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
Jim Procter [Wed, 18 Jul 2018 16:20:36 +0000 (17:20 +0100)]
JAL-3048 test for successful save with refactored saveAlignment method
Jim Procter [Wed, 18 Jul 2018 14:40:55 +0000 (15:40 +0100)]
Merge branch 'develop' into Jalview-BH/JAL-3026
clover artefacts added to gitignore. nb - .classpath is now ignored - may need to be redacted
Jim Procter [Wed, 18 Jul 2018 13:33:57 +0000 (14:33 +0100)]
JAL-3033 clean eclipse log before each new js-build
Jim Procter [Wed, 18 Jul 2018 13:30:44 +0000 (14:30 +0100)]
JAL-3033 clean the site directory before compilation in eclipse
Jim Procter [Wed, 18 Jul 2018 13:25:57 +0000 (14:25 +0100)]
JAL-3033 echo eclipse log to stdout for buildlog
gmungoc [Tue, 17 Jul 2018 15:44:24 +0000 (16:44 +0100)]
JAL-3068 LineartOptions for EPS/HTML/SVG, new preferences, i18n
gmungoc [Tue, 17 Jul 2018 07:46:10 +0000 (08:46 +0100)]
Revert "Revert "JAL-3032 net.sf.j2s.core_3.2.1 upgrade""
This reverts commit
75ce39c3308a69bafc2e7c5514e44de22dd3d6f0.
gmungoc [Mon, 16 Jul 2018 14:55:06 +0000 (15:55 +0100)]
JAL-3060 tidy Cancel dialog action handler code
gmungoc [Mon, 16 Jul 2018 13:57:57 +0000 (14:57 +0100)]
Revert "JAL-3032 net.sf.j2s.core_3.2.1 upgrade"
This reverts commit
c9810b8cc443bd2ccd8c42b7318c68f6ae463f47.
gmungoc [Mon, 16 Jul 2018 11:23:14 +0000 (12:23 +0100)]
JAL-3060 more extensive extract method refactoring of FeatureEditor
hansonr [Sat, 14 Jul 2018 14:51:03 +0000 (15:51 +0100)]
JAL-3032 net.sf.j2s.core_3.2.1 upgrade
- project build command back to org.eclipse.jdt.core.javabuilder
- uses JDT CompilationParticipant extension instead of a massive
specialized builder
- solves the Eclipse Photon (non)incremental build problem
- stamps transpiler version into trailer on each .js file
- best (but not critical) to use -clean option when starting Eclipse
after adding this new version of the transpiler.
Jim Procter [Thu, 12 Jul 2018 13:17:13 +0000 (14:17 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 11 Jul 2018 19:39:49 +0000 (20:39 +0100)]
JAL-3026 JLabel for SequenceFeature details in jalview-js
Jim Procter [Wed, 11 Jul 2018 19:39:10 +0000 (20:39 +0100)]
JAL-3026 JLabel for alignment properties in jalview-js
Jim Procter [Wed, 11 Jul 2018 13:50:07 +0000 (14:50 +0100)]
Merge branch 'Jalview-BH/JAL-3048_exportSettingsrefactor' into Jalview-BH/JAL-3026
Jim Procter [Wed, 11 Jul 2018 12:27:39 +0000 (13:27 +0100)]
JAL-1551 formatting
Jim Procter [Wed, 11 Jul 2018 12:25:36 +0000 (13:25 +0100)]
JAL-3048 refactored export settings to bean+dialog with callbacks - basically works but could do with more cleanup
admin [Tue, 10 Jul 2018 18:36:47 +0000 (19:36 +0100)]
JAL-3026 BH back online
Jim Procter [Tue, 10 Jul 2018 16:46:25 +0000 (17:46 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of source.jalview.org/git/jalview into Jalview-BH/JAL-3026
Jim Procter [Tue, 10 Jul 2018 16:44:40 +0000 (17:44 +0100)]
JAL-3026 j2sNative fix for About.. panel/splashscreen : use JLabel rather than JTextPane and use <img> tag rather than mediaTracker to display jalview logo in about pane.
