#  Copyright (c) 2006 John Gilman
#
#  This software is distributed under the MIT Open Source License.
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""" Transformations of Seqs (alphabetic sequences).



Classes :
- Transform   -- Simple transforms of alphabetic strings.
- GeneticCode -- The genetic mapping of DNA to protein.

Functions :
-  mask_low_complexity -- Implementation of Seg algorithm to remove low complexity
        regions from protein sequences.

Other:
-   reduced_protein_alphabets -- A dictionary of transforms that reduce the size of the protein
   alphabet, merging various amino acids into classes.

        "LiBn" where n is 2 to 19 are from Li et al (2003), table I, 2 to 19 groups.
        "LiBn" where n is 2 to 19 are from Li et al (2003), table II (no interlacing),
        2 to 19 groups.

        Ref: Li et al Reduction of protein sequence complexity by residue grouping,
            Prot. Eng. 16 323-330 (2003)

"""

from typing import Dict, List, Optional, Tuple

from numpy import log2
from scipy.stats import entropy

from .data import dna_ambiguity, dna_extended_letters
from .seq import Alphabet, Seq, dna_alphabet, protein_alphabet
from .seq import reduced_protein_alphabet as std_protein_alphabet

__all__ = [
    "Transform",
    "mask_low_complexity",
    "GeneticCode",
    "reduced_protein_alphabets",
]


class Transform(object):
    """A translation between alphabetic strings.
    (This class is not called 'Translation' to avoid confusion with the
    biological translation of RNA to protein.)

    Example:
    trans = Transform(
        Seq("ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~", dna_alphabet),
        Seq("ACGTRYSWKMNNNNN-acgtUuryswkmbnnnnXx?.~", reduced_nucleic_alphabet)
        )
    s0 = Seq("AAAAAV", nucleic_alphabet)
    s1 = trans(s0)
    assert(s1.alphabet == reduced_nucleic_alphabet)
    assert(s2 == Seq("AAAAAN",  reduced_nucleic_alphabet)

    Status : Beta
    """

    __slots__ = ["table", "source", "target", "name", "description"]

    def __init__(
        self,
        source: Seq,
        target: Seq,
        name: Optional[str] = None,
        description: Optional[str] = None,
    ) -> None:
        self.table = str.maketrans(source.tostring(), target.tostring())
        self.source = source
        self.target = target
        self.name = name
        self.description = description

    def __call__(self, seq: Seq) -> Seq:
        """Translate sequence."""
        if not self.source.alphabet.alphabetic(seq):
            raise ValueError("Incompatible alphabets")
        s = str.translate(seq, self.table)
        cls = self.target.__class__
        return cls(s, self.target.alphabet, seq.name, seq.description)


# End class Translation

# FIXME: Test, document, add to seq.
dna_complement = Transform(
    Seq("ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~", dna_alphabet),
    Seq("TGCAYRSWMKVHDBN-tgcaAayrswmkvhdbnXx?.~", dna_alphabet),
)


def mask_low_complexity(
    seq: Seq,
    width: int = 12,
    trigger: float = 1.8,
    extension: float = 2.0,
    mask: str = "X",
) -> Seq:
    """Mask low complexity regions in protein sequences.

    Uses the method of Seg [1] by Wootton & Federhen [2] to divide a sequence
    into regions of high and low complexity. The sequence is divided into
    overlapping windows. Low complexity windows either have a sequence entropy
    less than the trigger complexity, or have an entropy less than the extension
    complexity and neighbor other low-complexity windows. The sequence within
    a low complexity region is replaced with the mask character (default 'X'),
    and the masked alphabetic sequence is returned.

