bio-graphics 1.2 → 1.4

data/doc/files/TUTORIAL.html

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Thu Oct 18 14:19:48 +0100 2007</td>
+      <td>Thu Jan 24 20:03:15 +0000 2008</td>
     </tr>
     </table>
   </div>
@@ -74,7 +74,7 @@
 </p>
 <h1><a href="../classes/Bio/Graphics.html">Bio::Graphics</a> tutorial</h1>
 <p>
-Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
+Copyright (C) 2007, 2008 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
 </p>
 <p>
 License: The Ruby License
@@ -93,12 +93,19 @@ This <a href="../classes/Bio/Graphics.html">Bio::Graphics</a> library
 allows for drawing overviews of genomic regions, similar to the pictures
 drawn by <a href="http://www.gmod.org/wiki/index.php/Gbrowse">gbrowse</a>.
 Basically, it allows creating simple images that display features on a
-linear map. The code is based on the equivalent code in the <a
-href="http://www.bioperl.org/wiki/Main_Page">bioperl</a> project.
+linear map, including the position of subdomains in a protein (see
+picture). It&#8216;s now also possible to create vertical pictures.
+</p>
+<p>
+<img src="../images/protein_domains.png" />
+</p>
+<p>
+<img src="../images/vertical.png" />
 </p>
 <p>
 Any <a href="../classes/Bio/Graphics.html">Bio::Graphics</a> image consists
-of the following parts (nomenclature identical to that from bioperl):
+of the following parts (concepts and nomenclature identical to that from <a
+href="http://www.bioperl.org/wiki/Main_Page">bioperl</a>):
 </p>
 <ul>
 <li>one panel: container of all tracks
@@ -143,11 +150,12 @@ Each of these tracks has zero or more features.
 </p>
 <p>
 As a feature can only exist within the confines of a track and a track can
-only exist within the confines of a panel, these classes are encapsuled.
-This means that the Track class is not Bio::Graphics::Track, but <a
-href="../classes/Bio/Graphics/Panel/Track.html">Bio::Graphics::Panel::Track</a>;
+only exist within the confines of a panel, these classes are encapsulated.
+This means that the Track class is not <a
+href="../classes/Bio/Graphics/Track.html">Bio::Graphics::Track</a>, but <a
+href="../classes/Bio/Graphics/Track.html">Bio::Graphics::Panel::Track</a>;
 the same goes for <a
-href="../classes/Bio/Graphics/Panel/Track/Feature.html">Bio::Graphics::Panel::Track::Feature</a>.
+href="../classes/Bio/Graphics/Feature.html">Bio::Graphics::Panel::Track::Feature</a>.
 </p>
 <h2>Glyphs</h2>
 <p>
@@ -178,44 +186,60 @@ for an nicer example.
 For an explanation of the arguments with each method for this example, see
 the <a href="../classes/Bio/Graphics/Panel.html">Bio::Graphics::Panel</a>
 and <a
-href="../classes/Bio/Graphics/Panel/Track.html">Bio::Graphics::Panel::Track</a>
+href="../classes/Bio/Graphics/Track.html">Bio::Graphics::Panel::Track</a>
 object documentation.
 </p>
 <pre>
   1   # Load the library
-  2   require 'bio-graphics' # or require_gem 'bio-graphics'
+  2   require 'bio-graphics' # or require_gem 'bio-graphics' or gem 'bio-graphics'
   3
   4   # Create the panel
-  5   my_panel = Bio::Graphics::Panel.new(500, 600, true, 1, 500)
+  5   my_panel = Bio::Graphics::Panel.new(500, :width =&gt; 1000)
   6
   7   # Create the tracks
-  8   generic_track = my_panel.add_track('generic')
-  9   directed_track = my_panel.add_track('directed',[0,1,0],'directed_generic')
-  10  triangle_track = my_panel.add_track('triangle',[1,0,0],'triangle')
-  11  spliced_track = my_panel.add_track('spliced',[1,0,0],'spliced')
-  12  directed_spliced_track = my_panel.add_track('directed_spliced',[1,0,1],'directed_spliced')
-  13
-  14  # Add features to each track
-  15  generic_track.add_feature('clone1','250..375', 'http://www.newsforge.com')
-  16  generic_track.add_feature('clone2','54..124', 'http://www.thearkdb.org')
-  17  generic_track.add_feature('clone3','100..449', 'http://www.google.com')
-  18
-  19  directed_track.add_feature('marker1','50..60', 'http://www.google.com')
-  20  directed_track.add_feature('marker2','complement(80..120)', 'http://www.sourceforge.net')
-  21
-  22  triangle_track.add_feature('snp1','56')
