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bio-graphics 1.0

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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/ImageMap/ImageMapElement.src/M000003.html ADDED

@@ -0,0 +1,19 @@
+<?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 (ImageMap::ImageMapElement)</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/image_map.rb, line 25</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>, <span class="ruby-identifier">url</span> = <span class="ruby-keyword kw">nil</span>)
+      <span class="ruby-ivar">@left</span>, <span class="ruby-ivar">@top</span>, <span class="ruby-ivar">@right</span>, <span class="ruby-ivar">@bottom</span> = <span class="ruby-identifier">left</span>, <span class="ruby-identifier">top</span>, <span class="ruby-identifier">right</span>, <span class="ruby-identifier">bottom</span>
+      <span class="ruby-ivar">@url</span> = ( <span class="ruby-identifier">url</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-value str">''</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">url</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/classes/ImageMap/ImageMapElement.src/M000004.html ADDED

@@ -0,0 +1,20 @@
+<?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>to_s (ImageMap::ImageMapElement)</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/image_map.rb, line 31</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+      <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
+        <span class="ruby-keyword kw">return</span> <span class="ruby-value str">'&lt;area shape=&quot;rect&quot; coords=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@left</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@top</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@right</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">' '</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@bottom</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot; href=&quot;'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@url</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'&quot;/&gt;'</span>
+      <span class="ruby-keyword kw">end</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>

data/doc/created.rid ADDED

	@@ -0,0 +1 @@
1	+ Mon Oct 01 11:03:19 +0100 2007

data/doc/files/README_DEV.html ADDED

@@ -0,0 +1,432 @@
+<?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: README.DEV</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="fileHeader">
+    <h1>README.DEV</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>README.DEV
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Mon Oct 01 11:03:17 +0100 2007</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
+</p>
+<h2>README for developers</h2>
+<p>
+This README is mainly meant to explain how the code works (rather than how
+to <em>use</em> the library). It should help if you&#8216;re interested in
+contributing, or if you think you found a bug.
+</p>
+<h3>Overview</h3>
+<p>
+I&#8216;ve tried to document as much as possible in the code itself, see
+for example the comments that accompany the setting of the defaults for <a
+href="../classes/Bio/Graphics.html">Bio::Graphics</a> in the panel.rb file.
+However, the bigger picture can not be explained that way.
+</p>
+<h3>The files</h3>
+<p>
+There&#8216;s one file for each class: panel, track, feature, ruler and
+image_map. See the tutorial on a breakdown what each of these do. All of
+these except the image_map make up a picture. The image_map is used to
+describe the HTML map that can be created to make a picture clickable.
+</p>
+<p>
+Classes are embedded in each other: instead of
+</p>
+<pre>
+  Bio::Graphics::Panel
+  Bio::Graphics::Ruler
+  Bio::Graphics::Track
+  Bio::Graphics::Feature
+</pre>
+<p>
+we have:
+</p>
+<pre>
+  Bio::Graphics::Panel
+  Bio::Graphics::Panel::Ruler
+  Bio::Graphics::Panel::Track
+  Bio::Graphics::Panel::Track::Feature
+</pre>
+<p>
+There&#8216;s a reason for this. A track can only exist within the confines
+of a panel (i.e. a panel is a container for tracks), and a feature can only
+exist within the confines of a track. In addition, there are quite some
+instances where information from the panel is necessary for the track, and
+from the track for the features.
+</p>
+<h3>The workflow</h3>
+<h4>1. Creating the panel</h4>
+<p>
+The user has to start with a
+</p>
+<pre>
+  my_panel = Bio::Graphics::Panel.new(length, width, clickable, display_start, display_stop)
+</pre>
+<p>
+When this happens, among other things, the instance variable @tracks is
+created that will later contain the actual Track objects. In addition,
+there&#8216;s @number_of_times_bumped. You&#8216;ll later see that each
+Track object also has its @number_of_times_bumped. The panel needs this
+information to know how far it has to go down before it can start drawing a
+track: the first track will be just below the ruler, but the vertical
+coordinates of the second one depend on the height of all the ones that
+were drawn previously. And <em>that</em> in turn is defined by the number
+of times a feature would overlap with another one and therefore had to be
+<em>bumped</em> down.
+</p>
+<p>
+@display_start and @display_stop are used for zooming in on a region. Even
+though the full @length of the sequence can be really long, setting
+@display_start and @display_stop will only consider that region.
+</p>
+<p>
+Then there is @rescale_factor, which plays a crucial role in drawing the
+stuff: it tells the script how many basepairs are contained in one pixel.
+This variable will be used <em>very</em> extensively in the drawing code.
+</p>
+<p>
+So this covered the Panel#initialize&#8230;
+</p>
+<h4>2. Adding tracks to the panel</h4>
+<p>
+Because tracks are inherently part of a panel and cannot exist on their
+own, they can only be created by using a Panel method rather than a Track
+method.
+</p>
+<pre>
+  my_track_1 = my_panel.add_track(name, feature_colour = [0,0,1], feature_glyph = 'generic')
+</pre>
+<p>
+This creates a new Track object and adds it to the @tracks array of the
+Panel object. Several instance variables are set for the Track object,
+including @features (which is an array of Feature objects for that track)
+and @number_of_times_bumped. Every time a feature cannot be drawn because
+it would overlap with another one, it will be &#8216;bumped&#8217; down
+until it can be drawn. This effectively results in <em>rows</em> that
+contain the features. The @number_of_times_bumped is just the number of
+rows (to be able to calculate the height of the track afterwards). I admit
+that this variable should be renamed to something like
+@number_of_feature_rows or something, because the value is actually the
+number of times bumped + 1. In the example below, @number_of_times_bumped
+is 3 (instead of 2). (I&#8216;ll change that later&#8230;)
+</p>
+<pre>
+  ------------------------------------------------------
+    *******    ****  *********         *****    *****
+         *****                       ********
+                                    **
