X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FcolumnFilterByAnnotation.html;h=2651a100a5fea295921ebbe6408305b85c9240e6;hb=0bee8aadc22e41e4793db251a7d37a839bd77db8;hp=7e6b17ab5aca312017412e76179912da71c77d25;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/features/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html
index 7e6b17a..2651a10 100644
--- a/help/html/features/columnFilterByAnnotation.html
+++ b/help/html/features/columnFilterByAnnotation.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.
  * 
@@ -31,22 +31,30 @@
     The 'Select/Hide by Annotation' window allows columns to be selected
     or hidden according to annotation rows on the alignment. The dialog
     box is opened <em>via</em> &quot;<strong>Select&#8594;Select/Hide
-      Columns by Annotation...</strong>&quot;, and different filters are
-    presented dependent upon the data shown in the selected annotation
+      Columns by Annotation...</strong>&quot;, and different filters are then
+    presented for filtering data according to the selected annotation
     row.
   </p>
   <table>
     <tr>
-      <td><img src="AnnotationColumnSelectionWithSM.gif"></td>
+      <td><img src="AnnotationColumnSelectionWithSM.png"></td>
       <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
     </tr>
   </table>
-
-  <p>If an annotation with numeric values is selected, the threshold
+  <p>The drop down menu lists the annotation available on the
+    alignment. Sequence associated annotation rows will be shown with
+    the sequence ID appended to the annotation label. It is only
+    possible to select one row at a time.</p>
+  <p>
+    If an annotation with numeric values is selected, the threshold
     filter option is activated. For other types of annotation, use the
     text box and secondary structure check boxes (right). The radio
     buttons at the bottom of the dialog specify the action applied to
-    columns matching the query.</p>
+    columns matching the query.<br /> <em>Note: annotation
+      containing only numeric labels (e.g. T-COFFEE column confidence
+      scores) will not be treated as quantitative data. You will need to
+      enter search expressions to select columns in this case.</em>
+  </p>
   <ul>
     <li><strong>Search Filter</strong>
       <ul>
@@ -68,7 +76,9 @@
         <li>Select whether to filter the alignment above or below
           the threshold.</li>
         <li>Change the threshold value with the slider, or enter it
-          in the text box.</li>
+          in the text box.
+	<li>The <em>As Percentage</em> checkbox allows thresholds to
+          be set as a percentage rather than absolute value.</li>
       </ul>
     <li><strong>Actions</strong>
       <ul>
