jalview

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JAL-3762 syntax error typo

JAL-3762 check if Info.args already defined before overwriting it with URL args. Also stashes URL args at Info.urlargs

JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    • +53
    /test/jalview/util/MapListTest.java
JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    • +53
    /test/jalview/util/MapListTest.java
JAL-3760 fix tests for changed behaviour

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

    • -30
    • +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 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

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

JAL-3758 tweak what’s new for 2.11.1.2!

JAL-3758 release Fri 25th Sep

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

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

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

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

JAL-3758 2.11.1.2 patch release notes and version bump

JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

JAL-3751 only merge strictly contiguous ranges of mappings

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    • +88
    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3751 only merge strictly contiguous ranges of mappings

    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -10
    • +17
    /test/jalview/util/MappingUtilsTest.java
JAL-3751 only merge strictly contiguous ranges of mappings

    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -0
    • +7
    /test/jalview/util/MappingUtilsTest.java
JAL-3751 only merge strictly contiguous ranges of mappings

    • -112
    • +88
    /test/jalview/util/MapListTest.java
    • -0
    • +7
    /test/jalview/util/MappingUtilsTest.java
JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://

JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://

JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows testAlignProteinAsDna_incompleteStartCodon to pass

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