    The default parameters, width=12, trigger=1.8, extension=2.0, mask='X' are
    suitable for masking protein sequences before a database search. The
    standard default seg parameters are width=12, trigger=2.2, extension=2.5

    Arguments:
        Seq seq         -- An alphabetic sequence
        int width       -- Window width
        float trigger   -- Entropy in bits between 0 and 4.3.. ( =log_2(20) )
        float extension -- Entropy in bits between 0 and 4.3.. ( =log_2(20) )
        char mask       -- The mask character (default: 'X')
    Returns :
        Seq         -- A masked alphabetic sequence
    Raises :
        ValueError  -- On invalid arguments
    Refs:
        [1] seg man page:
            http://bioportal.weizmann.ac.il/education/materials/gcg/seg.html
        [2] Wootton & Federhen (Computers and Chemistry 17; 149-163, (1993))
    Authors:
        GEC 2005
    Future :
        - Optional mask character.
        - Option to lower case masked symbols.
        - Remove arbitary restriction to protein.
    """

    lg20 = log2(20)
    if trigger < 0 or trigger > lg20:
        raise ValueError("Invalid trigger complexity: %f" % trigger)
    if extension < 0 or extension > lg20 or extension < trigger:
        raise ValueError("Invalid extension complexity: %f" % extension)
    if width < 0:
        raise ValueError("Invalid width: %d" % width)

    if width > len(seq):
        return seq

    s = seq.ords()

    X = seq.alphabet.ord(mask)

    nwindows = len(seq) - width + 1
    ent = [0 for x in range(0, nwindows)]
    count = [0 for x in range(0, len(seq.alphabet))]

    for c in s[0:width]:
        count[c] += 1
    ent[0] = entropy(count, base=2)

    for i in range(1, nwindows):
        count[s[i - 1]] -= 1
        count[s[i + width - 1]] += 1
        ent[i] = entropy(count, base=2)

    prev_segged = False
    for i in range(0, nwindows):
        if (prev_segged and ent[i] < extension) or ent[i] < trigger:
            for j in range(0, width):
                s[i + j] = X
            prev_segged = True
        else:
            prev_segged = False

    # Redo, only backwards
    prev_segged = False
    for i in range(nwindows - 1, -1, -1):
        if (prev_segged and ent[i] < extension) or ent[i] < trigger:
            for j in range(0, width):
                s[i + j] = X
            prev_segged = True
        else:
            prev_segged = False

    segged = seq.alphabet.chrs(s)
    segged.name = seq.name
    segged.description = seq.description
    return segged


# end mask_low_complexity()


class GeneticCode(object):
    """An encoding of amino acids by DNA triplets.

    Example :

    Genetic Code [1]: Standard
          T         C         A         G
       +---------+---------+---------+---------+
     T | TTT F   | TCT S   | TAT Y   | TGT C   | T
     T | TTC F   | TCC S   | TAC Y   | TGC C   | C
     T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
     T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
       +---------+---------+---------+---------+
     C | CTT L   | CCT P   | CAT H   | CGT R   | T
     C | CTC L   | CCC P   | CAC H   | CGC R   | C
     C | CTA L   | CCA P   | CAA Q   | CGA R   | A
     C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
       +---------+---------+---------+---------+
     A | ATT I   | ACT T   | AAT N   | AGT S   | T
     A | ATC I   | ACC T   | AAC N   | AGC S   | C
     A | ATA I   | ACA T   | AAA K   | AGA R   | A
     A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
       +---------+---------+---------+---------+
     G | GTT V   | GCT A   | GAT D   | GGT G   | T
     G | GTC V   | GCC A   | GAC D   | GGC G   | C
     G | GTA V   | GCA A   | GAA E   | GGA G   | A
     G | GTG V   | GCG A   | GAG E   | GGG G   | G
       +---------+---------+---------+---------+


    See Also :
    -- http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
    -- http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.5
    Authors:
        JXG, GEC
    """

    # TODO: Explain use of '?' in translated sequence.
    # TODO: Does translate fails with aproriate execption when fed gaps?
    # TODO: Can back_translate handle gaps?

    def __init__(
        self,
        ident: int,
        description: str,
        amino_acid: str,
        start: str,
        base1: str,
        base2: str,
        base3: str,
    ) -> None:
        """Create a new GeneticCode.

