jalview

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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

JAL-3748 fix compilation error

JAL-3748 maximal test for JAL-3748 using covid19 CDS/Protein

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    /test/jalview/gui/SplitFrameTest.java
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.

JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region

JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch

JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.

JAL-3748 test data for SplitFrameTest

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    /examples/testdata/MN908947.jvp
JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

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    /src/jalview/analysis/SeqsetUtils.java
JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences

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    /test/jalview/datamodel/SeqCigarTest.java
JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

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    /test/jalview/datamodel/SeqCigarTest.java
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-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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    /resources/images/jalview_logos.ico
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Merge branch 'releases/Release_2_11_1_Branch'

JAL-3675 release notes for JAL-3750 JAL-3751

Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

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    /help/help/html/features/commandline.html
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    /help/help/html/features/jvlfiles.html
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    /help/help/html/groovy/featuresCounter.html
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    /help/help/html/webServices/newsreader.html
JAL-3750 parse protocol before checking if argument to -open can be opened as a file

JAL-3675 patch release date 17th September 2020

JAL-3700 additions and corrections to unit tests (trivial) Conflicts: test/jalview/util/MappingUtilsTest.java

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    /test/jalview/util/MappingUtilsTest.java
JAL-3700 additions and corrections to unit tests

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    /test/jalview/util/MappingUtilsTest.java
JAL-3748 preserve sequence IDs from original alignment view when alignment returned by web service or analysis method.

JAL-3748 recover complement alignment from complement alignmentView rather than let ‘alignAs’ to do the work

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    /src/jalview/ws/jws2/MsaWSThread.java
JAL-3748 make findAlignedSequence require mapped from/to to properly contain the given CDS or protein sequence

JAL-3748 pass a list to findAlignedSequence to return mapping that relates CDS and the returned Peptide sequence to avoid searching twice

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    /src/jalview/analysis/AlignmentUtils.java