bio-graphics 1.2 → 1.4

data/doc/fr_file_index.html

@@ -24,10 +24,24 @@
     <a href="files/TUTORIAL.html">TUTORIAL</a><br />
     <a href="files/lib/bio-graphics_rb.html">lib/bio-graphics.rb</a><br />
     <a href="files/lib/bio/graphics/feature_rb.html">lib/bio/graphics/feature.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/box_rb.html">lib/bio/graphics/glyphs/box.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/common_rb.html">lib/bio/graphics/glyphs/common.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/directed_box_rb.html">lib/bio/graphics/glyphs/directed_box.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/directed_generic_rb.html">lib/bio/graphics/glyphs/directed_generic.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/directed_spliced_rb.html">lib/bio/graphics/glyphs/directed_spliced.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/dot_rb.html">lib/bio/graphics/glyphs/dot.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/generic_rb.html">lib/bio/graphics/glyphs/generic.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/line_rb.html">lib/bio/graphics/glyphs/line.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/line_with_handles_rb.html">lib/bio/graphics/glyphs/line_with_handles.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/spliced_rb.html">lib/bio/graphics/glyphs/spliced.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/transcript_rb.html">lib/bio/graphics/glyphs/transcript.rb</a><br />
+    <a href="files/lib/bio/graphics/glyphs/triangle_rb.html">lib/bio/graphics/glyphs/triangle.rb</a><br />
     <a href="files/lib/bio/graphics/image_map_rb.html">lib/bio/graphics/image_map.rb</a><br />
     <a href="files/lib/bio/graphics/panel_rb.html">lib/bio/graphics/panel.rb</a><br />
     <a href="files/lib/bio/graphics/ruler_rb.html">lib/bio/graphics/ruler.rb</a><br />
+    <a href="files/lib/bio/graphics/subfeature_rb.html">lib/bio/graphics/subfeature.rb</a><br />
     <a href="files/lib/bio/graphics/track_rb.html">lib/bio/graphics/track.rb</a><br />
+    <a href="files/lib/feature_rb.html">lib/feature.rb</a><br />
   </div>
 </div>
 </body>

