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"""
Parser module specific to PSICOV predictions
"""

__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"

from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile


class PsicovParser(ContactFileParser):
    """Class to parse a PSICOV contact prediction
    """

    def read(self, f_handle, f_id="psicov"):
        """Read a contact file

        Parameters
        ----------
        f_handle
           Open file handle [read permissions]
        f_id : str, optional
           Unique contact file identifier

        Returns
        -------
        :obj:`~conkit.core.contactfile.ContactFile`

        """

        hierarchy = ContactFile(f_id)
        _map = ContactMap("map_1")
        hierarchy.add(_map)

        for line in f_handle:
            line = line.strip().split()

            if not line or line[0].isalpha():
                continue

            elif line[0].isdigit():
                _contact = Contact(
                    int(line[0]), int(line[1]), float(line[4]), distance_bound=(float(line[2]), float(line[3])))
                _map.add(_contact)

        hierarchy.method = 'Contact map predicted using PSICOV'

        return hierarchy

    def write(self, f_handle, hierarchy):
        """Write a contact file instance to to file

        Parameters
        ----------
        f_handle
           Open file handle [write permissions]
        hierarchy : :obj:`~conkit.core.contactfile.ContactFile`, :obj:`~conkit.core.contactmap.ContactMap`
                    or :obj:`~conkit.core.contact.Contact`

        Raises
        ------
        :exc:`RuntimeError`
           More than one contact map in the hierarchy

        """
        contact_file = self._reconstruct(hierarchy)
        if len(contact_file) > 1:
            raise RuntimeError('More than one contact map provided')
        content = ''
        for contact_map in contact_file:
            for contact in contact_map:
                line = '{} {} {} {} {:.6f}\n'
                lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
                ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
                content += line.format(contact.res1_seq, contact.res2_seq, lb, ub, contact.raw_score)
        f_handle.write(content)
