bio-graphics 1.0 → 1.2
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- data/doc/classes/Bio/Graphics.html +11 -1
- data/doc/classes/Bio/Graphics/Panel.html +5 -2
- data/doc/classes/Bio/Graphics/Panel.src/M000005.html +4 -4
- data/doc/classes/Bio/Graphics/Panel.src/M000006.html +3 -3
- data/doc/classes/Bio/Graphics/Panel.src/M000007.html +6 -5
- data/doc/classes/Bio/Graphics/Panel/Ruler.html +16 -16
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000014.html +6 -14
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000015.html +10 -41
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000016.html +59 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000017.html +20 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000018.html +28 -0
- data/doc/classes/Bio/Graphics/Panel/Ruler.src/M000019.html +59 -0
- data/doc/classes/Bio/Graphics/Panel/Track.html +30 -15
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000008.html +8 -5
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000009.html +2 -2
- data/doc/classes/Bio/Graphics/Panel/Track.src/M000010.html +12 -245
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.html +109 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000011.html +1 -1
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000012.html +39 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000013.html +27 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000014.html +209 -49
- data/doc/classes/Bio/Graphics/Panel/Track/Feature.src/M000015.html +48 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.html +5 -5
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000013.html +18 -0
- data/doc/classes/Bio/Graphics/Panel/Track/Feature/PixelRange.src/M000016.html +18 -0
- data/doc/created.rid +1 -1
- data/doc/files/README_DEV.html +7 -11
- data/doc/files/TUTORIAL.html +3 -3
- data/doc/files/lib/bio-graphics_rb.html +3 -1
- data/doc/files/lib/bio/graphics/feature_rb.html +6 -11
- data/doc/files/lib/bio/graphics/image_map_rb.html +1 -1
- data/doc/files/lib/bio/graphics/panel_rb.html +1 -1
- data/doc/files/lib/bio/graphics/ruler_rb.html +1 -1
- data/doc/files/lib/bio/graphics/track_rb.html +1 -1
- data/doc/fr_method_index.html +8 -4
- data/doc/images/example_labels.png +0 -0
- data/doc/images/glyph_showcase.png +0 -0
- data/doc/images/terms.png +0 -0
- data/doc/index.html +2 -2
- data/images/example_labels.png +0 -0
- data/images/glyph_showcase.png +0 -0
- data/images/terms.png +0 -0
- data/images/terms.svg +146 -132
- data/lib/bio-graphics.rb +2 -1
- data/lib/bio/graphics/feature.rb +304 -0
- data/lib/bio/graphics/panel.rb +15 -11
- data/lib/bio/graphics/ruler.rb +1 -1
- data/lib/bio/graphics/track.rb +23 -254
- data/samples/arkdb_features.rb +8 -8
- data/samples/glyph_showcase.rb +10 -6
- data/test/unit/test_creation.rb +51 -0
- metadata +14 -2
@@ -139,7 +139,7 @@ Schematically:
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track1.add_feature('gene3',100,500)
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# Add a second track (e.g. 'polymorphisms')
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track2 = g.add_track('polymorphisms','red','triangle')
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track2 = g.add_track('polymorphisms',, false, 'red','triangle')
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# And put features on this one
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track2.add_feature('polymorphism 1',56,56)
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@@ -224,6 +224,16 @@ The defaults
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<td>=</td>
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<td class="context-item-value">5</td>
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</tr>
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<tr class="top-aligned-row context-row">
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<td class="context-item-name">FONT</td>
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<td>=</td>
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<td class="context-item-value">['Georgia', 1, 1]</td>
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<td width="3em"> </td>
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<td class="context-item-desc">
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consecutive ticks. This is used for the calculation of tick distance.
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</td>
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</tr>
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</table>
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</div>
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</div>
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@@ -167,7 +167,7 @@ Class <a href="Panel/Track.html" class="link">Bio::Graphics::Panel::Track</a><br
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<td class="context-item-desc"></td>
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</tr>
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<tr class="top-aligned-row context-row">
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<td class="context-item-name">
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<td class="context-item-name">number_of_feature_rows</td>
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<td class="context-item-value"> [RW] </td>
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<td class="context-item-desc"></td>
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</tr>
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<div class="method-heading">
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<a href="Panel.src/M000006.html" target="Code" class="method-signature"
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onclick="popupCode('Panel.src/M000006.html');return false;">
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<span class="method-name">add_track</span><span class="method-args">(name, feature_colour = [0,0,1], feature_glyph = 'generic')</span>
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<span class="method-name">add_track</span><span class="method-args">(name, label = true, feature_colour = [0,0,1], feature_glyph = 'generic')</span>
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</a>
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</div>
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@@ -288,6 +288,9 @@ polymorphisms, ESTs, etc.
