bio-graphics 1.0 → 1.2

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

@@ -127,17 +127,22 @@ documentation for explanation of interplay between different classes.
       <div class="name-list">
         <table>
         <tr class="top-aligned-row context-row">
-          <td class="context-item-name">feature_colour</td>
+          <td class="context-item-name">colour</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">feature_glyph</td>
+          <td class="context-item-name">features</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">features</td>
+          <td class="context-item-name">glyph</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">grid</td>
           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
           <td class="context-item-desc"></td>
         </tr>
@@ -152,7 +157,7 @@ documentation for explanation of interplay between different classes.
           <td class="context-item-desc"></td>
         </tr>
         <tr class="top-aligned-row context-row">
-          <td class="context-item-name">number_of_times_bumped</td>
+          <td class="context-item-name">number_of_feature_rows</td>
           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
           <td class="context-item-desc"></td>
         </tr>
@@ -161,6 +166,16 @@ documentation for explanation of interplay between different classes.
           <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">show_label</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">vertical_offset</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
         </table>
       </div>
     </div>
@@ -177,7 +192,7 @@ documentation for explanation of interplay between different classes.
         <div class="method-heading">
           <a href="Track.src/M000008.html" target="Code" class="method-signature"
             onclick="popupCode('Track.src/M000008.html');return false;">
-          <span class="method-name">new</span><span class="method-args">(panel, name, feature_colour = [0,0,1], feature_glyph = 'generic')</span>
+          <span class="method-name">new</span><span class="method-args">(panel, name, label = true, colour = [0,0,1], glyph = :generic)</span>
           </a>
         </div>
       
@@ -200,6 +215,10 @@ belongs to
 <li><em>name</em> (required) :: Name of the track to be displayed (e.g.
 &#8216;genes&#8217;)
 
+</li>
+<li><em>label</em> :: Boolean: should the label for each feature be drawn or
+not
+
 </li>
 <li><em>colour</em> :: Colour to be used to <a
 href="Track.html#M000010">draw</a> the features within the track. Default =
@@ -207,11 +226,11 @@ href="Track.html#M000010">draw</a> the features within the track. Default =
 
 </li>
 <li><em>glyph</em> :: Glyph to use for drawing the features. Options are:
-&#8216;generic&#8217;, &#8216;directed_generic&#8217;, &#8216;spliced,
-&#8216;directed_spliced&#8217; and &#8216;triangle&#8217;. Triangles can be
-used for features whose start and stop positions are the same (e.g. SNPs).
-If you try to <a href="Track.html#M000010">draw</a> a feature that is
-longer with triangles, an error will be shown.
+:generic, :directed_generic, :spliced, :directed_spliced, :line and
+:triangle. Triangles can be used for features whose start and stop
+positions are the same (e.g. SNPs). If you try to <a
+href="Track.html#M000010">draw</a> a feature that is longer with triangles,
+an error will be shown.
 
 </li>
 </ul>
@@ -297,7 +316,7 @@ added. If it should be only partly visible, it is added completely.
         <div class="method-heading">
           <a href="Track.src/M000010.html" target="Code" class="method-signature"
             onclick="popupCode('Track.src/M000010.html');return false;">
-          <span class="method-name">draw</span><span class="method-args">(panel_drawing, vertical_offset)</span>
+          <span class="method-name">draw</span><span class="method-args">(panel_drawing)</span>
           </a>
         </div>
       
@@ -313,10 +332,6 @@ href="../Panel.html#M000007">Bio::Graphics::Panel.draw</a>
 <ul>
 <li><em>paneldrawing</em> (required) :: the panel cairo object
 
