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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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>Alignment Fileformats</title>
<style type="text/css">
</head>
<body>
-<p><strong>Alignment Fileformats</strong>
-<p>Jalview understands a wide range of sequence alignment formats. In
-order to determine which format has been used for an alignment,
-jalview tries to detect some text or formatting unique to one of the formats:
-</p>
-<table width="100%" border="1">
-<tr><td width="17%">Format</td>
-<td width="60%">Unique File Feature</td>
-<td width="23%">File Extension</td>
-<tr>
-<td width="17%">FASTA</td>
-<td width="60%">>SequenceName<br>
-THISISASEQENCE<br></td>
-<td width="23%">.fa, .fasta</td>
-</tr><tr><td width="17%">MSF</td>
-<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
-<em>..</em><br>
-//<br></td>
-<td width="23%">.msf</td>
-</tr><tr><td width="17%">CLUSTALW</td>
-<td width="60%">CLUSTAL</td>
-<td width="23%">.aln</td>
-</tr><tr><td width="17%">PILEUP</td>
-<td width="60%">PileUp</td>
-<td width="23%"></td>
-</tr><tr><td width="17%">PIR</td>
-<td width="60%">>P1;</td>
-<td width="23%">.pir</td>
-</tr><tr><td width="17%">BLC</td>
-<td width="60%">>Seq1<br>
->Seq2</td>
-<td width="23%">.blc</td>
-</tr><tr><td width="17%">PFAM</td>
-<td width="60%">SequenceName THISISASEQENCE</td>
-<td width="23%">.pfam</td>
-</tr>
-</table>
-<p>The file extensions are used to associate jalview alignment icons
-with alignment files: <img src="file.png" width=12 height=12 >
-</p>
+ <p>
+ <strong>Alignment File Formats</strong>
+ <p>Jalview understands a wide range of sequence alignment formats.
+ In order to determine which format has been used for an alignment,
+ Jalview tries to detect some text or formatting unique to one of the
+ formats:</p>
+ <table width="100%" border="1">
+ <tr>
+ <td width="17%">Format</td>
+ <td width="60%">Unique File Feature</td>
+ <td width="23%">File Extension</td>
+ <tr>
+ <td width="17%">FASTA</td>
+ <td width="60%">>SequenceName<br> THISISASEQUENCE<br></td>
+ <td width="23%">.fa, .fasta</td>
+ </tr>
+ <tr>
+ <td width="17%">MSF</td>
+ <td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br> <em>..</em><br>
+ //<br></td>
+ <td width="23%">.msf</td>
+ </tr>
+ <tr>
+ <td width="17%">CLUSTALW</td>
+ <td width="60%">CLUSTAL</td>
+ <td width="23%">.aln</td>
+ </tr>
+ <tr>
+ <td width="17%">PILEUP</td>
+ <td width="60%">PileUp</td>
+ <td width="23%"></td>
+ </tr>
+ <tr>
+ <td width="17%">PIR</td>
+ <td width="60%">>P1;</td>
+ <td width="23%">.pir</td>
+ </tr>
+ <tr>
+ <td width="17%">BLC</td>
+ <td width="60%">>Seq1<br> >Seq2
+ </td>
+ <td width="23%">.blc</td>
+ </tr>
+ <tr>
+ <td width="17%">PFAM</td>
+ <td width="60%">SequenceName THISISASEQUENCE</td>
+ <td width="23%">.pfam</td>
+ </tr>
+ <tr>
+ <td width="17%">Stockholm</td>
+ <td width="60%"># STOCKHOLM VersionNumber<br> <em>...</em><br>//
+ </td>
+ <td width="23%">.stk, .sto</td>
+ </tr>
+ <tr>
+ <td width="17%">Phylip</td>
+ <td width="60%">Line starts with two numbers separated by
+ white space<br> <em>...</em><br>//
+ </td>
+ <td width="23%">.phy</td>
+ </tr>
+ <tr>
+ <td width="17%">JSON</td>
+ <td width="60%">Data starts with '{' <br>Data ends with
+ '}' <br>
+ <br>See <a href="../features/bioJsonFormat.html">BioJSON</a>
+ for more infomation about the Jalview JSON format <br></td>
+ <td width="23%">.json</td>
+ </tr>
+
+ </table>
+ <p>
+ The file extensions are used to associate Jalview alignment icons
+ with alignment files: <img src="file.png" width=12 height=12>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff