text: # Copyright 2006-2009 by Peter Cock.  All rights reserved.
  # This code is part of the Biopython distribution and governed by its
  # license.  Please see the LICENSE file that should have been included
  # as part of this package.
  """
  Bio.SeqIO support module (not for general use).
  
  Unless you are writing a new parser or writer for Bio.SeqIO, you should not
  use this module.  It provides base classes to try and simplify things.
  """
  
  from Bio.Alphabet import generic_alphabet
  
  class SequenceIterator(object):
      """Base class for building SeqRecord iterators.
  
      You should write a next() method to return SeqRecord
      objects.  You may wish to redefine the __init__
      method as well.
      """
      def __init__(self, handle, alphabet=generic_alphabet):
          """Create a SequenceIterator object.
  
          handle - input file
          alphabet - optional, e.g. Bio.Alphabet.generic_protein
  
          Note when subclassing:
          - there should be a single non-optional argument,
            the handle.
          - you do not have to require an alphabet.
          - you can add additional optional arguments."""
          self.handle = handle
          self.alphabet = alphabet
          #####################################################
          # You may want to subclass this, for example        #
          # to read through the file to find the first record,#
          # or if additional arguments are required.          #
          #####################################################
  
      def next(self):
          """Return the next record in the file.
  
          This method should be replaced by any derived class to do something useful."""
          raise NotImplementedError("This object should be subclassed")
          #####################################################
          # You SHOULD subclass this, to split the file up    #
          # into your individual records, and convert these   #
          # into useful objects, e.g. return SeqRecord object #
          #####################################################
  
      def __iter__(self):
          """Iterate over the entries as a SeqRecord objects.
  
          Example usage for Fasta files:
  
          myFile = open("example.fasta","r")
          myFastaReader = FastaIterator(myFile)
          for record in myFastaReader:
              print record.id
              print record.seq
          myFile.close()"""
          return iter(self.next, None)
  
  class InterlacedSequenceIterator(SequenceIterator):
      """Base class for any iterator of a non-sequential file type.
  
      This object is not intended for use directly.
      
      When writing a parser for any interlaced sequence file where the whole
      file must be read in order to extract any single record, then you should
      subclass this object.
  
      All you need to do is to define your own:
      (1) __init__ method to parse the file and call self.move_start()
      (2) __len__ method to return the number of records
      (3) __getitem__ to return any requested record.
  
      This class will then provide the iterator methods including next(), but relies
      on knowing the total number of records and tracking the pending record index in
      as self._n
  
      It is up to the subclassed object to decide if it wants to generate a cache of
      SeqRecords when initialised, or simply use its own lists and dicts and create
      SeqRecords on request.
      """
  
      def __init__(self):
          """Create the object.
  
          This method should be replaced by any derived class to do something useful."""
          #We assume that your implementation of __init__ will ensure self._n=0
          self.move_start()
          raise NotImplementedError("This object method should be subclassed")
          #####################################################
          # You SHOULD subclass this                          #
          #####################################################
  
      def __len__(self):
          """Return the number of records.
  
          This method should be replaced by any derived class to do something useful."""
          raise NotImplementedError("This object method should be subclassed")
          #####################################################
          # You SHOULD subclass this                          #
          #####################################################
  
      def __getitem__(self, i):
          """Return the requested record.
  
          This method should be replaced by any derived class to do something
          useful.
  
          It should NOT touch the value of self._n"""
          raise NotImplementedError("This object method should be subclassed")
          #####################################################
          # You SHOULD subclass this                          #
          #####################################################
  
      def move_start(self):
          self._n = 0
  
      def next(self):
          next_record = self._n
          if next_record < len(self):
              self._n = next_record+1
              return self[next_record]
          else:
              #StopIteration
              return None
      
      def __iter__(self):
          return iter(self.next, None)
  
  class SequenceWriter(object):
      """This class should be subclassed.
  
      Interlaced file formats (e.g. Clustal) should subclass directly.
  
      Sequential file formats (e.g. Fasta, GenBank) should subclass
      the SequentialSequenceWriter class instead.
      """
      def __init__(self, handle):
          """Creates the writer object.
  
