Source code for pybrops.popgen.gmat.PhasedGenotypeMatrix

"""
Module defining basal matrix interfaces and associated error checking routines
for phased genotype matrices.
"""

from abc import ABCMeta
from pybrops.core.mat.PhasedTaxaVariantMatrix import PhasedTaxaVariantMatrix
from pybrops.popgen.gmat.GenotypeMatrix import GenotypeMatrix

# NOTE: GenotypeMatrix MUST GO FIRST: causes method resolution error otherwise!
# NOTE: this is because
#       GenotypeMatrix extends TaxaVariantMatrix
#       PhasedTaxaVariantMatrix extends TaxaVariantMatrix
# I think a situation is caused where TaxaVariantMatrix is needed to be imported
# before itself due to its ranking in the MRO algorithm for multiple inheritance


class PhasedGenotypeMatrix(
        GenotypeMatrix,
        PhasedTaxaVariantMatrix,
        metaclass = ABCMeta,
    ):
    """
    An abstract class for phased genoypte matrix objects.

    The purpose of this abstract class is to merge the following interfaces:
        1) GenotypeMatrix
        2) PhasedTaxaVariantMatrix
    """


    ########################## Special Object Methods ##########################



################################## Utilities ###################################


def check_is_PhasedGenotypeMatrix(v: object, vname: str) -> None:
    """
    Check if object is of type ``PhasedGenotypeMatrix``. Otherwise raise ``TypeError``.

    Parameters
    ----------
    v : object
        Any Python object to test.
    vname : str
        Name of variable to print in ``TypeError`` message.
    """
    if not isinstance(v, PhasedGenotypeMatrix):
        raise TypeError("'%s' must be a PhasedGenotypeMatrix." % vname)




def check_PhasedGenotypeMatrix_has_vrnt_xoprob(v: PhasedGenotypeMatrix, vname: str) -> None:
    """
    Check if a ``PhasedGenotypeMatrix`` has the ``vrnt_xoprob`` field that is non-None.

    Parameters
    ----------
    v : PhasedGenotypeMatrix
        A phased genotype matrix.
    vname : str
        Name of the variable to print in ``ValueError`` message.
    """
    if v.vrnt_xoprob is None:
        raise ValueError(
            "{0} '{0}' must have 'vrnt_xoprob' (variant xoprob) assigned".format(
                type(v).__name__,
                vname
            )
        )




def check_PhasedGenotypeMatrix_has_vrnt_mask(v: PhasedGenotypeMatrix, vname: str) -> None:
    """
    Check if a ``PhasedGenotypeMatrix`` has the ``vrnt_mask`` field that is non-None.

    Parameters
    ----------
    v : PhasedGenotypeMatrix
        A phased genotype matrix.
    vname : str
        Name of the variable to print in ``ValueError`` message.
    """
    if v.vrnt_mask is None:
        raise ValueError(
            "{0} '{0}' must have 'vrnt_mask' (variant mask) assigned".format(
                type(v).__name__,
                vname
            )
        )