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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
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-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
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- <p>
- <strong>Quick Links:<ul><li>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>
- </li>
- <li>Parameters are described <a href="#parameters">below</a></li>
- <li>The javascript API is described <a
- href="jalviewLiteJs.html">here</a></li>
- </ul></strong>
- </p>
- <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+<!-- content start -->
+<h2>JalviewLite Applet Parameter Documentation</h2>
+<p>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its
+<a href="javascript:doSubmit('jalviewLiteJs')">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings. </p>
+ <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
<p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
<a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
<tr>
<td>fileName</td>
<td>The file to open, must be on same server as the applet.</td>
</tr>
+ <tr>
+ <td>file2</td>
+ <td>fileName</td>
+ <td>A second file to open and show linked in a Split Frame
+ view. If one file is nucleotide and the other peptide, and at
+ least one peptide sequence matches the translation of one of the
+ nucleotide sequences, then gaps will be inserted into the
+ sequences in this file to match the aligned columns for
+ corresponding positions in the primary alignment file. This
+ parameter is ignored if enableSplitFrame is set to false (<em>since
+ 2.9</em>).
+ </td>
+ </tr>
+ <tr>
+ <td>enableSplitFrame</td>
+ <td>true or false (default true)</td>
+ <td>Enable or disable the display of linked cDNA and Protein alignments in a split frame (<em>since 2.9</em>).</td>
+ </tr>
<tr>
<td>sequence1,<br>
sequence2,<br>
<td>defaultColour</td>
<td> <em>One of: </em><br>
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
<td>Default is no colour.</td>
</tr>
<tr>
+ <td>defaultColourNuc</td>
+ <td>A colour scheme (from the list above) to apply to Nucleotide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
+ <td>defaultColourProt</td>
+ <td>A colour scheme (from the list above) to apply to Peptide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
<td>userDefinedColour</td>
<td><p><em>Example:</em><br>
D,E=red; K,R,H=0022FF; c=yellow</p></td>
</tr>
<tr>
<td>linkLabel_1</td>
- <td>Uniprot</td>
+ <td>EMBL-EBI Search</td>
<td rowspan="2"><p>Right click on sequence id to see list of available
links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
value. For multiple links, increment the label and url name by
<br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
</tr>
<tr>
- <td> <p><br>
+ <td> <p>
+ <br>
linkUrl_1<br>
</p></td>
<td><p><br>
- http://us.expasy.org/cgi-bin/<br>
- niceprot.pl?$SEQUENCE_ID$</p>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
</td>
</tr>
<tr>
<td>1.0 or greater</td>
<td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
</tr>
+ <tr><td>scaleProteinAsCdna</td><td>true or false (default is false)</td>
+ <td>Set true to shown protein residues the same width as their encoding codons.
+ For use with parameter file2 when showing a split frame of cDNA and protein. (<em>since 2.9</em>)</td></tr>
<tr><td>centrecolumnlabels</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
<tr><td>showUnconserved</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
</tr>
<tr><td>upperCase</td>
<td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
</tr>
<tr><td>automaticScrolling</td>
- <td>true of false (default is true)</td>
+ <td>true or false (default is true)</td>
<td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
</tr>
<tr><td>showGroupConsensus</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
</tr>
<tr><td>showGroupConservation</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
</tr>
<tr><td>showConsensusHistogram</td>
- <td>true of false (default is true)</td>
+ <td>true or false (default is true)</td>
<td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
</tr>
<tr><td>showSequenceLogo</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
</tr>
<tr><td>normaliseSequenceLogo</td>
- <td>true of false (default is false)</td>
+ <td>true or false (default is false)</td>
<td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.8</em>)</td>
</tr>
<tr><td>oninit</td>
archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
</pre></li>
<li> Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click <a href="formComplete.html">here</a>.
+ code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>.
<br>
</li>
<li>Embed Jalview into the web page, without the "Start Jalview"
<param name="embedded"
value="true"> </li>
</ul>
- <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
+
+ <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p>
+ <ul>
+ <li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
+ </li>
+ </ul>
+ </p>
+ <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
<ul>
<li>Normalised sequence logo display
</li>
<li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
<li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
</li>
- <li>New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+ <li>New <a href="javascript:doSubmit('jalviewLiteJs')">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
</li></ul>
<p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
<ul>
</pre>(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)</li>
</ul>
-
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-<div id="cite">
-<p>
-If you use Jalview in your work, please cite this publication:
-</p>
-<br />
-<p>
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
-"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
-</p>
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