#   Copyright 2018 Samuel Payne sam_payne@byu.edu
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#       http://www.apache.org/licenses/LICENSE-2.0
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.

# Function imports
from .stats_utils import (
        permutation_test_corr,
        permutation_test_means,
        wrap_pearson_corr,
        wrap_ttest
    )

from .pathway_utils import (
        # Pathway member query functions
        get_pathways_with_proteins,
        get_proteins_in_pathways,

        # WikiPathways functions
        get_interacting_proteins_wikipathways,
        list_pathways_wikipathways,

        # Reactome functions
        reactome_pathway_overlay,
        reactome_enrichment_analysis,

        # Other pathway databases functions
        get_interacting_proteins_biogrid,
        get_interacting_proteins_bioplex,
        get_interacting_proteins_string
    )

from .other_utils import (
        # Protein list getters
        get_corum_protein_lists,
        get_hgnc_protein_lists,

        # Other functions
        get_boxnote_text,
        # TODO: Fix in other_utils first:
        # get_frequently_mutated,
        reduce_multiindex,
        parse_hotspot,
        search
    )
