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
hansonr [Thu, 5 Jul 2018 09:50:01 +0000 (10:50 +0100)]
JAL-3026 comment in main test method in PDbFtsrestClient.java
hansonr [Thu, 5 Jul 2018 09:41:47 +0000 (10:41 +0100)]
JAL-3026 renaming build-zip-jars.xml to build-libjs.xml
this file is only to be used when new jar contents are tanspiled into
JavaScript. Preferably add these to src2, compile, and remove them from
src2. This could certainly be automated.
hansonr [Thu, 5 Jul 2018 09:39:15 +0000 (10:39 +0100)]
removing temp files for build of libjs
hansonr [Thu, 5 Jul 2018 09:38:40 +0000 (10:38 +0100)]
srcjar changes for JSONParser - just 'c' |'c' workaround (not necessary
after next transpiler update
hansonr [Thu, 5 Jul 2018 09:23:26 +0000 (10:23 +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 08:52:24 +0000 (09:52 +0100)]
JAL-3058 missed refactoring of JColorChooser
hansonr [Thu, 5 Jul 2018 08:38:35 +0000 (09:38 +0100)]
Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
hansonr [Thu, 5 Jul 2018 08:35:09 +0000 (09:35 +0100)]
JAL-3026 fixes MigLayout, JSON parser
MiG layout was referencing java.beans only for serialization
JSONParser was using a bitwise syntax for char not supported in
transpiler
SwingJS jalview.javascript.web proxy for WebResources not set up
properly
- JSONParser is working
- PDB REST service call is working
- MiGLayout is loading, but is not laying out properly.
gmungoc [Thu, 5 Jul 2018 08:03:39 +0000 (09:03 +0100)]
JAL-3058 refactored raising JColorChooser for JS compatibility
gmungoc [Wed, 4 Jul 2018 14:44:56 +0000 (15:44 +0100)]
JAL-3032 JAL-3048 adjust how colour chooser is shown
hansonr [Wed, 4 Jul 2018 04:26:18 +0000 (05:26 +0100)]
try(resource), TableRowSorter
hansonr [Wed, 4 Jul 2018 03:42:41 +0000 (04:42 +0100)]
JAL-3026 implements simple REST client
new transpiler adds support for try(resource);
hansonr [Tue, 3 Jul 2018 19:16:28 +0000 (20:16 +0100)]
JAL-3026 adds org.json.simple to srcjars and jsonsimple-site.zip
hansonr [Tue, 3 Jul 2018 18:55:27 +0000 (19:55 +0100)]
SwingJS-site.zip
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)
git://source.jalview.org / jalview.git / log