"""
Utility functions for working with `Bitset`s and treating lists of (start,end)
as `Bitset`s.
"""

from bx.bitset import (
    BinnedBitSet,
    MAX,
)


def bitset_intersect(ex1, ex2):
    bits1 = list2bits(ex1)
    bits2 = list2bits(ex2)
    bits1.iand(bits2)
    return bits2list(bits1)


def bitset_subtract(ex1, ex2):
    bits1 = list2bits(ex1)
    bits2 = list2bits(ex2)
    bits2.invert()
    bits1.iand(bits2)
    return bits2list(bits1)


def list2bits(ex):
    bits = BinnedBitSet(MAX)
    for start, end in ex:
        bits.set_range(start, end - start)
    return bits


def bits2list(bits):
    ex = []
    end = 0
    while True:
        start = bits.next_set(end)
        if start == bits.size:
            break
        end = bits.next_clear(start)
        ex.append((start, end))
    return ex


def bitset_complement(exons):
    bits = BinnedBitSet(MAX)
    introns = []
    for start, end in exons:
        bits.set_range(start, end - start)
    bits.invert()

    # only complement within the range of the list
    ex_start = min(a[0] for a in exons)
    ex_end = max(a[1] for a in exons)
    end = ex_start
    len = ex_end
    while True:
        start = bits.next_set(end)
        if start == bits.size:
            break
        end = bits.next_clear(start)
        if end > len:
            end = len
        if start != end:
            introns.append((start, end))
        if end == len:
            break
    return introns


def bitset_interval_intersect(bits, istart, iend):
    rval = []
    end = istart
    len = iend
    while True:
        start = bits.next_set(end)
        if start >= len:
            break
        end = bits.next_clear(start)
        if start != end:
            rval.append((start, end))
        if end >= len:
            break
    return rval


def bitset_union(exons):
    bits = list2bits(exons)
    return bits2list(bits)
