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JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this...
[jalview.git] / help / help / html / io / fileformats.html
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+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>Alignment Fileformats</title>
+<style type="text/css">
+<!--
+td {
+       text-align: center;
+}
+-->
+</style>
+</head>
+<body>
+
+  <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%">&gt;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%">&gt;P1;</td>
+      <td width="23%">.pir</td>
+    </tr>
+    <tr>
+      <td width="17%">BLC</td>
+      <td width="60%">&gt;Seq1<br> &gt;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>