jalview

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JAL-3660 Fix for specified output format when using command line arg to convert a file

JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

JAL-3765 fix test

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    /test/jalview/analysis/FinderTest.java
fix for JAL-3765

Merge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path

JAL-3760 fix tests for changed behaviour

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    /test/jalview/util/ComparisonTest.java
JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like

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    • +39
    /src/jalview/util/Comparison.java
JAL-3753 ensure correct dependencies for shadowJar task

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings
Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

JAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding errors (needed to fix failing test)

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    /test/jalview/bin/MemorySettingTest.java
JAL-3753 Resources seen in tests and appropriate filters now being used as file opt-in rather than opt-out.

Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop

JAL-3753 put resources in gradle run and test path

JAL-3753 JAL-3754 first rejig

JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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    /getdown/lib/getdown-launcher-local.jar
JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

Merge branch 'feature/JAL-3615gzipXfam' into develop