--- /dev/null
+<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>
git://source.jalview.org / jalview.git / blobdiff