X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=665fb3f55b9bf59e57d39d4fa3f22d959864f87b;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=260443083ca7287cfd09c59822aa7cfc894204a3;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 2604430..665fb3f 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -132,13 +132,13 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
 </ul></p>
 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
 <p>Groups of sequences can be defined using the tab delimited line</p>
-<pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences</pre>
+<pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	<em>Sequences</em></pre>
 <p>The sequences can be defined by alignment index and a range of sequences can 
   be defined in a comma delimited field such as</p>
 <p>2-5,8-15,20,22</p>
 <p>Enter * to select all groups. </p>
-<p>If the alignment indices are not known, enter -1 then a tab delimited list 
-  of sequence ids. </p>
+<p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list 
+specifying the sequence ids. </p>
 <p>If the SEQUENCE_REF has been defined, the group_start and group_end will be 
   relative to the sequence residue numbering, otherwise the group_start and group_end 
   will be the alignment column indices. </p>
@@ -178,6 +178,9 @@ property, then the idColour will also be used to colour the sequence.</li>
  <em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
  for the group will be set to the referenced sequence.<!-- <br><strong>Note:</strong> if the <em>hide</em> 
  property is set then only the representative sequence for the group will be shown in the alignment.--></li>
+ <li>The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
+ so that only annotation line graphs with the given names ands the same 
+ <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</li>
 </ul>
 <p> </p>
 <p>An example Annotation file is given below:
@@ -197,13 +200,14 @@ COLOUR&#9;Purple Letters&#9;151,52,228
 COMBINE&#9;Green Values&#9;Red Values
 GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;black
 
-SEQUENCE_GROUP Group_A 30 50 *
-SEQUENCE_GROUP Group_B 1 351 2-5
-SEQUENCE_GROUP Group_C 12 14 -1 seq1	seq2	seq3
-PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false	colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red
-PROPERTIES Group_C colour=Clustal
+SEQUENCE_GROUP&#9;Group_A&#9;30&#9;50&#9;*
+SEQUENCE_GROUP&#9;Group_B&#9;1&#9;351&#9;2-5
+SEQUENCE_GROUP&#9;Group_C&#9;12&#9;14&#9;-1&#9;seq1&#9;seq2&#9;seq3
+PROPERTIES&#9;Group_A&#9;description=This is the description&#9;colour=Helix Propensity&#9;pidThreshold=0&#9;outlineColour=red&#9;displayBoxes=true&#9;displayText=false&#9;colourText=false&#9;textCol1=black&#9;textCol2=black&#9;textColThreshold=0
+PROPERTIES&#9;Group_B&#9;outlineColour=red
+PROPERTIES&#9;Group_C&#9;colour=Clustal
 </pre>
 </p>
+<p><em>Last updated for version 2.8.1</em></p>
 </body>
 </html>
