# Copyright 2002 by Jeffrey Chang.
# Copyright 2016, 2019, 2020 by Markus Piotrowski.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Pairwise sequence alignment using a dynamic programming algorithm.

This provides functions to get global and local alignments between two
sequences. A global alignment finds the best concordance between all
characters in two sequences. A local alignment finds just the
subsequences that align the best. Local alignments must have a positive
score to be reported and they will not be extended for 'zero counting'
matches. This means a local alignment will always start and end with
a positive counting match.

When doing alignments, you can specify the match score and gap
penalties.  The match score indicates the compatibility between an
alignment of two characters in the sequences. Highly compatible
characters should be given positive scores, and incompatible ones
should be given negative scores or 0.  The gap penalties should be
negative.

The names of the alignment functions in this module follow the
convention
<alignment type>XX
where <alignment type> is either "global" or "local" and XX is a 2
character code indicating the parameters it takes.  The first
character indicates the parameters for matches (and mismatches), and
the second indicates the parameters for gap penalties.

The match parameters are::

    CODE  DESCRIPTION & OPTIONAL KEYWORDS
    x     No parameters. Identical characters have score of 1, otherwise 0.
    m     A match score is the score of identical chars, otherwise mismatch
          score. Keywords ``match``, ``mismatch``.
    d     A dictionary returns the score of any pair of characters.
          Keyword ``match_dict``.
    c     A callback function returns scores. Keyword ``match_fn``.

The gap penalty parameters are::

    CODE  DESCRIPTION & OPTIONAL KEYWORDS
    x     No gap penalties.
    s     Same open and extend gap penalties for both sequences.
          Keywords ``open``, ``extend``.
    d     The sequences have different open and extend gap penalties.
          Keywords ``openA``, ``extendA``, ``openB``, ``extendB``.
    c     A callback function returns the gap penalties.
          Keywords ``gap_A_fn``, ``gap_B_fn``.

All the different alignment functions are contained in an object
``align``. For example:

    >>> from Bio import pairwise2
    >>> alignments = pairwise2.align.globalxx("ACCGT", "ACG")

For better readability, the required arguments can be used with optional keywords:

    >>> alignments = pairwise2.align.globalxx(sequenceA="ACCGT", sequenceB="ACG")

The result is a list of the alignments between the two strings. Each alignment
is a named tuple consisting of the two aligned sequences, the score and the
start and end positions of the alignment:

   >>> print(alignments)
   [Alignment(seqA='ACCGT', seqB='A-CG-', score=3.0, start=0, end=5), ...

You can access each element of an alignment by index or name:

   >>> alignments[0][2]
   3.0
   >>> alignments[0].score
   3.0

For a nice printout of an alignment, use the ``format_alignment`` method of
the module:

    >>> from Bio.pairwise2 import format_alignment
    >>> print(format_alignment(*alignments[0]))
    ACCGT
    | || 
    A-CG-
      Score=3
    <BLANKLINE>

All alignment functions have the following arguments:

- Two sequences: strings, Biopython sequence objects or lists.
  Lists are useful for supplying sequences which contain residues that are
  encoded by more than one letter.

- ``penalize_extend_when_opening``: boolean (default: False).
  Whether to count an extension penalty when opening a gap. If false, a gap of
  1 is only penalized an "open" penalty, otherwise it is penalized
  "open+extend".

- ``penalize_end_gaps``: boolean.
  Whether to count the gaps at the ends of an alignment. By default, they are
  counted for global alignments but not for local ones. Setting
  ``penalize_end_gaps`` to (boolean, boolean) allows you to specify for the
  two sequences separately whether gaps at the end of the alignment should be
  counted.

- ``gap_char``: string (default: ``'-'``).
  Which character to use as a gap character in the alignment returned. If your
  input sequences are lists, you must change this to ``['-']``.

- ``force_generic``: boolean (default: False).
  Always use the generic, non-cached, dynamic programming function (slow!).
  For debugging.

- ``score_only``: boolean (default: False).
  Only get the best score, don't recover any alignments. The return value of
  the function is the score. Faster and uses less memory.

- ``one_alignment_only``: boolean (default: False).
  Only recover one alignment.

The other parameters of the alignment function depend on the function called.
Some examples:

- Find the best global alignment between the two sequences. Identical
  characters are given 1 point. No points are deducted for mismatches or gaps.

    >>> for a in pairwise2.align.globalxx("ACCGT", "ACG"):
    ...     print(format_alignment(*a))
    ACCGT
    | || 
    A-CG-
      Score=3
    <BLANKLINE>
    ACCGT
    || | 
    AC-G-
      Score=3
    <BLANKLINE>

- Same thing as before, but with a local alignment. Note that
  ``format_alignment`` will only show the aligned parts of the sequences,
  together with the starting positions.

    >>> for a in pairwise2.align.localxx("ACCGT", "ACG"):
    ...     print(format_alignment(*a))
    1 ACCG
      | ||
    1 A-CG
      Score=3
    <BLANKLINE>
    1 ACCG
      || |
    1 AC-G
      Score=3
    <BLANKLINE>

  To restore the 'historic' behaviour of ``format_alignment``, i.e., showing
  also the un-aligned parts of both sequences, use the new keyword parameter
  ``full_sequences``:

    >>> for a in pairwise2.align.localxx("ACCGT", "ACG"):
    ...     print(format_alignment(*a, full_sequences=True))
    ACCGT
    | || 
    A-CG-
      Score=3
    <BLANKLINE>
    ACCGT
    || | 
    AC-G-
      Score=3
    <BLANKLINE>


- Do a global alignment. Identical characters are given 2 points, 1 point is
  deducted for each non-identical character. Don't penalize gaps.

    >>> for a in pairwise2.align.globalmx("ACCGT", "ACG", 2, -1):
    ...     print(format_alignment(*a))
    ACCGT
    | || 
    A-CG-
      Score=6
    <BLANKLINE>
    ACCGT
    || | 
    AC-G-
      Score=6
    <BLANKLINE>

- Same as above, except now 0.5 points are deducted when opening a gap, and
  0.1 points are deducted when extending it.

    >>> for a in pairwise2.align.globalms("ACCGT", "ACG", 2, -1, -.5, -.1):
    ...     print(format_alignment(*a))
    ACCGT
    | || 
    A-CG-
      Score=5
    <BLANKLINE>
    ACCGT
    || | 
    AC-G-
      Score=5
    <BLANKLINE>

- Note that you can use keywords to increase the readability, e.g.:

    >>> a = pairwise2.align.globalms("ACGT", "ACG", match=2, mismatch=-1, open=-.5,
    ...                              extend=-.1)

- Depending on the penalties, a gap in one sequence may be followed by a gap in
  the other sequence.If you don't like this behaviour, increase the gap-open
  penalty:

    >>> for a in pairwise2.align.globalms("A", "T", 5, -4, -1, -.1):
    ...     print(format_alignment(*a))
    A-
    <BLANKLINE>
    -T
      Score=-2
    <BLANKLINE>
    >>> for a in pairwise2.align.globalms("A", "T", 5, -4, -3, -.1):
    ...	    print(format_alignment(*a))
    A
    .
    T
      Score=-4
    <BLANKLINE>

- The alignment function can also use known matrices already included in
  Biopython (in ``Bio.Align.substitution_matrices``):

    >>> from Bio.Align import substitution_matrices
    >>> matrix = substitution_matrices.load("BLOSUM62")
    >>> for a in pairwise2.align.globaldx("KEVLA", "EVL", matrix):
    ...     print(format_alignment(*a))
    KEVLA
     ||| 
    -EVL-
      Score=13
    <BLANKLINE>

- With the parameter ``c`` you can define your own match- and gap functions.
  E.g. to define an affine logarithmic gap function and using it:

    >>> from math import log
    >>> def gap_function(x, y):  # x is gap position in seq, y is gap length
    ...     if y == 0:  # No gap
    ...         return 0
    ...     elif y == 1:  # Gap open penalty
    ...         return -2
    ...     return - (2 + y/4.0 + log(y)/2.0)
    ...
    >>> alignment = pairwise2.align.globalmc("ACCCCCGT", "ACG", 5, -4,
    ...                                      gap_function, gap_function)

  You can define different gap functions for each sequence.
  Self-defined match functions must take the two residues to be compared and
  return a score.

To see a description of the parameters for a function, please look at
the docstring for the function via the help function, e.g.
type ``help(pairwise2.align.localds)`` at the Python prompt.

"""  # noqa: W291

import warnings
from collections import namedtuple

from Bio import BiopythonDeprecationWarning
from Bio import BiopythonWarning
from Bio.Align import substitution_matrices

warnings.warn(
    "Bio.pairwise2 has been deprecated, and we intend to remove it in a "
    "future release of Biopython. As an alternative, please consider using "
    "Bio.Align.PairwiseAligner as a replacement, and contact the "
    "Biopython developers if you still need the Bio.pairwise2 module.",
    BiopythonDeprecationWarning,
)


MAX_ALIGNMENTS = 1000  # maximum alignments recovered in traceback

Alignment = namedtuple("Alignment", ("seqA, seqB, score, start, end"))


class align:
    """Provide functions that do alignments.

    Alignment functions are called as:

      pairwise2.align.globalXX

    or

      pairwise2.align.localXX

    Where XX is a 2 character code indicating the match/mismatch parameters
    (first character, either x, m, d or c) and the gap penalty parameters
    (second character, either x, s, d, or c).

    For a detailed description read the main module's docstring (e.g.,
    type ``help(pairwise2)``).
    To see a description of the parameters for a function, please
    look at the docstring for the function, e.g. type
    ``help(pairwise2.align.localds)`` at the Python prompt.
    """

    class alignment_function:
        """Callable class which impersonates an alignment function.

        The constructor takes the name of the function.  This class
        will decode the name of the function to figure out how to
        interpret the parameters.
        """

        # match code -> tuple of (parameters, docstring)
        match2args = {
            "x": ([], ""),
            "m": (
                ["match", "mismatch"],
                "match is the score to given to identical characters.\n"
                "mismatch is the score given to non-identical ones.",
            ),
            "d": (
                ["match_dict"],
                "match_dict is a dictionary where the keys are tuples\n"
                "of pairs of characters and the values are the scores,\n"
                "e.g. ('A', 'C') : 2.5.",
            ),
            "c": (
                ["match_fn"],
                "match_fn is a callback function that takes two "
                "characters and returns the score between them.",
            ),
        }
        # penalty code -> tuple of (parameters, docstring)
        penalty2args = {
            "x": ([], ""),
            "s": (
                ["open", "extend"],
                "open and extend are the gap penalties when a gap is\n"
                "opened and extended.  They should be negative.",
            ),
            "d": (
                ["openA", "extendA", "openB", "extendB"],
                "openA and extendA are the gap penalties for sequenceA,\n"
                "and openB and extendB for sequenceB.  The penalties\n"
                "should be negative.",
            ),
            "c": (
                ["gap_A_fn", "gap_B_fn"],
                "gap_A_fn and gap_B_fn are callback functions that takes\n"
                "(1) the index where the gap is opened, and (2) the length\n"
                "of the gap.  They should return a gap penalty.",
            ),
        }

        def __init__(self, name):
            """Check to make sure the name of the function is reasonable."""
            if name.startswith("global"):
                if len(name) != 8:
                    raise AttributeError("function should be globalXX")
            elif name.startswith("local"):
                if len(name) != 7:
                    raise AttributeError("function should be localXX")
            else:
                raise AttributeError(name)
            align_type, match_type, penalty_type = name[:-2], name[-2], name[-1]
            try:
                match_args, match_doc = self.match2args[match_type]
            except KeyError:
                raise AttributeError(f"unknown match type {match_type!r}")
            try:
                penalty_args, penalty_doc = self.penalty2args[penalty_type]
            except KeyError:
                raise AttributeError(f"unknown penalty type {penalty_type!r}")

            # Now get the names of the parameters to this function.
            param_names = ["sequenceA", "sequenceB"]
            param_names.extend(match_args)
            param_names.extend(penalty_args)
            self.function_name = name
            self.align_type = align_type
            self.param_names = param_names

            self.__name__ = self.function_name
            # Set the doc string.
            doc = f"{self.__name__}({', '.join(self.param_names)}) -> alignments\n"
            doc += """\
\nThe following parameters can also be used with optional
keywords of the same name.\n\n
sequenceA and sequenceB must be of the same type, either
strings, lists or Biopython sequence objects.\n
"""
            if match_doc:
                doc += f"\n{match_doc}\n"
            if penalty_doc:
                doc += f"\n{penalty_doc}\n"
            doc += """\
\nalignments is a list of named tuples (seqA, seqB, score,
begin, end). seqA and seqB are strings showing the alignment
between the sequences.  score is the score of the alignment.
begin and end are indexes of seqA and seqB that indicate
where the alignment occurs.
"""
            self.__doc__ = doc

        def decode(self, *args, **keywds):
            """Decode the arguments for the _align function.

            keywds will get passed to it, so translate the arguments
            to this function into forms appropriate for _align.
            """
            keywds = keywds.copy()

            # Replace possible "keywords" with arguments:
            args += (len(self.param_names) - len(args)) * (None,)
            for key in keywds.copy():
                if key in self.param_names:
                    _index = self.param_names.index(key)
                    args = args[:_index] + (keywds[key],) + args[_index:]
                    del keywds[key]
            args = tuple(arg for arg in args if arg is not None)

            if len(args) != len(self.param_names):
                raise TypeError(
                    "%s takes exactly %d argument (%d given)"
                    % (self.function_name, len(self.param_names), len(args))
                )

            i = 0
            while i < len(self.param_names):
                if self.param_names[i] in [
                    "sequenceA",
                    "sequenceB",
                    "gap_A_fn",
                    "gap_B_fn",
                    "match_fn",
                ]:
                    keywds[self.param_names[i]] = args[i]
                    i += 1
                elif self.param_names[i] == "match":
                    assert self.param_names[i + 1] == "mismatch"
                    match, mismatch = args[i], args[i + 1]
                    keywds["match_fn"] = identity_match(match, mismatch)
                    i += 2
                elif self.param_names[i] == "match_dict":
                    keywds["match_fn"] = dictionary_match(args[i])
                    i += 1
                elif self.param_names[i] == "open":
                    assert self.param_names[i + 1] == "extend"
                    open, extend = args[i], args[i + 1]
                    pe = keywds.get("penalize_extend_when_opening", 0)
                    keywds["gap_A_fn"] = affine_penalty(open, extend, pe)
                    keywds["gap_B_fn"] = affine_penalty(open, extend, pe)
                    i += 2
                elif self.param_names[i] == "openA":
                    assert self.param_names[i + 3] == "extendB"
                    openA, extendA, openB, extendB = args[i : i + 4]
                    pe = keywds.get("penalize_extend_when_opening", 0)
                    keywds["gap_A_fn"] = affine_penalty(openA, extendA, pe)
                    keywds["gap_B_fn"] = affine_penalty(openB, extendB, pe)
                    i += 4
                else:
                    raise ValueError(f"unknown parameter {self.param_names[i]!r}")

            # Here are the default parameters for _align.  Assign
            # these to keywds, unless already specified.
            pe = keywds.get("penalize_extend_when_opening", 0)
            default_params = [
                ("match_fn", identity_match(1, 0)),
                ("gap_A_fn", affine_penalty(0, 0, pe)),
                ("gap_B_fn", affine_penalty(0, 0, pe)),
                ("penalize_extend_when_opening", 0),
                ("penalize_end_gaps", self.align_type == "global"),
                ("align_globally", self.align_type == "global"),
                ("gap_char", "-"),
                ("force_generic", 0),
                ("score_only", 0),
                ("one_alignment_only", 0),
            ]
            for name, default in default_params:
                keywds[name] = keywds.get(name, default)
            value = keywds["penalize_end_gaps"]
            try:
                n = len(value)
            except TypeError:
                keywds["penalize_end_gaps"] = tuple([value] * 2)
            else:
                assert n == 2
            return keywds

        def __call__(self, *args, **keywds):
            """Call the alignment instance already created."""
            keywds = self.decode(*args, **keywds)
            return _align(**keywds)

    def __getattr__(self, attr):
        """Call alignment_function() to check and decode the attributes."""
        # The following 'magic' is needed to rewrite the class docstring
        # dynamically:
        wrapper = self.alignment_function(attr)
        wrapper_type = type(wrapper)
        wrapper_dict = wrapper_type.__dict__.copy()
        wrapper_dict["__doc__"] = wrapper.__doc__
        new_alignment_function = type("alignment_function", (object,), wrapper_dict)

        return new_alignment_function(attr)


align = align()


def _align(
    sequenceA,
    sequenceB,
    match_fn,
    gap_A_fn,
    gap_B_fn,
    penalize_extend_when_opening,
    penalize_end_gaps,
    align_globally,
    gap_char,
    force_generic,
    score_only,
    one_alignment_only,
):
    """Return optimal alignments between two sequences (PRIVATE).