          Use the method write_file() to actually record your sequence records."""
          self.handle = handle
  
      def _get_seq_string(self, record):
          """Use this to catch errors like the sequence being None."""
          try:
              #The tostring() method is part of the Seq API, we could instead
              #use str(record.seq) but that would give a string "None" if the
              #sequence was None, and unpredicatable output if an unexpected
              #object was present.
              return record.seq.tostring()
          except AttributeError:
              if record.seq is None:
                  #We could silently treat this as an empty sequence, Seq(""),
                  #but that would be an implict assumption we should avoid.
                  raise TypeError("SeqRecord (id=%s) has None for its sequence." \
                                  % record.id)
              else:
                  raise TypeError("SeqRecord (id=%s) has an invalid sequence." \
                                  % record.id)
  
      def clean(self, text):
          """Use this to avoid getting newlines in the output."""
          return text.replace("\n", " ").replace("\r", " ").replace("  ", " ")
      
      def write_file(self, records):
          """Use this to write an entire file containing the given records.
  
          records - A list or iterator returning SeqRecord objects
  
          Should return the number of records (as an integer).
  
          This method can only be called once."""
          #Note when implementing this, your writer class should NOT close the
          #file at the end, but the calling code should.
          raise NotImplementedError("This object should be subclassed")
          #####################################################
          # You SHOULD subclass this                          #
          #####################################################
  
  class SequentialSequenceWriter(SequenceWriter):
      """This class should be subclassed.
  
      It is intended for sequential file formats with an (optional)
      header, repeated records, and an (optional) footer.
  
      In this case (as with interlaced file formats), the user may
      simply call the write_file() method and be done.
  
      However, they may also call the write_header(), followed
      by multiple calls to write_record() and/or write_records()
      followed finally by write_footer().
  
      Users must call write_header() and write_footer() even when
      the file format concerned doesn't have a header or footer.
      This is to try and make life as easy as possible when
      switching the output format.
      
      Note that write_header() cannot require any assumptions about
      the number of records.
      """
      def __init__(self, handle):
          self.handle = handle
          self._header_written = False
          self._record_written = False
          self._footer_written = False
  
      def write_header(self):
          assert not self._header_written, "You have aleady called write_header()"
          assert not self._record_written, "You have aleady called write_record() or write_records()"
          assert not self._footer_written, "You have aleady called write_footer()"
          self._header_written = True
          
      def write_footer(self):
          assert self._header_written, "You must call write_header() first"
          assert self._record_written, "You have not called write_record() or write_records() yet"
          assert not self._footer_written, "You have aleady called write_footer()"
          self._footer_written = True
  
      def write_record(self, record):
          """Write a single record to the output file.
  
          record - a SeqRecord object
  
          Once you have called write_header() you can call write_record()
          and/or write_records() as many times as needed.  Then call
          write_footer() and close()."""
          assert self._header_written, "You must call write_header() first"
          assert not self._footer_written, "You have already called write_footer()"
          self._record_written = True
          raise NotImplementedError("This object should be subclassed")
          #####################################################
          # You SHOULD subclass this                          #
          #####################################################
  
      def write_records(self, records):
          """Write multiple record to the output file.
  
          records - A list or iterator returning SeqRecord objects
  
          Once you have called write_header() you can call write_record()
          and/or write_records() as many times as needed.  Then call
          write_footer() and close().
  
          Returns the number of records written.
          """
          #Default implementation:
          assert self._header_written, "You must call write_header() first"
          assert not self._footer_written, "You have already called write_footer()"
          count = 0
          for record in records:
              self.write_record(record)
              count += 1
          #Mark as true, even if there where no records
          self._record_written = True
          return count
  
      def write_file(self, records):
          """Use this to write an entire file containing the given records.
  
          records - A list or iterator returning SeqRecord objects
  
          This method can only be called once.  Returns the number of records
          written.
          """
          self.write_header()
          count = self.write_records(records)
          self.write_footer()
          return count
  