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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>Sorting Sequences</title>
</head>
<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→Sort</strong>):
</p>
<ul>
<li><p><strong>Sort by ID</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>Sequences are ordered by decreasing fraction of conserved residues
-with respect to the first sequence in the alignment.
+<p>Places pairs of sequences together that align with the greatest
+fraction of conserved residues.
</p><p>
</li>
<li><p><strong>Sort by Tree Order</strong></p>
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->By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort→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
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:
+its corresponding entry in the Sort menu.
+</p>
</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>
-<strong>Reversing the Order</strong>
-<p>If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse
-order for that property. In the case of trees and alignment orderings, Jalview will
+<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 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>
git://source.jalview.org / jalview.git / blobdiff