RubyGems - bio-graphics - Versions diffs - 1.0 - Mend

bio-graphics 1.0

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Files changed (63) hide show

data/doc/classes/Bio.html +135 -0
data/doc/classes/Bio/Graphics.html +247 -0
data/doc/classes/Bio/Graphics/Panel.html +344 -0
data/doc/classes/Bio/Graphics/Panel.src/M000005.html +29 -0
data/doc/classes/Bio/Graphics/Panel.src/M000006.html +19 -0
data/doc/classes/Bio/Graphics/Panel.src/M000007.html +67 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.html +238 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000008.html +20 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000009.html +28 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000010.html +54 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000013.html +20 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +28 -0
data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +59 -0
data/doc/classes/Bio/Graphics/Panel/Track.html +342 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +23 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +42 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +285 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000011.html +23 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000012.html +43 -0
data/doc/classes/Bio/Graphics/Panel/Track.src/M000013.html +259 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +292 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +65 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +65 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +155 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000012.html +18 -0
data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000015.html +18 -0
data/doc/classes/ImageMap.html +185 -0
data/doc/classes/ImageMap.src/M000001.html +18 -0
data/doc/classes/ImageMap.src/M000002.html +24 -0
data/doc/classes/ImageMap/ImageMapElement.html +187 -0
data/doc/classes/ImageMap/ImageMapElement.src/M000003.html +19 -0
data/doc/classes/ImageMap/ImageMapElement.src/M000004.html +20 -0
data/doc/created.rid +1 -0
data/doc/files/README_DEV.html +432 -0
data/doc/files/TUTORIAL.html +358 -0
data/doc/files/lib/bio-graphics_rb.html +121 -0
data/doc/files/lib/bio/graphics/feature_rb.html +113 -0
data/doc/files/lib/bio/graphics/image_map_rb.html +113 -0
data/doc/files/lib/bio/graphics/panel_rb.html +113 -0
data/doc/files/lib/bio/graphics/ruler_rb.html +113 -0
data/doc/files/lib/bio/graphics/track_rb.html +113 -0
data/doc/fr_class_index.html +35 -0
data/doc/fr_file_index.html +34 -0
data/doc/fr_method_index.html +41 -0
data/doc/images/example.png +0 -0
data/doc/images/glyph_showcase.png +0 -0
data/doc/images/terms.png +0 -0
data/doc/images/terms.svg +166 -0
data/doc/index.html +24 -0
data/images/example.png +0 -0
data/images/glyph_showcase.png +0 -0
data/images/terms.png +0 -0
data/images/terms.svg +166 -0
data/lib/bio-graphics.rb +18 -0
data/lib/bio/graphics/feature.rb +136 -0
data/lib/bio/graphics/image_map.rb +37 -0
data/lib/bio/graphics/panel.rb +205 -0
data/lib/bio/graphics/ruler.rb +96 -0
data/lib/bio/graphics/track.rb +387 -0
data/samples/arkdb_features.rb +37 -0
data/samples/data.txt +32 -0
data/samples/glyph_showcase.rb +29 -0
metadata +137 -0

data/doc/classes/Bio/Graphics/Panel/Track/Feature.html ADDED

@@ -0,0 +1,292 @@
+<?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>Class: Bio::Graphics::Panel::Track::Feature</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 )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">Bio::Graphics::Panel::Track::Feature</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../../../files/lib/bio/graphics/feature_rb.html">
+                lib/bio/graphics/feature.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+The Bio::Graphics::Track::Feature class describes features to be placed on
+the graph. See <a href="../../../Graphics.html">Bio::Graphics</a>
+documentation for explanation of interplay between different classes.
+</p>
+<p>
+The position of the <a href="Feature.html">Feature</a> is a Bio::Locations
+object to make it possible to transparently work with simple and spliced
+features.
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+      <a href="#M000011">new</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="class-list">
+      <h3 class="section-bar">Classes and Modules</h3>
+      Class <a href="Feature/PixelRange.html" class="link">Bio::Graphics::Panel::Track::Feature::PixelRange</a><br />
+    </div>
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">chopped_at_start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Is the first subfeature incomplete?
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">chopped_at_stop</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Is the last subfeature incomplete?
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">hidden_subfeatures_at_start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Are there subfeatures out of view at the left side of the picture?
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">hidden_subfeatures_at_stop</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Are there subfeatures out of view at the right side of the picture?
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">link</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The URL to be followed when the glyph for this feature is clicked
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">location</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The location of the feature (which is a Bio::Locations object)
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">name</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The name of the feature
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">pixel_range_collection</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The array keeping the pixel ranges for the sub-features. Unspliced features
+will just have one element, while spliced features will have more than one.
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">start</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The start position of the feature (in bp)
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">stop</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The stop position of the feature (in bp)
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">strand</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The strand of the feature
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">track</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+The track that this feature belongs to
+</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000011" class="method-detail">
+        <a name="M000011"></a>
+        <div class="method-heading">
+          <a href="Feature.src/M000011.html" target="Code" class="method-signature"
+            onclick="popupCode('Feature.src/M000011.html');return false;">
+          <span class="method-name">new</span><span class="method-args">(track, name, location = Bio::Locations.new('1..' + track.panel.length.to_s), link = nil)</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+!!Not to be used directly. Use <a
+href="../Track.html#M000009">Bio::Graphics::Panel::Track.add_feature</a>
+instead!! A feature can not exist except within the confines of a <a
+href="../Track.html">Bio::Graphics::Panel::Track</a> object.
+</p>
+<hr size="1"></hr><p>
+<b>Arguments</b>:
+</p>
+<ul>
+<li><em>panel</em> (required) :: <a
+href="../Track.html">Bio::Graphics::Panel::Track</a> object that this
+feature belongs to
+</li>
+<li><em>name</em> (required) :: Name of the feature
+</li>
+<li><em>location</em> :: Bio::Locations object. Default = whole panel, forward
+strand
+</li>
+<li><em>link</em> :: URL for clickable images
+</li>
+</ul>
+<table>
+<tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track::Feature object
+</td></tr>
+</table>
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html ADDED