        Args:
        -- ident - Standard identifier (or zero). An integer
        -- description
        -- amino acid - A sequence of amino acids and stop codons. e.g.
            "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
        -- start - A sequence indicating start codons, e.g.,
            "---M---------------M---------------M----------------------------"
        -- base1 - The first base of each codon. e.g.,
            "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"
        -- base2 - The second base of each codon. e.g.,
            "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"
        -- base3 - The last base of each codon. e.g.,
            "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"
        """
        self.ident = ident
        self.description = description

        self.amino_acid = amino_acid
        self.start = start
        self.base1 = base1
        self.base2 = base2
        self.base3 = base3

        stop_codons = []
        start_codons = []
        for i, a in enumerate(amino_acid):
            codon = base1[i] + base2[i] + base3[i]
            if a == "*":
                stop_codons.append(codon)
            if start[i] == "M":
                start_codons.append(codon)

        self.stop_codons = tuple(stop_codons)
        self.start_codons = tuple(start_codons)

        # Building the full translation table is expensive,
        # so we avoid doing so until necessary.
        self._table: Optional[Dict[str, str]] = None
        self._back_table: Optional[Dict[str, str]] = None

    @staticmethod
    def std_list() -> Tuple[
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
        "GeneticCode",
    ]:
        "Return a list of standard genetic codes."
        return _codon_tables

    @staticmethod
    def std() -> "GeneticCode":
        "The standard 'universal' genetic code."
        return _codon_tables[0]

    @staticmethod
    def by_name(name: str) -> "GeneticCode":
        """Find a genetic code in the code list by name or identifier."""
        for t in _codon_tables:
            if t.ident == name or t.description == name:
                return t
        raise ValueError("No such translation table: %s" % str(name))

    @property
    def table(self) -> Optional[Dict[str, str]]:
        """A map between codons and amino acids"""
        if self._table is None:
            self._create_table()  # pragma: no cover

        return self._table

    @property
    def back_table(self) -> Optional[Dict[str, str]]:
        """A map between amino acids and codons"""
        if self._back_table is None:
            self._create_table()  # pragma: no cover
        return self._back_table

    def _create_table(self) -> None:
        aa = self.amino_acid
        base1 = self.base1
        base2 = self.base2
        base3 = self.base3

        # Construct a table of unambiguous codon translations
        table = {}
        for i, a in enumerate(aa):
            codon = base1[i] + base2[i] + base3[i]
            table[codon] = a

        # Build the back table.
        back_table = {}
        items = list(table.items())
        items.sort()
        for codon, aa in items[::-1]:
            back_table[aa] = codon  # Use first codon, alphabetically.
        back_table["X"] = "NNN"
        back_table["B"] = "NNN"
        back_table["Z"] = "NNN"
        back_table["J"] = "NNN"
        self._back_table = back_table

        ltable = {}
        letters = dna_extended_letters + "U"  # include RNA in table

        # Create a list of all possible codons
        codons = []
        for c1 in letters:
            for c2 in letters:
                for c3 in letters:
                    codons.append(c1 + c2 + c3)

        # For each ambiguous codon, construct all compatible unambiguous codons.
        # Translate and collect a set of all possible translated amino acids.
        # If more than one translation look for possible amino acid ambiguity
        # codes.
        for C in codons:
            pre_translate = dict()  # Use dict, because no set in py2.3
            c = C.replace("U", "T")  # Convert RNA codon to DNA
            for c1 in dna_ambiguity[c[0]]:
                for c2 in dna_ambiguity[c[1]]:
                    for c3 in dna_ambiguity[c[2]]:
                        aa = table[c1 + c2 + c3]
                        pre_translate[aa] = ""
            translated = list(pre_translate.keys())
            translated.sort()
            if len(translated) == 1:
                trans = list(translated)[0]
            elif translated == ["D", "N"]:
                trans = "B"
            elif translated == ["E", "Q"]:
                trans = "Z"
            elif translated == ["I", "L"]:
                trans = "J"
            elif "*" in translated:
                trans = "?"
            else:
                trans = "X"
            ltable[C] = trans

        self._table = ltable

    # End create tables

    def translate(self, seq: Seq, frame: int = 0) -> Seq:
        """Translate a DNA sequence to a polypeptide using full
        IUPAC ambiguities in DNA/RNA and amino acid codes.

