Jalview Launch Files - JVL

Files with a '.jvl' (or .JVL) extension can be opened by the Jalview desktop application, and allow you to:

- Switch between different Jalview Versions
- Configure the proportion of memory allocated to Jalview
- Import data and pass command line arguments

Some example JVL files are given below - copy and paste them into a text editor and save them as a file with the extension '.jvl'. To test, open your saved .jvl file via the OSX File Chooser or Windows file explorer, or pass it to Jalview via the command line

Passing command line arguments

    # Jalview Launch File
    # Please install the Jalview Desktop from
    # https://www.jalview.org/getdown/release
    # and then try to open this file again
    jalview.apparg=-open
    jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
    jalview.apparg=-annotations
    jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
    jalview.apparg=-colour
    jalview.apparg=Clustal

Launching a different version of Jalview

    # Jalview Launch File
    # Please install the Jalview Desktop from
    # http://www.jalview.org/getdown/release
    # and then try to open this file again
    appbase=https://www.jalview.org/getdown/archive/2_10_5/

For security, the Jalview application will only allow appbase URLs from www.jalview.org.