From: Ben Soares Date: Tue, 30 May 2023 10:36:12 +0000 (+0100) Subject: JAL-629 JAL-4121 Added documentation to Help docs and Usage statement X-Git-Tag: Release_2_11_4_0~285 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4ccb1103e2ac2a0e588cc12cf8cae28bbe48bd2c;p=jalview.git JAL-629 JAL-4121 Added documentation to Help docs and Usage statement --- diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 626fb8c..7a87602 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -408,6 +408,10 @@

+

+ Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless). To use Jalview with --output and not assume headless mode, use the --gui or --noheadless argument (the order doesn't matter). +

+

--format

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html index 6d65033..6b98b7c 100644 --- a/help/help/html/features/clarguments-reference.html +++ b/help/help/html/features/clarguments-reference.html @@ -65,8 +65,16 @@ ‑‑help‑allHelp for all arguments - ‑‑headless - Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. + ‑‑headless / ‑‑noheadless + Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed. +
+ If you use a command line argument to specify an output file of some kind (--output, --image or --structureimage) then headless mode will be assumed. If you don't want this behaviour use --noheadless or --gui. + + + + + ‑‑gui + Force Jalview to run in graphical mode. This can be used to counter the assumption of headless mode when an argument that creates an output file is used. --gui takes precedence over --headless. @@ -76,27 +84,27 @@ ‑‑news / ‑‑nonews - Show (or don't show) the news feed. + Show (/ or don't show) the news feed. ‑‑splash / ‑‑nosplash - Show (or don't show) the About Jalview splash screen. + Show (/ or don't show) the About Jalview splash screen. ‑‑questionnaire / ‑‑noquestionnaire - Show (or don't show) the questionnaire if one is available. + Show (/ or don't show) the questionnaire if one is available. ‑‑usagestats / ‑‑nousagestats - Send (or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview! + Send (/ or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview! ‑‑webservicediscovery / ‑‑nowebservicediscovery - Attempt (or don't attempt) to connect to JABAWS web services. + Attempt (/ or don't attempt) to connect to JABAWS web services. @@ -114,10 +122,12 @@ Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR. +