"""
Support for chopping a list of alignment blocks to only the portion that
intersects a particular interval.
"""


def chop_list(blocks, src, start, end):
    """
    For each alignment block in the sequence `blocks`, chop out the portion
    of the block that overlaps the interval [`start`,`end`) in the
    component/species named `src`.
    """
    new_blocks = []
    for block in blocks:
        ref = block.get_component_by_src(src)
        # If the reference component is on the '-' strand we should complement the interval
        if ref.strand == "-":
            slice_start = max(ref.src_size - end, ref.start)
            slice_end = max(ref.src_size - start, ref.end)
        else:
            slice_start = max(start, ref.start)
            slice_end = min(end, ref.end)
        sliced = block.slice_by_component(ref, slice_start, slice_end)
        good = True
        for c in sliced.components:
            if c.size < 1:
                good = False
        if good:
            new_blocks.append(sliced)
    return new_blocks