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<li><em>name</em> (required) :: Name of the track to be displayed (e.g.
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‘genes’)
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</li>
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<li>_label) :: Whether the feature labels should be displayed or not
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</li>
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<li><em>colour</em> :: Colour to be used to <a
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href="Panel.html#M000007">draw</a> the features within the track. Default =
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<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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</head>
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<body class="standalone-code">
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 103</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">width</span> = <span class="ruby-constant">DEFAULT_PANEL_WIDTH</span>, <span class="ruby-identifier">clickable</span> = <span class="ruby-keyword kw">false</span>, <span class="ruby-identifier">display_start</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">display_stop</span> = <span class="ruby-keyword kw">nil</span>)
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<span class="ruby-ivar">@length</span> = <span class="ruby-identifier">length</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">width</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@tracks</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
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<span class="ruby-ivar">@
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<span class="ruby-ivar">@number_of_feature_rows</span> = <span class="ruby-value">0</span>
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<span class="ruby-ivar">@clickable</span> = <span class="ruby-identifier">clickable</span>
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<span class="ruby-ivar">@image_map</span> = ( <span class="ruby-identifier">clickable</span> ) <span class="ruby-operator">?</span> <span class="ruby-constant">ImageMap</span>.<span class="ruby-identifier">new</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-ivar">@display_start</span> = ( <span class="ruby-identifier">display_start</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_start</span>
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<span class="ruby-ivar">@display_stop</span> = ( <span class="ruby-identifier">display_stop</span>.<span class="ruby-identifier">nil?</span> ) <span class="ruby-operator">?</span> <span class="ruby-ivar">@length</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_stop</span>
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<span class="ruby-ivar">@display_start</span> = ( <span class="ruby-identifier">display_start</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">display_start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span> ) <span class="ruby-operator">?</span> <span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_start</span>
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<span class="ruby-ivar">@display_stop</span> = ( <span class="ruby-identifier">display_stop</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">display_stop</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@length</span> ) <span class="ruby-operator">?</span> <span class="ruby-ivar">@length</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">display_stop</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@display_stop</span> <span class="ruby-operator"><=</span> <span class="ruby-ivar">@display_start</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."</span>
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<span class="ruby-keyword kw">end</span>
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<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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</head>
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<body class="standalone-code">
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</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>)
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<span class="ruby-ivar">@tracks</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-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">feature_colour</span>, <span class="ruby-identifier">feature_glyph</span>))
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 139</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">label</span> = <span class="ruby-keyword kw">true</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>)
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<span class="ruby-ivar">@tracks</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-identifier">new</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">label</span>, <span class="ruby-identifier">feature_colour</span>, <span class="ruby-identifier">feature_glyph</span>))
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<span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@tracks</span>[<span class="ruby-value">-1</span>]
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<span class="ruby-keyword kw">end</span></pre>
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</body>
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</head>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/panel.rb, line 151</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">draw</span>(<span class="ruby-identifier">file_name</span>)
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<span class="ruby-comment cmt"># Create a panel that is huge vertically
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<span class="ruby-identifier">huge_height</span> = <span class="ruby-value">2000</span>
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<span class="ruby-comment cmt"># Add tracks
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">
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<span class="ruby-
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<span class="ruby-
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">vertical_offset</span> = <span class="ruby-identifier">vertical_offset</span>
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<span class="ruby-identifier">track</span>.<span class="ruby-identifier">draw</span>(<span class="ruby-identifier">huge_panel_drawing</span>)
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<span class="ruby-ivar">@number_of_feature_rows</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</span>
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<span class="ruby-identifier">vertical_offset</span> <span class="ruby-operator">+=</span> ( <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_of_feature_rows</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-value">5</span>)) <span class="ruby-operator">+</span> <span class="ruby-value">10</span> <span class="ruby-comment cmt"># '10' is for the header
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># And create a smaller version of the panel
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<span class="ruby-identifier">height</span> = <span class="ruby-identifier">ruler</span>.<span class="ruby-identifier">height</span>
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<span class="ruby-ivar">@
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<span class="ruby-ivar">@number_of_feature_rows</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span>
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<span class="ruby-identifier">height</span> <span class="ruby-operator">+=</span> <span class="ruby-value">20</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">length</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-comment cmt">#To correct for the track headers
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<h3 class="section-bar">Methods</h3>
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<a href="#
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<a href="#
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<a href="#
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<a href="#M000018">calculate_tick_distance</a>
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<a href="#M000019">draw</a>
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<a href="#M000017">new</a>
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<div id="methods">
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<h3 class="section-bar">Public Class methods</h3>
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<a name="
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onclick="popupCode('Ruler.src/M000017.html');return false;">
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<span class="method-name">new</span><span class="method-args">(panel, colour = [0,0,0])</span>
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<p>
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Creates a <a href="Ruler.html#
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Creates a <a href="Ruler.html#M000017">new</a> <a
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href="Ruler.html">Bio::Graphics::Panel::Ruler</a> object.
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<hr size="1"></hr><p>
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<h3 class="section-bar">Public Instance methods</h3>
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<a name="
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onclick="popupCode('Ruler.src/M000018.html');return false;">
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<span class="method-name">calculate_tick_distance</span><span class="method-args">()</span>
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onclick="popupCode('Ruler.src/M000019.html');return false;">
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<span class="method-name">draw</span><span class="method-args">(panel_drawing, vertical_offset)</span>
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</a>
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<title>
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<title>new (Bio::Graphics::Panel::Ruler)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">
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|
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<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 28</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
|
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<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
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|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-comment cmt"># Draw ticks
|
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<span class="ruby-comment cmt"># * Find position of first tick.
|
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|
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|
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
|
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|
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<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
|
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|
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<span class="ruby-comment cmt"># So we want to find the position of the first tick.
|
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|
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|
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
|
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<span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
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|
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|
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|
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|
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<span class="ruby-comment cmt"># * And start drawing the rest.
|
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|
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<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
|
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|
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<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
|
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|
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
|
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|
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|
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|
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<span class="ruby-comment cmt"># Draw tick number
|
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|
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<span class="ruby-identifier">ruler_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>)
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 35</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">calculate_tick_distance</span>
|
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|
+
<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
|
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|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs.
|
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|
+
<span class="ruby-keyword kw">while</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">min_tick_distance_requirement_met</span>
|
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|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">>=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
|
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|
+
<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
|
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20
|
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|
49
|
-
<span class="ruby-
|
50
|
-
|
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|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
|
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|
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|
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|
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
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|
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|
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|
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|
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|
|
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|
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|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
|
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|
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|
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|
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|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 49</span>
|
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|
+
<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>)
|
15
|
+
<span class="ruby-identifier">ruler_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>)
|
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|
+
|
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|
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">calculate_tick_distance</span>
|
18
|
+
|
19
|
+
<span class="ruby-comment cmt"># Draw line
|
20
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
|
21
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
|
22
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
23
|
+
|
24
|
+
<span class="ruby-comment cmt"># Draw ticks
|
25
|
+
<span class="ruby-comment cmt"># * Find position of first tick.
|
26
|
+
<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first
|
27
|
+
<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the
|
28
|
+
<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
|
29
|
+
<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
|
30
|
+
<span class="ruby-comment cmt"># So we want to find the position of the first tick.
|
31
|
+
<span class="ruby-identifier">first_tick_position</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
|
32
|
+
<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
|
33
|
+
<span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
34
|
+
<span class="ruby-keyword kw">end</span>
|
35
|
+
|
36
|
+
<span class="ruby-comment cmt"># * And start drawing the rest.
|
37
|
+
<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
|
38
|
+
<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
|
39
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
|
40
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
41
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
|
42
|
+
|
43
|
+
<span class="ruby-comment cmt"># Draw tick number
|
44
|
+
<span class="ruby-identifier">ruler_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>)
|
45
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
46
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
|
47
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
|
48
|
+
<span class="ruby-keyword kw">else</span>
|
49
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
|
50
|
+
|
51
|
+
<span class="ruby-keyword kw">end</span>
|
52
|
+
<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
|
53
|
+
<span class="ruby-keyword kw">end</span>
|
54
|
+
|
55
|
+
|
56
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-value">25</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>
|
57
|
+
<span class="ruby-keyword kw">end</span></pre>
|
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|
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|
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|
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|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 28</span>
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">panel</span>, <span class="ruby-identifier">colour</span> = [<span class="ruby-value">0</span>,<span class="ruby-value">0</span>,<span class="ruby-value">0</span>])
|
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|
+
<span class="ruby-ivar">@panel</span> = <span class="ruby-identifier">panel</span>
|
16
|
+
<span class="ruby-ivar">@name</span> = <span class="ruby-value str">'ruler'</span>
|
17
|
+
<span class="ruby-ivar">@colour</span> = <span class="ruby-identifier">colour</span>
|
18
|
+
<span class="ruby-keyword kw">end</span></pre>
|
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|
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|
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|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 35</span>
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">calculate_tick_distance</span>
|
15
|
+
<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">false</span>
|
16
|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-value">1</span> <span class="ruby-comment cmt"># in basepairs.
