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
hansonr [Mon, 13 May 2019 02:14:04 +0000 (21:14 -0500)]
jalview.bin.AppletParams
hansonr [Mon, 13 May 2019 02:12:51 +0000 (21:12 -0500)]
new SwingJS-site.zip
hansonr [Mon, 13 May 2019 02:11:42 +0000 (21:11 -0500)]
VARNA fix for use of _border used by JSComponent (how to avoid this?)
hansonr [Fri, 10 May 2019 20:30:47 +0000 (15:30 -0500)]
trying to force a build at builds.jalview.org
hansonr [Fri, 10 May 2019 18:27:22 +0000 (13:27 -0500)]
minor edits
hansonr [Fri, 10 May 2019 18:24:32 +0000 (13:24 -0500)]
JAL-3253 FileFormats static removal
hansonr [Fri, 10 May 2019 18:18:12 +0000 (13:18 -0500)]
JAL-3253 jalview.bin.Instance for AppCache and FeatureAttribute
hansonr [Fri, 10 May 2019 18:00:33 +0000 (13:00 -0500)]
JAL-3253 jalview.bin.Instance streamlining
hansonr [Fri, 10 May 2019 12:03:42 +0000 (07:03 -0500)]
JAL-3253 jalview.bin.Instance handles all singleton instances -
preliminary
hansonr [Fri, 10 May 2019 02:53:36 +0000 (21:53 -0500)]
insignificant test file changes
hansonr [Fri, 10 May 2019 02:51:19 +0000 (21:51 -0500)]
Jalview-JS/JAL-3253-applet Desktop fix for null desktopPane in testing
hansonr [Thu, 9 May 2019 19:10:47 +0000 (14:10 -0500)]
Jalview-JS/JAL-3253-applet does not recognize \r\n as OK
hansonr [Thu, 9 May 2019 19:05:58 +0000 (14:05 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Thu, 9 May 2019 18:54:03 +0000 (13:54 -0500)]
Jalview-JS/JAL-3253-applet
hansonr [Thu, 9 May 2019 18:54:03 +0000 (13:54 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Thu, 9 May 2019 18:24:30 +0000 (13:24 -0500)]
JAL-3253/JAL-3258 FileLoader fix for use of file.separator
hansonr [Thu, 9 May 2019 18:24:30 +0000 (13:24 -0500)]
JAL-3253/JAL-3257
working on getting TestNG working with singletons
check for null property file in Cache.setProperty to avoid error message
in testng; fixes problems with FeatureFileTest and FeatureFile with
mixed or unconsidered line endings
hansonr [Thu, 9 May 2019 13:32:00 +0000 (08:32 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 4 of 3
working on getting TestNG working with singletons
hansonr [Thu, 9 May 2019 03:35:47 +0000 (22:35 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 3 of 3
More succinct singleton class instances stored in jalview.bin.Jalview.
All 2200 instances of "static" checked.
hansonr [Wed, 8 May 2019 21:42:23 +0000 (16:42 -0500)]
JAL-3253 preliminary static fixes for JavaScript part 2
Includes lazy dynamic loading of SequenceFetcher database options.
Note that if WebServices menu is enabled (Java, not JavaScript), then
all web-based database proxies are instantiated anyway.
hansonr [Wed, 8 May 2019 11:29:37 +0000 (06:29 -0500)]
JAL-3253 preliminary static fixes for JavaScript
Desktop.instance and Desktop.getInstance()
Jalview.instance and Jalview.getInstance()
AlignmentSorter.instance and AlignmentSorter.getInstance()
ArgsParser static final options
*SoapBindingStub static final _operations
Clean up of headless business
Clean up of ArgsParser options
hansonr [Wed, 8 May 2019 02:42:57 +0000 (21:42 -0500)]
JAL-3253 AppletParams class for processing applet-specific params
gmungoc [Fri, 26 Apr 2019 09:20:31 +0000 (10:20 +0100)]
JAL-3226 removal of superseded changes
gmungoc [Fri, 26 Apr 2019 09:17:09 +0000 (10:17 +0100)]
JAL-3010 borderless 'x' for "delete this filter condition"
hansonr [Tue, 23 Apr 2019 03:48:49 +0000 (22:48 -0500)]
[JAL-3226] problem that JavaScript (or Java) may consolidate multiple
repaint() requests in unpredictable ways. In this case, the issue was
that in response to a CTRL-C/CTRL-V paste request, in Java a fast
repaint request preceded two full requests, thus resulting
in a full request for paint. In constrast, in JavaScript, the three
requests were bundled together into one, so the fastPaint flag was
still present for the second and third request.
This resulted in incomplete painting.
The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false
in PaintRefresher when the target to be painted is one of those two
components.
BH 2019.04.22
hansonr [Mon, 22 Apr 2019 17:10:09 +0000 (12:10 -0500)]
update of SwingJS -- no changes known.
hansonr [Thu, 18 Apr 2019 18:15:55 +0000 (13:15 -0500)]
minor code clean up
hansonr [Thu, 18 Apr 2019 18:15:24 +0000 (13:15 -0500)]
minor code clean up
hansonr [Thu, 18 Apr 2019 17:59:40 +0000 (12:59 -0500)]
// BH 2018.04.18 comment: addNotify() is not appropriate here. We
// are not changing ancestors, and keyboard action listeners do
// not need to be reset. addNotify() is a very expensive operation,
// requiring a full re-layout of all parents and children.
