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ben soares <b.soares@dundee.ac.uk> in jalview

JAL-1544 version number typo, probably copy and paste

JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file

JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/... This is better in multiple ways including collating files needed for the hugo website and website docroot.

JAL-3989 Independent creation of JSON installer sections

Merge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989

Merge branch 'develop' into task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup

JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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    /src/jalview/gui/AnnotationChooser.java
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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationExporter.java
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    /src/jalview/gui/AnnotationRowFilter.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/ChimeraViewFrame.java
  1. … 26 more files in changeset.
JAL-3991 Made info displayed only when needed (Java 11+)

JAL-3991 Added information output about the slightly alarming 'WARNING: An illegal reflective access operation has occurred' error that occurs for linux users. It can't be avoided so informing the user should help with alarm levels.

JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM mismatch in jalview.bin.LaunchUtils. STDERR warning from jalview.bin.Launcher. Console and optional popup warning in jalview.bin.Jalview.

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    /resources/lang/Messages_es.properties
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    /src/jalview/util/LaunchUtils.java
JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places

JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.

Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir

Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3847 Add some dependencies that gradle 7 mildly complains about

JAL-3851 comment out some debugging

JAL-3851 Some streamlining of caching/removing from cache. 'Highlighting' in InputAlignment endpoint windows

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    /src/jalview/gui/CutAndPasteTransfer.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
JAL-3851 Add a redirect back to itself for working endpoints

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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 Allow specifying a sequence index in highlight

JAL-3851 allow multiple instances of Endpoints. Fixes to naming of IGV colour scheme

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/CutAndPasteTransfer.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/RestHandler.java
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    /src/jalview/schemes/IGVColourScheme.java
Merge branch 'ben/gecos_colour_schemes' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 Fix getRequestBody()

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Merge branch 'feature/JAL-3851_rest_api_for_genome_browser' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 merged to develop 2022-03-22

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    /doc/api_specification.md
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    /src/jalview/gui/Desktop.java
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    /src/jalview/rest/RestHandler.java
  1. … 3 more files in changeset.
JAL-3416 Updated FlatLaF to 2.1

    • binary
    /j11lib/flatlaf-2.1.jar
Merge branch 'develop' into ben/gecos_colour_schemes

JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.

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    /getdown/lib/getdown-launcher-local.jar
JAL-3978 Getdown add getdownappbase property to launched Jalview

    • binary
    /getdown/lib/getdown-launcher-local.jar