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getting_started.html
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<meta name="description" content="Phylojive : integrating
phylogenies with online biodiverstiy data sources">
<link rel="stylesheet" type="text/css" media="screen"
href="stylesheets/stylesheet.css">
<title>Phylojive</title>
</head>
<body>
<!-- HEADER -->
<div id="header_wrap" class="outer">
<header class="inner"> <a id="forkme_banner"
href="https://github.com/TRIN/phyloJIVE">View on GitHub</a>
<h1 id="project_title">getting started <img alt="darwin sketch"
src="images/Darwin_sketch.png" height="120" width="120"
align="right"></h1>
<h2 id="project_tagline">with <a href="index.html"><font
color="#ffcccc">phyloJIVE</font></a> and your own data<br>
</h2>
<p><br>
</p>
<p align="right"><font color="#ffff00"> <font
color="#ff99ff"> <font color="#ffcc66"><font
color="#ffff99"><a href="http://trin.github.io/jit/"><font
color="#ffff99"><font color="#ccccff">for
developers, </font></font></a></font> </font>
</font><a href="https://github.com/TRIN/phyloJIVE/wiki"><font
color="#ff99ff">wiki instructions + known problems,</font></a>
<a
href="https://github.com/TRIN/phyloJIVE/zipball/master"><font
color="#ffff00">download phyloJIVE</font></a></font><font
color="#ffff00"> </font> <br>
</p>
<section id="downloads"> <a class="zip_download_link"
href="https://github.com/TRIN/phyloJIVE/zipball/master">Download
this project as a .zip file</a> <a
class="tar_download_link"
href="https://github.com/TRIN/phyloJIVE/tarball/master">Download
this project as a tar.gz file</a> </section>
</header>
</div>
<!-- MAIN CONTENT -->
<div id="main_content_wrap" class="outer">
<section id="main_content" class="inner">
<h3>Quick Start Template... for the impatient</h3>
This <a href="SimpleTemplate_webApp.html">simple template</a>
provides a minimal set of features. The file structure in
the folder containing this template can be used to set-up your
own instance of PhyloJIVE on your desktop or embedded in a
webpage. For more details, see the phyloJIVE web
application parameters <a href="phyloJIVEparameters.html">page</a>.<br>
<br>
There are two ways to change the data. <br>
<br>
<ol>
<li>First you can click the ipad-like button at the top, click
on the Input tab and paste a newick tree in the box and
clickon Render. You cannot input trait data with this
method.<br>
<br>
</li>
<li>The second way utilizes the file structure.</li>
<ol>
<li> Parameters, trees and characters can be altered
by editing SimpleParams_PhyloJIVE.js Open <a
href="trees_characters/SimpleParams_PhyloJIVE.js">SimpleParams_PhyloJIVE.js</a>
in the trees_character folder. This file
contains the data that you can view on the right of this
screen, i.e. the tree and character data. <br>
There is also a blank <a
href="trees_characters/template.js">template.js</a>.</li>
<li>Simply paste the new tree over the old making sure
the punctuation is maintained. Should a
large newick tree fail to display then the first thing to
check for is escape characters such as quotes for informal
names or unnamed specimens.<br>
The character trait data can be updated by first
converting a csv file to charJson by using the supplied <a
href="about_charJSON.html">converter</a>. <br>
</li>
<li>Then paste the charJSON formatted character data
over the data in <a
href="trees_characters/SimpleParams_PhyloJIVE.js">SimpleParams_PhyloJIVE.js</a>.
located in the trees_characters <a
href="trees_characters">folder</a><br>
Character sets can be either qualitative or quantitative
or a mix of both types.</li>
</ol>
</ol>
<h3>Customisation</h3>
<p>If you wish a more appropriate name for the file which
contains trees and characters or you have more than one tree.
You simply need to edit the html file to replace the reference
to <a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/trees_characters/SimpleParams_PhyloJIVE.js">SimpleParams_PhyloJIVE.js</a>.
A text view of the html file is shown <a
href="images/Changing_tree_jsFile.png">here</a>. <br>
</p>
<img alt="what to change if you want to rename to file containg
trees and chars" title="what to change if you want to rename
to file containg trees and chars"
src="images/Changing_tree_jsFile.png" height="393" width="960">
<h4>Changing external links - using templates<<<
Reccomended<br>
</h4>
<p>Two examples of how to change the external links using the
link template<br>
<a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/Australian_bird3365.html">Australian
extent endemic birds</a> and <a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/Amphibia%20T48025.html">Amphibia</a>.
Details of the syntax are on the <a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/phyloJIVEparameters#template">parameter
page</a>.</p>
<p>Punctuation (syntax) is important. Commas, brackets and
braces must match. They should remain unchanged.<img alt="an
example of a templated list" title="an example of a
templated list" src="images/templated%20linked%20list.png"
height="234" width="1153"></p>
<h4><br>
</h4>
<h4>Changing external links- over riding the presentClade
function <<< The hard way<br>
</h4>
<p>More exquisite control can be achieved if you over ride the
presentClade function. This is done by including a new
definition of it on initialization as seen in <a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/syncarida.html">Syncarida
.</a><br>
<img alt="an example of how to override the presentClade
function" title="an example of how to override the
presentClade function" src="images/presentClade.png"
height="1047" width="1081"><br>
</p>
<h4>Changing what appears on hover (the tips function)<br>
</h4>
<p> <br>
<a href="syncarida.html">Syncarida </a> shows how
to change what appears as the mouse hovers over a taxon or
clade. <br>
</p>
<p> You need to override the tips function. <br>
This is done by creating a new one which is saved with
the tree and other initialization variables. <br>
</p>
<img alt="A screen grab showing how to override the tips
function" title="A screen grab showing how to override the
tips function" src="images/tipsFn.png" height="794"
width="1022">
<h4> GUID's (LSIDs) <br>
</h4>
<p>An example where GUIDs are used (<a
href="file:///Volumes/Text/Documents-working/3%20Current%20Projects/3%20PhyloJIVE/3.pj.%20Current%20Projects/WebApp/git/phyloJIVE/syncarida.html">Syncarida</a>
plus LSIDs). Taxon names are looked up with a nomenclator
then translated to the equivalent <a
href="http://en.wikipedia.org/wiki/LSID">LSID</a>. <br>
</p>
Strictly speaking any GUID's should be supplied with the
phylogeny Or the creator of the phylogeny should explicitly
state that they are using the taxon concepts as recorded
in a particular source at a particular time. However, such
perfection is rarely attainable. This template is provided as a
proof of concept.
<p> </p>
<br>
<p></p>
<br>
</section>
</div>
<!-- FOOTER -->
<div id="footer_wrap" class="outer">
<footer class="inner">
<p class="copyright">Phylojive maintained by <a
href="https://github.com/TRIN">TRIN</a></p>
<p>Published with <a href="http://pages.github.com">GitHub
Pages</a></p>
</footer>
</div>
</body>
</html>