<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
<TITLE>Applet Parameters</TITLE>
<!-- InstanceEndEditable -->
\r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
\r<style type="text/css">
\r<!--
\rtd {
\r font-family: Geneva, Arial, Helvetica, sans-serif;
\r font-size: 12px;
\r}
\r.plain {
\r font-family: Verdana, Arial, Helvetica, sans-serif;
\r font-size: 14px;
\r text-decoration: none;
\r}
\r.plain:hover{
\r background-color:#000000; color: #F2F2FF;
\r}
\r \r-->
\r</style>
\r\r<script language="JavaScript">
\rfunction genHref()
\r{
\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
\rfor(i=0; i<8; i++)
\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
\rwindow.location=href;
\r}
\rfunction getEventTarget(e)
\r{
\rif(!e)
\re = window.event;
\rif(e.target)
\rreturn e.target;
\rreturn e.srcElement;
\r}
\r\r</script>
\r</head>
\r\r<body alink="#000000" vlink="#000000" link="#000000">
\r<script type="text/javascript">
\rvar gaJsHost = (("https:" == document.location.protocol) ?
\r"https://ssl." : "http://www.");
\rdocument.write(unescape("%3Cscript src='" + gaJsHost +
\r"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
\r</script>
\r<script type="text/javascript">
\rtry{
\rvar pageTracker = _gat._getTracker("UA-9060947-1");
\rpageTracker._trackPageview();
\r} catch(err) {}
\r</script>
\r<div align="left">
\r <table width="805" height="100" cellpadding="5">
\r <tr>
\r <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
\r </tr>
\r </table>
\r <table width="805" border="0" cellpadding="5" cellspacing="5">
\r <tr>
\r <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
\r \r <div align="center">
\r <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
\r <tr>
\r <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
\r Version</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
\r history</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
\r Code</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
\r Mailing List</a></td>
\r </tr>
\r <tr>
\r <td align="left" valign="middle"><a
\r href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
\r class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
\r bug reports to the discussion list.</em></td>
\r </tr>
\r <tr></tr>
\r <tr>
\r <!--<td align="left" valign="middle"><br>
\r Please send problems<br>and
\r bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
\r </tr>
\r </table>
\r\r </div>
\r\r <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
\r <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
\r </div>
\r </td>
\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p><strong>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>. Parameters are described
- <a href="#parameters">below</a>, and the javascript API is described <a href="formComplete.html">here</a></strong>.
- </p>
+ <p>
\r <strong>Quick Links:<ul><li>Download the applet jar file from <a
\r href="jalviewApplet.jar">here</a>
\r </li>
\r <li>Parameters are described <a href="#parameters">below</a></li>
\r <li>The javascript API is described <a
\r href="jalviewLiteJs.html">here</a></li>
\r </ul></strong>
\r </p>
\r <h3 align="left">Useful to know!!</h3>
<ul>
<li>Package all your data files into a single (or multiple) zip / jar
button by setting the embed parameter to true;<br>
<param name="embedded"
value="true"> </li>
- </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>
\r </li>
\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have
\r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>
\r </ul>
+ </ul>
\r <p><strong><font size="2">** NEW FEATURES ** in Jalview 2.7.1</font></strong></p>
\r <ul><li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre></font>
\r </li>
\r <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
\r Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r \r </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
\r <ul>
\r <li><font size="2">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>
\r <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></font>
\r </li>
\r <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
\r </font></li></ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>
\r </ul>
<br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
\r <ul>
\r <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
\r </ul>
\r <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
<ul>
<li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
<tr><td>showbutton</td>
<td>true</td>
<td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
- </tr>\r </tr>\r <tr><td>sortByTree</td>\r <td>true or false (default is false)</td>\r <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>\r </tr>\r <tr>\r <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>\r </tr>\r <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>\r <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>\r </tr>\r <tr><td>heightScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.</td>\r </tr>
- <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>\r </tr>\r </table>
+ </tr>\r </tr>\r <tr><td>sortByTree</td>\r <td>true or false (default is false)</td>\r <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>\r </tr>\r <tr>\r <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>\r </tr>\r <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>\r <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>\r </tr>\r <tr><td>heightScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>\r </tr>
+ <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <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>\r </tr>\r <tr><td>centrecolumnlabels</td>\r <td>true of false (default is false)</td>\r <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>\r <tr><td>showUnconserved</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r <tr><td>upperCase</td>\r <td><em>bold</em> or other value</td>\r <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>\r </tr>\r <tr><td>automaticScrolling</td>\r <td>true of false (default is true)</td>\r <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>\r </tr>\r \r <tr><td>showGroupConsensus</td>\r <td>true of false (default is false)</td>\r <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>\r </tr>\r \r <tr><td>showGroupConservation</td>\r <td>true of false (default is false)</td>\r <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>showConsensusHistogram</td>\r <td>true of false (default is true)</td>\r <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>\r </tr>\r <tr><td>showSequenceLogo</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r <tr><td>oninit</td>\r <td><em>after_init()</em></td>\r <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>relaxedidmatch</td>\r <td><em>true or false (default is false)</em></td>\r <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>alignpdbfiles</td>\r <td><em>true or false (default is false)</em></td>\r <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>externalstructureviewer</td>\r <td><em>true or false (default is false)</em></td>\r <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>\r \r </tr>\r <tr><td>annotationcolour_max</td>\r <td>colour name or RGB hex triplet (default is red)</td>\r <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>annotationcolour_min</td>\r <td>colour name or RGB hex triplet (default is orange)</td>\r <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>jalviewhelpurl</td>\r <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>\r <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>\r </tr>\r <tr><td>resolvetocodebase</td>\r <td>True or False (False)</td>\r <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>\r </tr>\r \r </table>
<p align="center"> </p>
<!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff