From 18ec5585c00cf8f8833c30f4dae5c04bc9ecfc65 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 19 Sep 2016 17:43:13 +0100
Subject: [PATCH] JAL-2189 JAL-1369 JAL-192  expand referenceseq documentation

---
 help/html/calculations/referenceseq.html |   48 ++++++++++++++++++++++--------
 1 file changed, 35 insertions(+), 13 deletions(-)

diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 03d24a5..912be55 100644
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -26,25 +26,47 @@
   <p>
     <strong>Reference Sequence Alignment Views</strong>
   </p>
+  <p>Many alignment analysis tasks concern a query, or reference
+    sequence. For instance, when searching for sequences from other
+    organisms that are similar to a newly sequenced gene, or when
+    searching for structurally similar sequences for use in homology
+    modelling.</p>
+<p>
+    <strong>What happens when a reference sequence is defined ?</strong>
+  </p>
   <p>
     The reference sequence for an alignment is indicated by its ID being
-    shown in bold. When a reference sequence has been defined, the <strong>Format&#8594;Show
-      unconserved</strong> option highlights mutations with respect to the
-    reference sequence, rather than the alignment's consensus sequence.
-  </p>
+    shown in bold. In addition:</p>
+  <ul>
+    <li><strong>Reference sequence numbering</strong>. Instead of
+      column numbers, the alignment ruler shows the reference sequence
+      positions at each column. At each tick mark, either the reference
+      sequence symbol and position is given, or the column number when a
+      gap is present at that position in the reference sequence.</li>
+    <li><strong>Format&#8594;Show unconserved</strong> highlights
+      mutations with respect to the reference sequence, rather than the
+      alignment's consensus sequence.</li>
+  </ul>
   <p>
+    <strong>Defining the reference sequence</strong>
+  </p>
+  <p>Each alignment view can have its own reference sequence.</p>
   <ul>
-    <li>Jalview automatically assigns a reference sequence when <a
-      href="../webServices/jnet.html"
-    >JPred4</a> predictions are imported.
-    </li>
-    <li><strong>Assigning a reference sequence</strong><br /> A
-      sequence can be marked as the reference sequence by right-clicking
-      on it's ID to open the popup menu, and selecting the "<strong>(Sequence
-        ID)&#8594;Mark as Reference</strong>" entry."</li>
+    <li><strong>Manually assigning a reference sequence</strong><br />
+      A sequence can be marked as the reference sequence by
+      right-clicking on its ID to open the popup menu, and selecting the
+      "<strong>(Sequence ID)&#8594;Mark as Reference</strong>" entry.</li>
+    <li><strong>Defining a reference when importing
+        annotation</strong><br />Jalview automatically assigns a reference
+      sequence when importing analysis results, such as those returned
+      from <a href="../webServices/jnet.html">JPred4</a> . A reference
+      sequence can also be assigned via the <a
+      href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
+      an alignment annotation file.</li>
   </ul>
   <p>
     <em>Reference sequence based alignment visualisation was
-      introduced in Jalview 2.9.</em>
+      introduced in Jalview 2.9, and support for storage and retrieval
+      of reference sequence views in 2.10.</em>
   </p>
 </html>
-- 
1.7.10.2