JAL-2069 spike updated with latest (FeatureTypeSettings)

[jalview.git] / help / html / calculations / sorting.html

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 5b6f616..a0412d0 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -46,8 +46,7 @@
     <li><p>
         <strong>Sort by Pairwise Identity</strong>
       </p>
-      <p>Places pairs of sequences together that align with the
-        greatest fraction of conserved residues.</p>
+      <p>Sorts sequences in the selection or alignment according to percent identity with respect to the first sequence in the view.</p>
       <p></li>
     <li><p>
         <strong>Sort by Tree Order</strong>
@@ -75,22 +74,28 @@
       </p>
       <p>
         This menu appears if the alignment contains any <a
-          href="../features/annotationsFormat.html"
-        >sequence associated alignment annotation</a> with associated
-        score values. Each entry is the label for a distinct group of
-        sequence associated annotation scores which can be used for
-        sorting.
+          href="../features/annotationsFormat.html">sequence
+          associated alignment annotation</a> with associated score values.
+        Each entry is the label for a distinct group of sequence
+        associated annotation scores which can be used for sorting.
       </p>
   </ul>
   <p>
+    <strong>Sorting according to sequence features</strong><br />
+    Additional sort operations for alignments containing sequence
+    features are provided in the <strong><a
+      href="../features/featuresettings.html#sortbyfeature">Feature
+        Settings</a></strong> dialog, opened via <strong>View&#8594;Feature
+      Settings...</strong>
+  <p>
     <strong>Reversing the Order</strong>
   </p>
   <p>Selecting any item from the Sort menu will sort sequences in an
     ascending order according to the property defining the sort. If the
     same sort is re-applied, the sequences will be sorted in the inverse
-    order. In both cases, for sequences which are equivalent under the sort
-    operation, their order will be preserved (since version 2.10). In
-    the case of trees and alignment orderings, Jalview will remember
+    order. In both cases, for sequences which are equivalent under the
+    sort operation, their order will be preserved (since version 2.10).
+    In the case of trees and alignment orderings, Jalview will remember
     your last choice for sorting the alignment and only apply the
     inverse ordering if you select the same tree or alignment ordering
     item again.</p>