# Copyright (c) 2016. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from __future__ import (
    print_function,
    division,
    absolute_import,
)
import collections
from copy import copy

COMMON_AMINO_ACIDS = collections.OrderedDict(sorted({
    "A": "Alanine",
    "R": "Arginine",
    "N": "Asparagine",
    "D": "Aspartic Acid",
    "C": "Cysteine",
    "E": "Glutamic Acid",
    "Q": "Glutamine",
    "G": "Glycine",
    "H": "Histidine",
    "I": "Isoleucine",
    "L": "Leucine",
    "K": "Lysine",
    "M": "Methionine",
    "F": "Phenylalanine",
    "P": "Proline",
    "S": "Serine",
    "T": "Threonine",
    "W": "Tryptophan",
    "Y": "Tyrosine",
    "V": "Valine",
}.items()))
COMMON_AMINO_ACIDS_WITH_UNKNOWN = copy(COMMON_AMINO_ACIDS)
COMMON_AMINO_ACIDS_WITH_UNKNOWN["X"] = "Unknown"

AMINO_ACID_INDEX = dict(
    (letter, i) for (i, letter) in enumerate(COMMON_AMINO_ACIDS_WITH_UNKNOWN))
