# Copyright 2009 by Cymon J. Cox and Brad Chapman. 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.
"""Command line wrapper for the multiple alignment program TCOFFEE."""


from Bio.Application import _Option, _Switch, AbstractCommandline


class TCoffeeCommandline(AbstractCommandline):
    """Commandline object for the TCoffee alignment program.

    http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

    The T-Coffee command line tool has a lot of switches and options.
    This wrapper implements a VERY limited number of options - if you
    would like to help improve it please get in touch.

    Notes
    -----
    Last checked against: Version_6.92

    References
    ----------
    T-Coffee: A novel method for multiple sequence alignments.
    Notredame, Higgins, Heringa, JMB,302(205-217) 2000

    Examples
    --------
    To align a FASTA file (unaligned.fasta) with the output in ClustalW
    format (file aligned.aln), and otherwise default settings, use:

    >>> from Bio.Align.Applications import TCoffeeCommandline
    >>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
    ...                                    output="clustalw",
    ...                                    outfile="aligned.aln")
    >>> print(tcoffee_cline)
    t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln

    You would typically run the command line with tcoffee_cline() or via
    the Python subprocess module, as described in the Biopython tutorial.

    """

    SEQ_TYPES = ["dna", "protein", "dna_protein"]

    def __init__(self, cmd="t_coffee", **kwargs):
        """Initialize the class."""
        self.parameters = [
            _Option(
                ["-output", "output"],
                """Specify the output type.

                One (or more separated by a comma) of:
                'clustalw_aln', 'clustalw', 'gcg', 'msf_aln',
                'pir_aln', 'fasta_aln', 'phylip', 'pir_seq', 'fasta_seq'
                """,
                equate=False,
            ),
            _Option(
                ["-infile", "infile"],
                "Specify the input file.",
                filename=True,
                is_required=True,
                equate=False,
            ),
            # Indicates the name of the alignment output by t_coffee. If the
            # default is used, the alignment is named <your sequences>.aln
            _Option(
                ["-outfile", "outfile"],
                "Specify the output file. Default: <your sequences>.aln",
                filename=True,
                equate=False,
            ),
            _Switch(
                ["-convert", "convert"], "Specify you want to perform a file conversion"
            ),
            _Option(
                ["-type", "type"],
                "Specify the type of sequence being aligned",
                checker_function=lambda x: x in self.SEQ_TYPES,
                equate=False,
            ),
            _Option(
                ["-outorder", "outorder"],
                "Specify the order of sequence to output"
                "Either 'input', 'aligned' or <filename> of "
                "Fasta file with sequence order",
                equate=False,
            ),
            _Option(
                ["-matrix", "matrix"],
                "Specify the filename of the substitution matrix to use. "
                "Default: blosum62mt",
                equate=False,
            ),
            _Option(
                ["-gapopen", "gapopen"],
                "Indicates the penalty applied for opening a gap (negative integer)",
                checker_function=lambda x: isinstance(x, int),
                equate=False,
            ),
            _Option(
                ["-gapext", "gapext"],
                "Indicates the penalty applied for extending a gap (negative integer)",
                checker_function=lambda x: isinstance(x, int),
                equate=False,
            ),
            _Switch(["-quiet", "quiet"], "Turn off log output"),
            _Option(
                ["-mode", "mode"],
                "Specifies a special mode: genome, quickaln, dali, 3dcoffee",
                equate=False,
            ),
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)


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

    run_doctest()
