o Rŀg^@s*dZddlZddlmZGdddZdS)zFeatureSet module. Provides: - FeatureSet - container for Feature objects For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com N)Featurec@sneZdZdZdddZddZddZd d Zdd d Zd dZ ddZ dddZ ddZ ddZ ddZdS) FeatureSetzFeatureSet object.NcCs"||_t|_d|_i|_||_dS)zCreate the object. Arguments: - set_id: Unique id for the set - name: String identifying the feature set rN)parentidnext_idfeaturesname)selfset_idr rr Z/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py__init__#s  zFeatureSet.__init__cKst|j}t|||}||j|<|D] }|dks|dkr%|j|||qt|j||||q|jd7_|S)a%Add a new feature. Arguments: - feature: Bio.SeqFeature object - 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). colourcolorr)rrr set_colorsetattr)r featurekwargsrfkeyr r r add_feature1s  zFeatureSet.add_featurecCs |j|=dS)zDelete a feature. Arguments: - feature_id: Unique id of the feature to delete Remove a feature from the set, indicated by its id. Nr)r feature_idr r r del_featureLs zFeatureSet.del_featurecCs*|jD] }t||rt|||qdS)aSet an attribute of all the features. Arguments: - attr: An attribute of the Feature class - value: The value to set that attribute to Set the passed attribute of all features in the set to the passed value. N)rvalueshasattrr)r attrvaluerr r r set_all_featuresVs   zFeatureSet.set_all_featurescsdusdurt|jS|dur fdd|jDS|dkr1fdd|jDS|dkrBfdd|jDS|dkrSfd d|jDSgS) aRetrieve features. Arguments: - attribute: String, attribute of a Feature object - value: The value desired of the attribute - 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. Ncsg|] }t|kr|qSr getattr.0r attributerr r z+FeatureSet.get_features..notcsg|] }t|kr|qSr r r"r$r r r&r' startswithcs g|] }t|r|qSr )r!r)r"r$r r r&s likecs"g|] }tt|r|qSr )researchr!r"r$r r r&s )listrr)r r%r comparatorr r$r get_featuresjs&    zFeatureSet.get_featurescCst|jS)z-Return a list of all ids for the feature set.)r-rkeysr r r r get_idsszFeatureSet.get_idscCsjgg}}|jD]}|jD]\}}||||qq t|dkr3t|dkr3t|t|fSdS)z@Return the lowest and highest base (or mark) numbers as a tuple.r)rr)rr locationsappendlenminmax)r lowshighsrstartendr r r ranges   zFeatureSet.rangercCsb|s|Sd|jd|jdg}|dt|j|jD] }|d|j|qd|S)zReturn a formatted string with information about the set. Arguments: - verbose: Boolean indicating whether a short (default) or complete account of the set is required z z %d featuresz feature:  ) __class__r r4r5rjoin)r verboseoutstrrr r r to_strings  zFeatureSet.to_stringcCs t|jS)z)Return the number of features in the set.)r5rr1r r r __len__ zFeatureSet.__len__cCs |j|S)zReturn a feature, keyed by id.r)r rr r r __getitem__rEzFeatureSet.__getitem__cCs$d|j|jt|jfg}d|S)zAReturn a formatted string with information about the feature set.z <%s: %s %d features>r>)r?r r5rr@)r rBr r r __str__s zFeatureSet.__str__)NNN)r)__name__ __module__ __qualname____doc__rrrrr/r2r<rCrDrFrGr r r r r s  8  r)rKr+_Featurerrr r r r s