Package Bio :: Package Graphics :: Module BasicChromosome :: Class Organism
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Class Organism

             PropHolder --+        
                          |        
_DrawTimeResizeable --+   |        
                      |   |        
               UserNode --+        
                          |        
                     Widget --+    
                              |    
           _ChromosomeComponent --+
                                  |
                                 Organism


Top level class for drawing chromosomes.

This class holds information about an organism and all of it's chromosomes, and provides the top level object which could be used for drawing a chromosome representation of an organism.

Chromosomes should be added and removed from the Organism via the add and remove functions.
Method Summary
  __init__(self)
Initialize a chromosome component.
  draw(self, output_file, title)
Draw out the information for the Organism.
  _draw_legend(self, cur_drawing, start_y, width)
Draw a legend for the figure.
  _draw_title(self, cur_drawing, title, width, height)
Write out the title of the organism figure.
    Inherited from _ChromosomeComponent
  add(self, component)
Add a sub_component to the list of components under this item.
  remove(self, component)
Remove the specified component from the subcomponents.
    Inherited from Widget
  demo(self)
  getBounds(self)
Return outer boundary as x1,y1,x2,y2.
  provideNode(self)
Override this to create your own node.
    Inherited from PropHolder
  __setattr__(self, name, value)
By default we verify.
  dumpProperties(self, prefix)
Convenience.
  getProperties(self, recur)
Returns a list of all properties which can be edited and which are not marked as private.
  setProperties(self, propDict)
Permits bulk setting of properties.
  verify(self)
If the _attrMap attribute is not None, this checks all expected attributes are present; no unwanted attributes are present; and (if a checking function is found) checks each attribute has a valid value.
    Inherited from _DrawTimeResizeable
  _drawTimeResize(self, w, h)

Class Variable Summary
list VALID_FORMATS = ['pdf', 'eps']
    Inherited from PropHolder
NoneType _attrMap = None                                                                  

Method Details

__init__(self, output_format='pdf')
(Constructor)

Initialize a chromosome component.

Attributes:

o _sub_components -- Any components which are contained under this parent component. This attribute should be accessed through the add() and remove() functions.
Overrides:
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__ (inherited documentation)

draw(self, output_file, title)

Draw out the information for the Organism.

Arguments:

o output_file -- The name of a file specifying where the pdf document drawn should be saved.

o title -- The output title of the produced document.
Overrides:
Bio.Graphics.BasicChromosome._ChromosomeComponent.draw

_draw_legend(self, cur_drawing, start_y, width)

Draw a legend for the figure.

Subclasses should implement this to provide specialized legends.

_draw_title(self, cur_drawing, title, width, height)

Write out the title of the organism figure.

Class Variable Details

VALID_FORMATS

Type:
list
Value:
['pdf', 'eps']                                                         

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