-  23  triangle_track.add_feature('snp2','103','http://digg.com')
-  24
-  25  spliced_track.add_feature('gene1','join(34..52,109..183)','http://news.bbc.co.uk')
-  26  spliced_track.add_feature('gene2','complement(join(170..231,264..299,350..360,409..445))')
-  27  spliced_track.add_feature('gene3','join(134..152,209..283)')
-  28
-  29  directed_spliced_track.add_feature('gene4','join(34..52,109..183)', 'http://www.vrtnieuws.net')
-  30  directed_spliced_track.add_feature('gene5','complement(join(170..231,264..299,350..360,409..445))')
-  31  directed_spliced_track.add_feature('gene6','join(134..152,209..283)')
-  32
-  33  # Draw the thing
-  34  my_panel.draw('glyph_showcase.png')
+  8   generic_track = my_panel.add_track('generic', :label =&gt; false)
+  9   line_track = my_panel.add_track('line', :label =&gt; false, :glyph =&gt; :line, :colour =&gt; [0,0,1])
+ 10   line_with_handles_track = my_panel.add_track('line_with_handles', :label =&gt; false, :glyph =&gt; :line_with_handles, [1,0,0])
+ 11   directed_track = my_panel.add_track('directed', :label =&gt; false, :glyph =&gt; :directed_generic, :colour =&gt; [0,1,0])
+ 12   triangle_track = my_panel.add_track('triangle', :label =&gt; false, :glyph =&gt; :triangle, :colour =&gt; [1,0,0])
+ 13   spliced_track = my_panel.add_track('spliced', :label =&gt; false, :glyph =&gt; :spliced, :colour =&gt; [1,0,0])
+ 14   directed_spliced_track = my_panel.add_track('directed_spliced', :label =&gt; false, :glyph =&gt; :directed_spliced, :colour =&gt; [1,0,1])
+ 15   composite_track = my_panel.add_track('composite_features', :label =&gt; false, :glyph =&gt; { 'utr' =&gt; :line, 'cds' =&gt; :directed_spliced})
+ 16
+ 17   # Add features to each track
+ 18   generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :link =&gt; 'http://www.newsforge.com')
+ 19   generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :link =&gt; 'http://www.thearkdb.org')
+ 20   generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :link =&gt; 'http://www.google.com')
+ 21
+ 22   line_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
+ 23   line_track.add_feature(Bio::Feature.new('utr', '355..480'), :link =&gt; 'http://www.zdnet.co.uk')
+ 24
+ 25   line_with_handles_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
+ 26   line_with_handles_track.add_feature(Bio::Feature.new('utr', '355..480'), :link =&gt; 'http://www.zdnet.co.uk')
+ 27
+ 28   directed_track.add_feature(Bio::Feature.new('primer', '50..60'), :link =&gt; 'http://www.google.com')
+ 29   directed_track.add_feature(Bio::Feature.new('primer', 'complement(80..120)'), :link =&gt; 'http://www.sourceforge.net')
+ 30
+ 31   triangle_track.add_feature(Bio::Feature.new('snp', '56'))
+ 32   triangle_track.add_feature(Bio::Feature.new('snp', '103'), :link =&gt; 'http://digg.com')
+ 33
+ 34   spliced_track.add_feature(Bio::Feature.new('spliced', 'join(34..52,109..183)'), :link =&gt; 'http://news.bbc.co.uk')
+ 35   spliced_track.add_feature(Bio::Feature.new('spliced', 'complement(join(170..231,264..299,350..360,409..445))'))
+ 36   spliced_track.add_feature(Bio::Feature.new('spliced', 'join(134..152,209..283)'))
+ 37
+ 38   directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(34..52,109..183)'), :link =&gt; 'http://www.vrtnieuws.net')
+ 39   directed_spliced_track.add_feature(Bio::Feature.new('cds', 'complement(join(170..231,264..299,350..360,409..445))'), :link =&gt; 'http://bioinformatics.roslin.ac.uk')
+ 40   directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(134..152,209..283)'))
+ 41
+ 42   utr5 = Bio::Feature.new('utr', '100..150')
+ 43   cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
+ 44   utr3 = Bio::Feature.new('utr', '330..375')
+ 45
+ 46   transcript = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [utr5,cds,utr3])
+ 47   composite_track.add_feature(transcript, :label =&gt; 'my_transcript')
+ 48
+ 49   # Draw the thing
+ 50   my_panel.draw('glyph_showcase.png')
 </pre>
 <p>
 Let&#8216;s walk through this:
@@ -232,42 +256,41 @@ you&#8216;ll be working on. The following parameters were used:
 <li>The sequence is 500 bp long.
 
