X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FfeaturesFormat.html;h=fd6b99f5b1becbdd8ab9fb4d917293310b6b8d9d;hb=0bee8aadc22e41e4793db251a7d37a839bd77db8;hp=257d42cbd047c1fbbcf0e3ee624a9cca11418be6;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index 257d42c..fd6b99f 100755
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * 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.
  * 
@@ -83,7 +83,7 @@
         <li><em>label</em><br> Indicate that the feature
           description should be used to create a colour for features of
           this type.<br> <em>Note: if no threshold value is
-            needed then the final '|' may be ommitted.<br> This
+            needed then the final '|' may be omitted.<br> This
             keyword was added in Jalview 2.6
         </em></li>
 
@@ -121,11 +121,12 @@
     a colour the feature).</p>
 
   <p>
-    If your sequence annotation is already available in GFF Format (see
-    <a href="http://www.sanger.ac.uk/resources/software/gff/spec.html">http://www.sanger.ac.uk/resources/software/gff/spec.html</a>),
-    then you can leave it as is, after first adding a line containing
-    only 'GFF' after any Jalview feature colour definitions (<em>this
-      mixed format capability was added in Jalview 2.6</em>). Alternately,
+    If your sequence annotation is already available in <a href="http://gmod.org/wiki/GFF2">GFF2</a> (http://gmod.org/wiki/GFF2) or
+    <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">GFF3</a> 
+    (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, 
+    then you can leave it as is, after first adding a line containing only
+    'GFF' after any Jalview feature colour definitions (<em>this
+    mixed format capability was added in Jalview 2.6</em>). Alternately,
     you can use Jalview's own sequence feature annotation format, which
     additionally allows HTML and URLs to be directly attached to each
     piece of annotation.
@@ -141,13 +142,13 @@
 </pre>
 
   This format allows two alternate ways of referring to a sequence,
-  either by its text ID, or its index in an associated alignment.
-  Normally, sequence features are associated with sequences rather than
-  alignments, and the sequenceIndex field is given as &quot;-1&quot;. In
-  order to specify a sequence by its index in a particular alignment,
-  the sequenceId should be given as &quot;ID_NOT_SPECIFIED&quot;,
-  otherwise the sequenceId field will be used in preference to the
-  sequenceIndex field.
+  either by its text ID, or its index (base 0) in an associated
+  alignment. Normally, sequence features are associated with sequences
+  rather than alignments, and the sequenceIndex field is given as
+  &quot;-1&quot;. In order to specify a sequence by its index in a
+  particular alignment, the sequenceId should be given as
+  &quot;ID_NOT_SPECIFIED&quot;, otherwise the sequenceId field will be
+  used in preference to the sequenceIndex field.
   </p>
 
 
@@ -161,14 +162,14 @@
     description line will be translated into URL links. A link symbol
     will be displayed adjacent to any feature which includes links, and
     these are made available from the <a
-      href="../menus/popupMenu.html#sqid.popup"
-    >links submenu</a> of the popup menu which is obtained by
-    right-clicking when a link symbol is displayed in the tooltip.<br>
-    <em>Non-positional features</em><br> Specify the <em>start</em>
-    and <em>end</em> for a feature to be <strong>0</strong> in order to
-    attach it to the whole sequence. Non-positional features are shown
-    in a tooltip when the mouse hovers over the sequence ID panel, and
-    any embedded links can be accessed from the popup menu.<br /> <em>Scores</em><br>
+      href="../menus/popupMenu.html#sqid.popup">links submenu</a>
+    of the popup menu which is obtained by right-clicking when a link
+    symbol is displayed in the tooltip.<br> <em>Non-positional
+      features</em><br> Specify the <em>start</em> and <em>end</em> for
+    a feature to be <strong>0</strong> in order to attach it to the
+    whole sequence. Non-positional features are shown in a tooltip when
+    the mouse hovers over the sequence ID panel, and any embedded links
+    can be accessed from the popup menu.<br /> <em>Scores</em><br>
     Scores can be associated with sequence features, and used to sort
     sequences or shade the alignment (this was added in Jalview 2.5).
     The score field is optional, and malformed scores will be ignored.
