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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 ($$Version-Rel$$)
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*
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<div id="pageWrap">
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-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
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-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <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 JalviewLites</a></li>
+ </ul>
</div>
<div id="content" class="content">
- <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="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 width="80" ><strong>value=""></strong></td>
<td width="100%"><strong>Description</strong></td>
</tr>
+ <tr>
+ <td>permissions</td>
+ <td>sandbox</td>
+ <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
+ </tr>
<tr>
<td>file</td>
<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>
+ <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>
</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 2.8.3</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>
</li>
<li>Note parameter "PDBSeq" is no longer required.<br>
</li>
- <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
+ <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li>
<p> </p>
</li>
</ul>
new line in an alignment file must be entered as a parameter)</li>
</ul>
-</div>
+<!-- content end -->
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
-<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
<div id="cite">
<p>
If you use Jalview in your work, please cite this publication:
<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 doi: 10.1093/bioinformatics/btp033
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
</p>
</div>
</div>
git://source.jalview.org / jalview.git / blobdiff