hansonr [Tue, 3 Jul 2018 18:54:26 +0000 (19:54 +0100)]
adds log4j zip file
hansonr [Tue, 3 Jul 2018 18:30:06 +0000 (19:30 +0100)]
src2 directory added to class path, zipping/unzipping of JAR file source
JAR file source Java is in srcjar/
hansonr [Tue, 3 Jul 2018 18:16:18 +0000 (19:16 +0100)]
JAL-3026 MiGLayout-SwingJS source
hansonr [Tue, 3 Jul 2018 16:55:51 +0000 (17:55 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Tue, 3 Jul 2018 16:55:32 +0000 (17:55 +0100)]
JAL-3026 GD#91 "final" keyword deprecated
removed from FeatureTypeSettings
Jim Procter [Tue, 3 Jul 2018 16:35:51 +0000 (17:35 +0100)]
JAL-3026 workarounds and TODOs for JSplitPane setDividerLocation in SwingJS for CDS/Protein split view
Jim Procter [Tue, 3 Jul 2018 16:34:05 +0000 (17:34 +0100)]
JAL-2347 first pass at JAL-2347 - doesn’t quite work in Java or Javascript yet !
Jim Procter [Tue, 3 Jul 2018 16:30:43 +0000 (17:30 +0100)]
JAL-3048 openLinkedAlignment refactor to use dialogRunner plus a conditional callback (the default response) to process alignment data added to alignment if split frame not shown
Jim Procter [Tue, 3 Jul 2018 16:27:30 +0000 (17:27 +0100)]
JAL-3048 first pass at JvOptionDialog as property listener for dialog runner rather than Desktop.dialogdata based method
Jim Procter [Tue, 3 Jul 2018 16:26:30 +0000 (17:26 +0100)]
JAL-3048 allow a default response handler to be set
hansonr [Tue, 3 Jul 2018 15:24:48 +0000 (16:24 +0100)]
JAL-3026 varna README_SWINGJS
gmungoc [Tue, 3 Jul 2018 14:59:01 +0000 (15:59 +0100)]
JAL-3032 revised colour picker, now with ActionListener
hansonr [Tue, 3 Jul 2018 14:15:33 +0000 (15:15 +0100)]
JAL-3026 VARNA files
hansonr [Tue, 3 Jul 2018 13:52:59 +0000 (14:52 +0100)]
JAL-3026 new SwingJS-site.zip
just preliminary for editable combobox
hansonr [Tue, 3 Jul 2018 13:50:09 +0000 (14:50 +0100)]
JAL-3026 libjs and build-site.xml for updating site directory
when SwingJS-site.zip or VARNA-site.zip
hansonr [Tue, 3 Jul 2018 13:46:54 +0000 (14:46 +0100)]
JAL-3026 srcjar files for VARNA and log4j
hansonr [Tue, 3 Jul 2018 09:19:08 +0000 (10:19 +0100)]
Merge remote-tracking branch 'origin/Jalview-BH/JAL-3048_dialogs' into Jalview-BH/JAL-3026
hansonr [Tue, 3 Jul 2018 07:16:00 +0000 (08:16 +0100)]
JAL-3026 "final" removed in Desktop ; fixing #48. 80, 91, 94
new SwingJS-site.zip requires clean build
hansonr [Tue, 3 Jul 2018 03:49:42 +0000 (04:49 +0100)]
JAL-3026 SwingJS-site.zip PDF recognizes Printable.NO_SUCH_PAGE
hansonr [Mon, 2 Jul 2018 21:07:02 +0000 (22:07 +0100)]
JAL-3026 BH 7/2/2018 10:00:49 PM fix logic for FileReader for Chrome
Just bad, untested code in j2sApplet.js
hansonr [Mon, 2 Jul 2018 18:00:29 +0000 (19:00 +0100)]
JAL-3026 File...Reload working
hansonr [Mon, 2 Jul 2018 16:55:41 +0000 (17:55 +0100)]
JAL-3026 Java+JavaScript fix for GD#95
View...Features Settings... not disabled when there are no features.
Involves an anonymous subclassing of JMenu for viewMenu that checks that
there are features just before opening.
GAlignFrame, with a call into AlignFrame for checking the viewport.
hansonr [Mon, 2 Jul 2018 16:55:00 +0000 (17:55 +0100)]
JAL-3026 Java+JavaScript fix for GD#95
View...Features Settings... not disabled when there are no features.
Involves an anonymous subclassing of JMenu for viewMenu that checks that
there are features just before opening.
GAlignFrame, with a call into AlignFrame for checking the viewport.
Jim Procter [Mon, 2 Jul 2018 16:37:52 +0000 (17:37 +0100)]
JAL-3048 remove TODOs
Jim Procter [Mon, 2 Jul 2018 16:36:28 +0000 (17:36 +0100)]
JAL-3048 File->VCF load refactored
Jim Procter [Mon, 2 Jul 2018 16:36:07 +0000 (17:36 +0100)]
JAL-3048 attempt to catch Object(NaN) … probably doesn’t work!
Jim Procter [Mon, 2 Jul 2018 16:35:41 +0000 (17:35 +0100)]
JAL-3048 don’t execute dialog runner after dialog shown in js
hansonr [Mon, 2 Jul 2018 15:37:26 +0000 (16:37 +0100)]
JAL-3026 GD#75 Stockholm file load fails
Transpiler and runtime fixes for enhanced for syntax with implicit
variable type changing, boxing, and unboxing.
JavaScript alternative to using reflection method getClass().getFields()
Jim Procter [Mon, 2 Jul 2018 14:41:53 +0000 (15:41 +0100)]
Merge branch 'Jalview-BH/JAL-3026' into Jalview-BH/JAL-3048_dialogs
hansonr [Mon, 2 Jul 2018 14:40:05 +0000 (15:40 +0100)]
JAL-3026 Transpiler take 2
Jim Procter [Mon, 2 Jul 2018 14:40:01 +0000 (15:40 +0100)]
JAL-3048 todo for export SVG/PNG/EPS
Jim Procter [Mon, 2 Jul 2018 14:36:26 +0000 (15:36 +0100)]
JAL-3048 AlignFrame -> Save dialog refactored - patched ‘File exists - Overwrite ?’ dialog to be ignored in javascript
Jim Procter [Mon, 2 Jul 2018 14:34:02 +0000 (15:34 +0100)]
JAL-3048 allow a chain of responses for a particular response code (needed when intermediate dialogs are raised which determine if rest of chain executes)
hansonr [Mon, 2 Jul 2018 14:20:36 +0000 (15:20 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Mon, 2 Jul 2018 14:20:17 +0000 (15:20 +0100)]
JAL-3032 GX#75 Stockholm
transpiler and runtime
fixes for(char c : Character[] ca) and related conversion syntaxes
gmungoc [Mon, 2 Jul 2018 09:18:32 +0000 (10:18 +0100)]
JAL-3026 reinstated deleted file
hansonr [Mon, 2 Jul 2018 09:14:19 +0000 (10:14 +0100)]
JAL-3032 JTable work; JSUtil.jQuery object; drag-drop;
reflect.Constructor; adds core:"NONE" to {project}/template.html
fixes drag-drop for first call in Firefox/win
fixes java.lang.reflect.Constructor for Integer
Remove the core:"NONE" if you do not want to see all the core files
separately.
Jim Procter [Fri, 29 Jun 2018 16:14:21 +0000 (17:14 +0100)]
JAL-3048 use FileParse to transfer File to NewickFile parser
Jim Procter [Fri, 29 Jun 2018 15:39:12 +0000 (16:39 +0100)]
JAL-1551 JAL-3048 formatting
Jim Procter [Fri, 29 Jun 2018 15:38:29 +0000 (16:38 +0100)]
JAL-3048 AlignFrame->File->Load Tree adapted for js
Jim Procter [Fri, 29 Jun 2018 15:21:35 +0000 (16:21 +0100)]
JAL-3048 refactored Desktop->File->Open to use jalview.utils.dialogrunner.DialogRunner
Jim Procter [Fri, 29 Jun 2018 15:18:27 +0000 (16:18 +0100)]
JAL-3048 jalview.utils.dialogrunner.DialogRunner allows sequences of runnable methods to be sequentially triggered according to response codes from a dialog.
hansonr [Thu, 28 Jun 2018 16:19:23 +0000 (17:19 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Thu, 28 Jun 2018 16:17:38 +0000 (17:17 +0100)]
JAL-3032 JvOptionPane summary of issues with boilerplate modal dialogs.
90 cases no issue; 5 works.
Jim Procter [Thu, 28 Jun 2018 16:15:04 +0000 (17:15 +0100)]
Merge branch 'Jalview-BH/JAL-3048_dialogs' into Jalview-BH/JAL-3026
Jim Procter [Thu, 28 Jun 2018 15:53:36 +0000 (16:53 +0100)]
JAL-3026 JAL-1551 formatting
Jim Procter [Thu, 28 Jun 2018 15:52:56 +0000 (16:52 +0100)]
JAL-3048 TODOs for refactoring JalviewFileChooser pattern
JAL-3026 disable browser select dialog for default browser in javasript
Jim Procter [Thu, 28 Jun 2018 15:51:32 +0000 (16:51 +0100)]
JAL-3048 TODOs for refactoring JalviewFileChooser pattern
gmungoc [Thu, 28 Jun 2018 15:49:10 +0000 (16:49 +0100)]
JAL-3032 avoid use of lambda expression or BasicArrowButton
Jim Procter [Thu, 28 Jun 2018 15:48:06 +0000 (16:48 +0100)]
JAL-3048 todo and JAL-3026 disable VCF support
hansonr [Thu, 28 Jun 2018 13:54:21 +0000 (14:54 +0100)]
JAL-3032 SwingJS-site.zip for wrong case in filename in site/
hansonr [Thu, 28 Jun 2018 13:45:16 +0000 (14:45 +0100)]
FileAsBytes
hansonr [Thu, 28 Jun 2018 13:30:54 +0000 (14:30 +0100)]
Dialogs JAL-3032
hansonr [Thu, 28 Jun 2018 13:20:11 +0000 (14:20 +0100)]
JAL-3032 FileChooser missing correct call to JSToolkit.getFileAsBytes$
hansonr [Thu, 28 Jun 2018 07:08:42 +0000 (08:08 +0100)]
JAL-3032 GD#46 menu buttons not fully disabling
hansonr [Thu, 28 Jun 2018 06:44:22 +0000 (07:44 +0100)]
JAL-3032 fix for Array.sort
hansonr [Thu, 28 Jun 2018 05:06:49 +0000 (06:06 +0100)]
JAL-3032 GD#70 internalFrameClosed event not fired
hansonr [Thu, 28 Jun 2018 02:00:44 +0000 (03:00 +0100)]
JAL-3032 DND enabled; additional io changes for File vs. String
hansonr [Wed, 27 Jun 2018 17:33:09 +0000 (18:33 +0100)]
JAL-3032 support for JDesktop Drag and Drop
hansonr [Wed, 27 Jun 2018 14:09:25 +0000 (15:09 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Wed, 27 Jun 2018 14:08:33 +0000 (15:08 +0100)]
transpiler fix for arr[Integer]
gmungoc [Wed, 27 Jun 2018 14:05:02 +0000 (15:05 +0100)]
JAL-3032 explicit Integer.intValue() conversion for safety
hansonr [Wed, 27 Jun 2018 12:02:24 +0000 (13:02 +0100)]
JAL-3026 FileParser for JFileChooser results as ByteArrayInputStream;
does not imply text.
hansonr [Wed, 27 Jun 2018 10:26:01 +0000 (11:26 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Wed, 27 Jun 2018 10:25:33 +0000 (11:25 +0100)]
JAL-3032 just the changes pulled already
hansonr [Wed, 27 Jun 2018 10:24:43 +0000 (11:24 +0100)]
JAL-3032 Dialogs Color picker -- untested commit
hansonr [Wed, 27 Jun 2018 10:23:42 +0000 (11:23 +0100)]
JAL-3032 comments only - starting work on dialogs
hansonr [Wed, 27 Jun 2018 10:20:25 +0000 (11:20 +0100)]
JAL-3032 part2 local file reading by JFileChooser
This commit adds the ALignFrame changes for handling the
JalviewFileChooser callback.