        Returns :
        -- Seq - A polypeptide sequence
        """
        # TODO: Optimize.
        # TODO: Insanity check alphabet.
        seqs = seq
        table = self.table
        assert table is not None
        trans = []
        L = len(seq)
        for i in range(frame, L - 2, 3):
            codon = str(seqs[i : i + 3]).upper()
            trans.append(table[codon])

        return Seq("".join(trans), protein_alphabet)

    def back_translate(self, seq: Seq) -> Seq:
        """Convert protein back into coding DNA.

        Args:
        -- seq - A polypeptide sequence.

        Returns :
        -- Seq - A DNA sequence
        """
        # TODO: Optimize
        # TODO: Insanity check alphabet.
        table = self.back_table
        assert table is not None

        seqs = seq
        trans = [table[a] for a in seqs]
        return Seq("".join(trans), dna_alphabet)

    # TODO: translate_orf(self, seq, start) ?
    # TODO: translate_to_stop(self, seq, frame) ?
    # TODO: translate_all_frames(self,seq) -> 6 translations.

    def __repr__(self) -> str:
        string: List[str] = []
        string += 'GeneticCode( %d, "' % self.ident
        string += self.description
        string += '", \n'
        string += '    amino_acid = "'
        string += self.amino_acid
        string += '",\n'
        string += '    start =      "'
        string += self.start
        string += '",\n'
        string += '    base1 =      "'
        string += self.base1
        string += '",\n'
        string += '    base2 =      "'
        string += self.base2
        string += '",\n'
        string += '    base3 =      "'
        string += self.base3
        string += '" )'
        return "".join(string)

    def __str__(self) -> str:
        """Returns a text representation of this genetic code."""
        # Inspired by http://bugzilla.open-bio.org/show_bug.cgi?id=1963
        letters = "TCAG"  # Conventional ordering for codon tables.
        string: List[str] = []

        if self.ident:
            string += "Genetic Code [%d]: " % self.ident
        else:
            string += "Genetic Code: "  # pragma: no cover
        string += self.description or ""

        string += "\n    "
        string += " ".join(["  %s      " % c2 for c2 in letters])

        string += "\n   +"
        string += "+".join(["---------" for c2 in letters]) + "+  "

        table = self.table
        assert table is not None

        for c1 in letters:
            for c3 in letters:
                string += "\n "
                string += c1
                string += " |"
                for c2 in letters:
                    codon = c1 + c2 + c3
                    string += " " + codon
                    if codon in self.stop_codons:
                        string += " Stop|"
                    else:
                        amino = table.get(codon, "?")
                        if codon in self.start_codons:
                            string += " %s(s)|" % amino
                        else:
                            string += " %s   |" % amino
                string += " " + c3

            string += "\n   +"
            string += "+".join(["---------" for c2 in letters])
            string += "+  "
        string += "\n"
        return "".join(string)


# end class GeneticCode


# Data from http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.5
# Aug. 2006
# Genetic Code Tables
#
# Authority      International Sequence Databank Collaboration
# Contact        NCBI
# Scope          /transl_table qualifier
# URL            http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
_codon_tables = (
    GeneticCode(
        1,
        "Standard",
        "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "---M---------------M---------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        2,
        "Vertebrate Mitochondrial",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
        "--------------------------------MMMM---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        3,
        "Yeast Mitochondrial",
        "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "----------------------------------MM----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        4,
        "Mold, Protozoan, Coelenterate Mitochondrial & Mycoplasma/Spiroplasma",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "--MM---------------M------------MMMM---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        5,
        "Invertebrate Mitochondrial",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
        "---M----------------------------MMMM---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        6,
        "Ciliate, Dasycladacean and Hexamita Nuclear",
        "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        9,
        "Echinoderm and Flatworm Mitochondrial",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
        "-----------------------------------M---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        10,
        "Euplotid Nuclear",
        "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        11,
        "Bacterial and Plant Plastid",
        "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "---M---------------M------------MMMM---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        12,
        "Alternative Yeast Nuclear",
        "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-------------------M---------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        13,
        "Ascidian Mitochondrial",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        14,
        "Alternative Flatworm Mitochondrial",
        "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        15,
        "Blepharisma Nuclear",
        "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        16,
        "Chlorophycean Mitochondrial",
        "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        21,
        "Trematode Mitochondrial",
        "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
        "-----------------------------------M---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        22,
        "Scenedesmus obliquus Mitochondrial",
        "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "-----------------------------------M----------------------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
    GeneticCode(
        23,
        "Thraustochytrium Mitochondrial",
        "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
        "--------------------------------M--M---------------M------------",
        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG",
        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG",
        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG",
    ),
)