-</li>
-<li><em>verticaloffset</em> (required) :: number of pixels to offset the track
-downwards, based on the height of other tracks that were drawn above it
-
 </li>
 </ul>
 <table>

data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html

@@ -10,14 +10,17 @@
   <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/track.rb, line 38</span>
-        <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">feature_colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>], <span class="ruby-identifier">feature_glyph</span> = <span class="ruby-value str">'generic'</span>)
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 39</span>
+        <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">label</span> = <span class="ruby-keyword kw">true</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">1</span>], <span class="ruby-identifier">glyph</span> = <span class="ruby-identifier">:generic</span>)
           <span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
           <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
-          <span class="ruby-ivar">@feature_colour</span> = <span class="ruby-identifier">feature_colour</span>
-          <span class="ruby-ivar">@feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
+          <span class="ruby-ivar">@show_label</span> = <span class="ruby-identifier">label</span>
+          <span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
+          <span class="ruby-ivar">@glyph</span> = <span class="ruby-identifier">glyph</span>
           <span class="ruby-ivar">@features</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-          <span class="ruby-ivar">@number_of_times_bumped</span> = <span class="ruby-value">0</span>
+          <span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
+          <span class="ruby-ivar">@vertical_offset</span> = <span class="ruby-value">0</span>
+          <span class="ruby-ivar">@grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
         <span class="ruby-keyword kw">end</span></pre>
 </body>
 </html>

data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html

@@ -10,7 +10,7 @@
   <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/track.rb, line 76</span>
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 80</span>
         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_feature</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_string</span> = <span class="ruby-value str">'1..'</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@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-keyword kw">if</span> <span class="ruby-identifier">link</span> <span class="ruby-operator">==</span> <span class="ruby-value str">''</span>
             <span class="ruby-identifier">link</span> = <span class="ruby-keyword kw">nil</span>
@@ -29,7 +29,7 @@
           <span class="ruby-comment cmt"># looking at, don't bother storing the stuff. I think this makes huge
           <span class="ruby-comment cmt"># speed and memory differences if you've got a chromosome with
           <span class="ruby-comment cmt"># thousands of features.
-          <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
+          <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
             <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span>
           <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#elsif start &gt;= panel.display_start and stop &lt;= panel.display_stop
             <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Panel</span><span class="ruby-operator">::</span><span class="ruby-constant">Track</span><span class="ruby-operator">::</span><span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">location_object</span>, <span class="ruby-identifier">link</span>))

data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html

@@ -10,274 +10,41 @@
   <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/track.rb, line 113</span>
-        <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>, <span class="ruby-identifier">vertical_offset</span>)
+  <pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 115</span>
+        <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">panel_drawing</span>)
           <span class="ruby-identifier">track_drawing</span> = <span class="ruby-constant">Cairo</span><span class="ruby-operator">::</span><span class="ruby-constant">Context</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">panel_drawing</span>)
 
           <span class="ruby-comment cmt"># Draw thin line above title
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>,<span class="ruby-value">0</span><span class="ruby-value">.75</span>)
-          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span>)
-          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-identifier">vertical_offset</span>)
+          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
+          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span>)
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
 
           <span class="ruby-comment cmt"># Draw track title
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>)
-          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-value str">'Georgia'</span>,<span class="ruby-value">1</span>,<span class="ruby-value">1</span>)
+<span class="ruby-comment cmt">#          track_drawing.select_font_face('Georgia',1,1)
+          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-operator">*</span>(<span class="ruby-constant">FONT</span>))
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
-          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
+          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-constant">TRACK_HEADER_HEIGHT</span> <span class="ruby-operator">+</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-value">10</span>)
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>)
 
           <span class="ruby-comment cmt"># Draw the features
-          <span class="ruby-identifier">grid</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>
-
           <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">save</span> <span class="ruby-keyword kw">do</span>
-            <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
-            <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@feature_colour</span>)
+            <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">translate</span>(<span class="ruby-value">0</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>)
+            <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">set_source_rgb</span>(<span class="ruby-ivar">@colour</span>)
 
