jalview

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JAL-3420 JAL-3394 Correct format of XML in added file extensions for install4j8. Also progress indicator for adding file associations (which can be slow). Still not entirely working, see comments in issue.

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    /utils/install4j/Jalview-File.png
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    /utils/install4j/Jalview-Launch.icns
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    /utils/install4j/Jalview-Launch.ico
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    /utils/install4j/Jalview-Launch.png
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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
JAL-3253-applet JAL-3397 switch back to original (MC) IS+NCList after testing complete.

JAL-3253-applet JAL-3423

CacheableInputBox direct update mode for testing removes need for wait.

JalviewJS complete PASS on Windows

(other than the usual three Xref fails)

JAL-3253-applet JAL-3423

AlignFrameTest fixes for timing and lack of ResidueShading conservation

data.

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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3420 JAL-3394 Using install4j8 template with file associations. Attempts unix file associations but not working (only tested in Ubuntu) yet.

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    /utils/install4j/auto_file_associations-i4j8.pl
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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
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    /utils/install4j/install4j8_template.install4j
JAL-3253 JAL-3397 adds (original MC) intervalstore code to implement modified api interfaces

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    /src/intervalstore/impl/BinarySearcher.java
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    /src/intervalstore/impl/IntervalStore.java
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    /src/intervalstore/impl/NCList.java
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    /src/intervalstore/impl/NCListBuilder.java
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    /src/intervalstore/impl/NCNode.java
JAL-3253-applet JAL-3423 TestNG/Win

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    /test/jalview/gui/AlignViewportTest.java
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    /test/jalview/gui/AlignmentPanelTest.java
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    /test/jalview/gui/SeqCanvasTest.java
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    /test/jalview/gui/SeqPanelTest.java
fixes errant debug "return;" in j2sApplet key listener

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    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3210 Now includes creating the .project, .classpath and .settings as a depenedency

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)

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    /test/jalview/gui/JvSwingUtilsTest.java
JAL-3253-applet JAL-3423 Windows TestNG

Bob bug found in IntervalStore-noNCList

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

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    /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

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    /test/jalview/bin/CommandLineOperations.java
JAL-3253-applet JAL-3423 Windows TestNG

- PDBEntry file name needs to normalize \ and /.

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    /src/jalview/datamodel/PDBEntry.java
TestNG find for JAL-3253-applet

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

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

headless tests on Windows

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    /hs_err_pid20236.log
JAL-3253-applet headless branch - just experimenting.

Windows (at least) headless does not allow for JInternalFrame even

though, on paper, JInternalFrame should not be a heavy-weight component.

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    /src/jalview/bin/JalviewAppLoader.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /src/jalview/jbgui/GAlignmentPanel.java
  1. … 4 more files in changeset.
JAL-3210 Barebones gradle/buildship/eclipse. See README

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    /.externalToolBuilders/Help Indices Jalview Release [Builder].launch
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    /.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch
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    /.externalToolBuilders/Jalview Release indices [Builder].launch
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    /.settings/org.eclipse.jdt.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
  1. … 1976 more files in changeset.
hard-codes workingDir for TestNG for unknown necessity.

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    /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

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    /src/intervalstore/nonc/IntervalStore.java
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    /src/jalview/renderer/OverviewResColourFinder.java
JAL-3423 testNG fixes for Windows

- \r\n, slightly differerent font metrics

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    /test/jalview/analysis/TestAlignSeq.java
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    /test/jalview/gui/SeqCanvasTest.java
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    /test/jalview/math/RotatableMatrixTest.java