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@danmaclean
danmaclean committed Apr 10, 2013
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2 changes: 0 additions & 2 deletions README.md
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Expand Up @@ -67,13 +67,11 @@ This process is repeated for all the features and tracks you want to show in the

See the RDOC in the packages doc directory for more information.

####






### Contributing to bio-svgenes

* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
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10 changes: 1 addition & 9 deletions doc/created.rid
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@@ -1,9 +1 @@
Fri, 01 Mar 2013 15:52:41 +0000
./lib/bio/graphics/primitive.rb Fri, 01 Mar 2013 13:01:51 +0000
./lib/bio/graphics/svgee.rb Fri, 01 Mar 2013 14:31:26 +0000
./lib/bio-svgenes.rb Tue, 12 Feb 2013 12:53:21 +0000
./lib/bio/graphics/track.rb Fri, 01 Mar 2013 15:38:24 +0000
./lib/bio/graphics/glyph.rb Fri, 01 Mar 2013 14:55:52 +0000
./LICENSE.txt Tue, 12 Feb 2013 12:53:20 +0000
./lib/bio/graphics/mini_feature.rb Fri, 01 Mar 2013 15:52:40 +0000
./lib/bio/graphics/page.rb Fri, 01 Mar 2013 14:34:28 +0000
Thu, 04 Apr 2013 16:23:02 +0100
112 changes: 21 additions & 91 deletions doc/index.html
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@@ -1,94 +1,24 @@
<!DOCTYPE html>
<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">

<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">

<title>RDoc Documentation</title>

<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">

<script type="text/javascript">
var rdoc_rel_prefix = "./";
</script>

<script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
<script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
<script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
<script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
<script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
<script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>


<body>
<nav id="metadata">
<nav id="home-section" class="section">
<h3 class="section-header">
<a href="./index.html">Home</a>
<a href="./table_of_contents.html#classes">Classes</a>
<a href="./table_of_contents.html#methods">Methods</a>
</h3>
</nav>


<nav id="search-section" class="section project-section" class="initially-hidden">
<form action="#" method="get" accept-charset="utf-8">
<h3 class="section-header">
<input type="text" name="search" placeholder="Search" id="search-field"
title="Type to search, Up and Down to navigate, Enter to load">
</h3>
</form>

<ul id="search-results" class="initially-hidden"></ul>
</nav>
<!--
RDoc Documentation
<div id="project-metadata">
<nav id="fileindex-section" class="section project-section">
<h3 class="section-header">Pages</h3>

<ul>

<li class="file"><a href="./LICENSE_txt.html">LICENSE</a>

</ul>
</nav>

<nav id="classindex-section" class="section project-section">
<h3 class="section-header">Class and Module Index</h3>

<ul class="link-list">

<li><a href="./Bio.html">Bio</a>

<li><a href="./Bio/Graphics.html">Bio::Graphics</a>

<li><a href="./Bio/Graphics/Glyph.html">Bio::Graphics::Glyph</a>

<li><a href="./Bio/Graphics/MiniFeature.html">Bio::Graphics::MiniFeature</a>

<li><a href="./Bio/Graphics/Page.html">Bio::Graphics::Page</a>

<li><a href="./Bio/Graphics/Primitive.html">Bio::Graphics::Primitive</a>

<li><a href="./Bio/Graphics/SVGEE.html">Bio::Graphics::SVGEE</a>

<li><a href="./Bio/Graphics/Track.html">Bio::Graphics::Track</a>

</ul>
</nav>

</div>
</nav>

<div id="documentation" class="description">
<p>This is the API documentation for RDoc Documentation.
</div>


<footer id="validator-badges">
<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
</footer>

-->
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>RDoc Documentation</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
</head>
<frameset rows="20%, 80%">
<frameset cols="25%,35%,45%">
<frame src="fr_file_index.html" title="Files" name="Files" />
<frame src="fr_class_index.html" name="Classes" />
<frame src="fr_method_index.html" name="Methods" />
</frameset>
<frame src="files/lib/bio/graphics/glyph_rb.html" name="docwin" />
</frameset>
</html>
20 changes: 12 additions & 8 deletions examples/example.rb
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@@ -1,24 +1,28 @@
#!/usr/bin/env ruby
#
# untitled
# example.rb
#
# Created by Dan MacLean (TSL) on 2012-09-28.
# Copyright (c) . All rights reserved.
###################################################
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
$LOAD_PATH.unshift(File.dirname(__FILE__))

##A very straightforward example that creates all the features and tracks explicitly.


require 'bio-svgenes'

##create the page
p = Bio::Graphics::Page.new(:width => 800,
:height => 200,
:number_of_intervals => 10)

:number_of_intervals => 10
)

##add a generic glyph track
generic_track = p.add_track(:glyph => :generic,
:name => 'generic_features',
:label => true )


##and some features
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '+', :id => "MyFeature")
generic_track.add(feature1)
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
Expand All @@ -33,7 +37,7 @@
generic_track.add(feature2)



##another generic track
generic_track = p.add_track(:glyph => :generic, :name => 'more_generic_features', :label => true, :fill_color => 'green' )

feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
Expand All @@ -43,7 +47,7 @@
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)


##another generic
generic_track = p.add_track(:glyph => :generic,
:name => 'yet_more_generic_features',
:label => true,
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