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mungo carstairs <gmungoc@gmail.com> in jalview

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

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

relevant issue is JAL-3626

relevant issue is JAL-3626

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

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

    • -22
    • +26
    /src/jalview/analysis/AlignmentUtils.java
Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

JAL-3469 add "Number=." fields (all values) to all alleles in VCF record

    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3423 more System.lineSeparator() in place of \n

    • -9
    • +9
    /test/jalview/analysis/TestAlignSeq.java
    • -2
    • +5
    /test/jalview/math/RotatableMatrixTest.java
JAL-3423 test coverage

    • -0
    • +1
    /test/jalview/datamodel/PDBEntryTest.java
JAL-3253 rename method, add Javadoc

JAL-3423 use System.lineSeparator() in code and tests

    • -11
    • +9
    /src/jalview/analysis/AlignSeq.java
JAL-32423 tidying

    • -6
    • +6
    /test/jalview/gui/AlignViewportTest.java
    • -5
    • +5
    /test/jalview/gui/AlignmentPanelTest.java
    • -17
    • +3
    /test/jalview/gui/SeqCanvasTest.java
    • -13
    • +0
    /test/jalview/gui/SeqPanelTest.java
why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

JAL-2994 utility method to match a list of folder/file patterns

    • -3
    • +46
    /test/jalview/util/FileUtilsTest.java
JAL-2937 working Cygwin bash execution of hmmbuild on Windows

    • -25
    • +52
    /src/jalview/hmmer/HmmerCommand.java
JAL-2937 Cygwin path preference, method refactoring

    • -13
    • +50
    /src/jalview/gui/Preferences.java
    • -49
    • +51
    /src/jalview/hmmer/HmmerCommand.java
    • -32
    • +82
    /src/jalview/jbgui/GPreferences.java
JAL-2629 more error checking

JAL-2937 extract reusable utility method

    • -0
    • +56
    /src/jalview/util/FileUtils.java
JAL-845 reduced height to allow for Desktop decorators on Windows

JAL-1596 set HTTP 1.1 in HttpClient