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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git] / help / html / io / fileformats.html
diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index 7bfc435..8f88c26 100755 (executable)
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -31,50 +31,80 @@ td {
 </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%">&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>
-</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%">&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>