+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+#
+# 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/>.
+#-------------------------------------------------------------------------------
<html>
-<title>Jalview Command Line Arguments
-</title>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<title>Jalview Command Line Arguments</title>
<body>
- <p><strong>The Jalview Executable's Command Line
- Arguments</strong></p>
- See <a href="commandline.html">running Jalview from the command
- line</a> for more information.<br>
- <table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr >
- <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
- </tr>
-
- <tr>
- <td><div align="center">-props FILE</div></td>
- <td><div align="left">Use the given Jalview properties file instead
- of users default.</div></td>
- </tr>
- <tr>
- <td><div align="center">-features FILE</div></td>
- <td><div align="left">
- <p>Use the given file to add sequence features to an alignment.
- See <a href="featuresFormat.html" target="NEW">Features
- File</a> (Known as Groups file prior to 2.08) description. </p>
-
- </div></td>
- </tr>
+<p><strong>The Jalview Executable's Command Line Arguments</strong></p>
+See
+<a href="commandline.html">running Jalview from the command line</a>
+for more information.
+<br>
+<table width="100%" border="1" cellspacing="0" cellpadding="0">
<tr>
- <td>
- <div align="center">-annotations FILE</div>
+ <td width="27%">
+ <div align="center">-nodisplay</div>
+ </td>
+ <td width="73%">
+ <div align="left">Run Jalview without User Interface.
+ (automatically disables questionnaire, version and usage stats checks)</div>
</td>
- <td>Add precalculated annotations to the alignment. See <a
- href="annotationsFormat.html" target="NEW">Annotation File</a>
- description.</td>
</tr>
+
<tr>
<td>
- <div align="center"></div>
+ <div align="center">-props FILE</div>
+ </td>
<td>
- <div align="left"></div>
+ <div align="left">Use the given Jalview properties file instead
+ of users default.</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-nodisplay</div>
+ <div align="center">-features FILE</div>
+ </td>
<td>
- <div align="left">Run Jalview without User Interface</div>
+ <div align="left">
+ <p>Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features File</a>
+ (Known as Groups file prior to 2.08) description.</p>
+
+ </div>
</td>
</tr>
<tr>
<td>
- <div align="center">-props FILE</div>
- <td>
- <div align="left">Use the given Jalview properties file instead
- of users default</div>
+ <div align="center">-colour COLOURSCHEME</div>
</td>
+ <td>Set the colourscheme for the alignment. This can be any of
+ the built-in colourschemes, a name of a predefined colourscheme
+ (defined in the jalview properties file), or an 'inline' colourscheme
+ (see the applet's colour parameter for more information).</td>
</tr>
<tr>
<td>
- <div align="center">-tree FILE</div>
- <td>
- <div align="left">Load the given newick format tree file onto
- the alignment</div>
+ <div align="center">-annotations FILE</div>
</td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW">Annotation File</a>
+ description.</td>
</tr>
<tr>
<td>
- <div align="center">-features FILE</div>
+ <div align="center">-tree FILE</div>
<td>
- <div align="left">Use the given file to mark features on the
- alignment</div>
+ <div align="left">Load the given newick format tree file onto
+ the alignment</div>
</td>
</tr>
<tr>
<div align="left">Turn off questionnaire check</div>
</td>
</tr>
- <tr><td>
+ <tr>
+ <td>
<div align="center">-nousagestats</div>
<td>
<div align="left">Turn off google analytics usage tracking</div>
</tr>
<tr>
<td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of
+ associated view when a new tree is displayed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
<div align="center">-dasserver nickname=URL</div>
<td>
- <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments<br>
- Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
+ <div align="left">Add and enable a <a href="dassettings.html">DAS
+ server</a> with given nickname (alphanumeric or underscores only) for
+ retrieval of features for all alignments<br>
+ Sources that also support the sequence command may be specified by
+ prepending the URL with 'sequence:'<br>
<em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
</td>
</tr>
<td>
<div align="center">-fetchfrom nickname</div>
<td>
- <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
- and display them</div>
+ <div align="left">Query a <a href="dassettings.html">DAS
+ source</a> called nickname for features for the alignments and display
+ them</div>
</td>
</tr>
<tr>
<td>
<div align="center">-groovy FILE</div>
<td>
- <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
- arguments have been processed</div>
+ <div align="left">Execute groovy script in FILE (where FILE may
+ be 'STDIN' to read from the standard input) after all other arguments
+ have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
+ <td>
+ <div align="left">Import the given vamsas document into a new
+ session.<br>
+ <em>New in 2.5</em></div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-vsess VAMSAS SESSION URL</div>
+ <td>
+ <div align="left">Join the given vamsas session<br>
+ If a document was also specified, this will be imported first and then
+ committed as new data from Jalview to the specified session
+ (Experimental - not yet enabled!).<em>New in 2.5</em></div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where FILE may
+ be 'STDIN' to read from the standard input) after all other arguments
+ have been processed</div>
</td>
</tr>
<tr>
<div align="left">Create alignment file FILE in Fasta format.</div>
</td>
</tr>
- <tr>
- <td><div align="center">-clustal FILE</div></td>
- <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-msf FILE</div></td>
+ <tr>
+ <td>
+ <div align="center">-clustal FILE</div>
+ </td>
+ <td>
+ <div align="left">Create alignment file FILE in Clustal format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-msf FILE</div>
+ </td>
- <td><div align="left">Create alignment file FILE in MSF format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pileup FILE</div></td>
- <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pir FILE</div></td>
+ <td>
+ <div align="left">Create alignment file FILE in MSF format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-pileup FILE</div>
+ </td>
+ <td>
+ <div align="left">Create alignment file FILE in Pileup format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-pir FILE</div>
+ </td>
- <td><div align="left">Create alignment file FILE in PIR format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pfam FILE</div></td>
- <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-blc FILE</div></td>
- <td><div align="left">Create alignment file FILE in BLC format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-jalview FILE</div></td>
+ <td>
+ <div align="left">Create alignment file FILE in PIR format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-pfam FILE</div>
+ </td>
+ <td>
+ <div align="left">Create alignment file FILE in PFAM format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-blc FILE</div>
+ </td>
+ <td>
+ <div align="left">Create alignment file FILE in BLC format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-jalview FILE</div>
+ </td>
- <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-png FILE</div></td>
- <td><div align="left">Create PNG image FILE from alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-imgMap FILE</div></td>
+ <td>
+ <div align="left">Create alignment file FILE in Jalview format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-png FILE</div>
+ </td>
+ <td>
+ <div align="left">Create PNG image FILE from alignment.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-imgMap FILE</div>
+ </td>
- <td><div align="left">Create HTML file FILE with image map of PNG
- image.</div></td>
- </tr>
- <tr>
- <td><div align="center">-eps FILE</div></td>
- <td><div align="left">Create EPS file FILE from alignment.</div></td>
- </tr>
- </table>
+ <td>
+ <div align="left">Create HTML file FILE with image map of PNG
+ image.</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-eps FILE</div>
+ </td>
+ <td>
+ <div align="left">Create EPS file FILE from alignment.</div>
+ </td>
+ </tr>
+</table>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff