jalview

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JAL-3830 powershell wrapper tested on linux, macos and windows including spaces in paths. This is the way.

added untracked parsing attempts files

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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /test/jalview/fts/threedbeacons/.gitignore
Adding tests for 3DB, currently 2/4 corrects on PanelTest

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    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
Merge branch 'releases/Release_2_11_1_Branch'

JAL-3830 minor fix in powershell wrapper

JAL-3830 powershell follows symlinks as they do exist in NTFS, and of course in linux

JAL-3830 Powershell wrapper now works cross-platform. Who needs bash?!

JAL-3830 Make wrapper scripts executable

JAL-3830 powershell wrapper tested and fixed

JAL-3830 improved bash scripts. Added powershell script. Needs testing

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    /utils/getdown/jalviewc.ps1
JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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    /utils/getdown/jalviewc
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    /utils/getdown/jalviewc-macos
JAL-3523 Advanced the getdown version number

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    /getdown/lib/getdown-launcher-local.jar
JAL-3830 Improved for .app dir name with spaces, e.g. Jalview Local. Tested on mac to be working.

JAL-3523 Remove getdown setting the working directory to appdir

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    /getdown/lib/getdown-launcher-local.jar
JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

JAL-3830 first draft of wrapper script to go in macOS Jalview.app/Contents/MacOS/jalview

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    /utils/install4j/macos_jalview
JAL-3816 release date updated to 9th March

JAL-3816 release date set for 8th March and updated what's new

JAL-3816 new known defects JAL-3705 and JAL-3806

Merge branch 'task/JAL-3796_notarization' into develop

Merge branch 'develop' into task/JAL-3796_notarization

JAL-3796 minimal steps for notarization and the entitlements.txt file needed for the codesign tool

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    /utils/osx_signing/README
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    /utils/osx_signing/entitlements.txt
JAL-3618 Enable appBundleIsTraversable in JFileChooser on macOS

JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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    /src/jalview/util/ChannelProperties.java
JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

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    /test/jalview/util/MappingUtilsTest.java
Revert "JAL-3816 release notes for JAL-3806"

This reverts commit ead40d75a04715c80c61e34e277bb995cb2bef90.

JAL-3826 added root=true to editorconfig for IntelliJ

JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

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    /src/.editorconfig