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"""Sequence IO for NBRF/PIR format.

The format is similar to fasta. The header line consistins of '>', a two-
letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a
sequence ID. The next line is a textual description of the sequence,
followed by one or more lines containing the sequence data. The end of
the sequence is marked by a "*" (asterisk) character.

type_code -- A map between NBRF two letter type codes and Alphabets.


see:  http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html

--- Example NBRF File ---

>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P1;CRAB_BOVIN
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
  HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
  QASGPERTIP ITREEKPAVT AAPKK*

"""

from ..seq import Seq, SeqList, protein_alphabet, dna_alphabet, rna_alphabet, generic_alphabet

names = ("nbrf", "pir",)
extensions = ('nbrf', 'pir', 'ali')

type_code = {
    'P1': protein_alphabet,  # Protein (complete)
    'F1': protein_alphabet,  # Protein (fragment)
    'DL': dna_alphabet,  # DNA (linear)
    'DC': dna_alphabet,  # DNA (circular)
    'RC': rna_alphabet,  # RNA (linear)
    'RL': rna_alphabet,  # RNA (circular)
    'N3': rna_alphabet,  # tRNA
    'N1': rna_alphabet,  # other functional RNA
    'XX': generic_alphabet
}


def read(fin, alphabet=None):
    """Read and parse a NBRF seqquence file.

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data. If not supplied, then
                an appropriate alphabet will be inferred from the data.
    Returns:
        SeqList -- A list of sequences
    Raises:
        ValueError -- If the file is unparsable
    """
    seqs = [s for s in iterseq(fin, alphabet)]
    return SeqList(seqs)


def iterseq(fin, alphabet=None):
    """ Generate sequences from an NBRF file.

    arguments:
        fin -- A stream or file to read
        alphabet --
    yields :
        Seq
    raises :
        ValueError -- On a parse error.
    """

    body, header, sequence = range(3)  # Internal states

    state = body
    seq_id = None
    seq_desc = None
    seq_alpha = None
    seqs = []

    for lineno, line in enumerate(fin):
        if state == body:
            if line == "" or line.isspace():
                continue
            if line[0] == '>':
                seq_type, seq_id = line[1:].split(';')
                if alphabet:
                    seq_alpha = alphabet
                else:
                    seq_alpha = type_code[seq_type]
                state = header
                continue
            raise ValueError("Parse error on line: %d" % lineno)

        elif state == header:
            seq_desc = line.strip()
            state = sequence
            continue

        elif state == sequence:
            data = "".join(line.split())  # Strip out white space
            if data[-1] == '*':
                # End of sequence data
                seqs.append(data[:-1])

                seq = Seq("".join(seqs), name=seq_id.strip(),
                          description=seq_desc, alphabet=seq_alpha)

                yield seq
                state = body
                seq_id = None
                seq_desc = None
                seqs = []
                continue
            else:
                seqs.append(data)
                continue
        else:
            # If we ever get here something has gone terrible wrong
            assert False    # pragma: no cover

    # end for