jalview.git
5 years agoJAL-3253 adds simple stacktrace debugging
hansonr [Wed, 31 Jul 2019 23:50:23 +0000 (18:50 -0500)]
JAL-3253 adds simple stacktrace debugging

5 years agoJAL-3253-applet SwingJS-site.zip
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.

5 years agoJAL-3383 unneeded change
hansonr [Tue, 30 Jul 2019 19:24:22 +0000 (14:24 -0500)]
JAL-3383 unneeded change

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3253-applet JAL-3383
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.

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3383 JAL-3253-applet removes unnecessary updateOverviewImage()
hansonr [Mon, 29 Jul 2019 20:34:41 +0000 (15:34 -0500)]
JAL-3383 JAL-3253-applet removes unnecessary updateOverviewImage()

5 years agoJAL-3383 JAL-3253-applet Allows for possibility of a sequence caching
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

5 years agoJAL-3383 JAL-3253-applet ScalePanel bug -- should not have to cause an
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.

5 years agoJAL-3383 JAL-3253-applet FeatureColourFinder avoiding unnec. creation of
hansonr [Mon, 29 Jul 2019 20:32:06 +0000 (15:32 -0500)]
JAL-3383 JAL-3253-applet FeatureColourFinder avoiding unnec. creation of
image graphics

5 years agoJAL-3383 JAL-3253-applet bug in FontChooser calls for full redraw;
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.

5 years agoJAL-3383 JAL-3253-applet Java8 switches to clarify ViewportRanges
hansonr [Mon, 29 Jul 2019 20:29:36 +0000 (15:29 -0500)]
JAL-3383 JAL-3253-applet Java8 switches to clarify ViewportRanges
listeners

5 years agoJAL-3369 JAL-3253-applet adds embedded dim checking for overview frame
hansonr [Mon, 29 Jul 2019 20:24:46 +0000 (15:24 -0500)]
JAL-3369 JAL-3253-applet adds embedded dim checking for overview frame

5 years agoJAL-3369 JAL-3253-applet adds JS app.showOverview()
hansonr [Mon, 29 Jul 2019 20:14:51 +0000 (15:14 -0500)]
JAL-3369 JAL-3253-applet adds JS app.showOverview()

5 years agoJAL-3387 no-annotation too early
hansonr [Mon, 29 Jul 2019 20:09:16 +0000 (15:09 -0500)]
JAL-3387 no-annotation too early

5 years agoJAL-3380 allows JalviewJS to get embedded div attributes
hansonr [Mon, 29 Jul 2019 08:34:57 +0000 (10:34 +0200)]
JAL-3380 allows JalviewJS to get embedded div attributes

5 years agoJAL-3379 Javascript applet.app
hansonr [Mon, 29 Jul 2019 08:31:05 +0000 (10:31 +0200)]
JAL-3379 Javascript applet.app

5 years agoJAL-3778 moving Java logging to Platform.
hansonr [Mon, 29 Jul 2019 08:21:53 +0000 (10:21 +0200)]
JAL-3778 moving Java logging to Platform.

5 years agoJAL-3253-applet adds NOMENUBAR, NOSTATUS, NOCALCULATION, SHOWOVERVIEW
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.

5 years agoJAL-3374 "noannotation" and menu sync
hansonr [Wed, 24 Jul 2019 05:31:01 +0000 (06:31 +0100)]
JAL-3374 "noannotation" and menu sync

5 years agoissue JAL-3373, JAL-3253-applet SwingJS update
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

5 years agonew SwingJS-site.zip fixes menu persistence issues
hansonr [Fri, 19 Jul 2019 09:13:14 +0000 (10:13 +0100)]
new SwingJS-site.zip fixes menu persistence issues

5 years agoJAL-3253 embedded example1
hansonr [Fri, 19 Jul 2019 09:12:41 +0000 (10:12 +0100)]
JAL-3253 embedded example1

