<p/></p>Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are
linked, with these features supported:
<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>)</li>
+<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>)</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</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</li>
<li>editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)</li>
<li>on <strong><a href="../calculations/tree.html">"Calculate Tree"</a></strong> in either alignment, grouping, colouring and sorting by tree are applied to both</li>
-<li>the <strong><a href="../menus/alwformat.html">"Format | Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
+<li>the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
the same width as a DNA codon (so the alignments 'line up' vertically)</li>
+<li>menu option <strong>"View→Protein"</strong> (in the cDNA panel) or <strong>"View→Nucleotide"</strong> (in the protein panel) allows you to show or hide the complementary alignment</li>
+<li>you can adjust panel heights by dragging the divider between them using the mouse</li>
+<li>menu options <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.</p>
<p><strong><em>Add Sequences</em></strong></p>
<p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
-sequence.</p>
+sequence.<br>
+If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments.
<p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
The additional options below apply to Jalview Desktop only.</p>
<p><strong><em>Translate as cDNA</em></strong></p>
-<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its
calculated protein product in a Split Frame view.</p>
<p><strong><em>Get Cross-References</em></strong></p>
-<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate | Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
+<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
-<p><strong><em>Realign Split View</em></strong></p>
+<p><strong><em>Realign a Split View</em></strong></p>
<p>If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new
Split Frame.</p>
<ul>
</ul>
</li>
</ul>
-
-<p><em>Split Frame Views were introduced in Jalview 2.?.?</em></p>
+<p><strong><em>Applet</em></strong></p>
+<p>To see a split frame view in the Jalview applet, provide these applet parameters:
+<table border="1">
+<tr><th>Parameter</th><th>Value</th><th>Description</th>
+<tr><td>file</td><td>path to an alignment file</td><td>a cDNA (or protein) alignment</td>
+<tr><td>file</td><td>path to an alignment file</td><td>a protein (or cDNA) alignment</td>
+<tr><td>enableSplitFrame</td><td>true</td><td>to enable the Split Frame feature</td>
+</table>
+<p/>If compatible sequences are present in the input alignments, Jalview will open a Split Frame view.<br/>
+If not, only the first alignment will be opened (an error message is written to the Java console).
+
+<p><em>Split Frame Views were introduced in Jalview 2.9</em></p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff