jalview

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Commits this week: 8
Total Committers: 73
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Commits this week: 8

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Tuesday 15 Oct 2019
5:02 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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

Options
    • -4
    • +9
    /src/jalview/renderer/OverviewResColourFinder.java
4:54 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

Commit 113cc13-2019.09.28 with added transparency fix

Options
    • -2
    • +15
    /src/jalview/renderer/seqfeatures/FeatureColourFinder.java
    • binary
    /swingjs/SwingJS-site.zip
    • -0
    • +2
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • -0
    • +2
    /swingjs/ver/3.2.4/_j2sclasslist.txt
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
Wednesday 28 Aug 2019
6:27 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JalviewJS2 optional headless, output

commented out unless desired for testing

Options
    • -1
    • +13
    /src/jalview/bin/JalviewJS2.java
6:25 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

FeatureColourFinderTest error only in batch mode

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    • -0
    • +2
    /test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
6:12 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

SeqPanelTest error only in batch mode

Options
    • -2
    • +4
    /test/jalview/gui/SeqPanelTest.java
5:52 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

mac CTRL test is only for Macs.

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    • -4
    • +6
    /test/jalview/gui/PairwiseAlignmentPanelTest.java
    • -1
    • +6
    /test/jalview/util/PlatformTest.java
5:51 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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)

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    • -2
    • +14
    /src/jalview/gui/JvSwingUtils.java
    • -6
    • +28
    /test/jalview/gui/JvSwingUtilsTest.java
5:49 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

Bob bug found in IntervalStore-noNCList

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    • -2
    • +2
    /src/intervalstore/nonc/IntervalStore.java
5:49 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

note that identifier can be null, resulting in a null pointer exception

Options
    • -1
    • +3
    /src/jalview/urls/IdentifiersUrlProvider.java
5:48 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

Bob Bug found in boolean testing of FeatureRendererModel

Options
    • -2
    • +4
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
5:46 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

CommandLineOperations indicates absolute file path; adding output file

option to JavaScript

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    • -4
    • +6
    /src/jalview/bin/Jalview.java
    • -2
    • +4
    /test/jalview/bin/CommandLineOperations.java
5:41 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet JAL-3423 Windows TestNG

- PDBEntry file name needs to normalize \ and /.

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    • -13
    • +6
    /src/jalview/datamodel/PDBEntry.java
1:24 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

TestNG find for JAL-3253-applet

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    • -2
    • +2
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
12:25 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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

Options
    • -9
    • +12
    /src/jalview/bin/Jalview.java
    • -4
    • +4
    /src/jalview/gui/AlignViewport.java
    • -1
    • +1
    /src/jalview/gui/AssociatePdbFileWithSeq.java
    • -1
    • +1
    /src/jalview/gui/CrossRefAction.java
    • -1
    • +1
    /src/jalview/gui/Desktop.java
    • -2
    • +2
    /src/jalview/gui/SplitFrame.java
    • -1
    • +1
    /src/jalview/gui/VamsasApplication.java
    • -1
    • +1
    /src/jalview/io/FileLoader.java
    • -1
    • +1
    /src/jalview/io/VamsasAppDatastore.java
    • -1
    • +1
    /src/jalview/io/vamsas/Sequencemapping.java
    • -2
    • +2
    /src/jalview/project/Jalview2XML.java
    • binary
    /test-bh.png
    • -1
    • +5
    /test/jalview/bin/CommandLineOperations.java
    • -1
    • +1
    /test/jalview/gui/AlignViewportTest.java
Tuesday 27 Aug 2019
11:18 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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

Options
    • -1
    • +7
    /src/jalview/bin/Jalview.java
4:21 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

hard-codes workingDir for TestNG for unknown necessity.

Options
    • -0
    • +1126
    /build.Bob-Windows.xml
4:13 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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.

*

Options
    • -0
    • +6
    /src/jalview/api/AlignViewportI.java
4:12 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3397 JAL-3253-applet

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

Options
    • -1
    • +1
    /src/jalview/datamodel/features/SequenceFeatures.java
4:11 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3253-applet no-NCList IntervalStore fixes

Options
    • -3
    • +78
    /src/intervalstore/nonc/IntervalStore.java
    • -9
    • +52
    /src/jalview/datamodel/features/FeatureStoreJS.java
    • -5
    • +37
    /src/jalview/renderer/OverviewResColourFinder.java
    • -0
    • +1
    /test/jalview/datamodel/features/FeatureStoreJSTest.java
    • -8
    • +28
    /test/jalview/renderer/OverviewResColourFinderTest.java
4:05 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3423 testNG fixes for Windows

- \r\n, slightly differerent font metrics

Options
    • -4
    • +17
    /test/jalview/analysis/TestAlignSeq.java
    • -10
    • +17
    /test/jalview/gui/SeqCanvasTest.java
    • -1
    • +1
    /test/jalview/math/RotatableMatrixTest.java
Monday 26 Aug 2019
7:42 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3423 testNG fix for revised tooltip html format

Options
    • -1
    • +3
    /src/jalview/gui/JvSwingUtils.java
    • -3
    • +2
    /test/jalview/gui/JvSwingUtilsTest.java
    • -5
    • +4
    /test/jalview/gui/PopupMenuTest.java
6:40 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

Transpiler update fixes nuisance null-pointer error message when .j2s is set to disabled.

Options
    • binary
    /swingjs/net.sf.j2s.core.jar
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
6:39 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3423 TestNG test bugs

PDBEntry needs to normalize file names under Windows, particularly for

TestNG tests.

Options
    • -2
    • +2
    /src/jalview/datamodel/PDBEntry.java
6:38 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3423 TestNG test bugs

Cache logger not initializing early enough for some TestNG tests.

Options
    • -0
    • +3
    /src/jalview/gui/Desktop.java
6:35 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3422 JAL-3253-applet

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

dropdown.

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    • binary
    /swingjs/SwingJS-site.zip
    • -3
    • +0
    /swingjs/_j2sclasslist.txt
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • -3
    • +0
    /swingjs/ver/3.2.4/_j2sclasslist.txt
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
Wednesday 21 Aug 2019
10:23 am

Jim Procter

Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

Options
10:15 am

Jim Procter

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

Options
    • -1
    • +3
    /build.xml
10:15 am

Jim Procter

JAL-3253 fix scrollTo termination check.

Options
    • -1
    • +1
    /src/jalview/viewmodel/ViewportRanges.java
Tuesday 20 Aug 2019
6:49 pm

Jim Procter

JAL-3418 debug testng execution - verbosity=10

Options
    • -1
    • +1
    /build.xml
Saturday 17 Aug 2019
3:26 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

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

Options