5 years agoJAL-3269 ready for testing embedded interface
hansonr [Thu, 18 Jul 2019 07:47:10 +0000 (08:47 +0100)]
JAL-3269 ready for testing embedded interface

5 years agoJAL-3370 sep ignored in getAlignmentOrderFrom(AlignFrameI alf, String
hansonr [Thu, 18 Jul 2019 06:22:15 +0000 (07:22 +0100)]
JAL-3370 sep ignored in getAlignmentOrderFrom(AlignFrameI alf, String
sep)

5 years agoJAL-3269 JAL-3370 JalviewJS interface upgrade
hansonr [Thu, 18 Jul 2019 06:15:38 +0000 (07:15 +0100)]
JAL-3269 JAL-3370 JalviewJS interface upgrade

5 years agominor fixes for JComboBox and also fixes issue with menu accelerator
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.

5 years agoissue JAL-3368 and JAL-3253-applet
hansonr [Tue, 16 Jul 2019 21:46:06 +0000 (22:46 +0100)]
issue JAL-3368  and JAL-3253-applet

Color names not supported.

5 years agoJAL-3032 fine tuning appearance of button
gmungoc [Mon, 15 Jul 2019 12:12:47 +0000 (13:12 +0100)]
JAL-3032 fine tuning appearance of button

5 years agoJAL-3345 small tidying
gmungoc [Mon, 15 Jul 2019 10:49:13 +0000 (11:49 +0100)]
JAL-3345 small tidying

5 years agoJAL-3366 JAL-3253-applet
hansonr [Fri, 12 Jul 2019 07:02:25 +0000 (08:02 +0100)]
JAL-3366   JAL-3253-applet

adds RendererPanel default inner size.

5 years ago2/2 JAL-3253-applet several fixes in SwingJS only:
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.

5 years ago1/2 JAL-3253-applet several fixes in SwingJS only:
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

5 years agoJAL-3253-applet JAL-3360 HTML tooltips not trimming properly; need <div>
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

5 years agoJAL-3253-applet minor fix to reduce number of times cell renderer is
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.

5 years agoJal-3357 ISSUE JAL-3253-applet tooltip for PHOSPHORYLATION missing
hansonr [Tue, 9 Jul 2019 15:19:43 +0000 (16:19 +0100)]
Jal-3357 ISSUE JAL-3253-applet tooltip for PHOSPHORYLATION missing

5 years agoJAL-3354 key listener issue JS#213,215
hansonr [Thu, 4 Jul 2019 16:15:35 +0000 (17:15 +0100)]
JAL-3354 key listener issue JS#213,215

5 years agofixing failure issue in build server
hansonr [Wed, 3 Jul 2019 09:35:29 +0000 (10:35 +0100)]
fixing failure issue in build server

5 years agotemp only
hansonr [Wed, 3 Jul 2019 09:34:44 +0000 (10:34 +0100)]
temp only

5 years agoJAL-3346 JAL-3253-applet JS Code issue 131 Carried forward - no
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

5 years agoJAL-3345 JAL3253 Smoother ScalePanel-based scrolling
hansonr [Tue, 2 Jul 2019 18:27:13 +0000 (20:27 +0200)]
JAL-3345 JAL3253 Smoother ScalePanel-based scrolling

5 years agoJAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip
hansonr [Tue, 2 Jul 2019 13:31:52 +0000 (15:31 +0200)]
JAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip

5 years agoJAL-3253 srcjar_unused/ moved to unused/
hansonr [Tue, 2 Jul 2019 13:29:54 +0000 (15:29 +0200)]
JAL-3253 srcjar_unused/ moved to unused/

5 years agoSwingJS-site.zip update after Wuppertal.
hansonr [Tue, 2 Jul 2019 12:35:57 +0000 (14:35 +0200)]
SwingJS-site.zip update after Wuppertal.

