"""
Adapter finding and trimming classes

The ...Adapter classes are responsible for finding adapters.
The ...Match classes trim the reads.
"""
import logging
from enum import Enum
from collections import defaultdict
from typing import Optional, Tuple, Sequence, Dict, Any, List
from abc import ABC, abstractmethod

import ultraplex.align

logger = logging.getLogger()


class Where(Enum):
    # Constants for the Aligner.locate() function.
    # The function is called with SEQ1 as the adapter, SEQ2 as the read.
    # TODO get rid of those constants, use strings instead
    BACK = align.START_WITHIN_SEQ2 | align.STOP_WITHIN_SEQ2 | align.STOP_WITHIN_SEQ1
    FRONT = align.START_WITHIN_SEQ2 | align.STOP_WITHIN_SEQ2 | align.START_WITHIN_SEQ1
    PREFIX = align.STOP_WITHIN_SEQ2
    SUFFIX = align.START_WITHIN_SEQ2
    # Just like FRONT/BACK, but without internal matches
    FRONT_NOT_INTERNAL = align.START_WITHIN_SEQ1 | align.STOP_WITHIN_SEQ2
    BACK_NOT_INTERNAL = align.START_WITHIN_SEQ2 | align.STOP_WITHIN_SEQ1
    ANYWHERE = align.SEMIGLOBAL
    LINKED = 'linked'


def returns_defaultdict_int():
    # We need this function to make EndStatistics picklable.
    # Even a @staticmethod of EndStatistics is not sufficient
    # as that is not picklable before Python 3.5.
    return defaultdict(int)


class EndStatistics:
    """Statistics about the 5' or 3' end"""

    def __init__(self, adapter: "SingleAdapter"):
        self.max_error_rate = adapter.max_error_rate  # type: float
        self.sequence = adapter.sequence  # type: str
        self.effective_length = adapter.effective_length  # type: int
        self.has_wildcards = adapter.adapter_wildcards  # type: bool
        # self.errors[l][e] == n iff n times a sequence of length l matching at e errors was removed
        self.errors = defaultdict(returns_defaultdict_int)  # type: Dict[int, Dict[int, int]]
        self.adjacent_bases = {'A': 0, 'C': 0, 'G': 0, 'T': 0, '': 0}
        # TODO avoid hard-coding the list of classes
        self._remove_prefix = isinstance(adapter, (FrontAdapter, NonInternalFrontAdapter, PrefixAdapter))

    def __repr__(self):
        errors = {k: dict(v) for k, v in self.errors.items()}
        return "EndStatistics(max_error_rate={}, errors={}, adjacent_bases={})".format(
            self.max_error_rate,
            errors,
            self.adjacent_bases,
        )

    def __iadd__(self, other: Any):
        if not isinstance(other, self.__class__):
            raise ValueError("Cannot compare")
        if (
            self.max_error_rate != other.max_error_rate
            or self.sequence != other.sequence
            or self.effective_length != other.effective_length
        ):
            raise RuntimeError('Incompatible EndStatistics, cannot be added')
        for base in ('A', 'C', 'G', 'T', ''):
            self.adjacent_bases[base] += other.adjacent_bases[base]
        for length, error_dict in other.errors.items():
            for errors in error_dict:
                self.errors[length][errors] += other.errors[length][errors]
        return self

    @property
    def lengths(self):
        d = {length: sum(errors.values()) for length, errors in self.errors.items()}
        return d

    def random_match_probabilities(self, gc_content: float) -> List[float]:
        """
        Estimate probabilities that this adapter end matches a
        random sequence. Indels are not taken into account.

        Returns a list p, where p[i] is the probability that
        i bases of this adapter match a random sequence with
        GC content gc_content.
        """
        seq = self.sequence
        # FIXME this is broken for 'anywhere' adapters
        if self._remove_prefix:
            seq = seq[::-1]
        allowed_bases = 'CGRYSKMBDHVN' if self.has_wildcards else 'GC'
        p = 1.
        probabilities = [p]
        for i, c in enumerate(seq):
            if c in allowed_bases:
                p *= gc_content / 2.
            else:
                p *= (1. - gc_content) / 2.
            probabilities.append(p)
        return probabilities


