o Rŀg@s4dZGdddZGdddZGdddeZdS)zAlignIO support module (not for general use). Unless you are writing a new parser or writer for Bio.AlignIO, you should not use this module. It provides base classes to try and simplify things. c@s*eZdZdZd ddZddZddZdS) AlignmentIteratorzBase class for building MultipleSeqAlignment iterators. You should write a next() method to return Alignment objects. You may wish to redefine the __init__ method as well. NcCs||_||_dS)aCreate an AlignmentIterator object. Arguments: - handle - input file - count - optional, expected number of records per alignment Recommend for fasta file format. Note when subclassing: - there should be a single non-optional argument, the handle, and optional count IN THAT ORDER. - you can add additional optional arguments. N)handlerecords_per_alignment)selfr seq_countrJ/var/www/html/myenv/lib/python3.10/site-packages/Bio/AlignIO/Interfaces.py__init__s zAlignmentIterator.__init__cCtd)zReturn the next alignment in the file. This method should be replaced by any derived class to do something useful. This object should be subclassedNotImplementedErrorrrrr__next__,zAlignmentIterator.__next__cCs t|jdS)aIterate over the entries as MultipleSeqAlignment objects. Example usage for (concatenated) PHYLIP files:: with open("many.phy","r") as myFile: for alignment in PhylipIterator(myFile): print("New alignment:") for record in alignment: print(record.id) print(record.seq) N)iterrr rrr__iter__9s zAlignmentIterator.__iter__)N)__name__ __module__ __qualname____doc__rrrrrrrrs   rc@s(eZdZdZddZddZddZdS) AlignmentWriterzBase class for building MultipleSeqAlignment writers. You should write a write_alignment() method. You may wish to redefine the __init__ method as well. cC ||_dSzInitialize the class.NrrrrrrrP zAlignmentWriter.__init__cCr )a}Use this to write an entire file containing the given alignments. Arguments: - alignments - A list or iterator returning MultipleSeqAlignment objects In general, this method can only be called once per file. This method should be replaced by any derived class to do something useful. It should return the number of alignments.. r r )r alignmentsrrr write_fileTs zAlignmentWriter.write_filecCs|ddddS)z1Use this to avoid getting newlines in the output.   )replace)rtextrrrcleaneszAlignmentWriter.cleanN)rrrrrrr#rrrrrIs  rc@s8eZdZdZddZddZddZdd Zd d Zd S) SequentialAlignmentWriterzBase class for building MultipleSeqAlignment writers. This assumes each alignment can be simply appended to the file. You should write a write_alignment() method. You may wish to redefine the __init__ method as well. cCrrrrrrrrrrz"SequentialAlignmentWriter.__init__cCs4|d}|D] }|||d7}q||S)zUse this to write an entire file containing the given alignments. Arguments: - alignments - A list or iterator returning MultipleSeqAlignment objects In general, this method can only be called once per file. ) write_headerwrite_alignment write_footer)rrcount alignmentrrrrvs  z$SequentialAlignmentWriter.write_filecCdS)zUse this to write any header. This method should be replaced by any derived class to do something useful. Nrr rrrr'z&SequentialAlignmentWriter.write_headercCr,)zUse this to write any footer. This method should be replaced by any derived class to do something useful. Nrr rrrr)r-z&SequentialAlignmentWriter.write_footercCr )zUse this to write a single alignment. This method should be replaced by any derived class to do something useful. r r )rr+rrrr(rz)SequentialAlignmentWriter.write_alignmentN) rrrrrrr'r)r(rrrrr$js r$N)rrrr$rrrrs;!