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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
</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→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 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>
+ 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>
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