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Draw representations of organism chromosomes with added information.
These classes are meant to model the drawing of pictures of chromosomes. This can be useful for lots of things, including displaying markers on a chromosome (ie. for genetic mapping) and showing syteny between two chromosomes.
The structure of these classes is intended to be a Composite, so that it will be easy to plug in and switch different parts without breaking the general drawing capabilities of the system. The relationship between classes is that everything derives from _ChromosomeComponent, which specifies the overall interface. The parts then are related so that an Organism contains Chromosomes, and these Chromosomes contain ChromosomeSegments. This representation differents from the canonical composite structure in that we don't really have 'leaf' nodes here -- all components can potentially hold sub-components.
Most of the time the ChromosomeSegment class is what you'll want to customize for specific drawing tasks.
For providing drawing capabilities, these classes use reportlab:
http://www.reportlab.com
This provides nice output in PDF, SVG and postscript. If you have reportlab's renderPM module installed you can also use PNG etc.
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_ChromosomeComponent Base class specifying the interface for a component of the system. |
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Organism Top level class for drawing chromosomes. |
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Chromosome Class for drawing a chromosome of an organism. |
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ChromosomeSegment Draw a segment of a chromosome. |
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TelomereSegment A segment that is located at the end of a linear chromosome. |
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