hansonr [Wed, 27 Jun 2018 10:15:22 +0000 (11:15 +0100)]
Consensus LOGO done
hansonr [Wed, 27 Jun 2018 10:14:00 +0000 (11:14 +0100)]
Consensus LOGO done
hansonr [Wed, 27 Jun 2018 08:53:54 +0000 (09:53 +0100)]
JAL-3032 fixes missing ToolTip
Jim Procter [Wed, 27 Jun 2018 07:42:22 +0000 (08:42 +0100)]
JAL-3033 tarball from site
Jim Procter [Tue, 26 Jun 2018 17:39:35 +0000 (18:39 +0100)]
Merge branch 'develop' into Jalview-BH/JAL-3026
Jim Procter [Tue, 26 Jun 2018 17:38:03 +0000 (18:38 +0100)]
Merge branch 'task/JAL-3042_remove_SimpleDocument_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 17:37:27 +0000 (18:37 +0100)]
JAL-3042 remove mention of adjustable search box history length from docs
Jim Procter [Tue, 26 Jun 2018 14:37:38 +0000 (15:37 +0100)]
JAL-3042 don't allow user to change default history length for an input box
gmungoc [Tue, 26 Jun 2018 17:08:13 +0000 (18:08 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
Jim Procter [Tue, 26 Jun 2018 16:57:44 +0000 (17:57 +0100)]
JAL-3035 removed jdas in libs documentation and noted spring modules as candidates for removal
gmungoc [Tue, 26 Jun 2018 16:57:05 +0000 (17:57 +0100)]
JAL-3032 don't draw AlphaComposite.Clear on background
Jim Procter [Tue, 26 Jun 2018 16:55:04 +0000 (17:55 +0100)]
JAL-3033 JAL-3035 remove jdas.jar from .classpath.js
Jim Procter [Tue, 26 Jun 2018 16:08:17 +0000 (17:08 +0100)]
Merge branch 'develop' into Jalview-BH/JAL-3026
Jim Procter [Tue, 26 Jun 2018 16:07:02 +0000 (17:07 +0100)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 16:06:40 +0000 (17:06 +0100)]
JAL-3035 documentation in 2.11 release notes (and 2.11 fictional release date)
Jim Procter [Tue, 26 Jun 2018 16:06:12 +0000 (17:06 +0100)]
JAL-3035 remove DAS UI documentation
Jim Procter [Tue, 26 Jun 2018 15:40:46 +0000 (16:40 +0100)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 15:38:14 +0000 (16:38 +0100)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into Jalview-BH/JAL-3026
Jim Procter [Tue, 26 Jun 2018 15:16:15 +0000 (16:16 +0100)]
JAL-3035 - jalview-das is no more !
- jsdas lib removed
- DAS settings panel deleted (Feature settings pane has no tabs now)
- all code for wrapping DAS sources and retrieving sequences and features from them is gone
- test methods/main methods have been de-dasified or removed if their only purpose was to test DAS source discovery
- fancy sorting code to account for DAS sequence source names has been removed
Jim Procter [Tue, 26 Jun 2018 15:09:45 +0000 (16:09 +0100)]
JAL-3035 (unrelated) random XML error in nbbuild.xml
gmungoc [Tue, 26 Jun 2018 15:08:50 +0000 (16:08 +0100)]
JAL-3032 updateOverviewImage on construction
Jim Procter [Tue, 26 Jun 2018 09:29:09 +0000 (10:29 +0100)]
Merge branch 'Jalview-BH/JAL-3026' into task/JAL-3033_jalviewjs_ant
hansonr [Tue, 26 Jun 2018 09:13:07 +0000 (10:13 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
Jim Procter [Tue, 26 Jun 2018 09:13:03 +0000 (10:13 +0100)]
JAL-3033 force overwrite for .classpath from .classpath.js
hansonr [Tue, 26 Jun 2018 09:11:25 +0000 (10:11 +0100)]
synchronize fixed
Jim Procter [Tue, 26 Jun 2018 08:59:28 +0000 (09:59 +0100)]
Merge branch 'Jalview-BH/JAL-3026' into task/JAL-3033_jalviewjs_ant
Jim Procter [Tue, 26 Jun 2018 08:57:14 +0000 (09:57 +0100)]
JAL-3033 fail if the transpiler isn’t updated from swingjs/…
Jim Procter [Tue, 26 Jun 2018 08:56:51 +0000 (09:56 +0100)]
JAL-3033 local build server path for eclipse
gmungoc [Tue, 26 Jun 2018 07:50:54 +0000 (08:50 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
gmungoc [Tue, 26 Jun 2018 07:49:32 +0000 (08:49 +0100)]
JAL-3032 don't place desktop at negative x or y position
Jim Procter [Mon, 25 Jun 2018 16:03:49 +0000 (17:03 +0100)]
JAL-3033 more copy/git debugging of task
Jim Procter [Mon, 25 Jun 2018 15:53:54 +0000 (16:53 +0100)]
JAL-3033 copy the right .classpath.js !
git://source.jalview.org / jalview.git / log