from cpython cimport bool
from libcpp.vector cimport vector
from libcpp.string cimport string
from cython.operator cimport dereference as deref






"""
Create Cython definitions for the Interval API defined in Interval.h
"""
cdef extern from "bedFile.h":
    cdef enum BedLineStatus:
        BED_MALFORMED = -2
        BED_INVALID = -1
        BED_HEADER = 0
        BED_BLANK = 1
        BED_VALID = 2

    ctypedef unsigned int   CHRPOS
    ctypedef bint BOOL

    cdef cppclass BED:
        string chrom
        CHRPOS start
        CHRPOS end
        string name
        string score
        string strand
        CHRPOS o_start  # the start of an overlap with another interval
        CHRPOS o_end    # the end of an overlap with another interval
        unsigned short bedType
        string file_type
        BedLineStatus status
        vector[string] fields

        # constructors
        BED()
        BED(string chrom, CHRPOS start, CHRPOS end, string name,
             string score, string strand, vector[string] fields,
             CHRPOS o_start, CHRPOS o_end,
             unsigned short bedType, string file_type, BedLineStatus status)

        BED(string chrom, CHRPOS start, CHRPOS end)
        BED(string chrom, CHRPOS start, CHRPOS end, string strand)
        BED(string chrom, CHRPOS start, CHRPOS end, string name,
             string score, string strand, vector[string] fields)

        # methods
        string reportBed()


    cdef cppclass BedFile:
        BedFile(string)
        int Open()
        void Rewind()
        void Seek(unsigned long offset)
        void Close()
        BED  GetNextBed()
        void loadBedFileIntoMap()

        ### "all" ###
        # this version doesn't care if the strands match.
        vector[BED] FindOverlapsPerBin(BED bed, float overlapFraction)
        # if forceStrand is true, require that the strands match,
        vector[BED] FindOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)

        ### "any" ###
        int FindAnyOverlapsPerBin(BED bed, float overlapFraction)
        # if forceStrand is true, require that the strands match,
        int FindAnyOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)


        ### "count" ###
        int CountOverlapsPerBin(BED bed, float overlapFraction)
        # if forceStrand is true, require that the strands match,
        int CountOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
        string file_type
        bint _typeIsKnown


cdef class Interval:
    cdef BED *_bed
    cdef object _attrs
    cpdef append(Interval self, object value)
    cpdef deparse_attrs(Interval self)