jalview

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JAL-3449 ensuring latest getdown jar files after merge

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3449 merge from develop

JAL-3529 attempt to guess database for a sequence’s AC record based on the sequence type if the alignment had no PFAM or RFAM accession

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    • +17
    /src/jalview/io/StockholmFile.java
JAL-3529 test for AC <Uniprot/EMBL> rather than DR in Stockholm file

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    /test/jalview/io/StockholmFileTest.java
JAL-3529 assert Uniprot refs must be provided as primary ‘AC’ ref

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    /test/jalview/io/StockholmFileTest.java
JAl-3187 JAL-3535 JAL-3534 update open feature settings when a different view is selected or close when none shown

JAL-3536 JAL-3187 don't create duplicate CDS-to-protein mappings

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3289 Added option and documentation for a TEST-LOCAL channel to test OTA updates using local filesystem

JAL-3252 download-jres.sh helper script for keeping JREs for all platforms up to date changed to create .zip files for getdown OTA updates

JAL-3536 failing test and test data

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    /examples/testdata/CantShowEnsemblCrossrefsTwice.jvp
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    /test/jalview/io/CrossRef2xmlTests.java
JAL-3534 patch for simple case (Protein or Nucleotide, but not linked): transfer feature settings dialog ref to exploded views, and preserve one of the feature settings dialogs refs when views are gathered again

JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mentioning common-compress updated.

    • binary
    /getdown/lib/getdown-launcher-local.jar
  1. … 4 more files in changeset.
JAL-3187 fix for JAL-3533 on CDS/Protein tabbed feature settings

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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/gui/SplitFrame.java
JAL-3187 JAL-3533 JAL-3535 set feature settings dialog title from view, and stash geometry for a feature settings dialog when closed, and re-use any existing geometry when dialog re-opened.

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    /src/jalview/api/AlignViewControllerGuiI.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/gui/FeatureSettings.java
JAL-3187 better semantics for feature settings closed event handler

JAL-3394 A little streamlining and fixing of helper script

JAL-3394 remove no longer used files

JAL-3532 TODO comment

fix for JAL-3529

JAL-3531 failing test

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    /test/jalview/util/DBRefUtilsTest.java
JAL-3529 more detailed asserts to detect whitespace in DBRefs imported from Stockholm

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    /test/jalview/io/StockholmFileTest.java
JAL-3529 preferentially output source dbrefs or principle db for sequence type before others.

JAL-3529 failing test for bug

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    /test/jalview/io/StockholmFileTest.java
JAL-3187 alternative solution - gather feature settings for CDS/Protein as tabs in a window managed by SplitFrame

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    /src/jalview/api/SplitContainerI.java
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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/gui/SplitFrame.java
JAL-1354 JAL-3528 fix bug from b594d516dac69eebcccdc743933880b00fb6d44c only try to look up message via formatMessage once.

JAL-3449 getdown resilience change to launcher classpath, includes the backup getdown-launcher.jar

JAL-3227 helper shell scripts for setting up a build environment

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    /utils/download_jdks.sh
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    /utils/download_jres.sh
JAL-3449 fix a getdownAppDir error introduced in previous commit 55f545014

JAL-3449 More tidying of build.gradle for CHANNEL selection

JAL-3187 applet alignFrame needs new api method

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    /src/jalview/appletgui/AlignFrame.java