hansonr [Wed, 31 Jul 2019 23:50:23 +0000 (18:50 -0500)]
JAL-3253 adds simple stacktrace debugging
hansonr [Tue, 30 Jul 2019 19:39:06 +0000 (14:39 -0500)]
JAL-3253-applet SwingJS-site.zip
- improves String.toCharArray$()
- speeds processing by a factor of 3-10 just by using split("") followed
by streamlined array typing.
hansonr [Tue, 30 Jul 2019 19:24:22 +0000 (14:24 -0500)]
JAL-3383 unneeded change
hansonr [Tue, 30 Jul 2019 18:09:40 +0000 (13:09 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Mon, 29 Jul 2019 21:05:34 +0000 (16:05 -0500)]
JAL-3253-applet JAL-3383
Significant improvement to Overview rendering. See JAL-3383 issue for
details.
hansonr [Mon, 29 Jul 2019 21:05:34 +0000 (16:05 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Mon, 29 Jul 2019 20:34:41 +0000 (15:34 -0500)]
JAL-3383 JAL-3253-applet removes unnecessary updateOverviewImage()
hansonr [Mon, 29 Jul 2019 20:34:41 +0000 (15:34 -0500)]
JAL-3383 JAL-3253-applet Allows for possibility of a sequence caching
its colors for speed; not implemented
hansonr [Mon, 29 Jul 2019 20:33:47 +0000 (15:33 -0500)]
JAL-3383 JAL-3253-applet ScalePanel bug -- should not have to cause an
AlignmentPanel repaint as a result of an Overview range change.
hansonr [Mon, 29 Jul 2019 20:32:06 +0000 (15:32 -0500)]
JAL-3383 JAL-3253-applet FeatureColourFinder avoiding unnec. creation of
image graphics
hansonr [Mon, 29 Jul 2019 20:30:34 +0000 (15:30 -0500)]
JAL-3383 JAL-3253-applet bug in FontChooser calls for full redraw;
should be just a new box.
hansonr [Mon, 29 Jul 2019 20:29:36 +0000 (15:29 -0500)]
JAL-3383 JAL-3253-applet Java8 switches to clarify ViewportRanges
listeners
hansonr [Mon, 29 Jul 2019 20:24:46 +0000 (15:24 -0500)]
JAL-3369 JAL-3253-applet adds embedded dim checking for overview frame
hansonr [Mon, 29 Jul 2019 20:14:51 +0000 (15:14 -0500)]
JAL-3369 JAL-3253-applet adds JS app.showOverview()
hansonr [Mon, 29 Jul 2019 20:09:16 +0000 (15:09 -0500)]
JAL-3387 no-annotation too early
hansonr [Mon, 29 Jul 2019 08:34:57 +0000 (10:34 +0200)]
JAL-3380 allows JalviewJS to get embedded div attributes
hansonr [Mon, 29 Jul 2019 08:31:05 +0000 (10:31 +0200)]
JAL-3379 Javascript applet.app
hansonr [Mon, 29 Jul 2019 08:21:53 +0000 (10:21 +0200)]
JAL-3778 moving Java logging to Platform.
hansonr [Wed, 24 Jul 2019 06:42:25 +0000 (07:42 +0100)]
JAL-3253-applet adds NOMENUBAR, NOSTATUS, NOCALCULATION, SHOWOVERVIEW
adds "overview" name for overview panel.
hansonr [Wed, 24 Jul 2019 05:31:01 +0000 (06:31 +0100)]
JAL-3374 "noannotation" and menu sync
hansonr [Wed, 24 Jul 2019 04:25:57 +0000 (05:25 +0100)]
issue JAL-3373, JAL-3253-applet SwingJS update
sticky tooltip over menu items
hansonr [Fri, 19 Jul 2019 09:13:14 +0000 (10:13 +0100)]
new SwingJS-site.zip fixes menu persistence issues
hansonr [Fri, 19 Jul 2019 09:12:41 +0000 (10:12 +0100)]
JAL-3253 embedded example1
hansonr [Thu, 18 Jul 2019 07:47:10 +0000 (08:47 +0100)]
JAL-3269 ready for testing embedded interface
hansonr [Thu, 18 Jul 2019 06:22:15 +0000 (07:22 +0100)]
JAL-3370 sep ignored in getAlignmentOrderFrom(AlignFrameI alf, String
sep)
hansonr [Thu, 18 Jul 2019 06:15:38 +0000 (07:15 +0100)]
JAL-3269 JAL-3370 JalviewJS interface upgrade
hansonr [Tue, 16 Jul 2019 21:48:23 +0000 (22:48 +0100)]
minor fixes for JComboBox and also fixes issue with menu accelerator
(ESC in this case) not triggered when a non-key-active component has the
focus. (A result of focus traversal now working, with default focus
gained initially.) Upgrade of JTextPane and JEditorPane, but these are
not used in Jalview. Still issues there.
hansonr [Tue, 16 Jul 2019 21:46:06 +0000 (22:46 +0100)]
issue JAL-3368 and JAL-3253-applet
Color names not supported.
gmungoc [Mon, 15 Jul 2019 12:12:47 +0000 (13:12 +0100)]
JAL-3032 fine tuning appearance of button
gmungoc [Mon, 15 Jul 2019 10:49:13 +0000 (11:49 +0100)]
JAL-3345 small tidying
hansonr [Fri, 12 Jul 2019 07:02:25 +0000 (08:02 +0100)]
JAL-3366 JAL-3253-applet
adds RendererPanel default inner size.
hansonr [Wed, 10 Jul 2019 11:24:15 +0000 (12:24 +0100)]
2/2 JAL-3253-applet several fixes in SwingJS only:
JAL-3357 multiline HTML tooltips not wrapping
JAL-3358 tooltips in ComboBoxes
JAL-3359 custom ComboBoxes with detailed event callbacks
adds ToolTip for Search...Find; not perfect.
hansonr [Wed, 10 Jul 2019 08:59:06 +0000 (09:59 +0100)]
1/2 JAL-3253-applet several fixes in SwingJS only:
JAL-3357 multiline HTML tooltips not wrapping
JAL-3358 tooltips in ComboBoxes
JAL-3359 custom ComboBoxes with detailed event callbacks
hansonr [Wed, 10 Jul 2019 08:55:53 +0000 (09:55 +0100)]
JAL-3253-applet JAL-3360 HTML tooltips not trimming properly; need <div>
for sizing in JavaScript
hansonr [Wed, 10 Jul 2019 08:53:56 +0000 (09:53 +0100)]
JAL-3253-applet minor fix to reduce number of times cell renderer is
fired.
hansonr [Tue, 9 Jul 2019 15:19:43 +0000 (16:19 +0100)]
Jal-3357 ISSUE JAL-3253-applet tooltip for PHOSPHORYLATION missing
hansonr [Thu, 4 Jul 2019 16:15:35 +0000 (17:15 +0100)]
JAL-3354 key listener issue JS#213,215
hansonr [Wed, 3 Jul 2019 09:35:29 +0000 (10:35 +0100)]
fixing failure issue in build server
hansonr [Wed, 3 Jul 2019 09:34:44 +0000 (10:34 +0100)]
temp only
hansonr [Tue, 2 Jul 2019 18:34:22 +0000 (20:34 +0200)]
JAL-3346 JAL-3253-applet JS Code issue 131 Carried forward - no
mouseExited in ScalePanel on mouse drag out and right over SeqPanel
border
hansonr [Tue, 2 Jul 2019 18:27:13 +0000 (20:27 +0200)]
JAL-3345 JAL3253 Smoother ScalePanel-based scrolling
hansonr [Tue, 2 Jul 2019 13:31:52 +0000 (15:31 +0200)]
JAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip
hansonr [Tue, 2 Jul 2019 13:29:54 +0000 (15:29 +0200)]
JAL-3253 srcjar_unused/ moved to unused/
hansonr [Tue, 2 Jul 2019 12:35:57 +0000 (14:35 +0200)]
SwingJS-site.zip update after Wuppertal.
hansonr [Tue, 2 Jul 2019 12:35:33 +0000 (14:35 +0200)]
JAL-3253 FeatureTypeSettings use of override paint(g) for "x" button
allows same characterists in Mac and Windows for button background and
border
hansonr [Tue, 2 Jul 2019 12:34:02 +0000 (14:34 +0200)]
JAL-3253 AlignmentPanel opaque white may provide white earlier?
hansonr [Tue, 2 Jul 2019 12:32:19 +0000 (14:32 +0200)]
JAL-3253 simpler coding using MouseAdapter. Using JLabel.setOpaque(true)
to minimize unnecessary layout of status label.
