From 922ffe0c08b4ce25da2bf25f7dbdf0641d3fd46f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 4 Jul 2019 09:05:12 +0100 Subject: [PATCH] JAL-3111 JAL-3348 JVL file documentation --- help/help/help.jhm | 1 + help/help/helpTOC.xml | 5 ++- help/help/html/features/clarguments.html | 6 +++ help/help/html/features/jvlfiles.html | 70 ++++++++++++++++++++++++++++++ 4 files changed, 80 insertions(+), 2 deletions(-) create mode 100644 help/help/html/features/jvlfiles.html diff --git a/help/help/help.jhm b/help/help/help.jhm index 0802bf1..47f7d53 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -61,6 +61,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 179fb06..7e358d6 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -154,13 +154,14 @@ - - + + + diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index ebdfcf3..60db069 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -27,6 +27,12 @@ See running Jalview from the command line for more information. +
+
Jalview processes arguments on the command line sequentially. If + you would like to pass a 'JVL' file containing + memory settings or any other launch + parameters, then include it at the beginning of the command line to + ensure they are processed before any remaining arguments.
diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html new file mode 100644 index 0000000..15df5d4 --- /dev/null +++ b/help/help/html/features/jvlfiles.html @@ -0,0 +1,70 @@ + + +JVL - Jalview Launch Files + +

+ Jalview Launch Files - JVL +

+

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

+ +

+ 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 
+# http://www.jalview.org/getdown/release
+# and then try to open this file again
+jalview.apparg=-open
+jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=-annotations
+jalview.apparg=http://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=http://www.jalview.org/old/v2_10_5/
+
+ For security, the Jalview application will only allow + appbase URLs from www.jalview.org, or your local file system. + + -- 1.7.10.2