 </li>
-<li>The width of the picture will be 600 points.
-
-</li>
-<li>A HTML page will be created to make hyperlinks possible (the <em>true</em>)
-
-</li>
-<li>The picture will be zoomed in from bp 1 to 500 (i.e. completely zoomed
-out).
+<li>The width of the picture will be 1000 points.
 
 </li>
 </ul>
 </li>
-<li>Lines 8-12: Create the different tracks. Parameters are:
+<li>Lines 8-15: Create the different tracks. Parameters are:
 
 <ul>
 <li>name.
 
 </li>
-<li>colour. At the moment in RGB. (This will probably change to colour names in
-the future).
+<li>flag if feature labels should be drawn (here: false)
+
+</li>
+<li>the default glyph for features in this track. This can be overridden on a
+feature-by-feature basis. See the picture above and
+Bio::Graphics::Panel::Track#new for allowed values.
 
 </li>
-<li>type. See the picture above and Bio::Graphics::Panel::Track#new for allowed
-values.
+<li>the default colour for features in this track. This can also be overridden
+on a feature-by-feature basis. At the moment in RGB. (This will probably
+change to colour names in the future).
 
 </li>
 </ul>
 </li>
-<li>Lines 15-31: Add features to each track. Parameters are:
+<li>Lines 18-47: Add features to each track. Parameters are:
 
 <ul>
-<li>name.
+<li>a <a href="../classes/Bio/Feature.html">Bio::Feature</a> object. (See
+bioruby documentation at <a
+href="http://www.bioruby.org">www.bioruby.org</a>)
 
 </li>
-<li>location. This should be a location parsable by <a
-href="http://www.bioruby.org">bioruby's</a> Bio::Locations object.
+<li>the label to be used
 
 </li>
 <li>link.
@@ -275,12 +298,34 @@ href="http://www.bioruby.org">bioruby's</a> Bio::Locations object.
 </li>
 </ul>
 </li>
-<li>Line 34: Create the actual picture. If the third parameter to the initial
-Panel#new call (in line 5) is &#8216;true&#8217;, a HTML file is created as
-well.
+<li>Line 50: Create the actual picture. If the the initial Panel#new call
+contains the parameter &quot;:clickable =&gt; true&quot; (in line 5), a
+HTML file is created as well.
 
 </li>
 </ul>
+<p>
+That&#8216;s pretty clear, but what&#8216;s happening with the
+composite_track (on lines 15 and 42-47)?
+</p>
+<p>
+To set the glyph for a feature (or the default glyph in a track), you
+normally use a symbol, like :generic or :directed_spliced. For composite
+features, however, we&#8216;ve made it possible to have different
+subfeatures drawn in different ways. In this example: we want to draw the
+UTRs as thin lines, while the CDS is big boxes connected with thin lines.
+How does this work? See lines 42 to 47. If the feature you&#8216;re adding
+to a track has subfeatures, you can use the type of the subfeature to
+direct the glyph to use. In the example above: the utr5 and utr3 have
+&#8216;utr&#8217; as the first argument in the Bio::Feature#new, and the
+cds object has &#8216;cds&#8217;. The transcript that gets created in line
+46 takes these three <a href="../classes/Bio/Feature.html">Bio::Feature</a>
+objects as subfeatures (the last argument). Now up in line 15 we set the
+glyph of this track to the hash {&#8216;utr&#8217; =&gt; :line,
+&#8216;cds&#8217; =&gt; :directed_spliced}. What this does, is it takes
+each subfeature in turn, and draws it using the glyph that matches its
+type.
+</p>
 <h3>Hyperlinks</h3>
 <p>
 There are no graphic formats that are inherently clickable (SVG is a
@@ -290,6 +335,48 @@ file is created with the same name as the picture but obviously the .html
 extension. This file contains the map and will display a clickable picture
 when loaded in a webbrowser.
 </p>
+<h3>Custom glyphs</h3>
+<p>
+The user can easily create custom glyphs to add to the functionality of the
+<a href="../classes/Bio/Graphics.html">Bio::Graphics</a> library. The only
+thing that has to be done is add a file to lib/bio/graphics/glyphs. The
+file should look like this:
+</p>
+<pre>
+  module Bio::Graphics::Glyph
+    class Bio::Graphics::Glyph::SomeName &lt; Bio::Graphics::Glyph::Common
+      def draw
+        @feature_context.rectangle(x1, y1, x2, y2).fill
+      end
+    end
+  end
+</pre>
+<p>
+What are the properties of that file?
+</p>
+<ul>
+<li>It&#8216;s name has to be the same as the class name specified on the
+second line, but in snake_case instead of CamelCase. The above file
+therefore should be called some_name.rb.
+
+</li>
+<li>Give the class a sensible name (in CamelCase).
+
+</li>
+<li>Just define the draw method. Have a look at the other files in the glyphs/
+directory for examples. Some values you can use:
+
+<ul>
+<li>Bio::Graphics::FEATURE_HEIGHT = default height in pixels for a glyph
+
+</li>
+<li>Bio::Graphics::FEATURE_ARROW_LENGTH = default width in pixels of arrows on
+features
+
+</li>
+</ul>
+</li>
+</ul>
 <h2>Download and installation</h2>
 <p>
 Development of the library is at <a
@@ -299,12 +386,11 @@ href="http://rubyforge.org/projects/bio-graphics">rubyforge.org/projects/bio-gra
 There are different ways to install the library.
 </p>
 <ul>
-<li>Export for SVN (for the latest development version): &quot;svn checkout
-svn://rubyforge.org/var/svn/bio-graphics&quot;
+<li>The easy way: gem install bio-graphics
 
 </li>
-<li>As a rubygem: download the bio-graphics-1.0.gem from the website, and do
-&quot;gem install bio-graphics-1.0.gem&quot;
+<li>The hard (but cutting-edge) way: from SVN: svn checkout
+svn://rubyforge.org/var/svn/bio-graphics
 
 </li>
 </ul>
@@ -314,15 +400,44 @@ You&#8216;ll need to have the following installed to use this library:
 </p>
 <ul>
 <li>bioruby (<a href="http://www.bioruby.org">www.bioruby.org</a>), to parse
-the feature locations. On linux systems, type &quot;gem install bio&quot;.
+the feature locations.
 
 </li>
 <li>cairo (<a href="http://cairographics.org">cairographics.org</a>), to do the
-actual drawing. On Ubuntu, type &quot;sudo apt-get install
-libcairo-ruby&quot;.
+actual drawing.
+
+</li>
+<li>pango (<a href="http://www.pango.org">www.pango.org</a>), to do the high
+level text drawing.
 
 </li>
 </ul>
+<h3>Ubuntu</h3>
+<ul>
+<li>gem install bio
+
+</li>
+<li>sudo apt-get install libcairo-ruby
+
+</li>
+</ul>
+<h3>Windows (thanks to Naohisa Goto)</h3>
+<p>
+Install Ruby-GNOME2 Win32 GUI Installer, which contains rcairo-1.2.6. Get
+it from ruby-gnome2.sourceforge.jp/?News_20070212_1
+(ruby-gnome2-0.16.0-1-i386-mswin32.exe)
+</p>
+<p>
+During installation, check the &quot;Register enviroment variables&quot;
+option.
+</p>
+<h3>Mac OSX (thanks to Ed Allen)</h3>
+<p>
+We haven&#8216;t figured out yet how to install cairo and pango separately
+on a Mac. However, if you install Why The Lucky Stiff‘s Shoes GUI for
+Ruby toolkit, you get the pango and ruby-pango bindings for free. Get it
+from code.whytheluckystiff.net/shoes/wiki/DownloadShoes
+</p>
 
     </div>
 
@@ -354,5 +469,11 @@ libcairo-ruby&quot;.
   <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
 </div>
 
+<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
+</script>
+<script type="text/javascript">
+_uacct = "UA-2131816-4";
+urchinTracker();
+</script>
 </body>
-</html>
+</html>

data/doc/files/lib/bio-graphics_rb.html

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Thu Oct 18 18:13:09 +0100 2007</td>
+      <td>Thu Jan 24 20:03:22 +0000 2008</td>
     </tr>
     </table>
   </div>
@@ -71,7 +71,8 @@
     <div id="description">
       <h1>bio-graphics.rb - Loading all <a href="../../classes/Bio/Graphics.html">Bio::Graphics</a> modules</h1>
 <table>
-<tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
+<tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt; Charles Comstock
+&lt;dgtized@gmail.com&gt;
 
 </td></tr>
 <tr><td valign="top">License:</td><td>The Ruby License

data/doc/files/lib/bio/graphics/feature_rb.html

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Thu Oct 18 18:24:17 +0100 2007</td>
+      <td>Thu Jan 24 16:22:58 +0000 2008</td>
     </tr>
     </table>
   </div>
@@ -68,15 +68,21 @@
 
   <div id="contextContent">
 
+    <div id="description">
+      <h1>bio/graphics/feature.rb - feature class</h1>
+<table>
+<tr><td valign="top">Copyright:</td><td>Copyright (C) 2007, 2008 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt; Charles
+Comstock &lt;dgtized@gmail.com&gt;
 
-    <div id="requires-list">
-      <h3 class="section-bar">Required files</h3>
+</td></tr>
+<tr><td valign="top">License:</td><td>The Ruby License
+
+</td></tr>
+</table>
 
-      <div class="name-list">
-      yaml&nbsp;&nbsp;
-      </div>
     </div>
 
+
    </div>
 
 

data/doc/files/lib/bio/graphics/glyphs/box_rb.html

@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>File: box.rb</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+
+  function toggleCode( id ) {
+    if ( document.getElementById )
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+      elem = eval( "document.all." + id );
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+      return false;
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+    elemStyle = elem.style;
+    
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
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+
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+  
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  
+  // ]]>
+  </script>
+
+</head>
+<body>
+
+
+
+  <div id="fileHeader">
+    <h1>box.rb</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>lib/bio/graphics/glyphs/box.rb
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Thu Jan 24 16:23:42 +0000 2008</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+
+  <div id="bodyContent">
+
+
+
+  <div id="contextContent">
+
+    <div id="description">
+      <h1>bio/graphics/glyphs/box - box glyph</h1>
+<table>
+<tr><td valign="top">Copyright:</td><td>Copyright (C) 2007, 2008 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
+
+</td></tr>
+<tr><td valign="top">License:</td><td>The Ruby License
+
+</td></tr>
+</table>
+
+    </div>
+
+
+   </div>
+
+
+  </div>
+
+
+    <!-- if includes -->
+
+    <div id="section">
+
+
+
+
+
+      
+
+
+    <!-- if method_list -->
+
+
+  </div>
+
+
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+
+</body>
+</html>