-<html>\r
-<body>\r
-<p><strong>Input</strong></p>\r
-<p>Jalview can read alignment files in any of the following formats:</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>Use the menu at the top of the main application window to read in files from\r
-</p>\r
-<ul>\r
- <li> the local file system</li>\r
- <li>a remote website</li>\r
- <li>or by copying and pasting into the "Cut & Paste" text window</li>\r
-</ul>\r
-<p>If a file is of an unknown format or there is any other error reading the alignment\r
- file you will be given an error message, the alignment will not be read in.\r
-</p>\r
-<p><strong>Output</strong> </p>\r
-<p>Each alignment, whether it is the original or an edited version may be saved\r
- in the formats</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>The alignment may also be saved as a HTML web page. </p>\r
-<p>You may save a jpg image of your alignment. </p>\r
-<p>The alignment can be printed from a local printer.</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * 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.
+ *
+ * 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.
+ -->
+<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>.<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