class AdapterStatistics:
    """
    Statistics about an adapter. An adapter can work on the 5' end (front)
    or 3' end (back) of a read, and statistics for that are captured
    separately in EndStatistics objects.
    """

    def __init__(
        self,
        adapter: "Adapter",
        front: "SingleAdapter",
        back: Optional["SingleAdapter"] = None,
    ):
        self.name = adapter.name
        self.adapter = adapter
        self.front = EndStatistics(front)
        if back is None:
            self.back = EndStatistics(front)
        else:
            self.back = EndStatistics(back)
        self.reverse_complemented = 0

    def __repr__(self):
        return "AdapterStatistics(name={}, front={}, back={})".format(
            self.name,
            self.front,
            self.back,
        )

    def __iadd__(self, other: "AdapterStatistics"):
        self.front += other.front
        self.back += other.back
        self.reverse_complemented += other.reverse_complemented
        return self


class Match(ABC):

    @abstractmethod
    def remainder_interval(self) -> Tuple[int, int]:
        pass

    @abstractmethod
    def get_info_records(self, read) -> List[List]:
        pass

    @abstractmethod
    def trimmed(self, read):
        pass


class SingleMatch(Match, ABC):
    """
    Representation of a single adapter matched to a single string
    """
    __slots__ = ['astart', 'astop', 'rstart', 'rstop', 'matches', 'errors',
        'adapter', 'sequence', 'length', 'adjacent_base']

    def __init__(
        self,
        astart: int,
        astop: int,
        rstart: int,
        rstop: int,
        matches: int,
        errors: int,
        adapter: "SingleAdapter",
        sequence: str,
    ):
        self.adjacent_base = ""
        self.astart = astart  # type: int
        self.astop = astop  # type: int
        self.rstart = rstart  # type: int
        self.rstop = rstop  # type: int
        self.matches = matches  # type: int
        self.errors = errors  # type: int
        self.adapter = adapter  # type: SingleAdapter
        self.sequence = sequence
        # Number of aligned characters in the adapter. If there are
        # indels, this may be different from the number of characters
        # in the read.
        self.length = astop - astart  # type: int

    def __repr__(self):
        return 'SingleMatch(astart={}, astop={}, rstart={}, rstop={}, matches={}, errors={})'.format(
            self.astart, self.astop, self.rstart, self.rstop, self.matches, self.errors)

    def wildcards(self, wildcard_char: str = "N") -> str:
        """
        Return a string that contains, for each wildcard character,
        the character that it matches. For example, if the adapter
        ATNGNA matches ATCGTA, then the string 'CT' is returned.

        If there are indels, this is not reliable as the full alignment
        is not available.
        """
        wildcards = [self.sequence[self.rstart + i] for i in range(self.length)
            if self.adapter.sequence[self.astart + i] == wildcard_char and
                self.rstart + i < len(self.sequence)]
        return ''.join(wildcards)

    def get_info_records(self, read) -> List[List]:
        seq = read.sequence
        qualities = read.qualities
        info = [
            "",
            self.errors,
            self.rstart,
            self.rstop,
            seq[0:self.rstart],
            seq[self.rstart:self.rstop],
            seq[self.rstop:],
            self.adapter.name,
        ]
        if qualities:
            info += [
                qualities[0:self.rstart],
                qualities[self.rstart:self.rstop],
                qualities[self.rstop:],
            ]
        else:
            info += ["", "", ""]

        return [info]


class RemoveBeforeMatch(SingleMatch):
    """A match that removes sequence before the match"""

    def __repr__(self):
        return 'RemoveBeforeMatch(astart={}, astop={}, rstart={}, rstop={}, matches={}, errors={})'.format(
            self.astart, self.astop, self.rstart, self.rstop, self.matches, self.errors)

    def rest(self) -> str:
        """
        Return the part of the read before this match if this is a
        'front' (5') adapter,
        return the part after the match if this is not a 'front' adapter (3').
        This can be an empty string.
        """
        return self.sequence[:self.rstart]

    def remainder_interval(self) -> Tuple[int, int]:
        """
        Return an interval (start, stop) that describes the part of the read that would
        remain after trimming
        """
        return self.rstop, len(self.sequence)

    def trim_slice(self):
        # Same as remainder_interval, but as a slice() object
        return slice(self.rstop, None)

    def trimmed(self, read):
        return read[self.rstop:]

