#!/usr/bin/env python

#  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
#  in all copies or substantial portions of the Software.
#
#  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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#  THE SOFTWARE.
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"""Read and write a rectangular array of sequence data.

One sequence per line and nothing else. Each line must contain the same number
of characters. Blank lines and white space are ignored.

--- Example Array ---

--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
-----------------------------------YTSDN---------YSGSGDYDSNK
-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
-EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
"""

from typing import Generator, Optional, TextIO

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

example = """
--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
-----------------------------------YTSDN---------YSGSGDYDSNK
-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
-EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
"""

names = ("array", "flatfile")
extensions = ()


def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
    """Read a file of raw sequence alignment data.

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given
    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: TextIO, alphabet: Optional[Alphabet] = None) -> Generator:
    """Read one line of sequence data and yield the sequence.

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given
    Yields:
        Seq -- One alphabetic sequence at a time.
    Raises:
        ValueError -- If the file is unparsable
    """

    alphabet = Alphabet(alphabet)
    line_length = 0

    for linenum, line in enumerate(fin):
        if line.isspace():
            continue  # Blank line
        line = line.strip()

        if line[0] == ">":  # probably a fasta file. Fail.
            raise ValueError("Parse Error on input line: %d " % linenum)

        line = remove_whitespace(line)

        if not alphabet.alphabetic(line):
            raise ValueError(
                "Character on line: %d not in alphabet: %s : %s"
                % (linenum, alphabet, line)
            )

        if line_length and line_length != len(line):
            raise ValueError("Line %d has an incommensurate length." % linenum)
        line_length = len(line)

        yield Seq(line, alphabet)


def write(afile: TextIO, seqs: SeqList) -> None:
    """Write raw sequence data, one line per sequence.

    arguments:
        afile -- A writable stream.
        seqs  -- A list of Seq's
    """
    for s in seqs:
        writeseq(afile, s)


def writeseq(afile: TextIO, seq: SeqList) -> None:
    """Write a single sequence in raw format.

    arguments:
        afile -- A writable stream.
        seq  -- A Seq instance
    """
    print(seq, file=afile)