jalview

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JAL-3130 Some fixes to ant build xml, and the modules list file creation (to remove trailing newline) so it can be used with module-less AdoptOpenJDK barebones JRE

Java2Script/SwingJS 3.2.4.05

- fixes FeatureIcon painting

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3171 dataset reference tests now in Functional group

JAL-3171 record mapping between unmarshalled sequence’s dataset sequence ID and materialised dataset to allow belt-and-braces discovery of existing dataset - test now passes

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    /src/jalview/project/Jalview2XML.java
JAL-3171 raise warning when a dataset reference exists *and* a different dataset exists for the sequenceSetID

JAL-3171 more complex project test - where sequences were copied from one alignment view into a new alignment and more views created.

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    /examples/testdata/projects/manyViews.jvp
JAL-3171 resolve dataset for imported projects via the alignment’s SequenceSetId

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    /src/jalview/project/Jalview2XML.java
JAL-3171 failing test for legacy projects and fixing multiple dataset references

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    /examples/testdata/projects/twoViews.jvp
JAL-3171 register existing dataset for new view

JAL-3171 failing test checking preservation of dataset

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    /test/jalview/gui/AlignFrameTest.java
JAL-3130 single class testing on CLI with ant [ -Dclass.name=path/from/classpath/to/Test.class ], and 'fixed' some other tests [that I broke]

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    /test/jalview/bin/CommandLineOperations.java
SwingJS 3.2.4.05 should fix JFileChooser synthetic ref issue

adds better detection of HTTP_FILE_NOT_FOUND error if using jsmol.php

relay (which seems to always add \r\n and gives status 200, even if the

actual response was 404

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    /src/jalview/io/JalviewFileChooser.java
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3130 Fixing a few more tests that pass on a Mac but not on linux (e.g. jv-bamboo)

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    /test/jalview/ext/jmol/JmolParserTest.java
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    /test/jalview/io/IdentifyFileTest.java
JAL-3130 Use non-deprecated check for Mac CMD key press

JAL-3130 Attempting to fix 8 tests that pass on a Mac but not on linux (e.g. jv-bamboo)

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    /test/jalview/ext/htsjdk/TestHtsContigDb.java
JAL-3130 Turns out Quit/About/Preferences handlers are Mac specific, d'oh. Moved build.xml to build-j11.xml

Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into JAL-3048dialogRunner2

JAL-3130 another tweak for bamboo to add the JDK jmods to --module-path

JAL-3130 build.xml tweaks for clover-3.4.1

JAL-3048 wip externalise trigger from RunResponse

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    /src/jalview/gui/AlignExportOptions.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/TextColourChooser.java
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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/io/JalviewFileChooser.java
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Merge branch 'feature/JAL-3169cancelOverwrite' into JAL-3048dialogRunner2

Conflicts:

src/jalview/io/JalviewFileChooser.java

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    /src/jalview/io/JalviewFileChooser.java
JAL-1421 added type to List and Vector

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    /src/jalview/io/JalviewFileChooser.java
JAL-3169 leave file browser open on Cancel in overwrite check

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    /src/jalview/io/JalviewFileChooser.java
JAL-3130 tweaked build.xml to do java 11 bytecode compiling[git branchgit branch]. updated getJavaVersion and added showJDKVersion in utils.

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    /utils/showJVMVersion.java
JAL-3048 DialogRunner changes (wip)

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    /src/jalview/gui/JvOptionPane.java
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    /src/jalview/io/JalviewFileChooser.java
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    /src/jalview/util/dialogrunner/Response.java
JAL-1544 corrected 'adjunst' to 'adjust'

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/TextColourChooser.java
Faster JTable processing; fixes Annotation painting issues (?)

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    /src/jalview/gui/AnnotationPanel.java
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    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3130 Some re-reorganisation for build process

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    /j11lib/javax.activation-MODULE.jar
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    /j11lib/javax.annotation-api-MODULE.jar
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    /j11lib/javax.servlet-api-MODULE.jar
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    /j11lib/javax.ws.rs-api-2.1.1.jar
  1. … 473 more files in changeset.
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_all.sh which works out module dependencies (not as straightforward as it should be) and makes a java 11 JRE

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    /j11jre/openj9_macosx/bin/jarsigner
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    /j11jre/openj9_macosx/bin/jdeprscan
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    /j11jre/openj9_macosx/bin/jrunscript
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    /j11jre/openj9_macosx/bin/rmiregistry
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JAL-3048 response() renamed addResponse(); checkstyle warning fixes

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    /src/jalview/gui/AlignExportOptions.java
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    /src/jalview/gui/TextColourChooser.java
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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/io/JalviewFileChooser.java