@@ -0,0 +1,65 @@
+<?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>
+<head>
+  <title>new (Bio::Graphics::Panel::Track::Feature)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 37</span>
+          <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">track</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'1..'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>)
+            <span class="ruby-ivar">@track</span> = <span class="ruby-identifier">track</span>
+            <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+            <span class="ruby-ivar">@location</span> = <span class="ruby-identifier">location</span>
+            <span class="ruby-ivar">@start</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@stop</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">location</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">strand</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@link</span> = <span class="ruby-identifier">link</span>
+            <span class="ruby-ivar">@pixel_range_collection</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
+            <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-comment cmt"># Get all pixel ranges for the subfeatures
+            <span class="ruby-identifier">location</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
+              <span class="ruby-comment cmt">#   xxxxxx  [          ]
+              <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
+                <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-keyword kw">next</span>
+              <span class="ruby-comment cmt">#           [          ]   xxxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-keyword kw">next</span>
+              <span class="ruby-comment cmt">#      xxxx[xxx       ]
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
+                <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
+                <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#          [      xxxx]xxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
+                <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#      xxxx[xxxxxxxxxx]xxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
+                <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
+                <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#          [   xxxxx  ]
+              <span class="ruby-keyword kw">else</span>
+                <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+              <span class="ruby-keyword kw">end</span>
+              <span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">PixelRange</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>))
+            <span class="ruby-keyword kw">end</span>
+          <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html ADDED

@@ -0,0 +1,65 @@
+<?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>
+<head>
+  <title>new (Bio::Graphics::Panel::Track::Feature)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../../../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/feature.rb, line 36</span>
+          <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">track</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Locations</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value str">'0..'</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">width</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">rescale_factor</span>).<span class="ruby-identifier">to_s</span>), <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>)
+            <span class="ruby-ivar">@track</span> = <span class="ruby-identifier">track</span>
+            <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+            <span class="ruby-ivar">@location</span> = <span class="ruby-identifier">location</span>
+            <span class="ruby-ivar">@start</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span>}.<span class="ruby-identifier">min</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@stop</span> = <span class="ruby-identifier">location</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span>}.<span class="ruby-identifier">max</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">location</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">strand</span>.<span class="ruby-identifier">to_i</span>
+            <span class="ruby-ivar">@link</span> = <span class="ruby-identifier">link</span>
+            <span class="ruby-ivar">@pixel_range_collection</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
+            <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">false</span>
+            <span class="ruby-comment cmt"># Get all pixel ranges for the subfeatures
+            <span class="ruby-identifier">location</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
+              <span class="ruby-comment cmt">#   xxxxxx  [          ]
+              <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
+                <span class="ruby-ivar">@hidden_subfeatures_at_start</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-keyword kw">next</span>
+              <span class="ruby-comment cmt">#           [          ]   xxxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-ivar">@hidden_subfeatures_at_stop</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-keyword kw">next</span>
+              <span class="ruby-comment cmt">#      xxxx[xxx       ]
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
+                <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
+                <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#          [      xxxx]xxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
+                <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#      xxxx[xxxxxxxxxx]xxxx
+              <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+                <span class="ruby-identifier">start_pixel</span> = <span class="ruby-value">1</span>
+                <span class="ruby-identifier">stop_pixel</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
+                <span class="ruby-ivar">@chopped_at_start</span> = <span class="ruby-keyword kw">true</span>
+                <span class="ruby-ivar">@chopped_at_stop</span> = <span class="ruby-keyword kw">true</span>
+              <span class="ruby-comment cmt">#          [   xxxxx  ]
+              <span class="ruby-keyword kw">else</span>
+                <span class="ruby-identifier">start_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">from</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+                <span class="ruby-identifier">stop_pixel</span> = ( <span class="ruby-identifier">l</span>.<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
+              <span class="ruby-keyword kw">end</span>
+              <span class="ruby-ivar">@pixel_range_collection</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">PixelRange</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">stop_pixel</span>))
+            <span class="ruby-keyword kw">end</span>
+          <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html ADDED

@@ -0,0 +1,155 @@
+<?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>Class: Bio::Graphics::Panel::Track::Feature::PixelRange</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 )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">Bio::Graphics::Panel::Track::Feature::PixelRange</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../../../../files/lib/bio/graphics/feature_rb.html">
+                lib/bio/graphics/feature.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+      <a href="#M000012">new</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">start_pixel</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">stop_pixel</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000012" class="method-detail">
+        <a name="M000012"></a>
+        <div class="method-heading">
+          <a href="PixelRange.src/M000012.html" target="Code" class="method-signature"
+            onclick="popupCode('PixelRange.src/M000012.html');return false;">
+          <span class="method-name">new</span><span class="method-args">(start_pixel, stop_pixel)</span>
+          </a>
+        </div>
+        <div class="method-description">
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>