hansonr [Tue, 2 Jul 2019 12:30:50 +0000 (14:30 +0200)]
JAL-3253 Jalview2XML minor recoding; suggesting InvokeLater rather than
InvokeAndWait to allow some asynchronous updating
hansonr [Tue, 2 Jul 2019 12:14:13 +0000 (14:14 +0200)]
new _j2sclasslist.txt for tab-focus
hansonr [Thu, 23 May 2019 01:05:38 +0000 (20:05 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Wed, 22 May 2019 13:15:03 +0000 (08:15 -0500)]
Jalview-JS/JAL-3253-applet newick Regex coding error fix JAL-3271
hansonr [Wed, 22 May 2019 13:15:03 +0000 (08:15 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of
https://source.jalview.org/git/jalview.git into
Jalview-JS/JAL-3253-applet
Conflicts:
src/jalview/project/Jalview2XML.java
hansonr [Wed, 22 May 2019 08:29:07 +0000 (03:29 -0500)]
Jalview-JS/JAL-3253-applet also comments relating to JAL-3268
hansonr [Wed, 22 May 2019 08:29:07 +0000 (03:29 -0500)]
Jalview-JS/JAL-3253-applet fix for original desktop, centralizing regex
and loadStaticResource
hansonr [Tue, 21 May 2019 11:56:04 +0000 (06:56 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
gmungoc [Tue, 21 May 2019 10:29:59 +0000 (11:29 +0100)]
JAL-3253-applet disabling button size setting by applet param. Whatever
this should do in Java, it doesn't seem to do, and it looks better in
JavaScript just to let the button set its own size.
gmungoc [Tue, 21 May 2019 10:29:59 +0000 (11:29 +0100)]
JAL-3253 code tidies and tweaks to Desktop
gmungoc [Mon, 20 May 2019 11:10:33 +0000 (12:10 +0100)]
JAL-2176 unused MenuChooser removed
hansonr [Sun, 19 May 2019 05:24:48 +0000 (00:24 -0500)]
Jalview-JS/JAL-3253-applet JAL-3192 secondary core files
buildcore now creates core_stevesoft (350K uncompressed) and core_jvjmol
(2.9M uncompressed)
Still needs some tweaking, but the process is relatively
straightforward:
1) To know what files to include, make sure you are using the core
version of the html file, and, after exercizing the program, issue:
J2S._saveFile('_j2sclasslist.txt',
Clazz.ClassFilesLoaded.sort().join('\n'))
(Sorry, I could make that simpler, I know.)
2) add a section in buildcore.xml that concatenates the desired file set
and turns that into a core file.
3) in the FIRST class loaded for this option, add something like this
static block:
static
{
/**
* This is the entry class. Load the core file directly, if it
exists. See
* buildcore.xml.
*
*
* @j2sNative
*
* swingjs.JSUtil.loadStaticResource$S("core/core_stevesoft.z.js");
*/
}
3) run buildcore.xml
2)
hansonr [Sun, 19 May 2019 04:27:59 +0000 (23:27 -0500)]
Jalview-JS/JAL-3253-applet core file comment -- Regex() call
hansonr [Sun, 19 May 2019 03:35:43 +0000 (22:35 -0500)]
Jalview-JS/JAL-3253-applet Creating
site/swingjs/j2s/com/stevesoft/core.js
Applying a simple trick to use a custom core file.
1) In buildcore.xml:
<!-- concatentate the stevesoft files -->
<concat destfile="${site.path}/j2s/com/stevesoft/core.js">
<fileset dir="${site.path}/j2s/com/stevesoft">
<include name="**/*.js" />
<exclude name="core.js" />
<exclude name="Regex.js" />
</fileset>
</concat>
<antcall target="call-core">
<param name="call-core.name" value="_stevesoft" />
<param name="call-core.list" value="com/stevesoft/core.js" />
</antcall>
2) In com/stevesoft, add a line that loads j2s/core/core_stevesoft.z.js
static
{
/**
* @j2sNative
*
* swingjs.JSUtil.loadStaticResource$S("core/core_stevesoft.z.js");
*/
}
hansonr [Sun, 19 May 2019 03:35:43 +0000 (22:35 -0500)]
Jalview-JS/JAL-3253-applet SwingJS-site.zip update
hansonr [Sun, 19 May 2019 03:35:12 +0000 (22:35 -0500)]
Jalview-JS/JAL-3253-applet update for core_jalview
hansonr [Sun, 19 May 2019 03:34:19 +0000 (22:34 -0500)]
Jalview-JS/JAL-3253-applet adds AlignFrameI empty interface to allow
JalviewLiteJSApi to serve with jalview.gui.AppletFrame as well as
jalview.appletgui.AppletFrame.
hansonr [Sat, 18 May 2019 22:27:10 +0000 (17:27 -0500)]
Jalview-JS/JAL-3253-applet fixes SwingJS-zip.js issue with frames
disappearing
In swingjs/plaf/JSFrameUI, "Desktop" should be "DesktopPane"
hansonr [Sat, 18 May 2019 06:16:14 +0000 (01:16 -0500)]
Jalview-JS/JAL-3253-applet adds shell JalviewJSApi methods to Jalview
A starting point for introducing a JavaScript API for Jalview.
