Clone
 

hansonr <hansonr@sto24954w.ad.stolaf.edu> in jalview

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

relevant issue is JAL-3626

relevant issue is JAL-3626

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

JAL-3463 SwingJS-site.zip update for Thread.sleep()

- throws InterruptedException if called in JavaScript

    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3463 Thread.sleep()

setting sleep() to throw InterruptedException()

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3463 alert for Thread.sleep; JAL-3378 java.util.logging.Logger implemented.

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3436 broken reader - SwingJS issue (wrong JAL number in last commit)

- java.util.logging.Logger not fully implemented.

- this fix just removes Logger calls from javax.xml classes.

- see JAL-3461 for full fix TODO

JAL-3442 (Aug 28 commit) option to use/not use cache

Commit 113cc13-2019.09.28 with added transparency fix

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3368 retaining branch for future SwingJS reference

JAL-3437 Desktop File...Load Project fails in JalviewJS

- just needed to use the File object rather than the file name in the

call to Jalview2XML.loadJalviewAlign

JAL-3445 branch for BSML file reading development

    • -0
    • +225
    /src/jalview/io/BSMLFile.java
JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.

adding SwingJS notes for JAR file source in srcjar/

    • -0
    • +5
    /srcjar/intervalstore/README_SWINGJS.txt
    • -0
    • +6
    /srcjar/net/miginfocom/README_SWINGJS.txt
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3459 org.json code removed

- moved to unused/

- supplied by SwingJS-site.zip

- only differences are in a few JavaScript-specific issues

- this move has NO EFFECT on the JavaScript, as SwingJS-site.zip is

unzipped last, overwriting whatever this code would have placed in

site/swingjs/j2s anyway.

    • -2411
    • +0
    /src/org/json/JSONObject.java
    • -45
    • +0
    /src/org/json/JSONPointerException.java
    • -43
    • +0
    /src/org/json/JSONPropertyIgnore.java
    • -47
    • +0
    /src/org/json/JSONPropertyName.java
  1. … 55 more files in changeset.
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3444 translucent overview

- oops, that broke Java!

JAL-3444 translucent overview

- was missing 2nd isJS block

- JS was setting pixel background to white instead of defaultColour

prior to transparent color painting

JAL-3436 fix for reload not reloading files

-- fix for Jalview projects reload where reload was using just the file

name.

-- will test further to ensure this is only in relation to JVP files

    • -2
    • +14
    /src/jalview/project/Jalview2XML.java
JAL-3436 debug comments out in JSPopupMenuUI.js

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3453

test to see if the build testing passes this test.

Slight modifications from Mungo's last commit to account for recent

changes in public/private fields, but that is all.

Passing tests on Bob's Windows machine.

    • -23
    • +1
    /test/jalview/gui/AlignFrameTest.java
JAL-3453 Some tests require different Desktop constructor

even better, simpler idea:

static boolean instanceOnly

public static Desktop getInstanceOnly()

{

instanceOnly = true;

return getInstance();

}

JAL-3453 Some tests require different Desktop constructor

better idea:

Desktop.getInstanceOnly()

- creates an instance with no dialog prompting and no frame display,

similar to headless mode, but not fully bypassing the code that

Jalview.headless bypasses.

JAL-3453 better JavaDoc

JAL-2114 just noting where the exo-location error presents itself.

    • -1
    • +2
    /src/jalview/ws/dbsources/EmblXmlSource.java
JAL-3454 file loading string-only (testNG) fails for PDB file

    • -5
    • +5
    /src/jalview/io/AppletFormatAdapter.java