*ė ā@;csrdZ dkZdklZdklZdklZdkl Z dfd„ƒYZ dS(s‘Generic.py Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format. classes: o Alignment N(sSeq(s SeqRecord(sAlphabet(sIUPACs Alignmentcs_dZd„Z$d„Z+d„Z6d„ZEeedd„Zld„ZRS(s„Represent a set of alignments. This is a base class to represent alignments, which should be subclassed to deal with an alignment in a specific format. cs" ||_"g|_dS(sĄInitialize a new Alignment object. Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type. N(salphabetsselfs _alphabets_records(sselfsalphabet((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys__init__s cs$()|iSdS(syReturn all of the sequences involved in the alignment. The return value is a list of SeqRecord objects. N(sselfs_records(sself((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys get_all_seqs$scs+34|i|iSdS(sāRetrieve a sequence by the number of the sequence in the consensus. Returns: o A Seq object for the requested sequence. Raises: o IndexError - If the specified number is out of range. N(sselfs_recordssnumbersseq(sselfsnumber((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pysget_seq_by_num+scse6<=d}?xE|id?r5}@t|iƒ|joAt|iƒ}nqWC|SdS(sReturn the maximum length of the alignment. All objects in the alignment should (hopefully) have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment. iN(s max_lengthsselfs_recordssrecordslensseq(sselfs max_lengthsrecord((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pysget_alignment_length6s  f1.0cs“EXYt||iƒ}Zt|d|ƒ}c|od||i d no weight, 1.0 => highest weight) s descriptionsstartsendsweightN(sSeqssequencesselfs _alphabetsnew_seqs SeqRecords descriptors new_recordsstarts annotationssendsweights_recordssappend(sselfs descriptorssequencesstartsendsweightsnew_seqs new_record((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys add_sequenceEs  cs{lmnd}oto'|djo||iƒjpt‚px*|idpr}q||i|7}qOWr|SdS(s*Returns a string containing a given columnsiN( scol_strs __debug__scolsselfsget_alignment_lengthsAssertionErrors_recordssrecsseq(sselfscolscol_strsrec((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys get_columnls 1 (s__doc__s__init__s get_all_seqssget_seq_by_numsget_alignment_lengthsNones add_sequences get_column(((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys Alignments   '( s__doc__sstringsBio.SeqsSeqs Bio.SeqRecords SeqRecordsBiosAlphabets Bio.AlphabetsIUPACs Alignment(s SeqRecords AlignmentsIUPACsAlphabetsSeqsstring((s;/mit/seven/lib/python2.1/site-packages/Bio/Align/Generic.pys?s