<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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.
--->
+ -->
<head>
<title>Input/Output</title>
</head>
<body>
-<p><strong>Input</strong></p>
-<p>Jalview can read alignment files in any of the following standard
-formats:</p>
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
-NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em></p>
-<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
-of these file formats.</p>
-<p>Additionally, whole sets of coloured and annotated alignments and
-trees can be read from a <a href="../features/jalarchive.html">Jalview
-(jar) format</a> file using <strong>Desktop→Load Project</strong>.</p>
-<p>Press "Control O" to open a file browser, or use
-the <strong>Desktop→Input Alignment</strong> menu to read in
-alignments from:</p>
-<ul>
- <li><strong>From File</strong>: the local file system</li>
- <li><strong>From URL</strong>: the web (please use the full url)</li>
- <li><strong>from Textbox</strong>: a copy and paste into the
- "Cut & Paste" text window</li>
-</ul>
-<p>Jalview will try to recognise the file type automatically (using
-some special <a href="fileformats.html">features</a>). If a file is of
-an unknown format or there is any other error reading the alignment file
-then you will be given an error message. If you think Jalview really
-should be able to read your file, then send an email containing the
-problem file to help@jalview.org.</p>
-<p>Jalview can also read jalview specific files for <a
- href="../features/featuresFormat.html">sequence features</a> and <a
- href="../features/annotationsFormat.html">alignment annotation</a>.</p>
-<p><strong>Output</strong></p>
-<p>Each alignment, whether it is the original or an edited version
-may be saved in the standard formats using <strong>File→Save
-As</strong></p>
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
-NBRF/PIR, Pfam/Stockholm</em></p>
-Jalview will by default append the sequence start and end to each
-sequence name, in the format /start-end. If you do not want this
-behaviour for a particular file output, open the "Output" tab
-on the
-<a href="../features/preferences.html">Preferences</a>
-window where you can select which file formats you want to append the
-start and end sequence positions for. In the case of PIR format, the
-output tab also contains a switch for turning on the output of Modeller
-style structured description lines.
-<p>Quantitative and symbolic <a href="../features/annotation.html">alignment
-annotation</a> can be exported as a comma separated value file by right
-clicking on an annotation row under the alignment.</p>
-<p>You can also save the current set of alignments and their
-colours, annotations and trees in a Jalview archive file using <strong>Desktop→Save
-project</strong>.</p>
-<p> </p>
+ <p>
+ <strong>Input</strong>
+ </p>
+ <p>Jalview can read alignment files in any of the following
+ standard formats:</p>
+ <p>
+ <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
+ NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
+ </p>
+ <p>
+ The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
+ of these file formats.
+ </p>
+ <p>
+ Additionally, whole sets of coloured and annotated alignments and
+ trees can be read from a <a href="../features/jalarchive.html">Jalview
+ (jar) format</a> file using <strong>Desktop→Load
+ Project</strong>.
+ </p>
+ <p>
+ Press "Control O" to open a file browser, or use the <strong>Desktop→Input
+ Alignment</strong> menu to read in alignments from:
+ </p>
+ <ul>
+ <li><strong>From File</strong>: the local file system</li>
+ <li><strong>From URL</strong>: the web (please use the full
+ url)</li>
+ <li><strong>from Textbox</strong>: a copy and paste into the
+ "Cut & Paste" text window</li>
+ </ul>
+ <p>
+ Jalview will try to recognise the file type automatically (using
+ some special <a href="fileformats.html">features</a>). If a file is
+ of an unknown format or there is any other error reading the
+ alignment file then you will be given an error message. If you think
+ Jalview really should be able to read your file, then send an email
+ containing the problem file to help@jalview.org.
+ </p>
+ <p>
+ Jalview can also read Jalview specific files for <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> and <a
+ href="../features/annotationsFormat.html"
+ >alignment annotation</a>.
+ </p>
+ <p>
+ <strong>Output</strong>
+ </p>
+ <p>
+ Each alignment, whether it is the original or an edited version may
+ be saved in the standard formats using <strong>File→Save
+ As</strong>
+ </p>
+ <p>
+ <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
+ NBRF/PIR, Pfam/Stockholm</em>
+ </p>
+ Jalview will by default append the sequence start and end to each
+ sequence name, in the format /start-end. If you do not want this
+ behaviour for a particular file output, open the "Output"
+ tab on the
+ <a href="../features/preferences.html">Preferences</a> window where
+ you can select which file formats you want to append the start and end
+ sequence positions for. In the case of PIR format, the output tab also
+ contains a switch for turning on the output of Modeller style
+ structured description lines.
+ <p>
+ Quantitative and symbolic <a href="../features/annotation.html">alignment
+ annotation</a> can be exported as a comma separated value file by
+ right clicking on an annotation row under the alignment.
+ </p>
+ <p>
+ You can also save the current set of alignments and their colours,
+ annotations and trees in a Jalview archive file using <strong>Desktop→Save
+ project</strong>.<br>The project data includes the state of any open
+ structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera
+ and Varna).
+ </p>
+ <p> </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff