make fileparse errors easier to debug by dumping file parameter contents in debug...

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index b029e96..cc73162 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -52,6 +52,9 @@ definition with the line:
 All Annotations defined after a SEQUENCE_REF command will then be
 associated with that sequence, and the first field in the Value field
 list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
+<ul><em>New in Jalview 2.4</em>: the tooltip displayed when the mouse is moved over the row 
+label for sequence associated annotation  gives the associated 
+sequence's name followed by the annotation row's description.</ul> 
 <p>Sequence associations are turned off for subsequent annotation
 definitions by: 
 <pre>SEQUENCE_REF&#9;ALIGNMENT</pre>
@@ -95,14 +98,23 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
   textCol1=black<br>
   textCol2=black<br>
   textColThreshold=0<br>
-  idColour=ff3322</p>
-<em>New Features in 2.4:</em><ul><li>if the <strong>idColour</strong> property
+  idColour=ff3322<br>
+  hide=false<br>
+  hidecols=false<br>
+  showunconserved=false</p>
+<ul><li>if the <strong>idColour</strong> property
 is given without specifying a colour scheme with the <strong>colour</strong>
 property, then the idColour will also be used to colour the sequence.</li>
 <li>the <strong>colour</strong> property can take either a colour scheme name,
  or a single colour specification (either a colour name like 'red' or an RGB
  triplet like 'ff0066'). If a single colour is specified, then the group
  will be coloured with that colour.</li>
+ <li><em>New Features in 2.4.1</em></li>
+ <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li>
+  <li>Sequence associated Groups<br>If a group is defined after a valid
+ <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>
 </ul>
 <p> </p>
 <p>An example Annotation file is given below: