jalview

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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
JalviewJS2 optional headless, output

commented out unless desired for testing

JAL-3253-applet JAL-3423 Windows TestNG

FeatureColourFinderTest error only in batch mode

JAL-3253-applet JAL-3423 Windows TestNG

SeqPanelTest error only in batch mode

JAL-3253-applet JAL-3423 Windows TestNG

mac CTRL test is only for Macs.

JAL-3253-applet JAL-3423 Windows TestNG

Bug found in wrap tool tip (also in Jalview-Develop) due to some

messages having only one of <html> or </html> and some having neither

but still having <br> (potentially)

    • -6
    • +28
    /test/jalview/gui/JvSwingUtilsTest.java
JAL-3253-applet JAL-3423 Windows TestNG

Bob bug found in IntervalStore-noNCList

    • -2
    • +2
    /src/intervalstore/nonc/IntervalStore.java
note that identifier can be null, resulting in a null pointer exception

    • -1
    • +3
    /src/jalview/urls/IdentifiersUrlProvider.java
JAL-3253-applet JAL-3423 Windows TestNG

Bob Bug found in boolean testing of FeatureRendererModel

JAL-3253-applet JAL-3423 Windows TestNG

CommandLineOperations indicates absolute file path; adding output file

option to JavaScript

    • -2
    • +4
    /test/jalview/bin/CommandLineOperations.java
JAL-3253-applet JAL-3423 Windows TestNG

- PDBEntry file name needs to normalize \ and /.

    • -13
    • +6
    /src/jalview/datamodel/PDBEntry.java
TestNG find for JAL-3253-applet

JAL-3253-applet JAL-3424 headless fix for Windows

    • -1
    • +1
    /src/jalview/gui/AssociatePdbFileWithSeq.java
    • -1
    • +1
    /src/jalview/gui/VamsasApplication.java
    • -1
    • +1
    /src/jalview/io/VamsasAppDatastore.java
    • -1
    • +1
    /src/jalview/io/vamsas/Sequencemapping.java
    • -1
    • +5
    /test/jalview/bin/CommandLineOperations.java
    • -1
    • +1
    /test/jalview/gui/AlignViewportTest.java
JAL-3253-applet JAL-3424 headless fix for Windows

hard-codes workingDir for TestNG for unknown necessity.

    • -0
    • +1126
    /build.Bob-Windows.xml
developer note pnly

*

* BH Note: It is critical that any call to

* AlignViewportI.setGlobalColourScheme is followed closely, if not

* immediately, by a call to AlignPanel.repaint(true, true) so that

the

* overview is updated. When that happens, the sequence overview color

caches

* are cleared.

*

JAL-3397 JAL-3253-applet

TEMPORARY disabling of NCList due to incompatibility with API in TestNG.

JAL-3253-applet no-NCList IntervalStore fixes

    • -3
    • +78
    /src/intervalstore/nonc/IntervalStore.java
    • -5
    • +37
    /src/jalview/renderer/OverviewResColourFinder.java
JAL-3423 testNG fixes for Windows

- \r\n, slightly differerent font metrics

    • -4
    • +17
    /test/jalview/analysis/TestAlignSeq.java
    • -10
    • +17
    /test/jalview/gui/SeqCanvasTest.java
    • -1
    • +1
    /test/jalview/math/RotatableMatrixTest.java
JAL-3423 testNG fix for revised tooltip html format

    • -3
    • +2
    /test/jalview/gui/JvSwingUtilsTest.java
Transpiler update fixes nuisance null-pointer error message when .j2s is set to disabled.

    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3423 TestNG test bugs

PDBEntry needs to normalize file names under Windows, particularly for

TestNG tests.

JAL-3423 TestNG test bugs

Cache logger not initializing early enough for some TestNG tests.

JAL-3422 JAL-3253-applet

SwingJS-site.zip fix for FontChooser combobox missing all text and

dropdown.

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

JAL-3235 -Dtestng-verbosity=10 to trace execution of TestNG tests

JAL-3253 fix scrollTo termination check.

JAL-3418 debug testng execution - verbosity=10

Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet