jalview

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JAL-3335 much improved getdown background images

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    /utils/getdown/jalview_logo_background_fade-640x480.xcf
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    /utils/getdown/jalview_logo_background_getdown-640x480.png
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    /utils/getdown/jalview_logo_background_getdown_error-640x480.png
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    /utils/getdown/jalview_logo_background_getdown_instant-640x480.png
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    /utils/getdown/jalview_logo_background_getdown_instant-640x480.xcf
JAL-3322 Progress bar status tweaks

JAL-3322 getdown Application class fix

Merge branch 'develop' into JAL-3322_getdown_speed_improvement

merging in develop

JAL-3322 corrected fix to convertBuildingMD task fail. removed debugging warnings from getdown config backups

Merge branch 'JAL-3322_getdown_speed_improvement' of https://source.jalview.org/git/jalview into JAL-3322_getdown_speed_improvement

parallel dev

JAL-3322 fixed convertBuildingMD task skipping in Windows

Merge branch 'JAL-3322_getdown_speed_improvement' into develop

JAL-3322 linksCheck task output.

JAL-3322 Removed debug logging. Enabled backup install/getdown.txt config. Added a dev doc diagram.

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    /doc/getdown_installation_structure.pdf
JAL-3322 Once background displayed, allow asynchronous progress setting

JAL-3111 fixed an anchor name link preventing linkCheck task from completing successfully

Merge branch 'develop' into releases/Release_2_11_Branch

JAL-3111 sign the uninstaller script .. again

Merge branch 'improvement/JAL-3322_getdown_splashscreen_visibility' into develop also note JAL-3320 addressed (groovy console opening with Java 11)

Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility

Merge branch 'develop' into releases/Release_2_11_Branch

JAL-3111 release notes for JAL-3334 JAL-3330 and rejig others

Merge branch 'bug/JAL-3330' into develop

JAL-3334 fix - always load full SO to resolve the sequence features from Ensembl correctly

JAL-3111 get rid of nasty tab characters

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    /src/jalview/bin/Jalview.java
JAL-3332 test to check for duplicate db sources and patch to code. crept in after das source removal

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    /test/jalview/ws/SequenceFetcherTest.java
JAL-3130 Added all groovy jars for groovy console

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    /j11lib/groovy-2.5.7.jar
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    /j11lib/groovy-ant-2.5.7.jar
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    /j11lib/groovy-bsf-2.5.7.jar
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    /j11lib/groovy-cli-commons-2.5.7.jar
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    /j11lib/groovy-cli-picocli-2.5.7.jar
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    /j11lib/groovy-console-2.5.7.jar
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    /j11lib/groovy-datetime-2.5.7.jar
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    /j11lib/groovy-dateutil-2.5.7.jar
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    /j11lib/groovy-docgenerator-2.5.7.jar
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    /j11lib/groovy-groovydoc-2.5.7.jar
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    /j11lib/groovy-groovysh-2.5.7.jar
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    /j11lib/groovy-jaxb-2.5.7.jar
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    /j11lib/groovy-jmx-2.5.7.jar
  1. … 13 more files in changeset.
Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility

merging with develop

JAL-3322 Splashcreen now appears instantly with new setting ui.progress_sync = true. Some other minor improvements

  1. … 28 more files in changeset.
JAL-3330 JAL-3332 relocate and simplify BeforeClass/BeforeTest to avoid ambiguity in setup

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    /test/jalview/gui/AlignFrameTest.java
JAL-3330 test to verify sub/attributeName array is not shared between multiple instances after copy-via-copy constructor

JAL-3330 javadoc

JAL-3322 replaced invokeAndWait(r) with r.run() and fixed nullpointer error in jvl config reading

JAL-3289 Ehancements to ARCHIVE building and script to show how to batch build and rsync the archived versions

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    /utils/archive_building.sh