from openomics.database.base import Annotatable

from openomics.transcriptomics import Expression

__all__ = ['SomaticMutation', 'DNAMethylation', 'CopyNumberVariation']

class SingleNucleotideVariants(Expression, Annotatable):

    def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",

                 transform_fn=None, dropna=False, npartitions=None, cohort_name=None):

        """

        Args:

            data:

            transpose:

            gene_index:

            usecols:

            gene_level:

            sample_level:

            transform_fn:

            dropna:

            npartitions:

            cohort_name:

        """

        super().__init__(data=data, transpose=transpose, gene_index=gene_index,

                         usecols=usecols, gene_level=gene_level,

                         sample_level=sample_level, transform_fn=transform_fn,

                         dropna=dropna, npartitions=npartitions, cohort_name=cohort_name)

    @classmethod

    def name(cls):

        return cls.__name__

class SomaticMutation(Expression, Annotatable):

    def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",

                 transform_fn=None, dropna=False, npartitions=None, cohort_name=None):

        """

        Args:

            data:

            transpose:

            gene_index:

            usecols:

            gene_level:

            sample_level:

            transform_fn:

            dropna:

            npartitions:

            cohort_name:

        """

        super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols,

                         gene_level=gene_level, sample_level=sample_level,

                         transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,

                         cohort_name=cohort_name)

    @classmethod

    def name(cls):

        return cls.__name__

class DNAMethylation(Expression, Annotatable):

    def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",

                 transform_fn=None, dropna=False, npartitions=None, cohort_name=None):

        """

        Args:

            data:

            transpose:

            gene_index:

            usecols:

            gene_level:

            sample_level:

            transform_fn:

            dropna:

            npartitions:

            cohort_name:

        """

        super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols,

                         gene_level=gene_level, sample_level=sample_level,

                         transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,

                         cohort_name=cohort_name)

    @classmethod

    def name(cls):

        return cls.__name__

class CopyNumberVariation(Expression, Annotatable):

    def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",

                 transform_fn=None, dropna=False, npartitions=None, cohort_name=None):

        """

        Args:

            data:

            transpose:

            gene_index:

            usecols:

            gene_level:

            sample_level:

            transform_fn:

            dropna:

            npartitions:

            cohort_name:

        """

        super().__init__(data=data, transpose=transpose, gene_index=gene_index,

                         usecols=usecols, gene_level=gene_level, sample_level=sample_level,

                         transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,

                         cohort_name=cohort_name)

    @classmethod

    def name(cls):

        return cls.__name__