gmungoc [Tue, 28 Aug 2018 15:01:52 +0000 (16:01 +0100)]
JAL-3089 safer popup menu actions on AnnotationLabels
gmungoc [Tue, 28 Aug 2018 11:32:01 +0000 (12:32 +0100)]
JAL-3055 corrections to use of AffineTransform to scale characters
hansonr [Tue, 28 Aug 2018 03:43:18 +0000 (22:43 -0500)]
Button/mouse tests
hansonr [Tue, 28 Aug 2018 03:35:35 +0000 (22:35 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 28 Aug 2018 03:34:40 +0000 (22:34 -0500)]
JAL-3026 mouse event overhaul; Jmol working (some "black label" issue?
pull, build-site
hansonr [Mon, 27 Aug 2018 16:09:53 +0000 (11:09 -0500)]
JAL-3026 alignmentFrame.statusBar.setText -> .setStatus
gmungoc [Mon, 27 Aug 2018 14:30:25 +0000 (15:30 +0100)]
JAL-3055 restore original deriveFont code for Java runtime
hansonr [Mon, 27 Aug 2018 13:39:36 +0000 (08:39 -0500)]
Bob's site directory JAL-3026
hansonr [Mon, 27 Aug 2018 08:36:29 +0000 (03:36 -0500)]
JAL-3026 Jmol functioning; some issues
Reworked mouse event handling. Temporarily lost out-of-frame business.
Or, more specifically, hovering over the scroll bar to auto-scroll.
hansonr [Fri, 24 Aug 2018 07:35:44 +0000 (02:35 -0500)]
JAL-3026 Java bug associated with File/String mods
in AlignFrame lines 4586,4592
hansonr [Fri, 24 Aug 2018 07:26:06 +0000 (02:26 -0500)]
JAL-3026 GD#107,128,130,139 build-site.xml
JInternalFrame z-order issues resolved
EBIFeching via server proxy as no access-control-origin:*
Temp file creation by File.createTempFile
Jmol app fixes for virtual key issues and starting to display now. Still
not dynamic, though. (No mouse action)
URL downloads now allow checking of status code (actually a hack, just
200 or 404, but we can get access to the real code.
hansonr [Wed, 22 Aug 2018 16:32:03 +0000 (11:32 -0500)]
JAL-3026 GD#127 frame selection/toFront
hansonr [Wed, 22 Aug 2018 10:49:20 +0000 (05:49 -0500)]
JAL-3026 JavaScript tests moved to utils/test
gmungoc [Wed, 22 Aug 2018 10:31:04 +0000 (11:31 +0100)]
JAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration
hansonr [Tue, 21 Aug 2018 19:30:23 +0000 (14:30 -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 18:36:43 +0000 (13:36 -0500)]
JAL-3026 GD #118 tooltip not showing for components.
hansonr [Tue, 21 Aug 2018 18:36:43 +0000 (13:36 -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 18:30:37 +0000 (13:30 -0500)]
JAL-3026 Boolean upgrade to Java 8
hansonr [Tue, 21 Aug 2018 18:30:37 +0000 (13:30 -0500)]
Merge branch 'Jalview-BH/JAL-3026' of
https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
Conflicts:
swingjs/SwingJS-site.zip
swingjs/timestamp
swingjs/ver/3.2.2/SwingJS-site.zip
swingjs/ver/3.2.2/timestamp
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()
git://source.jalview.org / jalview.git / log