JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/help/html/features/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html
index 22a3c4c..b260cee 100644 (file)
--- a/help/html/features/columnFilterByAnnotation.html
+++ b/help/html/features/columnFilterByAnnotation.html
@@ -31,21 +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 row.
+      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="annotationColumnSelectionWithoutSM.gif"></td>
+      <td><img src="AnnotationColumnSelectionWithSM.gif"></td>
+      <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
     </tr>
   </table>
-
-  <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>
+  <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.<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>