<html>
<!--
- * 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.
*
<ul>
<li>Mouseover or scrolling of either alignment is followed by
the other (unless you turn off <strong><a
- href="../menus/alwview.html"
- >"View→Automatic Scrolling"</a></strong>)
+ href="../menus/alwview.html">"View→Automatic
+ Scrolling"</a></strong>)
</li>
<li>On selecting rows, columns or regions in one alignment, the
corresponding selection is made in the other</li>
<li>Sequence ordering in one alignment (using the cursor, or <strong><a
- href="../calculate/sorting.html"
- >"Calculate→Sort")</a></strong> is also applied to the other
+ href="../calculations/sorting.html">"Calculate→Sort")</a></strong>
+ is also applied to the other
</li>
<li>Editing (gap insertion / deletion) in the protein alignment
is reflected in the cDNA (but not vice versa)</li>
<li>Any trees imported or created with <strong><a
- href="../calculations/tree.html"
- >"Calculate Tree"</a></strong> on one of the views allow both cDNA and
- Protein views to be grouped, coloured or sorted.
+ href="../calculations/tree.html">"Calculate Tree"</a></strong> on
+ one of the views allow both cDNA and Protein views to be grouped,
+ coloured or sorted.
</li>
<li>To allow for the different widths in cDNA and Protein
alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
menu option has an option 'Scale protein residues to codons'. This
option will make each protein residue the same width as a DNA
- codon (so the alignments 'line up' vertically)
- </li>
+ codon (so the alignments 'line up' vertically).</li>
+ <li><a name="mirror" />The 'Use same font for cDNA and peptide'
+ checkbox, when enabled, ensures that font or font-size changes in
+ either the cDNA or Protein alignment will also be mirrored. (<em>Added
+ in 2.10.2</em>)</li>
<li><strong>"View→Protein"</strong> (in the cDNA panel)
or <strong>"View→Nucleotide"</strong> (in the protein panel)
allows you to show or hide one or other of the linked alignment
panels.</li>
- <li>Panel heights are adjusted dragging the divider between
+ <li>Panel heights are adjusted by dragging the divider between
them using the mouse</li>
- <li><a href="menus/alwview.html"><strong>"View→New
+ <li><a href="../menus/alwview.html"><strong>"View→New
View / Expand Views / Gather Views"</strong></a> behave as for a normal
alignment window, but always create new views as Split Frames</li>
</ul>
<p>
An alignment annotation row on the protein alignment shows the <strong><a
- href="../calculations/consensus.html"
- >cDNA consensus</a></strong> for each peptide column.<br /> This consensus may
- reveal variation in nucleotides coding for conserved protein
- residues.
+ href="../calculations/consensus.html">cDNA consensus</a></strong> for
+ each peptide column.<br /> This consensus may reveal variation in
+ nucleotides coding for conserved protein residues.
</p>
<a name="opensplit" />