-<html>\r
-<head><title>Input/Output</title></head>\r
-<body>\r
-<p><strong>Input</strong></p>\r
-<p>Jalview can read alignment files in any of the following standard formats:</p>\r
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
-<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of\r
- these file formats.</p>\r
-<p>Additionally, annotated whole sets of alignments and trees can be\r
-read from a Jalview\r
-(jar) format file using <strong>Desktop→Load Project</strong>. </p>\r
-<p>Use the <strong>Desktop→Input Alignment</strong> menu to read in files from:</p>\r
-<ul>\r
- <li><strong>From File</strong>: the local file system</li>\r
- <li><strong>From URL</strong>: the web (please use the full url)</li>\r
- <li><strong>from Textbox</strong>: a copy and paste into the\r
- "Cut & Paste" text window</li>\r
-</ul>\r
-<p>Jalview will try to recognise the file type automatically (using\r
-some special <a href="fileformats.html">features</a>). If a\r
-file is of an unknown format or there is any other error reading the\r
-alignment file then you will be given an error message. If you think\r
-Jalview really should be able to read your file, then send an email\r
-containing the problem file to jalview@jalview.org.\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 standard formats using <strong>File→Save As</strong></p>\r
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
-<p>You can also save the current set of alignments and their colours, annotations and\r
-trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
+-->
+<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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff