From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 Oct 2018 16:22:46 +0000 (+0100)
Subject: JAL-3127 updated colours menu and tree view documentation
X-Git-Tag: Release_2_11_0~17^2~46^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=45b21046f407e78f92b496083ffeff13a4790b2b;p=jalview.git

JAL-3127 updated colours menu and tree view documentation
---

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index 3d6245e..8cb2b59 100755
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -36,20 +36,20 @@
   </p>
   <p>
     <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
-    Selecting sequence ids at the leaves of the tree selects the
+    Selecting sequence IDs at the leaves of the tree selects the
     corresponding sequences in the original alignment. These selections
     are also reflected in any other analysis windows associated with the
     alignment, such as another tree viewer.
   </p>
   <p>
-    <strong><em>Grouping sequences by partitioning the
-        tree at a particular distanec</em></strong><br> Clicking anywhere along
+    <strong><em><a name="partitioning">Grouping sequences by partitioning</a> the
+        tree at a particular distance</em></strong><br> Clicking anywhere along
     the extent of the tree (but not on a leaf or internal node) defines
     a tree 'partition', by cutting every branch of the tree spanning the
     depth where the mouse-click occurred. Groups are created containing
     sequences at the leaves of each connected sub tree. These groups are
     each given a different colour, which are reflected in other windows
-    in the same way as if the sequence ids were selected, and can be
+    in the same way as if the sequence IDs were selected, and can be
     edited in the same way as user defined sequence groups.
   </p>
   <p>
@@ -58,7 +58,10 @@
     identifying specific patterns of conservation and mutation
     corresponding to the overall phylogenetic structure, when combined
     with the <a href="../colourSchemes/conservation.html">conservation
-      based colour scheme</a>.
+      based colour scheme</a>.To distinguish parts of the alignment assigned
+    to different groups, you may also enable the Sequence ID colour
+    scheme via the <a href="../menus/alwcolour.html">Alignment
+      window's Colours menu</a> (<em>Since 2.11</em>).
   </p>
   <p>
     <strong><em>Selecting Subtrees and changing the branch
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index f3ab75d..3a057a8 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -483,7 +483,13 @@
       </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
           for a description of all colour schemes.
       </em><br></li>
-      <li><strong>By Conservation<br>
+        <li><strong>Sequence ID<br></strong><em>Shades
+            sequences using their Sequence ID colour. Useful when
+            performing <a
+            href="../calculations/treeviewer.html#partitioning">tree
+              based subfamily analysis</a>.
+        </em></li>
+        <li><strong>By Conservation<br>
       </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
             by Conservation</a>.
       </em><br></li>
diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index e62a130..9a96595 100755
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -45,6 +45,11 @@
         a description of all colour schemes.
     </em><br>
     </li>
+    <li><strong>Sequence ID<br></strong><em>Shades
+        sequences using their Sequence ID colour. Useful when performing
+        <a href="../calculations/treeviewer.html#partitioning">tree
+          based subfamily analysis</a>.
+    </em></li>
     <li><strong>By Conservation<br>
     </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
           by Conservation</a>.