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<head>
<TITLE>Applet Parameters</TITLE>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
<li ><a href="formComplete.html">Access from Javascript</a></li>
<li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
- <li ><a href="linkedapplets_ng.html">Linked JalviewLite applets</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
</ul>
</div>
<!-- content start -->
- <p>
- <strong>Quick Links:<ul><li>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>
- </li>
- <li>As of Jalview 2.8b1, the applet is signed, with 'sandbox' permissions</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>
+<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="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>
+ <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>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>
+ <tr>
<td>sequence1,<br>
sequence2,<br>
sequence3</td>
<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>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 2.8.3</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>
<param name="embedded"
value="true"> </li>
</ul>
- <p><strong>**APPLET SECURITY WARNINGS**</strong><ul><li>Since January 2014, only signed applets are allowed to run in the web page by default. We provide a range of different signed version of JalviewLite and JmolApplet that can be used in various situations.</li>
- <li>The default version of JalviewLite is signed for sandbox execution.</li>
- </ul></p>
<p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
<ul>
<li>Normalised sequence logo display
git://source.jalview.org / jalview.git / blobdiff