+</pre>
+<p>
+The Panel#add_track method returns the Track object itself, because the
+latter has to be accessible to be able to assign features to it.
+</p>
+<h4>3. Adding features to a track</h4>
+<p>
+Same thing as adding a track to a panel: the feature can only be added by
+the user by using the Track#add_feature method. Parameters are the name of
+the feature, the location and the link.
+</p>
+<p>
+The location of a feature can be something like
+&#8216;complement(join(10..20,50..70))&#8217;. To be able to parse this, I
+use the Bio::Locations object from bioruby (see <a
+href="http://www.bioruby.org">www.bioruby.org</a>). A Bio::Locations
+(plural) object contains one or more Bio::Location (singular) objects,
+which are the subfeatures: 10..20 and 50..70. It&#8216;s these
+Bio::Location objects we use to calculate the ultimate start and stop of
+the feature.
+</p>
+<p>
+The Track#add_feature method returns the Track object itself.
+</p>
+<p>
+Now let&#8216;s look at the other end: the Feature object that gets
+created. In the Feature#initialize method, you&#8216;ll notice, apart from
+the obvious variables, the following instances variables:
+@pixel_range_collection, @chopped_at_start, @chopped_at_stop,
+@hidden_subfeatures_at_start and @hidden_subfeatures_at_stop. Let&#8216;s
+take these one by one:
+</p>
+<h5>@pixel_range_collection</h5>
+<p>
+Now <em>this</em> is the crucial bit: it will hold the information on what
+pixels (on the horizontal axis) should be covered. This means that any part
+of the feature that does not fall within the view is <em>not</em> in this
+collection. Basically, for every subfeature (e.g. exon for a gene), the
+location of that subfeature is compared to the region of the view. If a
+subfeature is not in the view at all, its positions are discarded (but
+other stuff does happen, see below); if a subfeature is at the left of the
+picture but actually extends outwith the view, the start pixel will become
+1. You get the picture. Also see the mini diagrams in the code itself.
+</p>
+<p>
+These start and stop positions are used to create
+Bio::Graphics::Panel::Track::PixelRange objects. Unspliced objects will
+have an array @pixel_range_collection with just one element.
+</p>
+<h5>@chopped_at_start and @chopped_at_stop</h5>
+<p>
+Suppose you&#8216;ve got a directed feature (so one with an arrow), and the
+3&#8217; end falls outside of the view. What would happen, is that the
+3&#8217; end that&#8216;s out of view would be chopped of (that&#8216;s
+good), but also that the end of the glyph (which is <em>not</em> the end of
+the feature) becomes an arrow. I don&#8216;t want that. Instead, the arrow
+should be removed.
+</p>
+<p>
+That&#8216;s where the @chopped_at_start and @chopped_at_stop come in. If
+these are set to true (while building the @pixel_range_collection), the
+arrow is not drawn.
+</p>
+<h5>@hidden_subfeatures_at_start and @hidden_subfeatures_at_stop</h5>
+<p>
+For spliced features, it might be that one or more of the subfeatures (e.g.
+exons) lies outwith the view. We normally draw e.g. genes by drawing the
+exons as boxes and connecting them with small lines. The drawing code
+itself (see later) takes all exons within view and draws those connections.
+However, if an exon is outside of the viewing area, this line is not drawn.
+The @hidden_subfeatures_at_start and @hidden_subfeatures_at_stop are just
+flags to capture this.
+</p>
+<h4>4. Drawing the thing</h4>
+<p>
+The Cairo library (<a
+href="http://cairographics.org">cairographics.org</a>) is used for the
+actual drawing. The main concepts in the Cairo drawing model are (please
+also see <a
+href="http://cairographics.org/tutorial">cairographics.org/tutorial</a>):
+</p>
+<ul>
+<li><b>source</b>: the <em>paint</em> you&#8216;ll be using
+</li>
+<li><b>destination</b>: the <em>surface</em> (Cairo::ImageSurface) that you
+want to draw onto
+</li>
+<li><b>mask</b>: controls where you apply the source to the destination. Stuff
+like &#8216;line_to&#8217;.
+</li>
+<li><b>context</b>: tracks one source, one mask and one destination.
+</li>
+</ul>
+<p>
+From the cairo tutorial: &quot;Before you can start to draw something with
+cairo, you need to create the context. &lt;SNIP&gt; When you create a cairo
+context, it must be tied to a specific surface - for example, an image
+surface if you want to create a PNG file.&quot; So that&#8216;s what we
+have to do: create a Cairo::ImageSurface and connect a Cairo::Context to
+it.
+</p>
+<p>
+Now let&#8216;s walk through the code itself&#8230;
+</p>
+<p>
+When a user draws a panel, the first thing that happens, is the creation of
+a Cairo::ImageSurface (the <em>destination</em>). To be able to do this, we
+need to know the dimensions. But there&#8216;s a slight problem: we
+can&#8216;t know the height of the picture until it&#8216;s actually drawn.
