InstallAnywhere 2009

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

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index c61481f..1c15890 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -6,7 +6,7 @@
 <p><strong>Sorting Sequences</strong></p>
 <p>Any group of selected sequences may be reordered by pressing the
 up or down arrow keys. The whole alignment may also be reordered by
 <p><strong>Sorting Sequences</strong></p>
 <p>Any group of selected sequences may be reordered by pressing the
 up or down arrow keys. The whole alignment may also be reordered by

-the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
+the use of the functions in the Sort menu (<strong>Calculate&#8594;Sort</strong>):

 </p>
 <ul>
 <li><p><strong>Sort by ID</strong></p>
 </p>
 <ul>
 <li><p><strong>Sort by ID</strong></p>

@@ -14,11 +14,11 @@ the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
 precedence of their names.</p><p>
 </li>
 <li><p><strong>Sort by Group</strong></p>
 precedence of their names.</p><p>
 </li>
 <li><p><strong>Sort by Group</strong></p>

-<p>Places sequences in the same group adjacent to eachother.</p><p>
+<p>Places sequences in the same group adjacent to each other.</p><p>

 </li>
 <li><p><strong>Sort by Pairwise Identity</strong></p>
 <p>Places pairs of sequences together that align with the greatest
 </li>
 <li><p><strong>Sort by Pairwise Identity</strong></p>
 <p>Places pairs of sequences together that align with the greatest

-fraction of conserved residues. 
+fraction of conserved residues.

 </p><p>
 </li>
 <li><p><strong>Sort by Tree Order</strong></p>
 </p><p>
 </li>
 <li><p><strong>Sort by Tree Order</strong></p>

@@ -26,7 +26,7 @@ fraction of conserved residues.
 order the sequences corresponding to those leaves in the
 alignment.<br>
 If a tree has been calculated from or associated with the current
 order the sequences corresponding to those leaves in the
 alignment.<br>
 If a tree has been calculated from or associated with the current

-alignment, its name will appear in the submenu <em>Sort-&gt;By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort&#8594;By Tree Order</strong>.</p><p>

 </li>
 <li><p><strong>Sort by alignment ordering</strong></p>
 <p>Multiple alignment methods often order the sequences in their
 </li>
 <li><p><strong>Sort by alignment ordering</strong></p>
 <p>Multiple alignment methods often order the sequences in their

@@ -34,8 +34,13 @@ alignments by some measure of sequence identity.<br>
 If the current alignment has been generated by one of Jalview's
 alignment web services, the alignment ordering can be recovered by
 its corresponding entry in the Sort menu.
 If the current alignment has been generated by one of Jalview's
 alignment web services, the alignment ordering can be recovered by
 its corresponding entry in the Sort menu.

-</p><p>
+</p>

 </li>
 </li>

+<li><p><strong>Sort by Score</strong></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.</p>

 </ul>
 <p><strong>Reversing the Order</strong></p>
 <p>Selecting any item from the Sort menu will sort sequences in an
 </ul>
 <p><strong>Reversing the Order</strong></p>
 <p>Selecting any item from the Sort menu will sort sequences in an