Class Feature
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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
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__init__(self,
parent=None,
feature_id=None,
feature=None,
color=colors.lightgreen,
label=0)
o parent FeatureSet containing the feature |
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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
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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
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__getattr__(self,
name)
If the Feature class doesn't have the attribute called for, check in
self._feature for it |
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__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
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o feature Bio.SeqFeature object to be wrapped
Defines the Bio.SeqFeature object to be wrapped
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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
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