Bob Hanson

JAL-3659 unnecessary duplication -- test is made in previous block

JAL-3446 unintentially left training message in code.

JAL-3659 proper headless check; skips setProperty for JS
JAL-3659 proper headless check; skips setProperty for JS
JAL-3659 proper headless check; skips setProperty for JS

JAL-3662 simple fix for CLI not using right format for output of alignment.
JAL-3662 simple fix for CLI not using right format for output of alignment.
JAL-3662 simple fix for CLI not using right format for output of alignment.

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3446 -- YEIKS! two checkURLLinks calls!

JAL-3446 proper call for headless state

JAL-3446 CommandLineOperation test

- cleaner headless check when adding JInternalFrame to Desktop

instance.

JAL-3446 CommandLineOperation test

- headless check must be before Desktop.getInstance(), as you can't

make an instance of JFrame() when headless.

JAL-3446 CTRL-DOWN check for headless operation

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3657 SwingJS HashMap.putEntries() coding mistake.

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3445 BSML BBB file format.

- merge of BSML test branch.

- includes BSMLFileTest

- preliminary; does not read complement

- See Jalview-JS/develop/temp/bbb.dtd.pdf

JAL-3653 SwingJS support for indeterminate JProgressBar

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3487 Splash screen

- cleaner code, more comments

- adds SwingJS support for 1-ms image finalization

(using JSToolkit.dispatch instead of invokeLater

    • -83
    • +72
    /src/jalview/gui/SplashScreen.java
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3487 Splash screen

- JS now uses StateMachine

- simple example of how StateMachine works.

    • -155
    • +118
    /src/jalview/gui/SplashScreen.java
Merge branch 'Jalview-JS/develop.JAL-3445-BSML-reader' into Jalview-JS/develop

minor changes

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • -3
    • +3
    /test/jalview/gui/JvSwingUtilsTest.java
JAL-3446 from applet -- reload; also fixes some repaint issues
JAL-3446 from applet -- reload; also fixes some repaint issues
It is not clear what ap.validate() is supposed to do here. Setting a preferred height does not invalidate anything. So what is there to validate? Suggestion is: if (ap != null && ap.isValid()) ......

It is not clear what ap.validate() is supposed to do here. Setting a preferred height does not invalidate anything. So what is there to validate? Suggestion is:

if (ap != null && ap.isValid())
...
if (!ap.annotationScroller.getVerticalScrollBar().isVisible())
ap.annotationScroller.getVerticalScrollBar().setVisible(true);

...

where the check for isValid() is to make sure the panel's peer has been created, and that it has been laid out, preventing the scrollbar from being shown initially.

JAL-3446 SwingJS update

-fixes desktop frame not taking focus when clicked, so not processing

menu shortcuts

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3664 shortcuts in Desktop not working from AlignFrame

- missing test for JInternalFrame in JComponent.processKeyBindings

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3446 removing mouse button test debug

SwingJS upgrade fixes AlignmentPanel keyPressed not called

- ContentPane was getting the message, not JInternalFrame

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3446 from applet -- reload; also fixes some repaint issues

    • -23
    • +56
    /src/jalview/gui/AlignFrame.java
    • -37
    • +56
    /src/jalview/gui/AnnotationPanel.java
    • -4
    • +15
    /src/jalview/gui/PaintRefresher.java
    • -2
    • +16
    /src/jalview/io/VamsasAppDatastore.java
    • -11
    • +18
    /src/jalview/project/Jalview2XML.java
    • -0
    • +6
    /src/jalview/util/jarInputStreamProvider.java