jalview

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JAL-3247 Script to produce auto file association files for mac and windows installer, and changes in build.gradle to read in the produced, and edited, auto files

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    /utils/auto_file_associations_info_plist.sh
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    /utils/install4j/Info_plist_file_associations-AUTO.xml
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    /utils/install4j/auto_file_associations.pl
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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j.xml
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    /utils/install4j/file_associations_template-Info_plist.xml
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    /utils/install4j/file_associations_template-install4j.xml
JAL-3251 SequenceToSequenceMapping now SequenceMapping, MappingType++

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/MappingType.java
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    /src/jalview/datamodel/SequenceMapping.java
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    /src/jalview/datamodel/SequenceMappings.java
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    /src/jalview/io/gff/ExonerateHelper.java
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    /src/jalview/io/gff/GffHelperBase.java
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    /test/jalview/analysis/CrossRefTest.java
JAL-3253 preliminary static fixes for JavaScript

Desktop.instance and Desktop.getInstance()

Jalview.instance and Jalview.getInstance()

AlignmentSorter.instance and AlignmentSorter.getInstance()

ArgsParser static final options

*SoapBindingStub static final _operations

Clean up of headless business

Clean up of ArgsParser options

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    /doc/parameters.xlsx
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    /src/ext/vamsas/JpredSoapBindingStub.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/analysis/scoremodels/ScoreModels.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignExportOptions.java
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    /src/jalview/gui/AlignFrame.java
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JAL-3247 Note in launcher.log when using a JVL file

JAL-3253 AppletParams class for processing applet-specific params

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    /src/jalview/bin/AppletParams.java
JAL-3247 Changed JVL file to be a props file, with appbase=... required for the new appbase URL

JAL-3247 Script to automatically install Jalview from the .dmg to /Applications

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    /utils/dev_macos_install.sh
JAL-3247 Auto generated file associations from jalview/io/FileFormat.java

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    /utils/auto_file_associations_info_plist.sh
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    /utils/install4j/Info_plist_file_associations-AUTO.xml
JAL-3247 Allowing 'file' protocol URL with empty domain in a .jvl file

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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
JAL-3252 some debugging

JAL-3247 Code changes to getdown. Double click open of .jvp files in Windows and macOS, and .jvl new appbase file working in macOS.

JAL-3247 improvements

JAL-3247 Some getdown image file changes/tidying

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    /resources/images/jalview_logo_background_getdown-640x480.png
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    /resources/images/jalview_logo_background_getdown-progress.png
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    /resources/images/jalview_logo_background_getdown-progress1.png
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    /resources/images/jalview_logo_background_getdown-progress2.png
JAL-3240 known issue for release notes

JAL-3239 release note

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    /src/jalview/gui/SequenceRenderer.java
JAL-3244 release note

Merge remote-tracking branch 'origin/bug/JAL-3239monospacedEps' into develop

JAL-3244 delete obsolete method

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3247 First attempt at getdown code to add macOS startup filenames to the appargs as -open filename

JAL-3247 Part way towards adding double-click opening in Jalview on .jvp file in macOS

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    /j11lib/i4jruntime.jar
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    /j8lib/i4jruntime.jar
JAL-3247 Improved file associations on macOS and Windows

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    /utils/install4j/Info_plist_file_associations.xml
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    /utils/install4j/Jalview-Version-Locator.icns
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    /utils/install4j/Jalview-Version-Locator.ico
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    /utils/install4j/Jalview-Version-Locator.png
JAL-3235 override entrySet() to output Properties sorted by key (Java 9)

JAL-3239 draw EPS or SVG one character at a time (even monospaced)

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    /src/jalview/gui/SequenceRenderer.java
Merge branch 'bug/JAL-3244jmolWindows' into develop

JAL-3244 renamed Platform method for clarity

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    /src/jalview/gui/ChimeraViewFrame.java
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    /test/jalview/util/PlatformTest.java
adding another getdown file (produced during a getdown build) to gitignore

JAL-3248 some progress on prerequesite installation instructions

JAL-3247 jvp jvl File associations, JRE variablised, Windows-Userspace path default

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    /utils/install4j/Info_plist_file_associations.txt
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    /utils/install4j/Jalview-File.icns
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    /utils/install4j/Jalview-File.ico
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    /utils/install4j/JalviewVersionLocator.png
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    /utils/install4j/bs_install4j_template.install4j
Fixed -Djvl=true in install4j JVM invocation

Extra JVL file association in the installer. Shadowed gradle-launcher.jar and classpath adjusted in install4j template. 'jre' folder made a compiler variable in install4j template.

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    /getdown/src/getdown/launcher/pom.xml
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    /resources/images/JalviewVersionLocator.png