# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------

import skbio
from skbio.util._decorator import classproperty, overrides
from skbio.util._decorator import stable
from ._nucleotide_mixin import NucleotideMixin, _motifs as _parent_motifs
from ._grammared_sequence import GrammaredSequence, DisableSubclassingMeta


class DNA(GrammaredSequence, NucleotideMixin,
          metaclass=DisableSubclassingMeta):
    """Store DNA sequence data and optional associated metadata.

    Only characters in the IUPAC DNA character set [1]_ are supported.

    Parameters
    ----------
    sequence : str, Sequence, or 1D np.ndarray (np.uint8 or '\|S1')
        Characters representing the DNA sequence itself.
    metadata : dict, optional
        Arbitrary metadata which applies to the entire sequence.
    positional_metadata : Pandas DataFrame consumable, optional
        Arbitrary per-character metadata. For example, quality data from
        sequencing reads. Must be able to be passed directly to the Pandas
        DataFrame constructor.
    interval_metadata : IntervalMetadata
        Arbitrary interval metadata which applies to intervals within
        a sequence to store interval features (such as genes on the
        DNA sequence).
    lowercase : bool or str, optional
        If ``True``, lowercase sequence characters will be converted to
        uppercase characters in order to be valid IUPAC DNA characters. If
        ``False``, no characters will be converted. If a str, it will be
        treated as a key into the positional metadata of the object. All
        lowercase characters will be converted to uppercase, and a ``True``
        value will be stored in a boolean array in the positional metadata
        under the key.
    validate : bool, optional
        If ``True``, validation will be performed to ensure that all sequence
        characters are in the IUPAC DNA character set. If ``False``, validation
        will not be performed. Turning off validation will improve runtime
        performance. If invalid characters are present, however, there is
        **no guarantee that operations performed on the resulting object will
        work or behave as expected.** Only turn off validation if you are
        certain that the sequence characters are valid. To store sequence data
        that is not IUPAC-compliant, use ``Sequence``.

    Attributes
    ----------
    values
    metadata
    positional_metadata
    interval_metadata
    alphabet
    gap_chars
    default_gap_char
    definite_chars
    degenerate_chars
    degenerate_map
    complement_map

    See Also
    --------
    RNA
    GrammaredSequence

    Notes
    -----
    Subclassing is disabled for DNA, because subclassing makes
    it possible to change the alphabet, and certain methods rely on the
    IUPAC alphabet. If a custom sequence alphabet is needed, inherit directly
    from ``GrammaredSequence``.

    References
    ----------
    .. [1] Nomenclature for incompletely specified bases in nucleic acid
       sequences: recommendations 1984.
       Nucleic Acids Res. May 10, 1985; 13(9): 3021-3030.
       A Cornish-Bowden

    Examples
    --------
    >>> from skbio import DNA
    >>> DNA('ACCGAAT')
    DNA
    --------------------------
    Stats:
        length: 7
        has gaps: False
        has degenerates: False
        has definites: True
        GC-content: 42.86%
    --------------------------
    0 ACCGAAT

    Convert lowercase characters to uppercase:

    >>> DNA('AcCGaaT', lowercase=True)
    DNA
    --------------------------
    Stats:
        length: 7
        has gaps: False
        has degenerates: False
        has definites: True
        GC-content: 42.86%
    --------------------------
    0 ACCGAAT

    """

    @classproperty
    @overrides(NucleotideMixin)
    def complement_map(cls):
        comp_map = {
            'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'Y': 'R', 'R': 'Y',
            'S': 'S', 'W': 'W', 'K': 'M', 'M': 'K', 'B': 'V', 'D': 'H',
            'H': 'D', 'V': 'B', 'N': 'N'
        }

        comp_map.update({c: c for c in cls.gap_chars})
        return comp_map

    @classproperty
    @overrides(GrammaredSequence)
    def definite_chars(cls):
        return set("ACGT")

    @classproperty
    @overrides(GrammaredSequence)
    def degenerate_map(cls):
        return {
            "R": set("AG"), "Y": set("CT"), "M": set("AC"), "K": set("TG"),
            "W": set("AT"), "S": set("GC"), "B": set("CGT"), "D": set("AGT"),
            "H": set("ACT"), "V": set("ACG"), "N": set("ACGT")
        }

    @classproperty
    @overrides(GrammaredSequence)
    def default_gap_char(cls):
        return '-'

    @classproperty
    @overrides(GrammaredSequence)
    def gap_chars(cls):
        return set('-.')

    @property
    def _motifs(self):
        return _motifs

    @stable(as_of="0.4.0")
    def transcribe(self):
        """Transcribe DNA into RNA.

        DNA sequence is assumed to be the coding strand. Thymine (T) is
        replaced with uracil (U) in the transcribed sequence.

        Returns
        -------
        RNA
            Transcribed sequence.

        See Also
        --------
        translate
        translate_six_frames

        Notes
        -----
        DNA sequence's metadata, positional, and interval
        metadata are included in the transcribed RNA sequence.

