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+<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletParameters"> here</a> to view decorated page</b></div>
<!-- content start -->
<h2>JalviewLite Applet Parameter Documentation</h2>
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="jalviewLiteJs.html">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 are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
-</p>
+<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" >
<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. If one file is nucleotide and the other peptide, and at least one peptide sequence
- is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.8.3</em>).</td>
+ <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>
<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>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 2.8.3</em>)</td></tr>
+ 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 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>
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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-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>
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git://source.jalview.org / jalview.git / blobdiff