PhyloWidget Plugin

A Foswiki integration of the PhyloWidget phylogeny browser

%META:TOPICINFO{author="TemiV" comment="reprev" date="1306970937" format="1.1" reprev="16" version="3"}%

PHYLOWIDGET{"Topic"} -- display phylogeny

• PHYLOWIDGET macro is used to display a newick formatted tree. The tree could be content of a topic or an attachment on the Foswiki instance. It can also accepts resource hosted on an external url.
• Syntax:

  %PHYLOWIDGET{"Web.Topic"
     attachment="example.nex"
     url="www.treebase.org/nexus.nex"
     height="800"
     width="600"}%

• Supported parameters:

Parameter:	Description:	Default:
"Web.Topic"	Topic name whose content is either in nexus format or has an nexus file attachment.	-
attachment="example.nex"	A nexus formatted file attachment.	-
url="www.treebase.org/nexus.nex"	Url to an external resource can be included in this parameter.	-
height="800"	Sets the height of the PhyloWidget applet.	-
width="600"	Sets the width of the PhyloWidget applet.	-
genus	Mention the genus of the displayed tree. It is important if the clade information is to be displayed.	-

* Examples:

    %PHYLOWIDGET{"%SYSTEMWEB%.PhyloWidgetExample"
    height="495"
    width="420"}%

* Result (if installed):

See also: PhyloWidgetPlugin, NEXUSTREES

%META:TOPICINFO{author="ProjectContributor" format="1.1" version="$Rev$"}%

NEXUSTREES{"Topic"} -- display phylogeny

* NEXUSTREES macro is used to view the tree block of a nexus file. It contains two panel. The left panel display PhyloWidget applet. The right panel contains a clickable tree list. In order for PhyloWidget to render the tree, click on the tree name. * Syntax:

%NEXUSTREES{"Web.Topic"
attachment="example.nex"
header="<h3>Tree List</h3>$n"
format="   * $treeid $treeName"
footer="<h3>End</h3>"
separator="$n"
}%

* Supported parameters:

Parameter:	Description:	Default:
"Web.Topic"	Topic name whose content is either in nexus format or has an nexus file attachment.	-
attachment="example.nex"	A nexus formatted file attachment.	-
header="<h3>Tree List</h3>$n"	String that will decorate the value of format parameter.	-
format="   * $treeid $treeName"	This string is repeated according to the number of trees in the nexus file. $treeid & $treeName are replace with serial number and tree name.	-
footer="<h3>End</h3>"	String that will decorate the value of format parameter.	-
separator="$n"	This value is used to separate format parameter values. It can contain Foswiki recognised parameters.	-

* Examples 1:

%NEXUSTREES{"%SYSTEMWEB%/PhyloWidgetExample"
    attachment="Tree.nex"
    header="<h3>Tree List</h3>$n"
    format="   * <a href='%SCRIPTURL{"rest"}%/PhyloWidgetPlugin/getNHX?web=System;topic=System.PhyloWidgetExample;attachment=Tree.nex;tree=$treeid'>$treeName</a>"
    footer="<h3>***********</h3>"
    separator="$n"
    }%

• Result (if installed): %NEXUSTREES{"System/PhyloWidgetExample" attachment="Tree.nex" header="

  Tree List

  $n" format=" * $treeName" footer="

  ***********

  $n" separator="$n" }% * Examples 2: PhyloViewTrees See also: PhyloWidgetPlugin, PHYLOWIDGET, PhyloViewTrees

Known Issues

If the tree to be displayed is not public (requires authentication), you must make sure the website uses Apache Authentication. For example, if the tree is hosted on secure Foswiki instance, make sure that you have configured the site using the setting {LoginManager} = ApacheLogin.

You could also run into trouble if the secure website holding the tree has a self signed certificate, or if the certificate is signed by an authority unknown to Java. In such cases, add the certificate to JRE keystore using keytool command.

Installation

You do not need to install anything in the browser to use this extension. The following instructions are for the administrator who installs the extension on the server.

Open configure, and open the "Extensions" section. Use "Find More Extensions" to get a list of available extensions. Select "Install".

If you have any problems, or if the extension isn't available in configure, then you can still install manually from the command-line. See http://foswiki.org/Support/ManuallyInstallingExtensions for more help.

Plugin Info

Author:	Foswiki:Main.TemiVarghese
Copyright:	© 2010, Taxonomy Research & Information Network http://trin.org.au
License:	GPL (GNU General Public License)
Release:	0.1.2
Version:	12045 (2011-06-24)
Change History:
30 Nov 2010 (0.1.1)	Foswikitask:10044 - initial version
Home:	http://foswiki.org/Extensions/PhyloWidgetPlugin
Support:	http://foswiki.org/Support/PhyloWidgetPlugin
Dependencies:	Name Version Description Bio::NEXUS >=0 Required Bio::TreeIO >=0 Required Bio::NexmlIO >=0 Required Bio::Phylo >=0 Required Foswiki::Plugins::DBCachePlugin >=0 Optional, For examples