-            <span class="ruby-comment cmt"># Now draw the features
-            <span class="ruby-comment cmt"># These are the basic steps:
-            <span class="ruby-comment cmt">#   A. find out what row to draw it on
-            <span class="ruby-comment cmt">#   B. see if we want to change the glyph type from directed to
-            <span class="ruby-comment cmt">#      undirected
-            <span class="ruby-comment cmt">#   C. draw the thing
-            <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
+            <span class="ruby-ivar">@features</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">feature</span><span class="ruby-operator">|</span>
               <span class="ruby-comment cmt"># Don't even bother if the feature is not in the view
               <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>
                 <span class="ruby-keyword kw">next</span>
               <span class="ruby-keyword kw">else</span>
-                <span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">false</span>
-                
-                <span class="ruby-comment cmt"># A. find out what row to draw it on
-                <span class="ruby-identifier">feature_range</span> = (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>.<span class="ruby-identifier">floor</span><span class="ruby-operator">..</span><span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>.<span class="ruby-identifier">ceil</span>)
-                <span class="ruby-identifier">row</span> = <span class="ruby-value">1</span>
-                <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
-                <span class="ruby-keyword kw">until</span> <span class="ruby-identifier">feature_drawn</span>
-                  <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
-                    <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">covered</span><span class="ruby-operator">|</span>
-                      <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">covered</span>.<span class="ruby-identifier">first</span>) <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">covered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">feature_range</span>.<span class="ruby-identifier">first</span>)
-                        <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">false</span>
-                      <span class="ruby-keyword kw">end</span>
-                    <span class="ruby-keyword kw">end</span>
-                  <span class="ruby-keyword kw">end</span>
-  
-                  <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">row_available</span>
-                    <span class="ruby-identifier">row</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-                    <span class="ruby-identifier">row_available</span> = <span class="ruby-keyword kw">true</span>
-                  <span class="ruby-keyword kw">else</span>
-                    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">nil?</span>
-                      <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>] = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-                    <span class="ruby-keyword kw">end</span>
-                    <span class="ruby-identifier">grid</span>[<span class="ruby-identifier">row</span>].<span class="ruby-identifier">push</span>(<span class="ruby-identifier">feature_range</span>)
-
-                    <span class="ruby-comment cmt"># B. see if we want to change the glyph type from directed to
-                    <span class="ruby-comment cmt">#    undirected
-                    <span class="ruby-comment cmt"># There are 2 cases where we don't want to draw arrows on
-                    <span class="ruby-comment cmt"># features:
-                    <span class="ruby-comment cmt"># (a) when the picture is really zoomed out, features are
-                    <span class="ruby-comment cmt">#     so small that the arrow itself is too big
-                    <span class="ruby-comment cmt"># (b) if a directed feature on the fw strand extends beyond
-                    <span class="ruby-comment cmt">#     the end of the picture, the arrow is out of view. This
-                    <span class="ruby-comment cmt">#     is the same as considering the feature as undirected.
-                    <span class="ruby-comment cmt">#     The same obviously goes for features on the reverse
-                    <span class="ruby-comment cmt">#     strand that extend beyond the left side of the image.
-                    <span class="ruby-comment cmt">#
-                    <span class="ruby-comment cmt"># (a) Zoomed out
-                    <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">false</span>
-                    <span class="ruby-keyword kw">if</span> (<span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span>).<span class="ruby-identifier">to_f</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">2</span>
-                      <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
-                    <span class="ruby-keyword kw">end</span>
-                    <span class="ruby-comment cmt"># (b) Extending beyond borders picture
-                    <span class="ruby-keyword kw">if</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_stop</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">1</span> ) <span class="ruby-keyword kw">or</span> ( <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">chopped_at_start</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> = <span class="ruby-value">-1</span> )
-                      <span class="ruby-identifier">replace_directed_with_undirected</span> = <span class="ruby-keyword kw">true</span>
-                    <span class="ruby-keyword kw">end</span>
-
-                    <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-keyword kw">nil</span>
-                    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_generic'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
-                      <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'generic'</span>
-                    <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">feature_glyph</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'directed_spliced'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">replace_directed_with_undirected</span>
-                      <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-value str">'spliced'</span>
-                    <span class="ruby-keyword kw">else</span>
-                      <span class="ruby-identifier">local_feature_glyph</span> = <span class="ruby-identifier">feature_glyph</span>
-                    <span class="ruby-keyword kw">end</span>
-  
-                    <span class="ruby-comment cmt"># C. And draw the thing.
-                    <span class="ruby-identifier">top_pixel_of_feature</span> = <span class="ruby-constant">FEATURE_V_DISTANCE</span> <span class="ruby-operator">+</span> (<span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_V_DISTANCE</span>)<span class="ruby-operator">*</span><span class="ruby-identifier">row</span>
-                    <span class="ruby-identifier">bottom_pixel_of_feature</span> = <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-constant">FEATURE_HEIGHT</span>
-
-                    <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">local_feature_glyph</span>
-                      <span class="ruby-comment cmt"># triangles are typical for features which have a 1 bp position (start == stop)
-                      <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'triangle'</span>
-                        <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Start and stop are not the same (necessary if you want triangle glyphs)&quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">stop</span>
-  
-                        <span class="ruby-comment cmt"># Need to get this for the imagemap
-                        <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-value">3</span>
-                        <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">+</span> <span class="ruby-value">3</span>
-                        <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-value">3</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
-                        <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">-3</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>)
-                        <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">6</span>, <span class="ruby-value">0</span>)
-                        <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
-  
-                      <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'directed_generic'</span>
-                        <span class="ruby-comment cmt"># Need to get this for the imagemap
-                        <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
-                        <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># Reverse strand
-                          <span class="ruby-comment cmt"># Draw main box
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-  
-                          <span class="ruby-comment cmt"># Draw arrow
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">left_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
-  
-                        <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#default is forward strand
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
-                        <span class="ruby-keyword kw">end</span>
-                      <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'spliced'</span>
-                        <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-                        <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-  
-                        <span class="ruby-comment cmt"># Need to get this for the imagemap
-                        <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
-                        <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
-  
-                        <span class="ruby-comment cmt"># First draw the parts
-                        <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                          <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">stop_pixel</span>)
-                          <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>)
-                        <span class="ruby-keyword kw">end</span>
-  
-                        <span class="ruby-comment cmt"># And then draw the connections in the gaps
-                        <span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
-                        <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
-                        <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
-  
-                        <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
-                          <span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
-                          <span class="ruby-identifier">middle</span> = <span class="ruby-identifier">from</span> <span class="ruby-operator">+</span> ((<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">from</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-                        
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</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">to</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-                        
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
-                          <span class="ruby-identifier">to</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-  
-                      <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'directed_spliced'</span>
-                        <span class="ruby-identifier">gap_starts</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-                        <span class="ruby-identifier">gap_stops</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
-                        <span class="ruby-comment cmt"># First draw the parts
-                        <span class="ruby-identifier">locations</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">location</span>.<span class="ruby-identifier">sort_by</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-comment cmt"># Need to get this for the imagemap
-                        <span class="ruby-identifier">left_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
-                        <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">-1</span>].<span class="ruby-identifier">stop_pixel</span>
-  
-                        <span class="ruby-comment cmt">#   Start with the one with the arrow
-                        <span class="ruby-identifier">pixel_ranges</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}
-                        <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-keyword kw">nil</span>
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">strand</span> <span class="ruby-operator">==</span> <span class="ruby-value">-1</span> <span class="ruby-comment cmt"># reverse strand =&gt; box with arrow is first one
-                          <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">shift</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>((<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)<span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span><span class="ruby-operator">+</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">close_path</span>.<span class="ruby-identifier">fill</span>
-                        <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt"># forward strand =&gt; box with arrow is last one
