From 0d50ab3cdf86523b239e7dcccc551164ed197467 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 30 Sep 2016 14:35:06 +0100
Subject: [PATCH] JAL-2236 release notes and additional docs

---
 help/html/colourSchemes/annotationColouring.html |   19 +++++++++++--------
 help/html/features/columnFilterByAnnotation.html |   16 ++++++++++++----
 help/html/releases.html                          |    1 +
 3 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 30b6396..ed0ab3f 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -39,14 +39,17 @@
   </div>
   <ul>
     <li>Select which annotation to base the colouring scheme on
-      using the top left selection box.<br />If the <strong>Per-sequence
-        only</strong> tick box is not greyed out, then ticking it will limit the
-      available annotation rows to just those that are sequence
-      associated (e.g. T-COFFEE scores and <a
-      href="../webServices/proteinDisorder.html"
-    >protein disorder predictions</a>), which will colour each sequence
-      according to its own per-residue scores.<br /> <em>Per-sequence
-        associated annotation colouring was introduced in Jalview 2.8</em>
+      using the top left selection box. Sequence associated alignment
+      annotation are shown with the seuqence's name appended.<br />If
+      the <strong>Per-sequence only</strong> tick box is not greyed out,
+      then ticking it will limit the list of available annotation rows
+      to just the labels for those that are sequence associated.
+      Annotation rows on each sequence with the same label (e.g.
+      T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
+        disorder predictions</a>) will then be used to colour its
+      corresponding positions in the alignment.<br /> <em>Per-sequence
+        associated annotation colouring is currently only available in
+        the Desktop.</em>
     </li>
     <li>If the &quot;Use Original Colours&quot; box is selected,
       the colouring scheme will use the colouring scheme present on the
diff --git a/help/html/features/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html
index 2b7d0ec..c53844b 100644
--- a/help/html/features/columnFilterByAnnotation.html
+++ b/help/html/features/columnFilterByAnnotation.html
@@ -32,7 +32,7 @@
     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
+    then presented for filtering data according to the selected annotation
     row.
   </p>
   <table>
@@ -41,12 +41,20 @@
       <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>
diff --git a/help/html/releases.html b/help/html/releases.html
index aedd419..9339b33 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -59,6 +59,7 @@
             <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
             <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
             <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+            <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
         </ul> <em>Application</em>
         <ul>
             <li><!-- JAL---></li>
-- 
1.7.10.2