Package Bio :: Package Graphics :: Package GenomeDiagram :: Module _Feature :: Class Feature
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Class Feature

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object --+
         |
        Feature

Class to wrap Bio.SeqFeature objects for GenomeDiagram

Provides:

Methods:

o __init__(self, parent=None, feature_id=None, feature=None,
         color=colors.lightgreen) Called when the feature is
         instantiated

o set_feature(self, feature) Wrap the passed feature

o get_feature(self) Return the unwrapped Bio.SeqFeature object

o set_color(self, color) Set the color in which the feature will
        be drawn (accepts multiple formats: reportlab color.Color()
        tuple and color.name, or integer representing Artemis color

o get_color(self) Returns color.Color tuple of the feature's color

o __getattr__(self, name) Catches attribute requests and passes them to
        the wrapped Bio.SeqFeature object

Attributes:

o parent    FeatureSet, container for the object

o id        Unique id

o color    color.Color, color to draw the feature

o hide      Boolean for whether the feature will be drawn or not

o sigil     String denoting the type of sigil to use for the feature.
            Currently either "BOX" or "ARROW" are supported.

o arrowhead_length  Float denoting length of the arrow head to be drawn,
                    relative to the bounding box height.  The arrow shaft
                    takes up the remainder of the bounding box's length.

o arrowshaft_height  Float denoting length of the representative arrow
                     shaft to be drawn, relative to the bounding box height.
                     The arrow head takes the full height of the bound box.
 
o name_qualifiers   List of Strings, describes the qualifiers that may
            contain feature names in the wrapped Bio.SeqFeature object

o label     Boolean, 1 if the label should be shown

o label_font    String describing the font to use for the feature label

o label_size    Int describing the feature label font size

o label_color  color.Color describing the feature label color

o label_angle   Float describing the angle through which to rotate the
            feature label in degrees (default = 45, linear only)

o label_position    String, 'start', 'end' or 'middle' denoting where
            to place the feature label (linear only)

o locations     List of tuples of (start, end) ints describing where the
            feature and any subfeatures start and end

o type      String denoting the feature type

o name      String denoting the feature name

o strand    Int describing the strand on which the feature is found

Instance Methods [hide private]
 
__init__(self, parent=None, feature_id=None, feature=None, color=colors.lightgreen, label=0)
o parent FeatureSet containing the feature
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set_feature(self, feature)
o feature Bio.SeqFeature object to be wrapped
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__process_feature(self)
Examine the feature to be wrapped, and set some of the Feature's properties accordingly
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Bio.SeqFeature
get_feature(self)
Returns the unwrapped Bio.SeqFeature object
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set_colour(self, colour)
Backwards compatible variant of set_color(self, color) using UK spelling.
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set_color(self, color)
o color The color to draw the feature - either a colors.Color object, an RGB tuple of floats, or an integer corresponding to colors in colors.txt
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various
__getattr__(self, name)
If the Feature class doesn't have the attribute called for, check in self._feature for it
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, parent=None, feature_id=None, feature=None, color=colors.lightgreen, label=0)
(Constructor)

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o parent    FeatureSet containing the feature

o feature_id    Unique id for the feature

o feature   Bio.SeqFeature object to be wrapped

o color    color.Color Color to draw the feature (overridden
           by backwards compatible argument with UK spelling,
           colour).  Either argument is overridden if 'color'
           is found in feature qualifiers

o label     Boolean, 1 if the label should be shown

Overrides: object.__init__

set_feature(self, feature)

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o feature Bio.SeqFeature object to be wrapped

Defines the Bio.SeqFeature object to be wrapped

set_color(self, color)

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o color    The color to draw the feature - either a colors.Color
           object, an RGB tuple of floats, or an integer
           corresponding to colors in colors.txt
               
Set the color in which the feature will be drawn