jalview

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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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    • +306
    /test/jalview/util/MappingUtilsTest.java
JAL-3700 additions and corrections to unit tests

    • -172
    • +306
    /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

    • -14
    • +18
    /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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    • +3
    /src/jalview/analysis/AlignmentUtils.java
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence

JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true) to verify mapping matches seq’s dataset sequence start/end rather than seq

Merge branch 'failingTest/JAL-3748_reconstructCDSafterProteinMSA' into cherry-pick/JAL-3700mapSequenceSelection

JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView so it can be recovered after a web service operation

    • -0
    • +31
    /src/jalview/datamodel/AlignmentView.java
    • -0
    • +185
    /test/jalview/gui/SplitFrameTest.java
JAL-3675 logged JAL-3748 as known defect

JAL-3765 JAL-3718 release notes

changeset discussion

  1. Jim Procter: not related to JAL-3765 ! Actually related to JAL-3675!
Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3718 fixed getdown auto-update for future updates. Getdown Jars and version files.

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3718 fixed getdown auto-update for future updates. Getdown src files only

JAL-3675 typo in release notes :(

JAL-3675 update release date and release notes for JAL-3732

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

    • binary
    /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

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

JAL-3746 bump release version for 2.11.2 series (currently on develop)

JAL-3744 this obvious attempt to detect/gunzip file input for jalviewjs fails

JAL-2422 comments updated re ALTLOC handling

JAL-3576 unit test for preserving order of colocated features

JAL-3679 Added externally specified plugins dir to J2sPlugin check