gmungoc [Tue, 10 Jul 2018 14:01:34 +0000 (15:01 +0100)]
JAL-3048 obsolete method deleted
gmungoc [Tue, 10 Jul 2018 14:01:18 +0000 (15:01 +0100)]
JAL-3048 code reordered for JalviewJS compliance
Jim Procter [Tue, 10 Jul 2018 11:53:51 +0000 (12:53 +0100)]
JAL-3048 switch from 'dialogdata' to DialogRunner for load Features/Annotations/Otherdata (also needed File object passed through directly)
gmungoc [Tue, 10 Jul 2018 10:58:14 +0000 (11:58 +0100)]
JAL-3048 adapt Cancel and refresh for JalviewJS
Jim Procter [Tue, 10 Jul 2018 10:51:54 +0000 (11:51 +0100)]
JAL-3033 unpack SwingJS last to ensure we always have the latest version of SwingJS in site/swingjs
gmungoc [Mon, 9 Jul 2018 19:03:03 +0000 (20:03 +0100)]
JAL-3048 EditNameDialog modified for JalviewJS (layout, i18n)
gmungoc [Mon, 9 Jul 2018 14:57:30 +0000 (15:57 +0100)]
JAL-3032 BorderLayout renders panel correctly in JalviewJS
gmungoc [Mon, 9 Jul 2018 14:11:40 +0000 (15:11 +0100)]
JAL-1858 separate method highlightSearchResults with fastPaint
gmungoc [Mon, 9 Jul 2018 12:55:48 +0000 (13:55 +0100)]
JAL-3048 _no_ fastPaint when higlighting features, ever
gmungoc [Mon, 9 Jul 2018 12:41:12 +0000 (13:41 +0100)]
JAL-3060 entry points for createFeatures, amendFeatures
gmungoc [Mon, 9 Jul 2018 11:34:22 +0000 (12:34 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Mon, 9 Jul 2018 11:21:58 +0000 (12:21 +0100)]
JAL-3060 extract FeatureEditor class
Jim Procter [Mon, 9 Jul 2018 10:19:28 +0000 (11:19 +0100)]
JAL-3026 'dropins' !
Jim Procter [Mon, 9 Jul 2018 10:16:41 +0000 (11:16 +0100)]
JAL-3026 update README with instructions on setting up Eclipse for java2script and running unzip-to-site to update the site directory after a build.
gmungoc [Mon, 9 Jul 2018 08:33:39 +0000 (09:33 +0100)]
JAL-3058 save modified colour from dialog
Jim Procter [Sun, 8 Jul 2018 11:55:07 +0000 (12:55 +0100)]
JAL-3033 hard reset to clean eclipse workspace before checking out
Jim Procter [Fri, 6 Jul 2018 14:06:01 +0000 (15:06 +0100)]
JAL-3026 unzip-to-site ant task to just update site (swingjs, jslibs, examples and resources)
Jim Procter [Fri, 6 Jul 2018 13:35:51 +0000 (14:35 +0100)]
JAL-3048 remove copied todo
Jim Procter [Fri, 6 Jul 2018 13:32:59 +0000 (14:32 +0100)]
JAL-3048 amendFeatures as dialog runner - repaint after amend not always reliable
Jim Procter [Fri, 6 Jul 2018 13:32:07 +0000 (14:32 +0100)]
JAL-3048 internalDialog with dialogRunner
Jim Procter [Fri, 6 Jul 2018 13:29:34 +0000 (14:29 +0100)]
JAL-3048 internalDialog with dialogRunner
gmungoc [Fri, 6 Jul 2018 11:31:08 +0000 (12:31 +0100)]
JAL-3059 use the right colour for group border
gmungoc [Fri, 6 Jul 2018 09:55:46 +0000 (10:55 +0100)]
JAL-3054 small y-overlap of tooltip and cell leads the eye better
gmungoc [Fri, 6 Jul 2018 09:49:56 +0000 (10:49 +0100)]
JAL-3032 register JTable with ToolTipManager
gmungoc [Fri, 6 Jul 2018 09:41:57 +0000 (10:41 +0100)]
Merge branch 'bug/JAL-3049colourCellTooltip' into Jalview-BH/JAL-3026
gmungoc [Fri, 6 Jul 2018 09:05:43 +0000 (10:05 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Fri, 6 Jul 2018 08:39:49 +0000 (09:39 +0100)]
JAL-3032 use Math.min/max not Float.min/max
hansonr [Fri, 6 Jul 2018 07:59:03 +0000 (08:59 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Fri, 6 Jul 2018 07:58:29 +0000 (08:58 +0100)]
JAL-3026 all tabbed panes use JavaScript option
jalview.jbui.swing.JTabbedPane
Jim Procter [Thu, 5 Jul 2018 13:38:42 +0000 (14:38 +0100)]
JAL-2808 JAL-3026 deleted all commented out tab code from the dialog
gmungoc [Thu, 5 Jul 2018 13:27:44 +0000 (14:27 +0100)]
JAL-2808 JAL-3032 drop tabbed layout for Colours and Filters
gmungoc [Thu, 5 Jul 2018 11:09:24 +0000 (12:09 +0100)]
JAL-3058 colour button / menu option use JalviewColourChooser
gmungoc [Thu, 5 Jul 2018 10:38:38 +0000 (11:38 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Thu, 5 Jul 2018 10:38:26 +0000 (11:38 +0100)]
JAL-2808 JAL-3058 code tidy for compiler warnings, column constants
hansonr [Thu, 5 Jul 2018 10:20:39 +0000 (11:20 +0100)]
JAL-3026 moves javajs to srcjars
- important because Java is using older code from the Jmol jar file
git://source.jalview.org / jalview.git / log