-                          <span class="ruby-identifier">range_with_arrow</span> = <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">pop</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span><span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-identifier">top_pixel_of_feature</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-operator">-</span><span class="ruby-constant">FEATURE_ARROW_LENGTH</span>, <span class="ruby-constant">FEATURE_HEIGHT</span><span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                        <span class="ruby-keyword kw">end</span>
-                        <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">stop_pixel</span>)
-                        <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range_with_arrow</span>.<span class="ruby-identifier">start_pixel</span>)
-  
-                        <span class="ruby-comment cmt">#   And then add the others
-                        <span class="ruby-identifier">pixel_ranges</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">range</span><span class="ruby-operator">|</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, <span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>, <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                          <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">stop_pixel</span>)
-                          <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">range</span>.<span class="ruby-identifier">start_pixel</span>)
-                        <span class="ruby-keyword kw">end</span>
-  
-                        <span class="ruby-comment cmt"># And then draw the connections in the gaps
-                        <span class="ruby-comment cmt"># Start with removing the very first start and the very last stop.
-                        <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">pop</span>
-                        <span class="ruby-identifier">gap_stops</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">shift</span>
-  
-                        <span class="ruby-identifier">gap_starts</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap_number</span><span class="ruby-operator">|</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-identifier">gap_starts</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
-                          <span class="ruby-identifier">to</span> = <span class="ruby-identifier">gap_stops</span>[<span class="ruby-identifier">gap_number</span>].<span class="ruby-identifier">to_f</span>
-                          <span class="ruby-identifier">middle</span> = <span class="ruby-identifier">from</span> <span class="ruby-operator">+</span> ((<span class="ruby-identifier">to</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">from</span>)<span class="ruby-operator">/</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">middle</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">7</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">2</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_stop</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</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">to</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-                        
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">hidden_subfeatures_at_start</span>
-                          <span class="ruby-identifier">from</span> = <span class="ruby-value">1</span>
-                          <span class="ruby-identifier">to</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>.<span class="ruby-identifier">sort_by</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">pr</span><span class="ruby-operator">|</span> <span class="ruby-identifier">pr</span>.<span class="ruby-identifier">start_pixel</span>}[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">from</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">to</span>, <span class="ruby-identifier">top_pixel_of_feature</span><span class="ruby-operator">+</span><span class="ruby-value">5</span>)
-                          <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">stroke</span>
-                        <span class="ruby-keyword kw">end</span>
-
-                      <span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">#treat as 'generic'
-                        <span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">right_pixel_of_feature</span> = <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">start_pixel</span>, <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">pixel_range_collection</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">stop_pixel</span>
-                        <span class="ruby-identifier">track_drawing</span>.<span class="ruby-identifier">rectangle</span>(<span class="ruby-identifier">left_pixel_of_feature</span>, <span class="ruby-identifier">top_pixel_of_feature</span>, (<span class="ruby-identifier">right_pixel_of_feature</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">left_pixel_of_feature</span>), <span class="ruby-constant">FEATURE_HEIGHT</span>).<span class="ruby-identifier">fill</span>
-                    <span class="ruby-keyword kw">end</span>
-  
-                    <span class="ruby-comment cmt"># And add the region to the image map
-                    <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">clickable</span>
-                      <span class="ruby-comment cmt"># Comment: we have to add the vertical_offset and TRACK_HEADER_HEIGHT!
-                      <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">image_map</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">push</span>(<span class="ruby-constant">ImageMap</span><span class="ruby-operator">::</span><span class="ruby-constant">ImageMapElement</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">left_pixel_of_feature</span>,
-                                                                                  <span class="ruby-identifier">top_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
-                                                                                  <span class="ruby-identifier">right_pixel_of_feature</span>,
-                                                                                  <span class="ruby-identifier">bottom_pixel_of_feature</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+</span> <span class="ruby-constant">TRACK_HEADER_HEIGHT</span>,
-                                                                                  <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">link</span>
-                                                                                  ))
-                    <span class="ruby-keyword kw">end</span>
-  
-  
-                    <span class="ruby-identifier">feature_drawn</span> = <span class="ruby-keyword kw">true</span>
-                  <span class="ruby-keyword kw">end</span>
-                <span class="ruby-keyword kw">end</span>
+                <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">track_drawing</span>)
               <span class="ruby-keyword kw">end</span>
             <span class="ruby-keyword kw">end</span>
 