data/doc/fr_method_index.html

@@ -20,25 +20,57 @@
 <div id="index">
   <h1 class="section-bar">Methods</h1>
   <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/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/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#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 />
+    <a href="classes/Bio/Features.html#M000041">[] (Bio::Features)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap.html#M000033">add_element (Bio::Graphics::ImageMap)</a><br />
+    <a href="classes/Bio/Graphics/Track.html#M000022">add_feature (Bio::Graphics::Track)</a><br />
+    <a href="classes/Bio/Feature.html#M000046">add_qualifier (Bio::Feature)</a><br />
+    <a href="classes/Bio/Feature.html#M000045">add_subfeature (Bio::Feature)</a><br />
+    <a href="classes/Bio/Graphics/Panel.html#M000030">add_track (Bio::Graphics::Panel)</a><br />
+    <a href="classes/Bio/Features.html#M000039">append (Bio::Features)</a><br />
+    <a href="classes/Bio/Feature.html#M000047">append_qualifier (Bio::Feature)</a><br />
+    <a href="classes/String.html#M000002">camel_case (String)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Dot.html#M000015">draw (Bio::Graphics::Glyph::Dot)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Generic.html#M000011">draw (Bio::Graphics::Glyph::Generic)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Spliced.html#M000012">draw (Bio::Graphics::Glyph::Spliced)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/DirectedGeneric.html#M000013">draw (Bio::Graphics::Glyph::DirectedGeneric)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Line.html#M000014">draw (Bio::Graphics::Glyph::Line)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/DirectedSpliced.html#M000010">draw (Bio::Graphics::Glyph::DirectedSpliced)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/LineWithHandles.html#M000016">draw (Bio::Graphics::Glyph::LineWithHandles)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/DirectedBox.html#M000009">draw (Bio::Graphics::Glyph::DirectedBox)</a><br />
+    <a href="classes/Bio/Graphics/SubFeature.html#M000028">draw (Bio::Graphics::SubFeature)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Triangle.html#M000008">draw (Bio::Graphics::Glyph::Triangle)</a><br />
+    <a href="classes/Bio/Graphics/Panel.html#M000031">draw (Bio::Graphics::Panel)</a><br />
+    <a href="classes/Bio/Graphics/Track.html#M000023">draw (Bio::Graphics::Track)</a><br />
+    <a href="classes/Bio/Graphics/Feature.html#M000025">draw (Bio::Graphics::Feature)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Box.html#M000004">draw (Bio::Graphics::Glyph::Box)</a><br />
+    <a href="classes/Bio/Graphics/Ruler.html#M000020">draw (Bio::Graphics::Ruler)</a><br />
+    <a href="classes/Bio/Features.html#M000040">each (Bio::Features)</a><br />
+    <a href="classes/Bio/Feature.html#M000049">each (Bio::Feature)</a><br />
+    <a href="classes/Bio/Feature.html#M000050">each_qualifier (Bio::Feature)</a><br />
+    <a href="classes/Bio/Feature.html#M000048">each_subfeature (Bio::Feature)</a><br />
+    <a href="classes/Bio/Graphics/Feature.html#M000026">find_row (Bio::Graphics::Feature)</a><br />
+    <a href="classes/Bio/Features.html#M000042">first (Bio::Features)</a><br />
+    <a href="classes/Bio/Graphics/Ruler.html#M000019">first_tick_position (Bio::Graphics::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap.html#M000035">flip_orientation (Bio::Graphics::ImageMap)</a><br />
+    <a href="classes/Bio/Features.html#M000043">last (Bio::Features)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Common.html#M000006">left_pixel (Bio::Graphics::Glyph::Common)</a><br />
+    <a href="classes/Bio/Graphics/SubFeature.html#M000027">new (Bio::Graphics::SubFeature)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap/Element.html#M000036">new (Bio::Graphics::ImageMap::Element)</a><br />
+    <a href="classes/Bio/Graphics/Track.html#M000021">new (Bio::Graphics::Track)</a><br />
+    <a href="classes/Bio/Features.html#M000038">new (Bio::Features)</a><br />
+    <a href="classes/Bio/Graphics/Ruler.html#M000017">new (Bio::Graphics::Ruler)</a><br />
+    <a href="classes/Bio/Graphics/Panel.html#M000029">new (Bio::Graphics::Panel)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Common.html#M000005">new (Bio::Graphics::Glyph::Common)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap.html#M000032">new (Bio::Graphics::ImageMap)</a><br />
+    <a href="classes/Bio/Graphics/Feature.html#M000024">new (Bio::Graphics::Feature)</a><br />
+    <a href="classes/Bio/Feature.html#M000044">new (Bio::Feature)</a><br />
+    <a href="classes/Bio/Feature/Qualifier.html#M000051">new (Bio::Feature::Qualifier)</a><br />
+    <a href="classes/Bio/Graphics/Glyph/Common.html#M000007">right_pixel (Bio::Graphics::Glyph::Common)</a><br />
+    <a href="classes/Bio/Graphics/Ruler.html#M000018">scaling_factor (Bio::Graphics::Ruler)</a><br />
+    <a href="classes/String.html#M000001">snake_case (String)</a><br />
+    <a href="classes/String.html#M000003">to_class (String)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap.html#M000034">to_s (Bio::Graphics::ImageMap)</a><br />
+    <a href="classes/Bio/Graphics/ImageMap/Element.html#M000037">to_s (Bio::Graphics::ImageMap::Element)</a><br />
   </div>
 </div>
 </body>

data/doc/images/terms.svg

@@ -9,17 +9,31 @@
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+   id="svg2288"
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-   sodipodi:docbase="/home/aertsj/Documents/Projects/20070924_RT3097_BioGraphics/images"
+   sodipodi:docbase="/home/aertsj/LocalDocuments/bio-graphics/trunk/images"
    sodipodi:docname="terms.svg"
-   inkscape:output_extension="org.inkscape.output.svg.inkscape">
+   inkscape:output_extension="org.inkscape.output.svg.inkscape"
+   inkscape:export-filename="/home/aertsj/LocalDocuments/bio-graphics/trunk/images/terms.png"
+   inkscape:export-xdpi="90"
+   inkscape:export-ydpi="90">
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+     id="metadata2293">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
   <defs
-     id="defs4">
+     id="defs2291">
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        inkscape:stockid="Arrow1Lend"
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@@ -35,132 +49,132 @@
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+     transform="matrix(4.2413793,0,0,1,-1493.3289,-185.20032)" />
+  <path
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;marker-end:url(#Arrow1Lend);stroke-opacity:1"
+     d="M 442.42126,117.66854 L 411.77262,95.298269"
+     id="path8263"
+     sodipodi:nodetypes="cc" />
+  <rect
+     style="fill:#6ae432;fill-opacity:0.46448089;stroke:none;stroke-width:1.40473521;stroke-linejoin:round;stroke-opacity:1"
+     id="rect3194"
+     width="805.83954"
+     height="88.185356"
+     x="-7.8217263"
+     y="261.10339" />
+  <path
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;marker-end:url(#Arrow1Lend);stroke-opacity:1"
+     d="M 727.89591,239.70636 L 668.34402,270.04133"
+     id="path5138"
+     sodipodi:nodetypes="cc" />
+  <text
+     xml:space="preserve"
+     style="font-size:12px;font-style:normal;font-weight:bold;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans;font-stretch:normal;font-variant:normal;text-anchor:start;text-align:start;writing-mode:lr;line-height:125%"
+     x="522.54974"
+     y="220.45403"
+     id="text2181"
+     sodipodi:linespacing="125%"><tspan
+       sodipodi:role="line"
+       id="tspan2183"
+       x="522.54974"
+       y="220.45403">Label</tspan></text>
+  <path
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;marker-end:url(#Arrow1Lend);stroke-opacity:1"
+     d="M 519.97202,211.59722 L 468.26327,187.03023"
+     id="path2185"
+     sodipodi:nodetypes="cc" />
 </svg>

data/lib/bio-graphics.rb

@@ -3,17 +3,49 @@
 #
 # Copyright::   Copyright (C) 2007
 #               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+#               Charles Comstock <dgtized@gmail.com>
 # License::     The Ruby License
 # 
-begin
-  require 'bio'
-  require 'cairo'
-  require 'pango'
-  require 'stringio'
+
+require 'bio'
+require 'cairo'
+require 'pango'
+require 'stringio'
+
+class Range
+  alias :lend :begin
+  alias :rend :end
 end
 
-require File.dirname(__FILE__) + '/bio/graphics/image_map.rb'
+class String
+  def snake_case
+   return self.to_s.gsub(/::/, '/').gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').gsub(/([a-z\d])([A-Z])/,'\1_\2').tr("-", "_").downcase
+  end
+    
+  def camel_case
+    return self.to_s.gsub(/\/(.?)/) { "::" + $1.upcase }.gsub(/(^|_)(.)/) { $2.upcase }.to_s.gsub(/\/(.?)/) { "::" + $1.upcase }.gsub(/(^|_)(.)/) { $2.upcase }
+  end
+  
+  def to_class
+    parts = self.split(/::/)
+    klass = Kernel
+    parts.each do |part|
+      klass = klass.const_get(part)
+    end
+    return klass
+  end
+end
+
+require File.dirname(__FILE__) + '/feature.rb'
 require File.dirname(__FILE__) + '/bio/graphics/panel.rb'
+require File.dirname(__FILE__) + '/bio/graphics/image_map.rb'
 require File.dirname(__FILE__) + '/bio/graphics/track.rb'
 require File.dirname(__FILE__) + '/bio/graphics/feature.rb'
+require File.dirname(__FILE__) + '/bio/graphics/subfeature.rb'
 require File.dirname(__FILE__) + '/bio/graphics/ruler.rb'
+
+# Load all the glyphs
+require File.dirname(__FILE__) + '/bio/graphics/glyphs/common.rb'
+Dir.new(File.dirname(__FILE__) + '/bio/graphics/glyphs').reject{|f| f == 'common.rb'}.select{|f| f =~ /\.rb$/}.each do |glyph_file_name|
+  require File.dirname(__FILE__) + '/bio/graphics/glyphs/' + glyph_file_name
+end