        Examples
        --------
        Transcribe DNA into RNA:

        >>> from skbio import DNA
        >>> dna = DNA('TAACGTTA')
        >>> dna
        DNA
        --------------------------
        Stats:
            length: 8
            has gaps: False
            has degenerates: False
            has definites: True
            GC-content: 25.00%
        --------------------------
        0 TAACGTTA
        >>> dna.transcribe()
        RNA
        --------------------------
        Stats:
            length: 8
            has gaps: False
            has degenerates: False
            has definites: True
            GC-content: 25.00%
        --------------------------
        0 UAACGUUA

        """
        seq = self._string.replace(b'T', b'U')

        metadata = None
        if self.has_metadata():
            metadata = self.metadata

        positional_metadata = None
        if self.has_positional_metadata():
            positional_metadata = self.positional_metadata

        interval_metadata = None
        if self.has_interval_metadata():
            interval_metadata = self.interval_metadata

        # turn off validation because `seq` is guaranteed to be valid
        return skbio.RNA(seq, metadata=metadata,
                         positional_metadata=positional_metadata,
                         interval_metadata=interval_metadata,
                         validate=False)

    @stable(as_of="0.4.0")
    def translate(self, *args, **kwargs):
        """Translate DNA sequence into protein sequence.

        DNA sequence is assumed to be the coding strand. DNA sequence is first
        transcribed into RNA and then translated into protein.

        Parameters
        ----------
        args : tuple
            Positional arguments accepted by ``RNA.translate``.
        kwargs : dict
            Keyword arguments accepted by ``RNA.translate``.

        Returns
        -------
        Protein
            Translated sequence.

        See Also
        --------
        RNA.reverse_transcribe
        RNA.translate
        translate_six_frames
        transcribe

        Notes
        -----
        DNA sequence's metadata are included in the translated protein
        sequence. Positional metadata are not included.

        Examples
        --------
        Translate DNA into protein using NCBI's standard genetic code (table ID
        1, the default genetic code in scikit-bio):

        >>> from skbio import DNA
        >>> dna = DNA('ATGCCACTTTAA')
        >>> dna.translate()
        Protein
        --------------------------
        Stats:
            length: 4
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: True
        --------------------------
        0 MPL*

        Translate the same DNA sequence using a different NCBI genetic code
        (table ID 3, the yeast mitochondrial code) and specify that translation
        must terminate at the first stop codon:

        >>> dna.translate(3, stop='require')
        Protein
        --------------------------
        Stats:
            length: 3
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: False
        --------------------------
        0 MPT

        """
        return self.transcribe().translate(*args, **kwargs)

    @stable(as_of="0.4.0")
    def translate_six_frames(self, *args, **kwargs):
        """Translate DNA into protein using six possible reading frames.

        DNA sequence is assumed to be the coding strand. DNA sequence is first
        transcribed into RNA and then translated into protein. The six possible
        reading frames are:

        * 1 (forward)
        * 2 (forward)
        * 3 (forward)
        * -1 (reverse)
        * -2 (reverse)
        * -3 (reverse)

        Translated sequences are yielded in this order.

        Parameters
        ----------
        args : tuple
            Positional arguments accepted by ``RNA.translate_six_frames``.
        kwargs : dict
            Keyword arguments accepted by ``RNA.translate_six_frames``.

        Yields
        ------
        Protein
            Translated sequence in the current reading frame.

        See Also
        --------
        RNA.translate_six_frames
        translate
        transcribe

        Notes
        -----
        This method is faster than (and equivalent to) performing six
        independent translations using, for example:

        ``(seq.translate(reading_frame=rf)
        for rf in GeneticCode.reading_frames)``

        DNA sequence's metadata are included in each translated protein
        sequence. Positional metadata are not included.

        Examples
        --------
        Translate DNA into protein using the six possible reading frames and
        NCBI's standard genetic code (table ID 1, the default genetic code in
        scikit-bio):

        >>> from skbio import DNA
        >>> dna = DNA('ATGCCACTTTAA')
        >>> for protein in dna.translate_six_frames():
        ...     protein
        ...     print('')
        Protein
        --------------------------
        Stats:
            length: 4
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: True
        --------------------------
        0 MPL*
        <BLANKLINE>
        Protein
        --------------------------
        Stats:
            length: 3
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: False
        --------------------------
        0 CHF
        <BLANKLINE>
        Protein
        --------------------------
        Stats:
            length: 3
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: False
        --------------------------
        0 ATL
        <BLANKLINE>
        Protein
        --------------------------
        Stats:
            length: 4
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: False
        --------------------------
        0 LKWH
        <BLANKLINE>
        Protein
        --------------------------
        Stats:
            length: 3
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: True
        --------------------------
        0 *SG
        <BLANKLINE>
        Protein
        --------------------------
        Stats:
            length: 3
            has gaps: False
            has degenerates: False
            has definites: True
            has stops: False
        --------------------------
        0 KVA
        <BLANKLINE>

        """
        return self.transcribe().translate_six_frames(*args, **kwargs)

    @overrides(GrammaredSequence)
    def _repr_stats(self):
        """Define custom statistics to display in the sequence's repr."""
        stats = super(DNA, self)._repr_stats()
        stats.append(('GC-content', '{:.2%}'.format(self.gc_content())))
        return stats


_motifs = _parent_motifs.copy()

# Leave this at the bottom
_motifs.interpolate(DNA, "find_motifs")