           <span class="ruby-keyword kw">end</span>
 
-          <span class="ruby-ivar">@number_of_times_bumped</span> = ( <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+          <span class="ruby-ivar">@number_of_feature_rows</span> = ( <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@grid</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">max</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
 
           <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">panel_drawing</span>
         <span class="ruby-keyword kw">end</span></pre>

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

@@ -99,6 +99,10 @@ features.
       <h3 class="section-bar">Methods</h3>
 
       <div class="name-list">
+      <a href="#M000012">arrow</a>&nbsp;&nbsp;
+      <a href="#M000013">connector</a>&nbsp;&nbsp;
+      <a href="#M000014">draw</a>&nbsp;&nbsp;
+      <a href="#M000015">find_row</a>&nbsp;&nbsp;
       <a href="#M000011">new</a>&nbsp;&nbsp;
       </div>
     </div>
@@ -272,6 +276,111 @@ strand
 <table>
 <tr><td valign="top"><b>Returns</b>:</td><td>Bio::Graphics::Track::Feature object
 
+</td></tr>
+</table>
+        </div>
+      </div>
+
+      <h3 class="section-bar">Public Instance methods</h3>
+
+      <div id="method-M000012" class="method-detail">
+        <a name="M000012"></a>
+
+        <div class="method-heading">
+          <a href="Feature.src/M000012.html" target="Code" class="method-signature"
+            onclick="popupCode('Feature.src/M000012.html');return false;">
+          <span class="method-name">arrow</span><span class="method-args">(track,direction,x,y,size)</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Method to <a href="Feature.html#M000014">draw</a> the arrows of directed
+glyphs. Not to be used directly, but called by <a
+href="Feature.html#M000014">Feature#draw</a>.
+</p>
+        </div>
+      </div>
+
+      <div id="method-M000013" class="method-detail">
+        <a name="M000013"></a>
+
+        <div class="method-heading">
+          <a href="Feature.src/M000013.html" target="Code" class="method-signature"
+            onclick="popupCode('Feature.src/M000013.html');return false;">
+          <span class="method-name">connector</span><span class="method-args">(track,from,to,top, color)</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Method to <a href="Feature.html#M000014">draw</a> the connections (introns)
+of spliced glyphs. Not to be used directly, but called by <a
+href="Feature.html#M000014">Feature#draw</a>.
+</p>
+        </div>
+      </div>
+
+      <div id="method-M000014" class="method-detail">
+        <a name="M000014"></a>
+
+        <div class="method-heading">
+          <a href="Feature.src/M000014.html" target="Code" class="method-signature"
+            onclick="popupCode('Feature.src/M000014.html');return false;">
+          <span class="method-name">draw</span><span class="method-args">(track_drawing)</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Adds the feature to the track cairo context. This method should not be used
+directly by the user, but is called by <a
+href="../Track.html#M000010">Bio::Graphics::Panel::Track.draw</a>
+</p>
+<hr size="1"></hr><p>
+<b>Arguments</b>:
+</p>
+<ul>
+<li><em>trackdrawing</em> (required) :: the track cairo object
+
+</li>
+<li><em>row</em> (required) :: row within the track that this feature has
+
+<pre>
+                    been bumped to
+</pre>
+</li>
+</ul>
+<table>
+<tr><td valign="top"><b>Returns</b>:</td><td>FIXME: I don&#8216;t know
+
+</td></tr>
+</table>
+        </div>
+      </div>
+
+      <div id="method-M000015" class="method-detail">
+        <a name="M000015"></a>
+
+        <div class="method-heading">
+          <a href="Feature.src/M000015.html" target="Code" class="method-signature"
+            onclick="popupCode('Feature.src/M000015.html');return false;">
+          <span class="method-name">find_row</span><span class="method-args">()</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+          <p>
+Calculates the row within the track where this feature should be drawn.
+This method should not be used directly by the user, but is called by <a
+href="Feature.html#M000014">Bio::Graphics::Panel::Track::Feature.draw</a>
+</p>
+<hr size="1"></hr><table>
+<tr><td valign="top"><b>Arguments</b>:</td><td>none
+
+</td></tr>
+<tr><td valign="top"><b>Returns</b>:</td><td>row number
+
 </td></tr>
 </table>
         </div>