jalview

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JAL-3829 attempt to fix my changes to follow the Jira issue

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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    /utils/getdown/bin/jalview.bat
JAL-3830 Follow all SymbolicLinks in Windows powershell wrapper

fixed last commit

Request now parses the whole structures, need to fix the result

JAL-3830 delete channel.props and channel.propsv when uninstalling

JAL-3633 new getdown jars

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3633 refactored/simplified LaunchUtils code

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    /src/jalview/util/ChannelProperties.java
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    /src/jalview/util/LaunchUtils.java
TDB.executeRequest fix & test passed

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    /src/jalview/fts/core/FTSRestResponse.java
Added (and passed !)all the FTS tests from test.fts.core

Created 3Dbeacons data_columns.txt Test passed for data columns

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    /resources/fts/tdbeacons_data_columns.txt
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    /src/jalview/fts/core/FTSRestResponse.java
JAL-3633 new getdown jars

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3633 getdown reads jalview_properties for proxy settings

JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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    /utils/getdown/bin/jalview.ps1
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    /utils/getdown/bin/jalview.sh
JAL-3503 Changed decimal display of memory in Prefences

JAL-3594 Making default .jalview_properties file separate. Now .jalview_nonrelease_properties

JAL-3503 missed a widget being disabled

JAL-3503 New getdown version and jar files

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/LaunchUtils.java
  1. … 6 more files in changeset.
JAL-3830 Allow paths to start with '~'. Make path check more succinct.

JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

JAL-3830 add the windows bash script to getdown files and install4j installers

JAL-3830 bash script that works in both cygwin and WSL (Windows Subsystem for Linux)

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    /utils/getdown/jalviewc-windows
JAL-3830 Delete wrapper scripts and getdown *v files when uninstalling

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