jalview

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fix for JAL-3765

fix for JAL-3765

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

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    /test/jalview/analysis/FinderTest.java
not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

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

JAL-3763 unused method removed

JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3763 failsafe check for null

JAL-3763 failsafe check for null

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 always make a new dataset sequence for CDS sequence

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3763 always make a new dataset sequence for CDS sequence

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3761 failing test, formatting, method renamed

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    /test/jalview/util/MapListTest.java
JAL-3762 check for !args || args=="" before overwriting

JAL-3762 more typo fixing :q

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-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

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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 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!