    This method either returns a list of optimal alignments (with the same
    score) or just the optimal score.
    """
    if not sequenceA or not sequenceB:
        return []
    try:
        sequenceA + gap_char
        sequenceB + gap_char
    except TypeError:
        raise TypeError(
            "both sequences must be of the same type, either "
            "string/sequence object or list. Gap character must "
            "fit the sequence type (string or list)"
        )

    if not isinstance(sequenceA, list):
        sequenceA = str(sequenceA)
    if not isinstance(sequenceB, list):
        sequenceB = str(sequenceB)
    if not align_globally and (penalize_end_gaps[0] or penalize_end_gaps[1]):
        warnings.warn(
            '"penalize_end_gaps" should not be used in local '
            "alignments. The resulting score may be wrong.",
            BiopythonWarning,
        )

    if (
        (not force_generic)
        and isinstance(gap_A_fn, affine_penalty)
        and isinstance(gap_B_fn, affine_penalty)
    ):
        open_A, extend_A = gap_A_fn.open, gap_A_fn.extend
        open_B, extend_B = gap_B_fn.open, gap_B_fn.extend
        matrices = _make_score_matrix_fast(
            sequenceA,
            sequenceB,
            match_fn,
            open_A,
            extend_A,
            open_B,
            extend_B,
            penalize_extend_when_opening,
            penalize_end_gaps,
            align_globally,
            score_only,
        )
    else:
        matrices = _make_score_matrix_generic(
            sequenceA,
            sequenceB,
            match_fn,
            gap_A_fn,
            gap_B_fn,
            penalize_end_gaps,
            align_globally,
            score_only,
        )

    score_matrix, trace_matrix, best_score = matrices

    # print("SCORE %s" % print_matrix(score_matrix))
    # print("TRACEBACK %s" % print_matrix(trace_matrix))

    # If they only want the score, then return it.
    if score_only:
        return best_score

    starts = _find_start(score_matrix, best_score, align_globally)

    # Recover the alignments and return them.
    alignments = _recover_alignments(
        sequenceA,
        sequenceB,
        starts,
        best_score,
        score_matrix,
        trace_matrix,
        align_globally,
        gap_char,
        one_alignment_only,
        gap_A_fn,
        gap_B_fn,
    )
    if not alignments:
        # This may happen, see recover_alignments for explanation
        score_matrix, trace_matrix = _reverse_matrices(score_matrix, trace_matrix)
        starts = [(z, (y, x)) for z, (x, y) in starts]
        alignments = _recover_alignments(
            sequenceB,
            sequenceA,
            starts,
            best_score,
            score_matrix,
            trace_matrix,
            align_globally,
            gap_char,
            one_alignment_only,
            gap_B_fn,
            gap_A_fn,
            reverse=True,
        )
    return alignments


def _make_score_matrix_generic(
    sequenceA,
    sequenceB,
    match_fn,
    gap_A_fn,
    gap_B_fn,
    penalize_end_gaps,
    align_globally,
    score_only,
):
    """Generate a score and traceback matrix (PRIVATE).

    This implementation according to Needleman-Wunsch allows the usage of
    general gap functions and is rather slow. It is automatically called if
    you define your own gap functions. You can force the usage of this method
    with ``force_generic=True``.
    """
    local_max_score = 0
    # Create the score and traceback matrices. These should be in the
    # shape:
    # sequenceA (down) x sequenceB (across)
    lenA, lenB = len(sequenceA), len(sequenceB)
    score_matrix, trace_matrix = [], []
    for i in range(lenA + 1):
        score_matrix.append([None] * (lenB + 1))
        if not score_only:
            trace_matrix.append([None] * (lenB + 1))

    # Initialize first row and column with gap scores. This is like opening up
    # i gaps at the beginning of sequence A or B.
    for i in range(lenA + 1):
        if penalize_end_gaps[1]:  # [1]:gap in sequence B
            score = gap_B_fn(0, i)
        else:
            score = 0.0
        score_matrix[i][0] = score
    for i in range(lenB + 1):
        if penalize_end_gaps[0]:  # [0]:gap in sequence A
            score = gap_A_fn(0, i)
        else:
            score = 0.0
        score_matrix[0][i] = score

    # Fill in the score matrix.  Each position in the matrix
    # represents an alignment between a character from sequence A to
    # one in sequence B.  As I iterate through the matrix, find the
    # alignment by choose the best of:
    #    1) extending a previous alignment without gaps
    #    2) adding a gap in sequenceA
    #    3) adding a gap in sequenceB
    for row in range(1, lenA + 1):
        for col in range(1, lenB + 1):
            # First, calculate the score that would occur by extending
            # the alignment without gaps.
            # fmt: off
            nogap_score = (
                score_matrix[row - 1][col - 1]
                + match_fn(sequenceA[row - 1], sequenceB[col - 1])
            )

            # fmt: on
            # Try to find a better score by opening gaps in sequenceA.
            # Do this by checking alignments from each column in the row.
            # Each column represents a different character to align from,
            # and thus a different length gap.
            # Although the gap function does not distinguish between opening
            # and extending a gap, we distinguish them for the backtrace.
            if not penalize_end_gaps[0] and row == lenA:
                row_open = score_matrix[row][col - 1]
                row_extend = max(score_matrix[row][x] for x in range(col))
            else:
                row_open = score_matrix[row][col - 1] + gap_A_fn(row, 1)
                row_extend = max(
                    score_matrix[row][x] + gap_A_fn(row, col - x) for x in range(col)
                )

            # Try to find a better score by opening gaps in sequenceB.
            if not penalize_end_gaps[1] and col == lenB:
                col_open = score_matrix[row - 1][col]
                col_extend = max(score_matrix[x][col] for x in range(row))
            else:
                col_open = score_matrix[row - 1][col] + gap_B_fn(col, 1)
                col_extend = max(
                    score_matrix[x][col] + gap_B_fn(col, row - x) for x in range(row)
                )

            best_score = max(nogap_score, row_open, row_extend, col_open, col_extend)
            local_max_score = max(local_max_score, best_score)
            if not align_globally and best_score < 0:
                score_matrix[row][col] = 0.0
            else:
                score_matrix[row][col] = best_score

            # The backtrace is encoded binary. See _make_score_matrix_fast
            # for details.
            if not score_only:
                trace_score = 0
                if rint(nogap_score) == rint(best_score):
                    trace_score += 2
                if rint(row_open) == rint(best_score):
                    trace_score += 1
                if rint(row_extend) == rint(best_score):
                    trace_score += 8
                if rint(col_open) == rint(best_score):
                    trace_score += 4
                if rint(col_extend) == rint(best_score):
                    trace_score += 16
                trace_matrix[row][col] = trace_score

    if not align_globally:
        best_score = local_max_score

    return score_matrix, trace_matrix, best_score


def _make_score_matrix_fast(
    sequenceA,
    sequenceB,
    match_fn,
    open_A,
    extend_A,
    open_B,
    extend_B,
    penalize_extend_when_opening,
    penalize_end_gaps,
    align_globally,
    score_only,
):
    """Generate a score and traceback matrix according to Gotoh (PRIVATE).

    This is an implementation of the Needleman-Wunsch dynamic programming
    algorithm as modified by Gotoh, implementing affine gap penalties.
    In short, we have three matrices, holding scores for alignments ending
    in (1) a match/mismatch, (2) a gap in sequence A, and (3) a gap in
    sequence B, respectively. However, we can combine them in one matrix,
    which holds the best scores, and store only those values from the
    other matrices that are actually used for the next step of calculation.
    The traceback matrix holds the positions for backtracing the alignment.
    """
    first_A_gap = calc_affine_penalty(1, open_A, extend_A, penalize_extend_when_opening)
    first_B_gap = calc_affine_penalty(1, open_B, extend_B, penalize_extend_when_opening)
    local_max_score = 0

    # Create the score and traceback matrices. These should be in the
    # shape:
    # sequenceA (down) x sequenceB (across)
    lenA, lenB = len(sequenceA), len(sequenceB)
    score_matrix, trace_matrix = [], []
    for i in range(lenA + 1):
        score_matrix.append([None] * (lenB + 1))
        if not score_only:
            trace_matrix.append([None] * (lenB + 1))

    # Initialize first row and column with gap scores. This is like opening up
    # i gaps at the beginning of sequence A or B.
    for i in range(lenA + 1):
        if penalize_end_gaps[1]:  # [1]:gap in sequence B
            score = calc_affine_penalty(
                i, open_B, extend_B, penalize_extend_when_opening
            )
        else:
            score = 0
        score_matrix[i][0] = score
    for i in range(lenB + 1):
        if penalize_end_gaps[0]:  # [0]:gap in sequence A
            score = calc_affine_penalty(
                i, open_A, extend_A, penalize_extend_when_opening
            )
        else:
            score = 0
        score_matrix[0][i] = score

    # Now initialize the col 'matrix'. Actually this is only a one dimensional
    # list, since we only need the col scores from the last row.
    col_score = [0]  # Best score, if actual alignment ends with gap in seqB
    for i in range(1, lenB + 1):
        col_score.append(
            calc_affine_penalty(i, 2 * open_B, extend_B, penalize_extend_when_opening)
        )

    # The row 'matrix' is calculated on the fly. Here we only need the actual
    # score.
    # Now, filling up the score and traceback matrices:
    for row in range(1, lenA + 1):
        row_score = calc_affine_penalty(
            row, 2 * open_A, extend_A, penalize_extend_when_opening
        )
        for col in range(1, lenB + 1):
            # Calculate the score that would occur by extending the
            # alignment without gaps.
            # fmt: off
            nogap_score = (
                score_matrix[row - 1][col - 1]
                + match_fn(sequenceA[row - 1], sequenceB[col - 1])
            )
            # fmt: on
            # Check the score that would occur if there were a gap in
            # sequence A. This could come from opening a new gap or
            # extending an existing one.
            # A gap in sequence A can also be opened if it follows a gap in
            # sequence B:  A-
            #              -B
            if not penalize_end_gaps[0] and row == lenA:
                row_open = score_matrix[row][col - 1]
                row_extend = row_score
            else:
                row_open = score_matrix[row][col - 1] + first_A_gap
                row_extend = row_score + extend_A
            row_score = max(row_open, row_extend)

            # The same for sequence B:
            if not penalize_end_gaps[1] and col == lenB:
                col_open = score_matrix[row - 1][col]
                col_extend = col_score[col]
            else:
                col_open = score_matrix[row - 1][col] + first_B_gap
                col_extend = col_score[col] + extend_B
            col_score[col] = max(col_open, col_extend)

            best_score = max(nogap_score, col_score[col], row_score)
            local_max_score = max(local_max_score, best_score)
            if not align_globally and best_score < 0:
                score_matrix[row][col] = 0
            else:
                score_matrix[row][col] = best_score

            # Now the trace_matrix. The edges of the backtrace are encoded
            # binary: 1 = open gap in seqA, 2 = match/mismatch of seqA and
            # seqB, 4 = open gap in seqB, 8 = extend gap in seqA, and
            # 16 = extend gap in seqB. This values can be summed up.
            # Thus, the trace score 7 means that the best score can either
            # come from opening a gap in seqA (=1), pairing two characters
            # of seqA and seqB (+2=3) or opening a gap in seqB (+4=7).
            # However, if we only want the score we don't care about the trace.
            if not score_only:
                row_score_rint = rint(row_score)
                col_score_rint = rint(col_score[col])
                row_trace_score = 0
                col_trace_score = 0
                if rint(row_open) == row_score_rint:
                    row_trace_score += 1  # Open gap in seqA
                if rint(row_extend) == row_score_rint:
                    row_trace_score += 8  # Extend gap in seqA
                if rint(col_open) == col_score_rint:
                    col_trace_score += 4  # Open gap in seqB
                if rint(col_extend) == col_score_rint:
                    col_trace_score += 16  # Extend gap in seqB

                trace_score = 0
                best_score_rint = rint(best_score)
                if rint(nogap_score) == best_score_rint:
                    trace_score += 2  # Align seqA with seqB
                if row_score_rint == best_score_rint:
                    trace_score += row_trace_score
                if col_score_rint == best_score_rint:
                    trace_score += col_trace_score
                trace_matrix[row][col] = trace_score

    if not align_globally:
        best_score = local_max_score

    return score_matrix, trace_matrix, best_score


def _recover_alignments(
    sequenceA,
    sequenceB,
    starts,
    best_score,
    score_matrix,
    trace_matrix,
    align_globally,
    gap_char,
    one_alignment_only,
    gap_A_fn,
    gap_B_fn,
    reverse=False,
):
    """Do the backtracing and return a list of alignments (PRIVATE).

    Recover the alignments by following the traceback matrix.  This
    is a recursive procedure, but it's implemented here iteratively
    with a stack.

    sequenceA and sequenceB may be sequences, including strings,
    lists, or list-like objects.  In order to preserve the type of
    the object, we need to use slices on the sequences instead of
    indexes.  For example, sequenceA[row] may return a type that's
    not compatible with sequenceA, e.g. if sequenceA is a list and
    sequenceA[row] is a string.  Thus, avoid using indexes and use
    slices, e.g. sequenceA[row:row+1].  Assume that client-defined
    sequence classes preserve these semantics.
    """
    lenA, lenB = len(sequenceA), len(sequenceB)
    ali_seqA, ali_seqB = sequenceA[0:0], sequenceB[0:0]
    tracebacks = []
    in_process = []

    for start in starts:
        score, (row, col) = start
        begin = 0
        if align_globally:
            end = None
        else:
            # If this start is a zero-extension: don't start here!
            if (score, (row - 1, col - 1)) in starts:
                continue
            # Local alignments should start with a positive score!
            if score <= 0:
                continue
            # Local alignments should not end with a gap!:
            trace = trace_matrix[row][col]
            if (trace - trace % 2) % 4 == 2:  # Trace contains 'nogap', fine!
                trace_matrix[row][col] = 2
            # If not, don't start here!
            else:
                continue
            end = -max(lenA - row, lenB - col)
            if not end:
                end = None
            col_distance = lenB - col
            row_distance = lenA - row

            # fmt: off
            ali_seqA = (
                (col_distance - row_distance) * gap_char
                + sequenceA[lenA - 1 : row - 1 : -1]
            )
            ali_seqB = (
                (row_distance - col_distance) * gap_char
                + sequenceB[lenB - 1 : col - 1 : -1]
            )
            # fmt: on
        in_process += [
            (ali_seqA, ali_seqB, end, row, col, False, trace_matrix[row][col])
        ]
    while in_process and len(tracebacks) < MAX_ALIGNMENTS:
        # Although we allow a gap in seqB to be followed by a gap in seqA,
        # we don't want to allow it the other way round, since this would
        # give redundant alignments of type: A-  vs.  -A
        #                                    -B       B-
        # Thus we need to keep track if a gap in seqA was opened (col_gap)
        # and stop the backtrace (dead_end) if a gap in seqB follows.
        #
        # Attention: This may fail, if the gap-penalties for both strands are
        # different. In this case the second alignment may be the only optimal
        # alignment. Thus it can happen that no alignment is returned. For
        # this case a workaround was implemented, which reverses the input and
        # the matrices (this happens in _reverse_matrices) and repeats the
        # backtrace. The variable 'reverse' keeps track of this.
        dead_end = False
        ali_seqA, ali_seqB, end, row, col, col_gap, trace = in_process.pop()

        while (row > 0 or col > 0) and not dead_end:
            cache = (ali_seqA[:], ali_seqB[:], end, row, col, col_gap)

            # If trace is empty we have reached at least one border of the
            # matrix or the end of a local alignment. Just add the rest of
            # the sequence(s) and fill with gaps if necessary.
            if not trace:
                if col and col_gap:
                    dead_end = True
                else:
                    ali_seqA, ali_seqB = _finish_backtrace(
                        sequenceA, sequenceB, ali_seqA, ali_seqB, row, col, gap_char
                    )
                break
            elif trace % 2 == 1:  # = row open = open gap in seqA
                trace -= 1
                if col_gap:
                    dead_end = True
                else:
                    col -= 1
                    ali_seqA += gap_char
                    ali_seqB += sequenceB[col : col + 1]
                    col_gap = False
            elif trace % 4 == 2:  # = match/mismatch of seqA with seqB
                trace -= 2
                row -= 1
                col -= 1
                ali_seqA += sequenceA[row : row + 1]
                ali_seqB += sequenceB[col : col + 1]
                col_gap = False
            elif trace % 8 == 4:  # = col open = open gap in seqB
                trace -= 4
                row -= 1
                ali_seqA += sequenceA[row : row + 1]
                ali_seqB += gap_char
                col_gap = True
            elif trace in (8, 24):  # = row extend = extend gap in seqA
                trace -= 8
                if col_gap:
                    dead_end = True
                else:
                    col_gap = False
                    # We need to find the starting point of the extended gap
                    x = _find_gap_open(
                        sequenceA,
                        sequenceB,
                        ali_seqA,
                        ali_seqB,
                        end,
                        row,
                        col,
                        col_gap,
                        gap_char,
                        score_matrix,
                        trace_matrix,
                        in_process,
                        gap_A_fn,
                        col,
                        row,
                        "col",
                        best_score,
                        align_globally,
                    )
                    ali_seqA, ali_seqB, row, col, in_process, dead_end = x
            elif trace == 16:  # = col extend = extend gap in seqB
                trace -= 16
                col_gap = True
                x = _find_gap_open(
                    sequenceA,
                    sequenceB,
                    ali_seqA,
                    ali_seqB,
                    end,
                    row,
                    col,
                    col_gap,
                    gap_char,
                    score_matrix,
                    trace_matrix,
                    in_process,
                    gap_B_fn,
                    row,
                    col,
                    "row",
                    best_score,
                    align_globally,
                )
                ali_seqA, ali_seqB, row, col, in_process, dead_end = x

            if trace:  # There is another path to follow...
                cache += (trace,)
                in_process.append(cache)
            trace = trace_matrix[row][col]
            if not align_globally:
                if score_matrix[row][col] == best_score:
                    # We have gone through a 'zero-score' extension, discard it
                    dead_end = True
                elif score_matrix[row][col] <= 0:
                    # We have reached the end of the backtrace
                    begin = max(row, col)
                    trace = 0
        if not dead_end:
            if not reverse:
                tracebacks.append((ali_seqA[::-1], ali_seqB[::-1], score, begin, end))
            else:
                tracebacks.append((ali_seqB[::-1], ali_seqA[::-1], score, begin, end))
            if one_alignment_only:
                break
    return _clean_alignments(tracebacks)


def _find_start(score_matrix, best_score, align_globally):
    """Return a list of starting points (score, (row, col)) (PRIVATE).

