08 +0100)]
Merge branch 'bug/JAL-3082selectRegex' into Jalview-BH/JAL-3026
gmungoc [Thu, 16 Aug 2018 09:00:07 +0000 (10:00 +0100)]
JAL-3082 one more test condition
gmungoc [Thu, 16 Aug 2018 08:56:36 +0000 (09:56 +0100)]
JAL-3082 handle regex error, exclusive threshold, unit tests
hansonr [Thu, 16 Aug 2018 02:11:55 +0000 (21:11 -0500)]
Java2Script 3.2.2_04 fixes Clazz._exceptionOf P$ issue
gmungoc [Wed, 15 Aug 2018 11:17:27 +0000 (12:17 +0100)]
JAL-3048 use JS-compatible JvOptionPane method
gmungoc [Wed, 15 Aug 2018 10:02:47 +0000 (11:02 +0100)]
Merge branch 'feature/JAL-3080clearTreeGroups' into Jalview-BH/JAL-3026
gmungoc [Wed, 15 Aug 2018 10:01:27 +0000 (11:01 +0100)]
JAL-3080 remove tree partition if no groups created
gmungoc [Tue, 14 Aug 2018 15:55:13 +0000 (16:55 +0100)]
JAL-3078 reset Tree font (only!) on Cancel
gmungoc [Tue, 14 Aug 2018 13:04:06 +0000 (14:04 +0100)]
JAL-3032 tidy AlignmentProperties display for JalviewJS
gmungoc [Tue, 14 Aug 2018 10:04:02 +0000 (11:04 +0100)]
JAL-3056 no Save/Load colours xml in JalviewJS
hansonr [Sun, 12 Aug 2018 12:27:30 +0000 (07:27 -0500)]
JAL-3026 refines, generalizes build-site.xml
hansonr [Sun, 12 Aug 2018 12:21:37 +0000 (07:21 -0500)]
JAL-3026 refines, generalizes build-site.xml
hansonr [Sun, 12 Aug 2018 11:37:05 +0000 (06:37 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Sun, 12 Aug 2018 05:19:01 +0000 (00:19 -0500)]
Java2Script 3.2.2 upgrade
gmungoc [Thu, 26 Jul 2018 15:42:14 +0000 (16:42 +0100)]
JAL-3026 major update 1/2
- Java2Script 3.2.2 Java 8 ready
- fix for scrollbar returning 3.
99999996 instead of 4
- fix for checkboxes too low
- drop in new transpiler
- run eclipsec -clean
- run build-site.xml
gmungoc [Fri, 10 Aug 2018 15:44:24 +0000 (16:44 +0100)]
JAL-3056 suppress Lineart option in JalviewJS
gmungoc [Thu, 26 Jul 2018 15:42:14 +0000 (16:42 +0100)]
JAL-3071 turn off 'mousedDragging' when stopping scrolling
gmungoc [Thu, 26 Jul 2018 12:38:12 +0000 (13:38 +0100)]
JAL-3071 IdPanel.ScrollThread for JalviewJS, Javadoc
gmungoc [Thu, 26 Jul 2018 10:15:44 +0000 (11:15 +0100)]
JAL-3071 SeqPanel scroll thread now interruptible in JalviewJS
gmungoc [Thu, 26 Jul 2018 06:59:46 +0000 (07:59 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-3072scrollThread' into Jalview-BH/JAL-3026
gmungoc [Wed, 25 Jul 2018 16:36:13 +0000 (17:36 +0100)]
JAL-3073 select columns if dragging sideways in a graph annotation
gmungoc [Wed, 25 Jul 2018 15:41:02 +0000 (16:41 +0100)]
JAL-3074 don't scroll up/down on drag out of scale or annotation panel, performance tweaks
gmungoc [Wed, 25 Jul 2018 10:43:21 +0000 (11:43 +0100)]
JAL-3072 SeqPanel.stopScrolling on mouse up in scale or annotation panel
hansonr [Wed, 25 Jul 2018 07:11:13 +0000 (02:11 -0500)]
JAL-3026 Java 8 upgrade and JTabbedPane
hansonr [Wed, 25 Jul 2018 07:09:41 +0000 (02:09 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Wed, 25 Jul 2018 07:08:29 +0000 (02:08 -0500)]
merged
hansonr [Tue, 24 Jul 2018 11:55:10 +0000 (06:55 -0500)]
JAL-3032 minor SwingJS fixes for java.lang.reflect
adds java.lang.reflect.Field
gmungoc [Mon, 23 Jul 2018 14:47:07 +0000 (15:47 +0100)]
JAL-3056 suppress News menu item, remove unneeded j2sNative
gmungoc [Mon, 23 Jul 2018 14:44:36 +0000 (15:44 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
Jim Procter [Mon, 23 Jul 2018 14:38:56 +0000 (15:38 +0100)]
JAL-3026 JAL-3033 update classpath.js with new Jmol library version
gmungoc [Mon, 23 Jul 2018 13:42:08 +0000 (14:42 +0100)]
JAL-3056 suppress menu options, and repoint Help, for JalviewJS
hansonr [Mon, 23 Jul 2018 10:58:18 +0000 (05:58 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 23 Jul 2018 10:57:35 +0000 (05:57 -0500)]
JAL-3032 adds missing Character.valueOf(C)
gmungoc [Mon, 23 Jul 2018 10:56:11 +0000 (11:56 +0100)]
JAL-3048 javadoc and code tidy
gmungoc [Mon, 23 Jul 2018 10:54:56 +0000 (11:54 +0100)]
JAL-3048 check for headless
gmungoc [Mon, 23 Jul 2018 10:53:22 +0000 (11:53 +0100)]
JAL-3032 test updates to match change to implementation
gmungoc [Mon, 23 Jul 2018 10:19:54 +0000 (11:19 +0100)]
JAL-3049 corrected code and unit tests
gmungoc [Mon, 23 Jul 2018 09:30:26 +0000 (10:30 +0100)]
JAL-3048 all image export (alignment, tree, PCA, Jmol) now via ImageExporter and JalviewJS compatible
hansonr [Mon, 23 Jul 2018 03:57:06 +0000 (22:57 -0500)]
adds Boolean.prototype.objectValue()
hansonr [Mon, 23 Jul 2018 03:46:44 +0000 (22:46 -0500)]
MigInfo.com layout fixe (again?) libjs rebuilt
hansonr [Mon, 23 Jul 2018 03:15:05 +0000 (22:15 -0500)]
adds java.util.ComparableTimSort
hansonr [Mon, 23 Jul 2018 03:05:21 +0000 (22:05 -0500)]
Jal-3032 adds Font.getPSName()
hansonr [Sun, 22 Jul 2018 22:58:16 +0000 (17:58 -0500)]
JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory
probably should put .gitignore on src2. Sorry about that.
