bio-graphics 1.0 → 1.2

data/doc/created.rid

@@ -1 +1 @@
-Mon Oct 01 11:03:19 +0100 2007
+Thu Oct 18 18:24:47 +0100 2007

data/doc/files/README_DEV.html

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Mon Oct 01 11:03:17 +0100 2007</td>
+      <td>Thu Oct 18 14:49:59 +0100 2007</td>
     </tr>
     </table>
   </div>
@@ -128,8 +128,8 @@ The user has to start with a
 <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
+there&#8216;s @number_of_feature_rows. You&#8216;ll later see that each
+Track object also has its @number_of_feature_rows. 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
@@ -157,21 +157,17 @@ 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')
+  my_track_1 = my_panel.add_track(name, label = false, 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
+and @number_of_feature_rows. 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;)
+contain the features. The @number_of_feature_rows is just the number of
+rows (to be able to calculate the height of the track afterwards).
 </p>
 <pre>
   ------------------------------------------------------

data/doc/files/TUTORIAL.html

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Sat Sep 29 18:23:07 +0100 2007</td>
+      <td>Thu Oct 18 14:19:48 +0100 2007</td>
     </tr>
     </table>
   </div>
@@ -70,7 +70,7 @@
 
     <div id="description">
       <p>
-<img src="../images/example.png" />
+<img src="../images/example_labels.png" />
 </p>
 <h1><a href="../classes/Bio/Graphics.html">Bio::Graphics</a> tutorial</h1>
 <p>
@@ -300,7 +300,7 @@ There are different ways to install the library.
 </p>
 <ul>
 <li>Export for SVN (for the latest development version): &quot;svn checkout
-svn+ssh://jandot@rubyforge.org//var/svn/bio-graphics&quot;
+svn://rubyforge.org/var/svn/bio-graphics&quot;
 
 </li>
 <li>As a rubygem: download the bio-graphics-1.0.gem from the website, and do

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Fri Sep 28 20:03:31 +0100 2007</td>
+      <td>Thu Oct 18 18:13:09 +0100 2007</td>
     </tr>
     </table>
   </div>
@@ -87,6 +87,8 @@
       <div class="name-list">
       bio&nbsp;&nbsp;
       cairo&nbsp;&nbsp;
+      pango&nbsp;&nbsp;
+      stringio&nbsp;&nbsp;
       </div>
     </div>
 

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Fri Sep 28 20:39:05 +0100 2007</td>
+      <td>Thu Oct 18 18:24:17 +0100 2007</td>
     </tr>
     </table>
   </div>
@@ -68,20 +68,15 @@
 
   <div id="contextContent">
 
-    <div id="description">
-      <h1>bio/graphics/feature.rb - feature class</h1>
-<table>
-<tr><td valign="top">Copyright:</td><td>Copyright (C) 2007 Jan Aerts &lt;jan.aerts@bbsrc.ac.uk&gt;
 
-</td></tr>
-<tr><td valign="top">License:</td><td>The Ruby License
-
-</td></tr>
-</table>
+    <div id="requires-list">
+      <h3 class="section-bar">Required files</h3>
 
+      <div class="name-list">
+      yaml&nbsp;&nbsp;
+      </div>
     </div>
 
-
    </div>
 
 

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Fri Sep 28 20:03:31 +0100 2007</td>
+      <td>Tue Oct 09 20:42:28 +0100 2007</td>
     </tr>
     </table>
   </div>

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Mon Oct 01 11:00:37 +0100 2007</td>
+      <td>Thu Oct 18 14:47:09 +0100 2007</td>
     </tr>
     </table>
   </div>

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Sat Sep 29 19:35:12 +0100 2007</td>
+      <td>Thu Oct 18 05:05:46 +0100 2007</td>
     </tr>
     </table>
   </div>

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

@@ -56,7 +56,7 @@
     </tr>
     <tr class="top-aligned-row">
       <td><strong>Last Update:</strong></td>
-      <td>Mon Oct 01 10:51:11 +0100 2007</td>
+      <td>Thu Oct 18 18:18:39 +0100 2007</td>
     </tr>
     </table>
   </div>

data/doc/fr_method_index.html

@@ -22,17 +22,21 @@
   <div id="index-entries">
     <a href="classes/Bio/Graphics/Panel/Track.html#M000009">add_feature (Bio::Graphics::Panel::Track)</a><br />
     <a href="classes/Bio/Graphics/Panel.html#M000006">add_track (Bio::Graphics::Panel)</a><br />
-    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000014">calculate_tick_distance (Bio::Graphics::Panel::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Track/Feature.html#M000012">arrow (Bio::Graphics::Panel::Track::Feature)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000018">calculate_tick_distance (Bio::Graphics::Panel::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Track/Feature.html#M000013">connector (Bio::Graphics::Panel::Track::Feature)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Track/Feature.html#M000014">draw (Bio::Graphics::Panel::Track::Feature)</a><br />
     <a href="classes/Bio/Graphics/Panel.html#M000007">draw (Bio::Graphics::Panel)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000019">draw (Bio::Graphics::Panel::Ruler)</a><br />
     <a href="classes/Bio/Graphics/Panel/Track.html#M000010">draw (Bio::Graphics::Panel::Track)</a><br />
-    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000015">draw (Bio::Graphics::Panel::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Track/Feature.html#M000015">find_row (Bio::Graphics::Panel::Track::Feature)</a><br />
     <a href="classes/Bio/Graphics/Panel/Track.html#M000008">new (Bio::Graphics::Panel::Track)</a><br />
     <a href="classes/Bio/Graphics/Panel.html#M000005">new (Bio::Graphics::Panel)</a><br />
     <a href="classes/ImageMap.html#M000001">new (ImageMap)</a><br />
     <a href="classes/ImageMap/ImageMapElement.html#M000003">new (ImageMap::ImageMapElement)</a><br />
     <a href="classes/Bio/Graphics/Panel/Track/Feature.html#M000011">new (Bio::Graphics::Panel::Track::Feature)</a><br />
-    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000013">new (Bio::Graphics::Panel::Ruler)</a><br />
-    <a href="classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html#M000012">new (Bio::Graphics::Panel::Track::Feature::PixelRange)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Ruler.html#M000017">new (Bio::Graphics::Panel::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html#M000016">new (Bio::Graphics::Panel::Track::Feature::PixelRange)</a><br />
     <a href="classes/ImageMap.html#M000002">to_s (ImageMap)</a><br />
     <a href="classes/ImageMap/ImageMapElement.html#M000004">to_s (ImageMap::ImageMapElement)</a><br />
   </div>

data/doc/index.html

@@ -5,12 +5,12 @@
 
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-    RDoc Documentation
+    Bio::Graphics documentation
 
   -->
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 <head>
-  <title>RDoc Documentation</title>
+  <title>Bio::Graphics documentation</title>
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 </head>
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