Ri^0dZddlZddlmZGddZy)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)FeaturecXeZdZdZddZdZdZdZddZdZ d Z dd Z d Z d Z d Zy) FeatureSetzFeatureSet object.NcR||_t|_d|_i|_||_y)zCreate the object. Arguments: - set_id: Unique id for the set - name: String identifying the feature set rN)parentidnext_idfeaturesname)selfset_idr rs ^/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py__init__zFeatureSet.__init__#s'    c |j}t|||}||j|<|D]K}|dk(s|dk(r"|j|j||/t |j||||M|xjdz c_|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)r rr set_colorsetattr)r featurekwargsr fkeys r add_featurezFeatureSet.add_feature1s\\ D"g & b 9Ch#.  b!++F3K8 DMM"%sF3K 8 9  rc|j|=y)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_ids r del_featurezFeatureSet.del_featureLs MM* %rcv|jjD]}t||st|||y)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)r valueshasattrr)r attrvaluers rset_all_featureszFeatureSet.set_all_featuresVs6}}++- .Gw%u- .rc ||#t|jjS|7|jjDcgc]}t|||k(r|c}S|dk(r7|jjDcgc]}t|||k7r|c}S|dk(rC|jjDcgc]}t||j |r|!c}S|dk(rH|jjDcgc]$}t j |t||r|&c}SgScc}wcc}wcc}wcc}w)aRetrieve features. Arguments: - attribute: String, attribute of a Feature object - value: The value desired of the attribute - comparator: String, how to compare the Feature attribute to the passed value If no attribute or value is given, return a list of all features in the feature set. If both an attribute and value are given, then depending on the comparator, then a list of all features in the FeatureSet matching (or not) the passed value will be returned. Allowed comparators are: 'startswith', 'not', 'like'. The user is expected to make a responsible decision about which feature attributes to use with which passed values and comparator settings. not startswithlike)listr r!getattrr(research)r attributer$ comparatorrs r get_featureszFeatureSet.get_featuresjsW&    ,,./ /   $}}3357I.%7 5  $}}3357I.%7 < ' $}}3357I.99%@ 6 ! $}}33599UGGY$?@   =sD4D9>$D>)EcHt|jjS)z-Return a list of all ids for the feature set.)r*r keysr s rget_idszFeatureSet.get_idssDMM&&())rcgg}}|jjD]8}|jD]'\}}|j||j|):t |dk7r$t |dk7rt |t |fSy)z@Return the lowest and highest base (or mark) numbers as a tuple.r)rr)r r! locationsappendlenminmax)r lowshighsrstartends rrangezFeatureSet.ranges"e}}++- "G%// " s E" S! " " t9>c%jAoIs5z* *rc|s|Sd|jd|jdg}|jdt|jz|jD]#}|jd|j|%dj |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 r7r8r join)r verboseoutstrrs r to_stringzFeatureSet.to_stringsV DNN+2dii[:;F MM-#dmm*<< =}} @ $--*<)=>? @99V$ $rc,t|jS)z)Return the number of features in the set.)r8r r3s r__len__zFeatureSet.__len__s4==!!rc |j|S)zReturn a feature, keyed by id.r)r rs r __getitem__zFeatureSet.__getitem__s}}S!!rcd|j|jt|jfzg}dj |S)zAReturn a formatted string with information about the feature set.z <%s: %s %d features>rB)rCr r8r rD)r rFs r__str__zFeatureSet.__str__s< % 3t}}CU'V V yy  r)NNN)r)__name__ __module__ __qualname____doc__rrrr%r0r4r?rGrIrKrMrrrr s= 6& .(6p* %"""!rr)rQr,_FeaturerrrRrrrTs$ o!o!r