reduced_protein_alphabets = {
    #
    "LiB2": Transform(
        Seq("CFYWMLIV-GPATSNHQEDRKX*-", std_protein_alphabet),
        Seq("IIIIIIII-SSSSSSSSSSSSX*-", Alphabet("ISX*-")),
        "Li et al (2003), table II, group 2",
    ),
    #
    "LiB3": Transform(
        Seq("CFYWMLIV-GPATS-NHQEDRKX*-", std_protein_alphabet),
        Seq("IIIIIIII-SSSSS-EEEEEEEX*-", Alphabet("ISEX*-")),
        "Li et al (2003), table II, group 3",
    ),
    #
    "LiB4": Transform(
        Seq("CFYW-MLIV-GPATS-NHQEDRKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-SSSSS-EEEEEEEX*-", Alphabet("YISEX*-")),
        "Li et al (2003), table II, group 4",
    ),
    #
    "LiB5": Transform(
        Seq("CFYW-MLIV-G-PATS-NHQEDRKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-G-SSSS-EEEEEEEX*-", Alphabet("YIGSEX*-")),
        "Li et al (2003), table II, group 5",
    ),
    #
    "LiB6": Transform(
        Seq("CFYW-MLIV-G-P-ATS-NHQEDRKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-G-P-SSS-EEEEEEEX*-", Alphabet("YIGPSEX*-")),
        "Li et al (2003), table II, group 6",
    ),
    #
    "LiB7": Transform(
        Seq("CFYW-MLIV-G-P-ATS-NHQED-RKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-G-P-SSS-EEEEE-KKX*-", Alphabet("YIGPSEKX*-")),
        "Li et al (2003), table II, group 7",
    ),
    #
    "LiB8": Transform(
        Seq("CFYW-MLIV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-G-P-SSS-NN-EEE-KKX*-", Alphabet("YIGPSNEKX*-")),
        "Li et al (2003), table II, group 8",
    ),
    #
    "LiB9": Transform(
        Seq("CFYW-ML-IV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet),
        Seq("YYYY-LL-II-G-P-SSS-NN-EEE-KKX*-", Alphabet("YLIGPSNEKX*-")),
        "Li et al (2003), table II, group 9",
    ),
    #
    "LiB10": Transform(
        Seq("C-FYW-ML-IV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-SSS-NN-EEE-KKX*-", Alphabet("CYLIGPSNEKX*-")),
        "Li et al (2003), table II, group 10",
    ),
    #
    "LiB11": Transform(
        Seq("C-FYW-ML-IV-G-P-A-TS-NH-QED-RKX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-A-SS-NN-EEE-KKX*-", Alphabet("CYLIGPASNEKX*-")),
        "Li et al (2003), table II, group 11",
    ),
    #
    "LiB12": Transform(
        Seq("C-FYW-ML-IV-G-P-A-TS-NH-QE-D-RKX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-A-SS-NN-EE-D-KKX*-", Alphabet("CYLIGPASNEDKX*-")),
        "Li et al (2003), table II, group 12",
    ),
    #
    "LiB13": Transform(
        Seq("C-FYW-ML-IV-G-P-A-T-S-NH-QE-D-RKX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-A-T-S-NN-EE-D-KKX*-", Alphabet("CYLIGPATSNEDKX*-")),
        "Li et al (2003), table II, group 13",
    ),
    #
    "LiB14": Transform(
        Seq("C-FYW-ML-IV-G-P-A-T-S-N-H-QE-D-RKX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-A-T-S-N-H-EE-D-KKX*-", Alphabet("CYLIGPATSNHEDKX*-")),
        "Li et al (2003), table II, group 14",
    ),
    #
    "LiB15": Transform(
        Seq("C-FYW-ML-IV-G-P-A-T-S-N-H-QE-D-R-KX*-", std_protein_alphabet),
        Seq("C-YYY-LL-II-G-P-A-T-S-N-H-EE-D-R-KX*-", Alphabet("CYLIGPATSNHEDRKX*-")),
