X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=fcdb90802df39a161304463cf9209768b1d99ae4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=afd35861a6f4d994089cdd69fdc327d1327ad698;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index afd3586..fcdb908 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -31,9 +31,8 @@
     Alignment annotations can be imported onto an alignment since
     version 2.08 of Jalview, via an annotations file. It is a simple
     ASCII text file consisting of tab delimited records similar to the <a
-      href="featuresFormat.html"
-    >Sequence Features File</a>, and introduced primarily for use with the
-    Jalview applet.
+      href="featuresFormat.html">Sequence Features File</a>, and
+    introduced primarily for use with the Jalview applet.
   </p>
 
   <p>
@@ -55,8 +54,8 @@
     alignment window.
   </p>
   <p>
-    <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation file
-    consists of lines containing an instruction followed by tab
+    <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation
+    file consists of lines containing an instruction followed by tab
     delimited fields. Any lines starting with &quot;#&quot; are
     considered comments, and ignored. The sections below describe the
     structure of an annotation file.
@@ -83,11 +82,10 @@
   </ul>
   <p>
     At the end of this document, you can also find notes on <a
-      href="#compatibility"
-    >compatibility</a> of annotation files across different versions of
-    Jalview. An <a href="#exampleann">example annotation file</a> is
-    also provided along with instructions on how to import it to
-    Jalview.
+      href="#compatibility">compatibility</a> of annotation files
+    across different versions of Jalview. An <a href="#exampleann">example
+      annotation file</a> is also provided along with instructions on how to
+    import it to Jalview.
   </p>
   <hr />
   <p>
@@ -110,8 +108,9 @@
     followed by a <em>description</em> for the row, which is shown in a
     tooltip when the user mouses over the annotation row's label. Since
     Jalview 2.7, the description field may also contain HTML tags (in
-    the same way as a <a href="featuresFile.html">sequence feature's</a>
-    label), providing the text is enclosed in an &lt;html/&gt; tag.
+    the same way as a <a href="featuresFormat.html">sequence
+      feature's</a> label), providing the text is enclosed in an
+    &lt;html/&gt; tag.
   <ul>
     <em>Please note: URL links embedded in HTML descriptions are
       not yet supported.</em>
@@ -124,6 +123,7 @@
     <em>GRAPH_TYPE</em>. The allowed values of <em>GRAPH_TYPE</em> and
     corresponding interpretation of each <em>Value</em> are shown below:
 
+
   
   <ul>
     <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
@@ -190,9 +190,9 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
   </ul>
   </p>
   <p>
-    <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br /> Groups
-    of sequences and column ranges can be defined using a tab delimited
-    statement like:
+    <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br />
+    Groups of sequences and column ranges can be defined using a tab
+    delimited statement like:
   </p>
   <pre>SEQUENCE_GROUP&#9;Group_Name&#9;Group_Start&#9;Group_End&#9;<em>Sequences</em>
   </pre>
@@ -296,8 +296,8 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
       <tr>
         <td width="50%">hide</td>
         <td>Boolean (default false) indicating whether the rows in
-          this group should be marked as hidden.<br />
-        <em>Note:</em> if the group is sequence associated (specified by
+          this group should be marked as hidden.<br /> <em>Note:</em>
+          if the group is sequence associated (specified by
           SEQUENCE_REF), then all members will be hidden and marked as
           represented by the reference sequence.
         </td>