5 years agoJAL-3253 FeatureTypeSettings use of override paint(g) for "x" button
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

5 years agoJAL-3253 AlignmentPanel opaque white may provide white earlier?
hansonr [Tue, 2 Jul 2019 12:34:02 +0000 (14:34 +0200)]
JAL-3253 AlignmentPanel opaque white may provide white earlier?

5 years agoJAL-3253 simpler coding using MouseAdapter. Using JLabel.setOpaque(true)
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.

5 years agoJAL-3253 Jalview2XML minor recoding; suggesting InvokeLater rather than
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

5 years agonew _j2sclasslist.txt for tab-focus
hansonr [Tue, 2 Jul 2019 12:14:13 +0000 (14:14 +0200)]
new _j2sclasslist.txt for tab-focus

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJalview-JS/JAL-3253-applet newick Regex coding error fix JAL-3271
hansonr [Wed, 22 May 2019 13:15:03 +0000 (08:15 -0500)]
Jalview-JS/JAL-3253-applet  newick Regex coding error fix JAL-3271

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of
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

5 years agoJalview-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 also comments relating to JAL-3268

5 years agoJalview-JS/JAL-3253-applet fix for original desktop, centralizing regex
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

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3253-applet disabling button size setting by applet param. Whatever
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.

5 years agoJAL-3253 code tidies and tweaks to Desktop
gmungoc [Tue, 21 May 2019 10:29:59 +0000 (11:29 +0100)]
JAL-3253 code tidies and tweaks to Desktop

5 years agoJAL-2176 unused MenuChooser removed
gmungoc [Mon, 20 May 2019 11:10:33 +0000 (12:10 +0100)]
JAL-2176 unused MenuChooser removed

5 years agoJalview-JS/JAL-3253-applet JAL-3192 secondary core files
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)

5 years agoJalview-JS/JAL-3253-applet core file comment -- Regex() call
hansonr [Sun, 19 May 2019 04:27:59 +0000 (23:27 -0500)]
Jalview-JS/JAL-3253-applet core file comment -- Regex() call

5 years agoJalview-JS/JAL-3253-applet Creating
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");
     */
  }

5 years agoJalview-JS/JAL-3253-applet SwingJS-site.zip update
hansonr [Sun, 19 May 2019 03:35:43 +0000 (22:35 -0500)]
Jalview-JS/JAL-3253-applet SwingJS-site.zip update

5 years agoJalview-JS/JAL-3253-applet update for core_jalview
hansonr [Sun, 19 May 2019 03:35:12 +0000 (22:35 -0500)]
Jalview-JS/JAL-3253-applet update for core_jalview

5 years agoJalview-JS/JAL-3253-applet adds AlignFrameI empty interface to allow
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.

5 years agoJalview-JS/JAL-3253-applet fixes SwingJS-zip.js issue with frames
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"

5 years agoJalview-JS/JAL-3253-applet adds shell JalviewJSApi methods to Jalview
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.

5 years agoJalview-JS/JAL-3253-applet more argument parsing
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).

5 years agoJalview-JS/JAL-3253-applet more argument parsing
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.

5 years agoJalview-JS/JAL-3253-applet additional static final preferences
hansonr [Fri, 17 May 2019 13:26:33 +0000 (08:26 -0500)]
Jalview-JS/JAL-3253-applet additional static final preferences

5 years agoJalview-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

5 years agoJalview-JS/JAL-3253-applet adding more applet parameters and setting
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" ....'

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJalview-JS/JAL-3253-applet JAL-3266 Varna fix.
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!