    def update_statistics(self, statistics: AdapterStatistics):
        """Update AdapterStatistics in place"""
        statistics.front.errors[self.rstop][self.errors] += 1


class RemoveAfterMatch(SingleMatch):
    """A match that removes sequence after the match"""

    def __repr__(self):
        return "RemoveAfterMatch(astart={}, astop={}, rstart={}, rstop={}, matches={}, errors={})".format(
            self.astart, self.astop, self.rstart, self.rstop, self.matches, self.errors)

    def rest(self) -> str:
        """
        Return the part of the read before this match if this is a
        'front' (5') adapter,
        return the part after the match if this is not a 'front' adapter (3').
        This can be an empty string.
        """
        return self.sequence[self.rstop:]

    def remainder_interval(self) -> Tuple[int, int]:
        """
        Return an interval (start, stop) that describes the part of the read that would
        remain after trimming
        """
        return 0, self.rstart

    def trim_slice(self):
        # Same as remainder_interval, but as a slice() object
        return slice(None, self.rstart)

    def trimmed(self, read):
        return read[:self.rstart]

    def update_statistics(self, statistics: AdapterStatistics):
        """Update AdapterStatistics in place"""
        adjacent_base = self.sequence[self.rstart - 1:self.rstart]
        statistics.back.errors[len(self.sequence) - self.rstart][self.errors] += 1
        try:
            statistics.back.adjacent_bases[adjacent_base] += 1
        except KeyError:
            statistics.back.adjacent_bases[''] = 1


def _generate_adapter_name(_start=[1]) -> str:
    name = str(_start[0])
    _start[0] += 1
    return name


class Adapter(ABC):

    description = "adapter with one component"  # this is overriden in subclasses

    def __init__(self, name: Optional[str], *args, **kwargs):
        self.name = name

    @abstractmethod
    def enable_debug(self):
        pass

    @abstractmethod
    def match_to(self, sequence: str):
        pass


class SingleAdapter(Adapter, ABC):
    """
    This class can find a single adapter characterized by sequence, error rate,
    type etc. within reads.

    where --  A Where enum value. This influences where the adapter is allowed to appear within the
        read.

    sequence -- The adapter sequence as string. Will be converted to uppercase.
        Also, Us will be converted to Ts.

    max_error_rate -- Maximum allowed error rate. The error rate is
        the number of errors in the alignment divided by the length
        of the part of the alignment that matches the adapter.

    minimum_overlap -- Minimum length of the part of the alignment
        that matches the adapter.

    read_wildcards -- Whether IUPAC wildcards in the read are allowed.

    adapter_wildcards -- Whether IUPAC wildcards in the adapter are
        allowed.

    name -- optional name of the adapter. If not provided, the name is set to a
        unique number.
    """

    def __init__(
        self,
        sequence: str,
        max_error_rate: float = 0.1,
        min_overlap: int = 3,
        read_wildcards: bool = False,
        adapter_wildcards: bool = True,
        name: Optional[str] = None,
        indels: bool = True,
    ):
        super().__init__(name)
        self._debug = False  # type: bool
        self.name = _generate_adapter_name() if name is None else name  # type: str
        self.sequence = sequence.upper().replace("U", "T")  # type: str
        if not self.sequence:
            raise ValueError("Adapter sequence is empty")
        self.max_error_rate = max_error_rate  # type: float
        self.min_overlap = min(min_overlap, len(self.sequence))  # type: int
        iupac = frozenset('XACGTURYSWKMBDHVN')
        if adapter_wildcards and not set(self.sequence) <= iupac:
            for c in self.sequence:
                if c not in iupac:
                    raise ValueError('Character {!r} in adapter sequence {!r} is '
                        'not a valid IUPAC code. Use only characters '
                        'XACGTURYSWKMBDHVN.'.format(c, self.sequence))
        # Optimization: Use non-wildcard matching if only ACGT is used
        self.adapter_wildcards = adapter_wildcards and not set(self.sequence) <= set("ACGT")  # type: bool
        self.read_wildcards = read_wildcards  # type: bool
        self.indels = indels  # type: bool
        self.aligner = self._aligner()

    def _make_aligner(self, flags):
        # TODO
        # Indels are suppressed by setting their cost very high, but a different algorithm
        # should be used instead.
        indel_cost = 1 if self.indels else 100000
        return align.Aligner(
            self.sequence,
            self.max_error_rate,
            flags=flags,
            wildcard_ref=self.adapter_wildcards,
            wildcard_query=self.read_wildcards,
            indel_cost=indel_cost,
            min_overlap=self.min_overlap,
        )

    def __repr__(self):
        return '<{cls}(name={name!r}, sequence={sequence!r}, '\
            'max_error_rate={max_error_rate}, min_overlap={min_overlap}, '\
            'read_wildcards={read_wildcards}, '\
            'adapter_wildcards={adapter_wildcards}, '\
            'indels={indels})>'.format(cls=self.__class__.__name__, **vars(self))

    @property
    def is_anchored(self):
        """Return whether this adapter is anchored"""
        return self.where in {Where.PREFIX, Where.SUFFIX}

    @property
    def effective_length(self):
        return self.aligner.effective_length

    def enable_debug(self):
        """
        Print out the dynamic programming matrix after matching a read to an
        adapter.
        """
        self._debug = True
        self.aligner.enable_debug()

    @abstractmethod
    def _aligner(self):
        pass

    @abstractmethod
    def match_to(self, sequence: str):
        """
        Attempt to match this adapter to the given string.

        Return a Match instance if a match was found;
        return None if no match was found given the matching criteria (minimum
        overlap length, maximum error rate).
        """

    def __len__(self):
        return len(self.sequence)

    def create_statistics(self):
        return AdapterStatistics(self, self)


class FrontAdapter(SingleAdapter):
    """A 5' adapter"""

    description = "regular 5'"

    def __init__(self, *args, **kwargs):
        self._force_anywhere = kwargs.pop("force_anywhere", False)
        super().__init__(*args, **kwargs)

    def _aligner(self):
        return self._make_aligner(Where.ANYWHERE.value if self._force_anywhere else Where.FRONT.value)

    def match_to(self, sequence: str):
        """
        Attempt to match this adapter to the given read.

        Return a Match instance if a match was found;
        return None if no match was found given the matching criteria (minimum
        overlap length, maximum error rate).
        """
        alignment = self.aligner.locate(sequence.upper())  # type: Optional[Tuple[int,int,int,int,int,int]]
        if self._debug:
            print(self.aligner.dpmatrix)  # pragma: no cover
        if alignment is None:
            return None
        return RemoveBeforeMatch(*alignment, adapter=self, sequence=sequence)


class BackAdapter(SingleAdapter):
    """A 3' adapter"""

    description = "regular 3'"

    def __init__(self, *args, **kwargs):
        self._force_anywhere = kwargs.pop("force_anywhere", False)
        super().__init__(*args, **kwargs)

    def _aligner(self):
        return self._make_aligner(Where.ANYWHERE.value if self._force_anywhere else Where.BACK.value)

    def match_to(self, sequence: str):
        """
        Attempt to match this adapter to the given read.

        Return a Match instance if a match was found;
        return None if no match was found given the matching criteria (minimum
        overlap length, maximum error rate).
        """
        alignment = self.aligner.locate(sequence.upper())  # type: Optional[Tuple[int,int,int,int,int,int]]
        if self._debug:
            print(self.aligner.dpmatrix)  # pragma: no cover
        if alignment is None:
            return None
        return RemoveAfterMatch(*alignment, adapter=self, sequence=sequence)


class AnywhereAdapter(SingleAdapter):
    """
    An adapter that can be 5' or 3'. If a match involves the first base of
    the read, it is assumed to be a 5' adapter and a 3' otherwise.
    """

    description = "variable 5'/3'"

    def _aligner(self):
        return self._make_aligner(Where.ANYWHERE.value)

    def match_to(self, sequence: str):
        """
        Attempt to match this adapter to the given string.

        Return a Match instance if a match was found;
        return None if no match was found given the matching criteria (minimum
        overlap length, maximum error rate).
        """
        alignment = self.aligner.locate(sequence)
        if self._debug:
            print(self.aligner.dpmatrix)  # pragma: no cover
        if alignment is None:
            return None
        # guess: if alignment starts at pos 0, it’s a 5' adapter
        if alignment[2] == 0:  # index 2 is rstart
            match = RemoveBeforeMatch(*alignment, adapter=self, sequence=sequence)  # type: ignore
        else:
            match = RemoveAfterMatch(*alignment, adapter=self, sequence=sequence)  # type: ignore
        return match


class NonInternalFrontAdapter(FrontAdapter):
    """A non-internal 5' adapter"""

    description = "non-internal 5'"

    def _aligner(self):
        return self._make_aligner(Where.FRONT_NOT_INTERNAL.value)

    def match_to(self, sequence: str):
        if not self.adapter_wildcards and sequence.startswith(self.sequence):
            n = len(self.sequence)
            return RemoveBeforeMatch(
                0, n, 0, n, n, 0, adapter=self, sequence=sequence
            )  # type: ignore
        alignment = self.aligner.locate(sequence)
        if self._debug:
            try:
                print(self.aligner.dpmatrix)  # pragma: no cover
            except AttributeError:
                pass
        if alignment is None:
            return None
        return RemoveBeforeMatch(*alignment, adapter=self, sequence=sequence)  # type: ignore


class NonInternalBackAdapter(BackAdapter):
    """A non-internal 3' adapter"""

    description = "non-internal 3'"

    def _aligner(self):
        return self._make_aligner(Where.BACK_NOT_INTERNAL.value)

    def match_to(self, sequence: str):
        if not self.adapter_wildcards and sequence.endswith(self.sequence):
            # Exact match found
            # astart, astop, rstart, rstop, matches, errors
            n = len(self.sequence)
            return RemoveAfterMatch(
                0, n, len(sequence) - n, len(sequence), n, 0, adapter=self, sequence=sequence
            )  # type: ignore
        alignment = self.aligner.locate(sequence)
        if self._debug:
            try:
                print(self.aligner.dpmatrix)  # pragma: no cover
            except AttributeError:
                pass
        if alignment is None:
            return None
        return RemoveAfterMatch(*alignment, adapter=self, sequence=sequence)  # type: ignore


class PrefixAdapter(NonInternalFrontAdapter):
    """An anchored 5' adapter"""

    description = "anchored 5'"

    def _aligner(self):
        if not self.indels:  # TODO or if error rate allows 0 errors anyway
            return align.PrefixComparer(
                self.sequence,
                self.max_error_rate,
                wildcard_ref=self.adapter_wildcards,
                wildcard_query=self.read_wildcards,
                min_overlap=self.min_overlap
            )
        else:
            return self._make_aligner(Where.PREFIX.value)


class SuffixAdapter(NonInternalBackAdapter):
    """An anchored 3' adapter"""

    description = "anchored 3'"

    def _aligner(self):
        if not self.indels:  # TODO or if error rate allows 0 errors anyway
            return align.SuffixComparer(
                self.sequence,
                self.max_error_rate,
                wildcard_ref=self.adapter_wildcards,
                wildcard_query=self.read_wildcards,
                min_overlap=self.min_overlap
            )
        else:
            return self._make_aligner(Where.SUFFIX.value)


class LinkedMatch(Match):
    """
    Represent a match of a LinkedAdapter
    """
    def __init__(self, front_match: RemoveBeforeMatch, back_match: RemoveAfterMatch, adapter: "LinkedAdapter"):
        assert front_match is not None or back_match is not None
        self.front_match = front_match  # type: RemoveBeforeMatch
        self.back_match = back_match  # type: RemoveAfterMatch
        self.adapter = adapter  # type: LinkedAdapter

    def __repr__(self):
        return '<LinkedMatch(front_match={!r}, back_match={}, adapter={})>'.format(
            self.front_match, self.back_match, self.adapter)

    @property
    def matches(self):
        """Number of matching bases"""
        m = 0
        if self.front_match is not None:
            m += self.front_match.matches
        if self.back_match is not None:
            m += self.back_match.matches
        return m

    @property
    def errors(self):
        e = 0
        if self.front_match is not None:
            e += self.front_match.errors
        if self.back_match is not None:
            e += self.back_match.errors
        return e

    def trimmed(self, read):
        if self.front_match:
            read = self.front_match.trimmed(read)
        if self.back_match:
            read = self.back_match.trimmed(read)
        return read

