| Trees | Indices | Help |
|---|
|
|
object --+
|
FeatureSet
FeatureSet
Provides:
Methods:
o __init__(self, set_id=None, name=None) Called on instantiation
o add_feature(self, feature, color=colors.lightgreen) Add a Feature
object to the set
o del_feature(self, feature_id) Remove a feature from the set, by id
o set_all_features(self, attr, value) Set the passed attribute to the
passed value in all features in the set
o get_features(self) Returns a list of Features from the set
o get_ids(self) Returns a list of unique ids for features in the set
o range(self) Returns the range of bases covered by features in
the set
o to_string(self, verbose=0) Returns a string describing the set
o __len__(self) Returns the length of sequence covered by the set
o __getitem__(self, key) Returns a feature from the set, keyed by id
o __str__(self) Returns a string describing the set
Attributes:
o id Unique id for the set
o name String describing the set
|
|||
|
|||
|
|||
|
|||
|
|||
| [Feature, Feature, ...] |
|
||
| [int, int, ...] |
|
||
|
|||
| "" |
|
||
| int |
|
||
| Feature |
|
||
| "" |
|
||
|
Inherited from |
|||
|
|||
|
Inherited from |
|||
|
|||
o set_id Unique id for the set o name String identifying the feature set
|
o feature Bio.SeqFeature object
o **kwargs Keyword arguments for Feature. Named attributes
of the Feature
Add a Bio.SeqFeature object to the diagram (will be stored
internally in a Feature wrapper
|
o feature_id Unique id of the feature to delete Remove a feature from the set, indicated by its id |
o attr An attribute of the Feature class o value The value to set that attribute Set the passed attribute of all features in the set to the passed value |
o attribute String, attribute of a Feature object
o value The value desired of the attribute
o comparator String, how to compare the Feature attribute to the
passed value
If no attribute or value is given, return a list of all features in the
feature set. If both an attribute and value are given, then depending
on the comparator, then a list of all features in the FeatureSet
matching (or not) the passed value will be returned. Allowed comparators
are: 'startswith', 'not', 'like'.
The user is expected to make a responsible decision about which feature
attributes to use with which passed values and comparator settings.
|
o verbose Boolean indicating whether a short or complete
account of the set is required
Returns a formatted string with information about the set
|
Returns a formatted string with information about the feature set
|
| Trees | Indices | Help |
|---|
| Generated by Epydoc 3.0.1 on Sun May 3 17:14:20 2009 | http://epydoc.sourceforge.net |