        "Li et al (2003), table II, group 15",
    ),
    #
    "LiB16": Transform(
        Seq("C-FY-W-ML-IV-G-P-A-T-S-N-H-QE-D-R-KX*-", std_protein_alphabet),
        Seq("C-YY-W-LL-II-G-P-A-T-S-N-H-EE-D-R-KX*-", Alphabet("CYWLIGPATSNHEDRKX*-")),
        "Li et al (2003), table II, group 16",
    ),
    #
    "LiB17": Transform(
        Seq("C-FY-W-ML-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet),
        Seq(
            "C-YY-W-LL-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-", Alphabet("CYWLIGPATSNHQEDRKX*-")
        ),
        "Li et al (2003), table II, group 17",
    ),
    #
    "LiB18": Transform(
        Seq("C-FY-W-M-L-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet),
        Seq(
            "C-YY-W-M-L-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-",
            Alphabet("CYWMLIGPATSNHQEDRKX*-"),
        ),
        "Li et al (2003), table II, group 18",
    ),
    #
    "LiB19": Transform(
        Seq("C-F-Y-W-M-L-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet),
        Seq(
            "C-F-Y-W-M-L-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-",
            Alphabet("CFYWMLIGPATSNHQEDRKX*-"),
        ),
        "Li et al (2003), table II, group 19",
    ),
    #
    "LiB20": Transform(
        Seq("C-F-Y-W-M-L-I-V-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet),
        Seq(
            "C-F-Y-W-M-L-I-V-G-P-A-T-S-N-H-Q-E-D-R-KX*-",
            Alphabet("CFYWMLIVGPATSNHQEDRKX*-"),
        ),
        "Li et al (2003), table II, group 20",
    ),
    #
    "LiA2": Transform(
        Seq("CMFILVWY-AGTSNQDEHRKPX*-", std_protein_alphabet),
        Seq("IIIIIIII-SSSSSSSSSSSSX*-", Alphabet("ISX*-")),
        "Li et al (2003), table I, group 2",
    ),
    #
    "LiA3": Transform(
        Seq("CMFILVWY-AGTSP-NQDEHRKX*-", std_protein_alphabet),
        Seq("IIIIIIII-SSSSS-EEEEEEEX*-", Alphabet("ISEX*-")),
        "Li et al (2003), table I, group 3",
    ),
    #
    "LiA4": Transform(
        Seq("CMFWY-ILV-AGTS-NQDEHRKPX*-", std_protein_alphabet),
        Seq("YYYYY-III-SSSS-EEEEEEEEX*-", Alphabet("YISEX*-")),
        "Li et al (2003), table I, group 4",
    ),
    #
    "LiA5": Transform(
        Seq("FWYH-MILV-CATSP-G-NQDERKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-SSSSS-G-EEEEEEX*-", Alphabet("YISGEX*-")),
        "Li et al (2003), table I, group 5",
    ),
    #
    "LiA6": Transform(
        Seq("FWYH-MILV-CATS-P-G-NQDERKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-SSSS-P-G-EEEEEEX*-", Alphabet("YISPGEX*-")),
        "Li et al (2003), table I, group 6",
    ),
    #
    "LiA7": Transform(
        Seq("FWYH-MILV-CATS-P-G-NQDE-RKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-SSSS-P-G-EEEE-KKX*-", Alphabet("YISPGEKX*-")),
        "Li et al (2003), table I, group 7",
    ),
    #
    "LiA8": Transform(
        Seq("FWYH-MILV-CA-NTS-P-G-DE-QRKX*-", std_protein_alphabet),
        Seq("YYYY-IIII-AA-SSS-P-G-NN-KKKX*-", Alphabet("YIASPGNKX*-")),
        "Li et al (2003), table I, group 8",
    ),
    #
    "LiA9": Transform(