// Note in JComponent:
// This method is called by the toolkit internally and should
// not be called directly by programs.
// I note that addNotify() is called in several areas of Jalview.
hansonr [Thu, 18 Apr 2019 17:55:55 +0000 (12:55 -0500)]
Adds check for gap padding to disallow fast paint upon pasting if
alignment has been modified.
hansonr [Thu, 18 Apr 2019 17:54:46 +0000 (12:54 -0500)]
removes unnecessary clearFastPaint
hansonr [Thu, 18 Apr 2019 17:54:08 +0000 (12:54 -0500)]
Corrects incorrect calls to ViewportRanges.setEndSeq()
This function has the limit of height - 1, not height. Also adds safety
for start < 0 in ViewportRanges.setEndSeq();
hansonr [Thu, 18 Apr 2019 15:03:30 +0000 (10:03 -0500)]
pushing again, just comments
hansonr [Thu, 18 Apr 2019 14:32:42 +0000 (09:32 -0500)]
hack for fastpaint Java bug upshifting one line after a sequence
selection paste. Covered in Java by a full paint by ConsensusThread.
hansonr [Thu, 18 Apr 2019 11:53:00 +0000 (06:53 -0500)]
reverting seqPanel.seqCanvas.clearFastPaint();
gmungoc [Thu, 18 Apr 2019 08:36:57 +0000 (09:36 +0100)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"
gmungoc [Thu, 18 Apr 2019 08:31:17 +0000 (09:31 +0100)]
Merge branch 'develop' into Jalview-JS/develop
hansonr [Thu, 18 Apr 2019 03:54:33 +0000 (22:54 -0500)]
explicit Hashtable objects
hansonr [Thu, 18 Apr 2019 03:53:59 +0000 (22:53 -0500)]
adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport
adjustment
gmungoc [Wed, 17 Apr 2019 15:34:58 +0000 (16:34 +0100)]
JAL-3026 fix bug loading Jalview Project (in Java)
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 17 Apr 2019 14:32:36 +0000 (15:32 +0100)]
JAL-3111 Jalview 2.11 what’s New and estimated release date
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
gmungoc [Wed, 17 Apr 2019 10:48:28 +0000 (11:48 +0100)]
Merge branch 'develop' into Jalview-JS/develop
hansonr [Tue, 16 Apr 2019 22:29:07 +0000 (17:29 -0500)]
better resource loading/file caching
hansonr [Tue, 16 Apr 2019 22:28:14 +0000 (17:28 -0500)]
caching of DnD files dropped
hansonr [Tue, 16 Apr 2019 21:07:20 +0000 (16:07 -0500)]
jmol-app updated for SwingJS ZipTools upgrade
hansonr [Tue, 16 Apr 2019 21:06:36 +0000 (16:06 -0500)]
localizes Thread colourby so that it does not cause ThreadStateException
in Java
hansonr [Tue, 16 Apr 2019 21:05:41 +0000 (16:05 -0500)]
comments only
hansonr [Tue, 16 Apr 2019 13:39:31 +0000 (08:39 -0500)]
missing check for JavaScript in client response for String (Java) vs.
Map (JavaScript) -- since JavaScript has already done the conversion to
a Map and needs no further JSON parsing.
hansonr [Tue, 16 Apr 2019 13:20:31 +0000 (08:20 -0500)]
unused old SwingJS dependencies
hansonr [Tue, 16 Apr 2019 13:16:30 +0000 (08:16 -0500)]
unused old SwingJS dependencies
hansonr [Tue, 16 Apr 2019 12:34:10 +0000 (07:34 -0500)]
Adds _j2sclasslist.txt to SwingJS distribution; fixes missing
menuListener
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
gmungoc [Mon, 15 Apr 2019 08:47:50 +0000 (09:47 +0100)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0
Jim Procter [Wed, 10 Apr 2019 13:56:32 +0000 (14:56 +0100)]
JAL-3033 and more classes for examples core
Jim Procter [Tue, 9 Apr 2019 13:23:56 +0000 (14:23 +0100)]
JAL-3033 jalview.org/jalview-js/JalviewJS.shtml?open%20http://www.jalview.org/examples/uniref50.fa
hansonr [Tue, 9 Apr 2019 04:41:36 +0000 (23:41 -0500)]
JTable improvements
- prevents loss of tool tip when clicking or editing
- corrects offset of center label in variable color option
- speed somewhat improved
hansonr [Tue, 9 Apr 2019 04:39:28 +0000 (23:39 -0500)]
better comment regarding setting recognized ajax-enabled sites
hansonr [Tue, 9 Apr 2019 04:38:42 +0000 (23:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
hansonr [Tue, 9 Apr 2019 04:38:21 +0000 (23:38 -0500)]
code formatting only
git://source.jalview.org / jalview.git / log