JalviewApplet.js now automatically creates a "LiveConnect-like" set
of unqualified methods when the main class has a getInstance()
method, using reflection to get that instance's method list and
then using that list to create an interface that allows
overloading of methods (as long as they have a different arity.
So, for example, if Jalview is started as the "jalview1" applet
(using the <applet> or <jvapplet> tag), then we have:
Jalview1.setSelectionListener(alignFrame, listener)
Jalview1.setSelectionListener(listener)
and about 50 other methods.
To keep this simple, all methods that are not private, not
static, and that do not start with $ are included in the interface.
hansonr [Fri, 17 May 2019 18:45:28 +0000 (13:45 -0500)]
Jalview-JS/JAL-3253-applet more argument parsing
trying to simplify the sourcing of parametric data:
applet origin: <applet><param>
application origin: Info.args
preference file origin: Info.XXXX_YYYY
Close to full implementation of all three.
Next: Moving Jalview API to a jointly accessible class for Jalview(JS) and JalviewLite (deprecated, but still there).
hansonr [Fri, 17 May 2019 18:41:49 +0000 (13:41 -0500)]
Jalview-JS/JAL-3253-applet more argument parsing
allows for web component <jvapplet> as well as deprecated <applet>
adds applets-nocore.html for testing;
sets applets.html to be with core loading, for demo.
hansonr [Fri, 17 May 2019 13:26:33 +0000 (08:26 -0500)]
Jalview-JS/JAL-3253-applet additional static final preferences
hansonr [Fri, 17 May 2019 12:22:49 +0000 (07:22 -0500)]
Jalview-JS/JAL-3253-applet additional static final preferences
Consolidates UserDefinedColours.USER_DEFINED_COLOURS and
Preferences.USER_DEFINED_COLOURS
hansonr [Fri, 17 May 2019 04:59:29 +0000 (23:59 -0500)]
Jalview-JS/JAL-3253-applet adding more applet parameters and setting
more static final constants
Three types of parameters are being read:
1. Property file values, from Info.Jalview_XXX_XXXX:
Info.Jalview_ENABLE_SPLIT_FRAME = true;
2. Applet parameters:
<applet><param name="enableSplitPane" value="true">...</applet>
3. Jalview Command-line parameters:
Info.args='open "xxxxx.fa" ....'
hansonr [Thu, 16 May 2019 19:54:27 +0000 (14:54 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Thu, 16 May 2019 18:32:18 +0000 (13:32 -0500)]
Jalview-JS/JAL-3253-applet JAL-3266 Varna fix.
For some reason, the JPopupMenu was being added to the JPanel with
Component.add(), and then removed with Component.removeAll()
-- during the painting process. This caused it to appear on the
window as its unstyled <ul><li>... list.
Also, during painting, Component.setBackground() was being set.
This is very nonstandard and cannot be recommended.
I am surprised it works in Java.
Working now in JavaScript. Export to SVG and PNG are very nice!
hansonr [Thu, 16 May 2019 18:32:18 +0000 (13:32 -0500)]
Jalview-JS/JAL-3253-applet JAL-3267 URLConnection POST option broken in
SwingJS
hansonr [Thu, 16 May 2019 16:00:25 +0000 (11:00 -0500)]
Jalview-JS/JAL-3253-applet SwingJS upgrade for case-insensitive Applet
parameters
hansonr [Thu, 16 May 2019 15:59:35 +0000 (10:59 -0500)]
Jalview-JS/JAL-3253 applet param PDBFILE
hansonr [Thu, 16 May 2019 15:58:25 +0000 (10:58 -0500)]
Jalview-JS/JAL-3253 allow for dialog-free StructureViewer launch
hansonr [Thu, 16 May 2019 15:57:34 +0000 (10:57 -0500)]
Jalview-JS/JAL-3253 honor Applet param case insensitive
hansonr [Thu, 16 May 2019 15:56:32 +0000 (10:56 -0500)]
Jalview-JS/JAL-3253 applet param GROUPS
hansonr [Thu, 16 May 2019 05:17:03 +0000 (00:17 -0500)]
Jalview-JS/JAL-3253 applet params jpredfile, jnetfile
debug comments out, fixes for missing annotation file post-load tasks
hansonr [Thu, 16 May 2019 05:11:56 +0000 (00:11 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Thu, 16 May 2019 03:07:08 +0000 (22:07 -0500)]
Jalview-JS/JAL-3253 debug comments out
hansonr [Thu, 16 May 2019 03:07:08 +0000 (22:07 -0500)]
Jalview-JS/JAL-3253 AppletParams color params
"defaultcolour" -> "DEFAULT_COLOUR"
"defaultcolournuc" -> "DEFAULT_COLOUR_NUC"
"defaultcolourprot" -> "DEFAULT_COLOUR_PROT"
hansonr [Thu, 16 May 2019 01:17:42 +0000 (20:17 -0500)]
Jalview-JS/JAL-3253, JAL-3266 Varna preliminary upgrade
hansonr [Wed, 15 May 2019 23:29:53 +0000 (18:29 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Wed, 15 May 2019 23:27:06 +0000 (18:27 -0500)]
JAL-3253-applet,JAL-3263 SwingJS-site.zip clean build for 秘foo
hansonr [Wed, 15 May 2019 23:27:06 +0000 (18:27 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Wed, 15 May 2019 23:26:47 +0000 (18:26 -0500)]
JAL-3253-applet Platform getDocumentBase() and getCodeBase() as if
applet fixed
uses g.秘html5Applet instead of J2S.thisApplet
gmungoc [Wed, 15 May 2019 16:01:43 +0000 (17:01 +0100)]
JAL-3253-applet feature parameter processing fixed
gmungoc [Wed, 15 May 2019 16:01:43 +0000 (17:01 +0100)]
JAL-3253 ApplicationSingletonProvider replaces Instance
hansonr [Wed, 15 May 2019 14:53:39 +0000 (09:53 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Wed, 15 May 2019 14:52:42 +0000 (09:52 -0500)]
JAL-3253-applet, reading applet tag parameters needed toLowerCase()
hansonr [Wed, 15 May 2019 14:51:22 +0000 (09:51 -0500)]
JAL-3253-applet, JAL-3263 new SwingJS-site.zip for "_"
gmungoc [Wed, 15 May 2019 10:51:28 +0000 (11:51 +0100)]
JAL-3263 variable name now 秘html5Applet
hansonr [Tue, 14 May 2019 21:47:14 +0000 (16:47 -0500)]
Fix to not create lasting static instance in JavaScript; trims up code
hansonr [Tue, 14 May 2019 02:19:32 +0000 (21:19 -0500)]
removes temporary debugging line
hansonr [Tue, 14 May 2019 02:07:39 +0000 (21:07 -0500)]
JAL-3263, JAL 3264 New Transpiler fixes FunctionalInterface issues,
_xxxx issues,
privatizes SwingJS-private fields with Mandarin first "secret" character
\u79D8 (only affects File._byte; left here in both forms _byte and
秘byte
SwingJS bug in transpiler caused java.util.stream.MatchOps to fail. Adds
back in the IntervalStore classes into srcjar, which use Java8
FunctionalInterfaces.
hansonr [Mon, 13 May 2019 02:26:58 +0000 (21:26 -0500)]
Site resources for running pages with swingjs/JalviewJS.js
JalviewJS.js just a very thin implementation, enough to show a "Start
Jalview" button, read the <applet> tag for parameters, and to start the
applet when that button is pressed.
Using the applet tags allows support for both Java and JavaScript for
pages that have Jalview <applet> tags. (Java right now requires
?_USE=JAVA)
Info.resourcePath is used by jalview.bin.AppletParams to ensure that the
directory with the resources is found.
applets.html is functioning in a preliminary demo mode
- <applet> tag read successfully
- Info.resourcePath read successfully
- Info and applet parameters transferred successfully
- .fa and features files read successfully
- embedding and floating frames supported
- initial "Start Jalview" buttons working
- when VARNA 2D or other window is displays, others hide.
(probably because Desktop is in the DOM but hidden).
hansonr [Mon, 13 May 2019 02:17:12 +0000 (21:17 -0500)]
JalviewAppLoader for moving code from JalviewLite relating to applet
parameters
hansonr [Mon, 13 May 2019 02:15:37 +0000 (21:15 -0500)]
better preferences/properties
git://source.jalview.org / jalview.git / log