<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>Split Frame Views</title>
</head>
<body>
-<p><strong>Split Frame Views</strong></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.
+ 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.
+ 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:
-
+ <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>)
+ 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="../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>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>
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>
-
-<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>
+ 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>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>
+ <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><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>
+ <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>
+ Frame.</p>
<ul>
<li>the alignment you chose to realign (for example, peptide)
is displayed as aligned by the external web service</li>
this case, cDNA) by inserting gaps in the corresponding positions</li>
</ul>
<p>
- <a name="reconalignment" /><strong>Reconstructed Alignments</strong>
+ <a name="reconalignment" /><strong>Reconstructed
+ Alignments</strong>
</p>
<p>
Reconstructed alignments are typically <em>not</em> the same as the
kinds of molecular evolution analysis.
</p>
<p>
- <em>Split Frame Views were introduced in Jalview 2.9</em>
- </p>
+ <em>Split Frame Views were introduced in Jalview 2.9</em>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff