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JAL-3111 JAL-3348 JVL file documentation
authorJim Procter <jprocter@issues.jalview.org>
Thu, 4 Jul 2019 08:05:12 +0000 (09:05 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Thu, 4 Jul 2019 08:05:12 +0000 (09:05 +0100)
help/help/help.jhm patch | blob | history
help/help/helpTOC.xml patch | blob | history
help/help/html/features/clarguments.html patch | blob | history
help/help/html/features/jvlfiles.html [new file with mode: 0644] patch | blob

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 0802bf1..47f7d53 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -61,6 +61,7 @@
    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
+   <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 179fb06..7e358d6 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -154,13 +154,14 @@
                        </tocitem>
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
-               <tocitem text="Memory Settings" target="memory" expand="false"/>
                <tocitem text="Scripting with Groovy" target="groovy">
                        <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
                </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
                        <tocitem text="Command Line Arguments" target="clarguments" />
-               </tocitem>
+    <tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
+    </tocitem>
                <tocitem text="Privacy" target="privacy" />
        </tocitem>
        <tocitem text="Useful information" expand="true">
diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index ebdfcf3..60db069 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -27,6 +27,12 @@
   See
   <a href="commandline.html">running Jalview from the command line</a>
   for more information.
+  <br />
+  <br />Jalview processes arguments on the command line sequentially. If
+  you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
+  <a href="../memory.html">memory settings</a> or any other launch
+  parameters, then include it at the beginning of the command line to
+  ensure they are processed before any remaining arguments.
   <br>
   <table width="100%" border="1" cellspacing="0" cellpadding="0">
     <tr>
diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html
new file mode 100644 (file)
index 0000000..15df5d4
--- /dev/null
+++ b/help/help/html/features/jvlfiles.html
@@ -0,0 +1,70 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<title>JVL - Jalview Launch Files</title>
+<body>
+  <p>
+    <strong>Jalview Launch Files - JVL</strong>
+  </p>
+  <p>Files with a '.jvl' (or .JVL) extension can be opened by the
+    Jalview desktop application, and allow you to:</p>
+  <ul>
+    <li><strong>Switch between different Jalview Versions</strong></li>
+    <li><strong>Configure the <a href="../memory.html">proportion
+          of memory</a> allocated to Jalview
+    </strong></li>
+    <li><strong>Import data and pass <a
+        href="clarguments.html">command line arguments</a></strong></li>
+  </ul>
+  <p>
+    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 <a
+      href="../commandline.html">command line</a>
+  </p>
+  <p>
+    <strong>Passing command line arguments</strong>
+  <pre>
+# 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
+</pre>
+  <p>
+    <strong>Launching a different version of Jalview</strong>
+  <pre>
+# 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/
+</pre>
+  For security, the Jalview application will only allow
+  <em>appbase</em> URLs from www.jalview.org, or your local file system.
+</body>
+</html>