|
17
|
+
<span class="ruby-keyword kw">while</span> <span class="ruby-operator">!</span> <span class="ruby-identifier">min_tick_distance_requirement_met</span>
|
18
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">/</span><span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span> <span class="ruby-operator">>=</span> <span class="ruby-constant">RULER_MIN_DISTANCE_TICKS_PIXEL</span>
|
19
|
+
<span class="ruby-identifier">min_tick_distance_requirement_met</span> = <span class="ruby-keyword kw">true</span>
|
20
|
+
<span class="ruby-keyword kw">else</span>
|
21
|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span><span class="ruby-operator">*</span><span class="ruby-value">5</span>
|
22
|
+
<span class="ruby-keyword kw">end</span>
|
23
|
+
<span class="ruby-keyword kw">end</span>
|
24
|
+
|
25
|
+
<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">major_tick_distance</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">minor_tick_distance</span> <span class="ruby-operator">*</span> <span class="ruby-value">10</span>
|
26
|
+
<span class="ruby-keyword kw">end</span></pre>
|
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<title>draw (Bio::Graphics::Panel::Ruler)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/ruler.rb, line 49</span>
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<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>)
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<span class="ruby-identifier">ruler_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>)
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<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">calculate_tick_distance</span>
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<span class="ruby-comment cmt"># Draw line
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-value">0</span>,<span class="ruby-value">10</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">line_to</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">width</span>, <span class="ruby-value">10</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-comment cmt"># Draw ticks
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<span class="ruby-comment cmt"># * Find position of first tick.
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<span class="ruby-comment cmt"># Most of the time, we don't want the first tick on the very first
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<span class="ruby-comment cmt"># basepair of the view. Suppose that would be position 333 in the
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<span class="ruby-comment cmt"># sequence. Then the numbers under the major tickmarks would be:
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<span class="ruby-comment cmt"># 343, 353, 363, 373 and so on. Instead, we want 350, 360, 370, 380.
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<span class="ruby-comment cmt"># So we want to find the position of the first tick.
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<span class="ruby-identifier">first_tick_position</span> = <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
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<span class="ruby-identifier">first_tick_position</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt"># * And start drawing the rest.
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<span class="ruby-identifier">first_tick_position</span>.<span class="ruby-identifier">step</span>(<span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_stop</span>, <span class="ruby-identifier">minor_tick_distance</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">tick</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">tick_pixel_position</span> = (<span class="ruby-identifier">tick</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">display_start</span>) <span class="ruby-operator">/</span> <span class="ruby-identifier">panel</span>.<span class="ruby-identifier">rescale_factor</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">5</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">tick</span>.<span class="ruby-identifier">modulo</span>(<span class="ruby-identifier">major_tick_distance</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">15</span>)
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<span class="ruby-comment cmt"># Draw tick number
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">select_font_face</span>(<span class="ruby-operator">*</span>(<span class="ruby-constant">FONT</span>))
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">set_font_size</span>(<span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">move_to</span>(<span class="ruby-identifier">tick_pixel_position</span>.<span class="ruby-identifier">floor</span>, <span class="ruby-value">20</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>)
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">show_text</span>(<span class="ruby-identifier">tick</span>.<span class="ruby-identifier">to_i</span>.<span class="ruby-identifier">to_s</span>)
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">rel_line_to</span>(<span class="ruby-value">0</span>, <span class="ruby-value">5</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">ruler_drawing</span>.<span class="ruby-identifier">stroke</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@height</span> = <span class="ruby-value">25</span> <span class="ruby-operator">+</span> <span class="ruby-constant">RULER_TEXT_HEIGHT</span>
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<span class="ruby-keyword kw">end</span></pre>
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