hansonr [Sun, 22 Jul 2018 22:27:03 +0000 (17:27 -0500)]
allows for null Jmol viewer
hansonr [Sun, 22 Jul 2018 19:56:56 +0000 (14:56 -0500)]
JAL-3032 Jmol upgrade org.jmol.java.BS -> javajs.util.BS
hansonr [Sun, 22 Jul 2018 19:44:06 +0000 (14:44 -0500)]
JAL-3026 upgrades Jmol to 14.29.17 for Java.
hansonr [Sun, 22 Jul 2018 19:09:20 +0000 (14:09 -0500)]
JAL-3026 Transpiler fix for GD#75 stockholm
hansonr [Sun, 22 Jul 2018 18:11:46 +0000 (13:11 -0500)]
PAL-3026 missing vertical numbers for wrapped pane
hansonr [Sun, 22 Jul 2018 12:39:06 +0000 (07:39 -0500)]
JAL-3026 scrollbar fix GD#, not compiling on Mac issue
hansonr [Fri, 20 Jul 2018 18:43:31 +0000 (13:43 -0500)]
PAL-3026 Java 8 stream fix for
.stream().filter().map().sorted().forEach()
hansonr [Fri, 20 Jul 2018 16:56:00 +0000 (11:56 -0500)]
adds README for srcjar directory
hansonr [Fri, 20 Jul 2018 16:51:55 +0000 (11:51 -0500)]
adds comment
hansonr [Fri, 20 Jul 2018 16:51:46 +0000 (11:51 -0500)]
JAL-3032 moving Mungo's original JalviewJS.java out of src
adding unused/ for legacy reference.
hansonr [Fri, 20 Jul 2018 16:47:58 +0000 (11:47 -0500)]
JAL-3032 adds Java 8 functionality (2/2)
the "::" operator
lambda expressions
java.util.function.*
java.util.stream.*
default methods in interfaces
hansonr [Fri, 20 Jul 2018 16:47:31 +0000 (11:47 -0500)]
JAL-3032 adds Java 8 functionality (1/2)
the "::" operator
lambda expressions
java.util.function.*
java.util.stream.*
default methods in interfaces
gmungoc [Fri, 20 Jul 2018 10:15:20 +0000 (11:15 +0100)]
JAL-3048 test updated for AlignExportSettings changes
gmungoc [Fri, 20 Jul 2018 10:04:30 +0000 (11:04 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Fri, 20 Jul 2018 10:04:19 +0000 (11:04 +0100)]
JAL-3048 JalviewJS compliant use of LineartOptions dialog
gmungoc [Fri, 20 Jul 2018 10:03:31 +0000 (11:03 +0100)]
JAL-3048 revised AlignExportSettings dialog with response action
Jim Procter [Thu, 19 Jul 2018 15:40:18 +0000 (16:40 +0100)]
Merge branch 'develop' into Jalview-BH/JAL-3026
Jim Procter [Thu, 19 Jul 2018 15:37:40 +0000 (16:37 +0100)]
Merge branch 'task/JAL-3047_clovercoverage' into develop
Jim Procter [Thu, 19 Jul 2018 15:36:30 +0000 (16:36 +0100)]
JAL-3047 don't set classes unconditionally (forgot to delete it in earlier patch)
gmungoc [Thu, 19 Jul 2018 10:46:04 +0000 (11:46 +0100)]
JAL-3048 inlined 1-line methods, small refactor of ImageMaker.TYPE
gmungoc [Thu, 19 Jul 2018 10:42:59 +0000 (11:42 +0100)]
JAL-3048 revert saveAs action so it works in Javascript too
Jim Procter [Wed, 18 Jul 2018 16:23:17 +0000 (17:23 +0100)]
JAL-3026 updated featurecolourtooltip method signature in tests
Jim Procter [Wed, 18 Jul 2018 16:22:58 +0000 (17:22 +0100)]
JAL-3048 JAL-1353 bug demo update for refactored edit name dialog
Jim Procter [Wed, 18 Jul 2018 16:22:09 +0000 (17:22 +0100)]
JAL-3048 update tests for alignment export bean refactoring
Jim Procter [Wed, 18 Jul 2018 16:21:52 +0000 (17:21 +0100)]
JAL-3048 add additional wrapper methods for JOptionPane to ensure JvOptionPane tests can run unattended
git://source.jalview.org / jalview.git / log