#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
#  This software is distributed under the MIT Open Source License.
#  <http://www.opensource.org/licenses/mit-license.html>
#
#  Permission is hereby granted, free of charge, to any person obtaining a
#  copy of this software and associated documentation files (the "Software"),
#  to deal in the Software without restriction, including without limitation
#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
#  and/or sell copies of the Software, and to permit persons to whom the
#  Software is furnished to do so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included
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#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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"""Read a multiple sequence alignment in STOCKHOLM format.

This file format is used by PFAM and HMMER. At present, all annotation
information is ignored.

See:
    - http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html
    - HMMER manual

"""

import re
from typing import Iterator, Optional, TextIO

from ..seq import Alphabet, Seq, SeqList
from ..utils import Token

example = """
# STOCKHOLM 1.0
#=GF ID CBS
#=GF AC PF00571
#=GF DE CBS domain
#=GF AU Bateman A
#=GF CC CBS domains are small intracellular modules mostly found
#=GF CC in 2 or four copies within a protein.
#=GF SQ 67
#=GS O31698/18-71 AC O31698
#=GS O83071/192-246 AC O83071
#=GS O83071/259-312 AC O83071
#=GS O31698/88-139 AC O31698
#=GS O31698/88-139 OS Bacillus subtilis
O83071/192-246          MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS
#=GR O83071/192-246 SA  999887756453524252..55152525....36463774777
O83071/259-312          MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY
#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE
O31698/18-71            MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS
#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH
O31698/88-139           EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH
#=GC SS_cons            CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH
O31699/88-139           EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31699/88-139 AS   ________________*__________________________
#=GR_O31699/88-139_IN   ____________1______________2__________0____
//
"""

names = (
    "stockholm",
    "pfam",
)
extensions = ("sth", "stockholm", "align")

header_line = re.compile(r"#\s+STOCKHOLM\s+1.\d\s+$")


def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]:
    """Iterate over the sequences in the file."""
    # Default implementation
    return iter(read(fin, alphabet))


def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
    alphabet = Alphabet(alphabet)
    seq_ids = []
    seqs: list = []
    block_count = 0

    for token in _scan(fin):
        if token.typeof == "begin_block":
            block_count = 0
        elif token.typeof == "seq_id":
            if len(seqs) <= block_count:
                seq_ids.append(token.data)
                seqs.append([])
        elif token.typeof == "seq":
            data = token.data
            assert data is not None

            if not alphabet.alphabetic(data):
                raise ValueError(
                    "Character on line: %d not in alphabet: %s : %s"
                    % (token.lineno, alphabet, data)
                )
            seqs[block_count].append(data)
            block_count += 1

    seqs = [Seq("".join(s), alphabet, name=i) for s, i in zip(seqs, seq_ids)]
    return SeqList(seqs)


def _scan(fin: TextIO) -> Iterator[Token]:
    header, body, block = range(3)

    yield Token("begin")
    state = header
    for L, line in enumerate(fin):
        if state == header:
            if line.isspace():
                continue
            m = header_line.match(line)
            state = body
            if m is not None:
                # print("header: ", m.group())
                yield Token("header", m.group())
                continue
            else:
                raise ValueError("Parse error on line: %d" % L)

        if state == body:
            if line.isspace():
                continue  # pragma: no cover
            yield Token("begin_block")
            state = block
            # fall through to block

        if state == block:
            if line.isspace():
                yield Token("end_block")
                state = body
                continue
            if line.strip() == "//":
                yield Token("end_block")
                return

            if line[0] == "#":  # Comment or annotation line
                continue

            name_seq = line.split(None, 1)  # Split into two parts at first whitespace
            if len(name_seq) != 2:
                raise ValueError("Parse error on line: %d" % L)  # pragma: no cover

            yield Token("seq_id", name_seq[0].strip())
            yield Token("seq", name_seq[1].strip())
            continue

        # END state blocks. If I ever get here something has gone terrible wrong
        raise RuntimeError()  # pragma: no cover