<title>Split Frame Views</title>
</head>
<body>
-<p><strong>Split Frame Views</strong></p>
-<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>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>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
-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>Split Frame Views</strong>
+ </p>
+ <p>
+ Jalview provides a special viewing mode to show Coding DNA (cDNA)
+ and protein product alignments as a split view, with cDNA above and
+ protein below. The two alignments are linked, allowing editing and
+ analysis to be performed at both the peptide and nucleotide level.
+ Linked protein alignments also have an additional <strong>cDNA
+ Consensus</strong> annotation row, showing the distribution of codons at
+ each column of the protein alignment.
+ </p>
+ <p>
+ Split Frame views can be <a href="#opensplit">created in a
+ number of ways</a>. In the Jalview Desktop, Split Frame views are
+ saved in Jalview Projects, like any other alignment view.
+ </p>
+ <p>
+ <strong>Operations supported in Split Frame Mode</strong>
+ </p>
+ <p>Split Frame views allow the following:
+ <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>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="../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.
+ </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>
+ <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
+ them using the mouse</li>
+ <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.
+ </p>
-<p><strong>Opening a Split Frame View</strong></p>
-<p>A Split Frame View can be opened in one of the following ways:</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.<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.
+ <a name="opensplit" />
+ <p>
+ <strong>Opening a Split Frame View</strong>
+ </p>
+ <p>A Split Frame View can be opened in one of the following ways:</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.<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>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 calculated protein product in a Split
+ Frame view.
+ </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
-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. 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>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.
-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 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>
-<li>the alignment you chose to realign (for example, peptide) is displayed as aligned by the external web service</li>
-<li>Jalview 'aligns' its complement (in this case, cDNA) similarly, by inserting corresponding gaps
- <ul>
- <li>NB this is <em>not</em> the same as aligning the complement using the external service, which may give different results</li>
- </ul>
-</li>
-</ul>
-
-<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>
+ <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>
+ <li>the alignment you chose to realign (for example, peptide)
+ is displayed as aligned by the external web service</li>
+ <li>Jalview reconstructs the alignment of its complement (in
+ this case, cDNA) by inserting gaps in the corresponding positions</li>
+ </ul>
+ <p>
+ <a name="reconalignment" /><strong>Reconstructed
+ Alignments</strong>
+ </p>
+ <p>
+ Reconstructed alignments are typically <em>not</em> the same as the
+ alignment produced by aligning the complement sequence set directly
+ with the external service. However, in the case of protein
+ alignments, a reconstructed cDNA alignment is often more reliable
+ than one calculated without coding information. Reconstructed cDNA
+ alignments are also more informative than the original protein
+ alignment when calculating phylogenetic trees or performing other
+ kinds of molecular evolution analysis.
+ </p>
+ <p>
+ <em>Split Frame Views were introduced in Jalview 2.9</em>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff