# Copyright 2003 by Bartek Wilczynski.  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.

"""Parsing AlignACE files: AlignAceParser
"""

from Bio.Motif import Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq


class Record(object):
    def __init__(self):
        self.motifs = []
        self.current_motif = None
        self.param_dict = None


def read(handle):
    """read(handle)"""
    record = Record()
    record.ver = next(handle)
    record.cmd_line = next(handle)
    for line in handle:
        if line.strip() == "":
            pass
        elif line[:4] == "Para":
            record.param_dict = {}
        elif line[0] == "#":
            seq_name = line.split("\t")[1]
            record.seq_dict.append(seq_name)
        elif "=" in line:
            par_name = line.split("=")[0].strip()
            par_value = line.split("=")[1].strip()
            record.param_dict[par_name] = par_value
        elif line[:5] == "Input":
            record.seq_dict = []
        elif line[:5] == "Motif":
            record.current_motif = Motif()
            record.motifs.append(record.current_motif)
            record.current_motif.alphabet = IUPAC.unambiguous_dna
        elif line[:3] == "MAP":
            record.current_motif.score = float(line.split()[-1])
        elif len(line.split("\t")) == 4:
            seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
            record.current_motif.add_instance(seq)
        elif "*" in line:
            record.current_motif.set_mask(line.strip("\n\c"))
        else:
            raise ValueError(line)
    return record