    Indicating every possible place to start the tracebacks.
    """
    nrows, ncols = len(score_matrix), len(score_matrix[0])
    # In this implementation of the global algorithm, the start will always be
    # the bottom right corner of the matrix.
    if align_globally:
        starts = [(best_score, (nrows - 1, ncols - 1))]
    else:
        # For local alignments, there may be many different start points.
        starts = []
        tolerance = 0  # XXX do anything with this?
        # Now find all the positions within some tolerance of the best
        # score.
        for row in range(nrows):
            for col in range(ncols):
                score = score_matrix[row][col]
                if rint(abs(score - best_score)) <= rint(tolerance):
                    starts.append((score, (row, col)))
    return starts


def _reverse_matrices(score_matrix, trace_matrix):
    """Reverse score and trace matrices (PRIVATE)."""
    reverse_score_matrix = []
    reverse_trace_matrix = []
    # fmt: off
    reverse_trace = {
        1: 4, 2: 2, 3: 6, 4: 1, 5: 5, 6: 3, 7: 7, 8: 16, 9: 20, 10: 18, 11: 22, 12: 17,
        13: 21, 14: 19, 15: 23, 16: 8, 17: 12, 18: 10, 19: 14, 20: 9, 21: 13, 22: 11,
        23: 15, 24: 24, 25: 28, 26: 26, 27: 30, 28: 25, 29: 29, 30: 27, 31: 31,
        None: None,
    }
    # fmt: on
    for col in range(len(score_matrix[0])):
        new_score_row = []
        new_trace_row = []
        for row in range(len(score_matrix)):
            new_score_row.append(score_matrix[row][col])
            new_trace_row.append(reverse_trace[trace_matrix[row][col]])
        reverse_score_matrix.append(new_score_row)
        reverse_trace_matrix.append(new_trace_row)
    return reverse_score_matrix, reverse_trace_matrix


def _clean_alignments(alignments):
    """Take a list of alignments and return a cleaned version (PRIVATE).

    Remove duplicates, make sure begin and end are set correctly, remove
    empty alignments.
    """
    unique_alignments = []
    for align in alignments:
        if align not in unique_alignments:
            unique_alignments.append(align)
    i = 0
    while i < len(unique_alignments):
        seqA, seqB, score, begin, end = unique_alignments[i]
        # Make sure end is set reasonably.
        if end is None:  # global alignment
            end = len(seqA)
        elif end < 0:
            end = end + len(seqA)
        # If there's no alignment here, get rid of it.
        if begin >= end:
            del unique_alignments[i]
            continue
        unique_alignments[i] = Alignment(seqA, seqB, score, begin, end)
        i += 1
    return unique_alignments


def _finish_backtrace(sequenceA, sequenceB, ali_seqA, ali_seqB, row, col, gap_char):
    """Add remaining sequences and fill with gaps if necessary (PRIVATE)."""
    if row:
        ali_seqA += sequenceA[row - 1 :: -1]
    if col:
        ali_seqB += sequenceB[col - 1 :: -1]
    if row > col:
        ali_seqB += gap_char * (len(ali_seqA) - len(ali_seqB))
    elif col > row:
        ali_seqA += gap_char * (len(ali_seqB) - len(ali_seqA))
    return ali_seqA, ali_seqB


def _find_gap_open(
    sequenceA,
    sequenceB,
    ali_seqA,
    ali_seqB,
    end,
    row,
    col,
    col_gap,
    gap_char,
    score_matrix,
    trace_matrix,
    in_process,
    gap_fn,
    target,
    index,
    direction,
    best_score,
    align_globally,
):
    """Find the starting point(s) of the extended gap (PRIVATE)."""
    dead_end = False
    target_score = score_matrix[row][col]
    for n in range(target):
        if direction == "col":
            col -= 1
            ali_seqA += gap_char
            ali_seqB += sequenceB[col : col + 1]
        else:
            row -= 1
            ali_seqA += sequenceA[row : row + 1]
            ali_seqB += gap_char
        actual_score = score_matrix[row][col] + gap_fn(index, n + 1)
        if not align_globally and score_matrix[row][col] == best_score:
            # We have run through a 'zero-score' extension and discard it
            dead_end = True
            break
        if rint(actual_score) == rint(target_score) and n > 0:
            if not trace_matrix[row][col]:
                break
            else:
                in_process.append(
                    (
                        ali_seqA[:],
                        ali_seqB[:],
                        end,
                        row,
                        col,
                        col_gap,
                        trace_matrix[row][col],
                    )
                )
        if not trace_matrix[row][col]:
            dead_end = True
    return ali_seqA, ali_seqB, row, col, in_process, dead_end


_PRECISION = 1000


def rint(x, precision=_PRECISION):
    """Print number with declared precision."""
    return int(x * precision + 0.5)


class identity_match:
    """Create a match function for use in an alignment.

    match and mismatch are the scores to give when two residues are equal
    or unequal.  By default, match is 1 and mismatch is 0.
    """

    def __init__(self, match=1, mismatch=0):
        """Initialize the class."""
        self.match = match
        self.mismatch = mismatch

    def __call__(self, charA, charB):
        """Call a match function instance already created."""
        if charA == charB:
            return self.match
        return self.mismatch


class dictionary_match:
    """Create a match function for use in an alignment.

    Attributes:
     - score_dict     - A dictionary where the keys are tuples (residue 1,
       residue 2) and the values are the match scores between those residues.
     - symmetric      - A flag that indicates whether the scores are symmetric.

    """

    def __init__(self, score_dict, symmetric=1):
        """Initialize the class."""
        if isinstance(score_dict, substitution_matrices.Array):
            score_dict = dict(score_dict)  # Access to dict is much faster
        self.score_dict = score_dict
        self.symmetric = symmetric

    def __call__(self, charA, charB):
        """Call a dictionary match instance already created."""
        if self.symmetric and (charA, charB) not in self.score_dict:
            # If the score dictionary is symmetric, then look up the
            # score both ways.
            charB, charA = charA, charB
        return self.score_dict[(charA, charB)]


class affine_penalty:
    """Create a gap function for use in an alignment."""

    def __init__(self, open, extend, penalize_extend_when_opening=0):
        """Initialize the class."""
        if open > 0 or extend > 0:
            raise ValueError("Gap penalties should be non-positive.")
        if not penalize_extend_when_opening and (extend < open):
            raise ValueError(
                "Gap opening penalty should be higher than "
                "gap extension penalty (or equal)"
            )
        self.open, self.extend = open, extend
        self.penalize_extend_when_opening = penalize_extend_when_opening

    def __call__(self, index, length):
        """Call a gap function instance already created."""
        return calc_affine_penalty(
            length, self.open, self.extend, self.penalize_extend_when_opening
        )


def calc_affine_penalty(length, open, extend, penalize_extend_when_opening):
    """Calculate a penalty score for the gap function."""
    if length <= 0:
        return 0.0
    penalty = open + extend * length
    if not penalize_extend_when_opening:
        penalty -= extend
    return penalty


def print_matrix(matrix):
    """Print out a matrix for debugging purposes."""
    # Transpose the matrix and get the length of the values in each column.
    matrixT = [[] for x in range(len(matrix[0]))]
    for i in range(len(matrix)):
        for j in range(len(matrix[i])):
            matrixT[j].append(len(str(matrix[i][j])))
    ndigits = [max(x) for x in matrixT]
    for i in range(len(matrix)):
        # Using string formatting trick to add leading spaces,
        print(
            " ".join("%*s " % (ndigits[j], matrix[i][j]) for j in range(len(matrix[i])))
        )


def format_alignment(align1, align2, score, begin, end, full_sequences=False):
    """Format the alignment prettily into a string.

    IMPORTANT: Gap symbol must be "-" (or ['-'] for lists)!

    Since Biopython 1.71 identical matches are shown with a pipe
    character, mismatches as a dot, and gaps as a space.

    Prior releases just used the pipe character to indicate the
    aligned region (matches, mismatches and gaps).

    Also, in local alignments, if the alignment does not include
    the whole sequences, now only the aligned part is shown,
    together with the start positions of the aligned subsequences.
    The start positions are 1-based; so start position n is the
    n-th base/amino acid in the *un-aligned* sequence.

    NOTE: This is different to the alignment's begin/end values,
    which give the Python indices (0-based) of the bases/amino acids
    in the *aligned* sequences.

    If you want to restore the 'historic' behaviour, that means
    displaying the whole sequences (including the non-aligned parts),
    use ``full_sequences=True``. In this case, the non-aligned leading
    and trailing parts are also indicated by spaces in the match-line.
    """
    align_begin = begin
    align_end = end
    start1 = start2 = ""
    start_m = begin  # Begin of match line (how many spaces to include)
    # For local alignments:
    if not full_sequences and (begin != 0 or end != len(align1)):
        # Calculate the actual start positions in the un-aligned sequences
        # This will only work if the gap symbol is '-' or ['-']!
        start1 = str(len(align1[:begin]) - align1[:begin].count("-") + 1) + " "
        start2 = str(len(align2[:begin]) - align2[:begin].count("-") + 1) + " "
        start_m = max(len(start1), len(start2))
    elif full_sequences:
        start_m = 0
        begin = 0
        end = len(align1)

    if isinstance(align1, list):
        # List elements will be separated by spaces, since they can be
        # of different lengths
        align1 = [a + " " for a in align1]
        align2 = [a + " " for a in align2]

    s1_line = ["{:>{width}}".format(start1, width=start_m)]  # seq1 line
    m_line = [" " * start_m]  # match line
    s2_line = ["{:>{width}}".format(start2, width=start_m)]  # seq2 line

    for n, (a, b) in enumerate(zip(align1[begin:end], align2[begin:end])):
        # Since list elements can be of different length, we center them,
        # using the maximum length of the two compared elements as width
        m_len = max(len(a), len(b))
        s1_line.append("{:^{width}}".format(a, width=m_len))
        s2_line.append("{:^{width}}".format(b, width=m_len))
        if full_sequences and (n < align_begin or n >= align_end):
            m_line.append("{:^{width}}".format(" ", width=m_len))  # space
            continue
        if a == b:
            m_line.append("{:^{width}}".format("|", width=m_len))  # match
        elif a.strip() == "-" or b.strip() == "-":
            m_line.append("{:^{width}}".format(" ", width=m_len))  # gap
        else:
            m_line.append("{:^{width}}".format(".", width=m_len))  # mismatch

    s2_line.append(f"\n  Score={score:g}\n")
    return "\n".join(["".join(s1_line), "".join(m_line), "".join(s2_line)])


# Try and load C implementations of functions. If I can't,
# then throw a warning and use the pure Python implementations.
# The redefinition is deliberate, thus the no quality assurance
# flag for when using flake8.
# Before, we secure access to the pure Python functions (for testing purposes):

_python_make_score_matrix_fast = _make_score_matrix_fast
_python_rint = rint

try:
    from .cpairwise2 import rint, _make_score_matrix_fast  # noqa
except ImportError:
    warnings.warn(
        "Import of C module failed. Falling back to pure Python "
        "implementation. This may be slooow...",
        BiopythonWarning,
    )

if __name__ == "__main__":
    from Bio._utils import run_doctest

    run_doctest()