        Seq("FWYH-ML-IV-CA-NTS-P-G-DE-QRKX*-", std_protein_alphabet),
        Seq("YYYY-LL-VV-AA-SSS-P-G-NN-KKKX*-", Alphabet("YLVASPGNKX*-")),
        "Li et al (2003), table I, group 9",
    ),
    #
    "LiA10": Transform(
        Seq("FWY-ML-IV-CA-TS-NH-P-G-DE-QRKX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-AA-TT-NN-P-G-DD-KKKX*-", Alphabet("YLVATNPGDKX*-")),
        "Li et al (2003), table I, group 10",
    ),
    #
    "LiA11": Transform(
        Seq("FWY-ML-IV-CA-TS-NH-P-G-D-QE-RKX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-AA-TT-NN-P-G-D-EE-KKX*-", Alphabet("YLVATNPGDEKX*-")),
        "Li et al (2003), table I, group 11",
    ),
    #
    "LiA12": Transform(
        Seq("FWY-ML-IV-C-A-TS-NH-P-G-D-QE-RKX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-C-A-TT-NN-P-G-D-EE-KKX*-", Alphabet("YLVCATNPGDEKX*-")),
        "Li et al (2003), table I, group 12",
    ),
    #
    "LiA13": Transform(
        Seq("FWY-ML-IV-C-A-T-S-NH-P-G-D-QE-RKX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-C-A-T-S-NN-P-G-D-EE-KKX*-", Alphabet("YLVCATSNPGDEKX*-")),
        "Li et al (2003), table I, group 13",
    ),
    #
    "LiA14": Transform(
        Seq("FWY-ML-IV-C-A-T-S-NH-P-G-D-QE-R-KX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-C-A-T-S-NN-P-G-D-EE-R-KX*-", Alphabet("YLVCATSNPGDERKX*-")),
        "Li et al (2003), table I, group 14",
    ),
    #
    "LiA15": Transform(
        Seq("FWY-ML-IV-C-A-T-S-N-H-P-G-D-QE-R-KX*-", std_protein_alphabet),
        Seq("YYY-LL-VV-C-A-T-S-N-H-P-G-D-EE-R-KX*-", Alphabet("YLVCATSNHPGDERKX*-")),
        "Li et al (2003), table I, group 15",
    ),
    #
    "LiA16": Transform(
        Seq("W-FY-ML-IV-C-A-T-S-N-H-P-G-D-QE-R-KX*-", std_protein_alphabet),
        Seq("W-YY-LL-VV-C-A-T-S-N-H-P-G-D-EE-R-KX*-", Alphabet("WYLVCATSNHPGDERKX*-")),
        "Li et al (2003), table I, group 16",
    ),
    #
    "LiA17": Transform(
        Seq("W-FY-ML-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet),
        Seq(
            "W-YY-LL-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", Alphabet("WYLVCATSNHPGDQERKX*-")
        ),
        "Li et al (2003), table I, group 17",
    ),
    #
    "LiA18": Transform(
        Seq("W-FY-M-L-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet),
        Seq(
            "W-YY-M-L-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-",
            Alphabet("WYMLVCATSNHPGDQERKX*-"),
        ),
        "Li et al (2003), table I, group 18",
    ),
    #
    "LiA19": Transform(
        Seq("W-F-Y-M-L-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet),
        Seq(
            "W-F-Y-M-L-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-",
            Alphabet("WFYMLVCATSNHPGDQERKX*-"),
        ),
        "Li et al (2003), table I, group 19",
    ),
    #
    "LiA20": Transform(
        Seq("W-F-Y-M-L-I-V-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet),
        Seq(
            "W-F-Y-M-L-I-V-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-",
            Alphabet("WFYMLIVCATSNHPGDQERKX*-"),
        ),
        "Li et al (2003), table I, group 20",
    ),
}