    @property
    def adjacent_base(self):
        return self.back_match.adjacent_base

    def update_statistics(self, statistics):
        """Update AdapterStatistics in place"""
        if self.front_match:
            statistics.front.errors[self.front_match.rstop][self.front_match.errors] += 1
        if self.back_match:
            length = len(self.back_match.sequence) - self.back_match.rstart
            statistics.back.errors[length][self.back_match.errors] += 1

    def remainder_interval(self) -> Tuple[int, int]:
        matches = [match for match in [self.front_match, self.back_match] if match is not None]
        return remainder(matches)

    def get_info_records(self, read) -> List[List]:
        records = []
        for match, namesuffix in [
            (self.front_match, ";1"),
            (self.back_match, ";2"),
        ]:
            if match is None:
                continue
            record = match.get_info_records(read)[0]
            record[7] = ("none" if self.adapter.name is None else self.adapter.name) + namesuffix
            records.append(record)
            read = match.trimmed(read)
        return records


class LinkedAdapter(Adapter):
    """A 5' adapter combined with a 3' adapter"""

    description = "linked"

    def __init__(
        self,
        front_adapter,
        back_adapter,
        front_required,
        back_required,
        name,
    ):
        super().__init__(name)
        self.front_required = front_required
        self.back_required = back_required

        # The following attributes are needed for the report
        self.where = Where.LINKED
        self.name = _generate_adapter_name() if name is None else name
        self.front_adapter = front_adapter
        self.front_adapter.name = self.name
        self.back_adapter = back_adapter

    def enable_debug(self):
        self.front_adapter.enable_debug()
        self.back_adapter.enable_debug()

    def match_to(self, sequence: str) -> Optional[LinkedMatch]:
        """
        Match the two linked adapters against a string
        """
        front_match = self.front_adapter.match_to(sequence)
        if self.front_required and front_match is None:
            return None
        if front_match is not None:
            sequence = sequence[front_match.trim_slice()]
        back_match = self.back_adapter.match_to(sequence)
        if back_match is None and (self.back_required or front_match is None):
            return None
        return LinkedMatch(front_match, back_match, self)

    def create_statistics(self):
        return AdapterStatistics(self, self.front_adapter, self.back_adapter)

    @property
    def sequence(self):
        return self.front_adapter.sequence + "..." + self.back_adapter.sequence

    @property
    def remove(self):
        return None


class MultiAdapter(Adapter, ABC):
    """
    Represent multiple adapters of the same type at once and use an index data structure
    to speed up matching. This acts like a "normal" Adapter as it provides a match_to
    method, but is faster with lots of adapters.

    There are quite a few restrictions:
    - no indels are allowed
    - the error rate allows at most 2 mismatches
    - wildcards in the adapter are not allowed
    - wildcards in the read are not allowed

    Use the is_acceptable() method to check individual adapters.
    """
    MultiAdapterIndex = Dict[str, Tuple[SingleAdapter, int, int]]

    def __init__(self, adapters):
        """All given adapters must be of the same type"""
        super().__init__(name="multi_adapter")
        if not adapters:
            raise ValueError("Adapter list is empty")
        for adapter in adapters:
            self._accept(adapter)
        self._adapters = adapters
        self._lengths, self._index = self._make_index()
        self._make_affix = self._get_make_affix()

    def __repr__(self):
        return "MultiAdapter(adapters={!r})".format(self._adapters)

    @abstractmethod
    def _get_make_affix(self):
        pass

    @abstractmethod
    def _make_match(self, adapter, length, matches, errors, sequence) -> SingleMatch:
        pass

    @classmethod
    def _accept(cls, adapter):
        """Raise a ValueError if the adapter is not acceptable"""
        if adapter.read_wildcards:
            raise ValueError("Wildcards in the read not supported")
        if adapter.adapter_wildcards:
            raise ValueError("Wildcards in the adapter not supported")
        k = int(len(adapter) * adapter.max_error_rate)
        if k > 0 and adapter.indels:
            raise ValueError("Indels not allowed")
        if k > 2:
            raise ValueError("Error rate too high")

    @classmethod
    def is_acceptable(cls, adapter):
        """
        Return whether this adapter is acceptable for being used by MultiAdapter