5 years agoJalview-JS/JAL-3253-applet JAL-3267 URLConnection POST option broken in
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

5 years agoJalview-JS/JAL-3253-applet SwingJS upgrade for case-insensitive Applet
hansonr [Thu, 16 May 2019 16:00:25 +0000 (11:00 -0500)]
Jalview-JS/JAL-3253-applet SwingJS upgrade for case-insensitive Applet
parameters

5 years agoJalview-JS/JAL-3253 applet param PDBFILE
hansonr [Thu, 16 May 2019 15:59:35 +0000 (10:59 -0500)]
Jalview-JS/JAL-3253 applet param PDBFILE

5 years agoJalview-JS/JAL-3253 allow for dialog-free StructureViewer launch
hansonr [Thu, 16 May 2019 15:58:25 +0000 (10:58 -0500)]
Jalview-JS/JAL-3253 allow for dialog-free StructureViewer launch

5 years agoJalview-JS/JAL-3253 honor Applet param case insensitive
hansonr [Thu, 16 May 2019 15:57:34 +0000 (10:57 -0500)]
Jalview-JS/JAL-3253 honor Applet param case insensitive

5 years agoJalview-JS/JAL-3253 applet param GROUPS
hansonr [Thu, 16 May 2019 15:56:32 +0000 (10:56 -0500)]
Jalview-JS/JAL-3253 applet param GROUPS

5 years agoJalview-JS/JAL-3253 applet params jpredfile, jnetfile
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

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJalview-JS/JAL-3253 debug comments out
hansonr [Thu, 16 May 2019 03:07:08 +0000 (22:07 -0500)]
Jalview-JS/JAL-3253 debug comments out

5 years agoJalview-JS/JAL-3253 AppletParams color params
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"

5 years agoJalview-JS/JAL-3253, JAL-3266 Varna preliminary upgrade
hansonr [Thu, 16 May 2019 01:17:42 +0000 (20:17 -0500)]
Jalview-JS/JAL-3253, JAL-3266 Varna preliminary upgrade

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3253-applet,JAL-3263 SwingJS-site.zip clean build for 秘foo
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

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3253-applet Platform getDocumentBase() and getCodeBase() as if
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

5 years agoJAL-3253-applet feature parameter processing fixed
gmungoc [Wed, 15 May 2019 16:01:43 +0000 (17:01 +0100)]
JAL-3253-applet feature parameter processing fixed

5 years agoJAL-3253 ApplicationSingletonProvider replaces Instance
gmungoc [Wed, 15 May 2019 16:01:43 +0000 (17:01 +0100)]
JAL-3253 ApplicationSingletonProvider replaces Instance

5 years agoMerge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...
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

5 years agoJAL-3253-applet, reading applet tag parameters needed toLowerCase()
hansonr [Wed, 15 May 2019 14:52:42 +0000 (09:52 -0500)]
JAL-3253-applet, reading applet tag parameters needed toLowerCase()

5 years agoJAL-3253-applet, JAL-3263 new SwingJS-site.zip for "_"
hansonr [Wed, 15 May 2019 14:51:22 +0000 (09:51 -0500)]
JAL-3253-applet, JAL-3263 new SwingJS-site.zip for "_"

5 years agoJAL-3263 variable name now 秘html5Applet
gmungoc [Wed, 15 May 2019 10:51:28 +0000 (11:51 +0100)]
JAL-3263 variable name now 秘html5Applet

5 years agoFix to not create lasting static instance in JavaScript; trims up code
hansonr [Tue, 14 May 2019 21:47:14 +0000 (16:47 -0500)]
Fix to not create lasting static instance in JavaScript; trims up code

5 years agoremoves temporary debugging line
hansonr [Tue, 14 May 2019 02:19:32 +0000 (21:19 -0500)]
removes temporary debugging line

5 years agoJAL-3263, JAL 3264 New Transpiler fixes FunctionalInterface issues,
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.

5 years agoSite resources for running pages with swingjs/JalviewJS.js
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).

5 years agoJalviewAppLoader for moving code from JalviewLite relating to applet
hansonr [Mon, 13 May 2019 02:17:12 +0000 (21:17 -0500)]
JalviewAppLoader for moving code from JalviewLite relating to applet
parameters

5 years agobetter preferences/properties
hansonr [Mon, 13 May 2019 02:15:37 +0000 (21:15 -0500)]
better preferences/properties