+The way we&#8216;ll circumvent this, is that we create a really high
+picture (called &quot;huge_panel_drawing&quot;) that we&#8216;ll crop
+afterwards.
+</p>
+<h5>Drawing the ruler</h5>
+<p>
+A ruler consists of a line with tickmarks on it. The major issue with
+drawing the ruler, is determining the distance between those ticks. Suppose
+we have zoomed into a small region, we&#8216;d still want to see usable
+ticks; and if we&#8216;ve zoomed out to a huge region, we don&#8216;t want
+to have those ticks all bumping into each other.
+</p>
+<p>
+To calculate the distance between consecutive ticks, we start with a
+distance of 1 basepair, and increase it until the minimal distance
+criterion is met. We also set the distance between major tickmarks (which
+are the ones that will get a number). There&#8216;s a small issue when you
+actually start drawing the ticks. Most of the time, we don&#8216;t want the
+first tick on the very first basepair of the view. Suppose that would be
+position 333 in the sequence. Then the numbers under the major tickmarks
+would be: 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370,
+380. So we want to find the position of the first tick. If we&#8216;ve
+found that one, it&#8216;s simple to add the rest of them.
+</p>
+<p>
+The ruler height @height consists of the height of the ruler itself plus
+the height of the numbers.
+</p>
+<h5>Drawing the tracks</h5>
+<p>
+Drawing each track starts out with the general header: a line above it and
+the title. Obviously, the more challenging part is drawing the features
+themselves.
+</p>
+<p>
+First thing we have to do, is figure out what the <b>vertical</b>
+<b>coordinates</b> of the glyph should be (i.e. the row). To keep track of
+what parts of the screen are already occupied by features (so that we know
+when a new feature has to be bumped down), I make use of a <b>grid</b>. The
+grid is basically a hash with the keys being the row number, and the values
+arrays of ranges. (These ranges use basepair units rather than pixels, but
+that&#8216;s completely arbitrary.) For each feature, we first check if we
+can draw it at the top of the track (i.e. row 1) and if we can&#8216;t move
+it down a row at a time until there&#8216;s room for it.
+</p>
+<p>
+So for example, suppose we&#8216;ve already drawn two features that have
+the following positions: 100..150 and 200..225. The grid would then look
+like this:
+</p>
+<pre>
+  grid = { 1 =&gt; [(100..150),(200..225)] }
+</pre>
+<p>
+If we&#8216;d like to draw a new feature from 125..175 (which overlaps the
+first of the two ranges above), we see that row_available becomes false,
+and the row number is increased. The grid after adding this feature looks
+like:
+</p>
+<pre>
+  grid = { 1 =&gt; [(100..150),(200..225)],
+           2 =&gt; [(125..175)] }
+</pre>
+<p>
+So now we know what the vertical coordinates of the glyph should be. Next
+step is to check if there&#8216;s reasons we would like to <b>change</b>
+<b>the</b> <b>requested</b> <b>glyph</b> <b>type</b> <b>from</b>
+<b>directed</b> <b>to</b> <b>undirected</b>. If the user asks for directed
+glyphs (i.e. ones with an arrow at the end), but the view is zoomed
+<em>way</em> out, there&#8216;s no way the arrow will be visible. If
+we&#8216;d try to draw that arrow anyway, it would become bigger than the
+feature itself. Another reason would be if the feature&#8216;s 3&#8217; end
+extends outwith the picture.
+</p>
+<p>
+Finally, we can <b>draw</b>. The actual drawing bit should be quite
+self-explanatory (<em>move_to</em>, <em>line_to</em>, &#8230;).
+</p>
+<p>
+For the spliced features (<em>spliced</em> itself and
+<em>directed_spliced</em>), we first draw the components (i.e. the exons)
+keeping track of the start and stop positions of the gaps (i.e. introns).
+We then add the connections in those gaps. In addition, we draw a line that
+extends to the side of the picture if there are exons out of view. This
+flag was set when the feature was created (see above:
+@hidden_subfeatures_at_start and @hidden_subfeatures_at_stop).
+</p>
+<p>
+When the user wants a clickable map, we also have to record that this
+region should be added to the image map.
+</p>
+<p>
+When everything has been drawn, we finally know the number of rows for that
+track (i.e. the number_of_times_bumped).
+</p>
+<h5>Finalizing the panel</h5>
+<p>
+So now we have a huge panel (see &quot;huge_panel_drawing&quot; above)
+which is way to high. This is converted to a panel of the right size by
+creating a new panel (i.e. the cairo destination), and then using the huge
+panel as a source to be transferred on that new destination.
+</p>
+<p>
+And we just write the PNG to a file. If the user wanted a clickable map,
+also create the HTML file.
+</p>
+    </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>