        Adapters are not acceptable if they allow wildcards, allow too many errors,
        or would lead to a very large index.
        """
        try:
            cls._accept(adapter)
        except ValueError:
            return False
        return True

    def _make_index(self) -> Tuple[List[int], "MultiAdapterIndex"]:
        logger.info('Building index of %s adapters ...', len(self._adapters))
        index = dict()  # type: MultiAdapter.MultiAdapterIndex
        lengths = set()
        has_warned = False
        for adapter in self._adapters:
            sequence = adapter.sequence
            k = int(adapter.max_error_rate * len(sequence))
            for s, errors, matches in align.hamming_environment(sequence, k):
                if s in index:
                    other_adapter, other_errors, other_matches = index[s]
                    if matches < other_matches:
                        continue
                    if other_matches == matches and not has_warned:
                        logger.warning(
                            "Adapters %s %r and %s %r are very similar. At %s allowed errors, "
                            "the sequence %r cannot be assigned uniquely because the number of "
                            "matches is %s compared to both adapters.",
                            other_adapter.name, other_adapter.sequence, adapter.name,
                            adapter.sequence, k, s, matches
                        )
                        has_warned = True
                else:
                    index[s] = (adapter, errors, matches)
                lengths.add(len(s))
        logger.info('Built an index containing %s strings.', len(index))

        return sorted(lengths, reverse=True), index

    def match_to(self, sequence: str):
        """
        Match the adapters against a string and return a Match that represents
        the best match or None if no match was found
        """
        # Check all the prefixes or suffixes (affixes) that could match
        best_adapter = None  # type: Optional[SingleAdapter]
        best_length = 0
        best_m = -1
        best_e = 1000
        for length in self._lengths:
            if length < best_m:
                # No chance of getting the same or a higher number of matches, so we can stop early
                break

            affix = self._make_affix(sequence, length)
            try:
                adapter, e, m = self._index[affix]
            except KeyError:
                continue
            if m > best_m or (m == best_m and e < best_e):
                best_adapter = adapter
                best_e = e
                best_m = m
                best_length = length

        if best_m == -1:
            return None
        else:
            assert best_adapter is not None
            return self._make_match(best_adapter, best_length, best_m, best_e, sequence)

    def enable_debug(self):
        pass


class MultiPrefixAdapter(MultiAdapter):

    @classmethod
    def _accept(cls, adapter):
        if not isinstance(adapter, PrefixAdapter):
            raise ValueError("Only 5' anchored adapters are allowed")
        return super()._accept(adapter)

    def _make_match(self, adapter, length, matches, errors, sequence):
        return RemoveBeforeMatch(
            astart=0,
            astop=len(adapter.sequence),
            rstart=0,
            rstop=length,
            matches=matches,
            errors=errors,
            adapter=adapter,
            sequence=sequence,
        )

    def _get_make_affix(self):
        return self._make_prefix

    @staticmethod
    def _make_prefix(s, n):
        return s[:n]


class MultiSuffixAdapter(MultiAdapter):

    @classmethod
    def _accept(cls, adapter):
        if not isinstance(adapter, SuffixAdapter):
            raise ValueError("Only anchored 3' adapters are allowed")
        return super()._accept(adapter)

    def _make_match(self, adapter, length, matches, errors, sequence):
        return RemoveAfterMatch(
            astart=0,
            astop=len(adapter.sequence),
            rstart=len(sequence) - length,
            rstop=len(sequence),
            matches=matches,
            errors=errors,
            adapter=adapter,
            sequence=sequence,
        )

    def _get_make_affix(self):
        return self._make_suffix

    @staticmethod
    def _make_suffix(s, n):
        return s[-n:]


def warn_duplicate_adapters(adapters):
    d = dict()
    for adapter in adapters:
        key = (adapter.__class__, adapter.sequence)
        if key in d:
            logger.warning("Adapter %r (%s) was specified multiple times! "
                "Please make sure that this is what you want.",
                adapter.sequence, adapter.description)
        d[key] = adapter.name


def remainder(matches: Sequence[Match]) -> Tuple[int, int]:
    """
    Determine which section of the read would not be trimmed. Return a tuple (start, stop)
    that gives the interval of the untrimmed part relative to the original read.

    matches must be non-empty
    """
    if not matches:
        raise ValueError("matches must not be empty")
    start = 0
    for match in matches:
        match_start, match_stop = match.remainder_interval()
        start += match_start
    length = match_stop - match_start
    return (start, start + length)
