How to supress opening any files on startup?

Jalview Discussion
1

Per The Jalview Executable’s Command Line Arguments, I see the -open startup option allows me to Specify the alignment file to open or process by providing additional arguments, thereby overriding the default example files that are loaded on startup. However, I do not see how to launch Jalview without opening any file at all.

I tried -open "\path\to\non-existent\file" but this creates a display whose sequence is “\path\to\non-existent\file”

I tried -open "" but this raises:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0 at java.lang.String.charAt(String.java:658) at jalview.bin.ArgsParser.<init>(ArgsParser.java:45) at jalview.bin.Jalview.doMain(Jalview.java:301) at jalview.bin.Jalview.main(Jalview.java:222)

Might this issue be a variation of: Unwanted opening of the example file at start up on a 64-bit install ?

2

I now see that my need may be accomplished by un-checking Preferences > Visual > Open File.

I’d still like to control this from the command line, if possible.

3

Adjusting Jalview’s preferences to disable the startup file is the first exercise in our introductory jalview training courses ! See https://www.jalview.org/tutorial/exercises/ex-1-Downloading/.

For Jalview 2.11.2.6 you can just specify a properties file containing your desired user preferences configuration - what I’d suggest is first configure Jalview as you need it, then make a copy of the .jalview_properties file (should be in the top level of your user’s home directory) and pass it in via -props

Jalview 2.11.3 has a completely new CLI system - it should allow the startup file preference to be ignored, but @ben_soares can provide clarification there.

I’m presuming, however, you’d like to launch jalview with the -groovy argument to pass in a groovy script. Ideally, jalview ought to ignore the startup file when an argument like that is passed in… I think we can perhaps raise that as an enhancement and squeeze in a patch before the next release.

You could also insert this additional line in the server groovy script:

// close all windows
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

// start listening for commands
new groovy.ui.GroovySocketServer(
    new GroovyShell(
        new Binding(['process':process])),

Jim

4

For the upcoming release of Jalview, as part of a completely revamped command line argument interface, I’ve added a

jalview --nostartupfile

argument which will prevent the startup file from showing just for that session.
Look out for Jalview 2.11.3!

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