# FIXME all of this belongs somewhere else (probably either pbcore.io.dataset
# or a future base module for resequencing apps)

from collections import namedtuple
import itertools
import math
import re
import os

from pbcore.io import ReferenceSet

# FIXME pbcore keys contigs by name, but kineticsTools usually keys by ID
ReferenceWindow = namedtuple(
    "ReferenceWindow", ["refId", "refName", "start", "end"])


def loadReferenceContigs(referencePath, alignmentSet, windows=None):
    # FIXME we should get rid of this entirely, but I think it requires
    # fixing the inconsistency in how contigs are referenced here versus in
    # pbcore.io
    """
    Load the reference contigs, and tag each one with the ref.alignmentID it
    was assigned in the alignment file(s).  Return a list of contigs,
    which are used to set up IpdModel.
    """

    # Read contigs from FASTA file (or XML dataset)
    refReader = ReferenceSet(referencePath)
    contigs = []
    if windows is not None:
        refNames = set([rw.refName for rw in windows])
        for contig in refReader:
            if contig.id in refNames:
                contigs.append(contig)
    else:
        contigs.extend([x for x in refReader])
    contigDict = dict([(x.id, x) for x in contigs])

    # initially each contig has an id of None -- this will be overwritten with the id from the alignments if there are any
    # reads mapped to it.
    for x in contigs:
        x.alignmentID = None

    # Mark each contig with it's ID from the alignments - match them up using
    # MD5s
    for x in alignmentSet.referenceInfoTable:
        if x.FullName in contigDict:
            contigDict[x.FullName].alignmentID = x.ID

    return contigs


def referenceWindowsFromAlignment(ds, refInfoLookup):
    return [ReferenceWindow(refId=refInfoLookup(w[0]).ID,
                            refName=w[0],
                            start=w[1],
                            end=w[2]) for w in ds.refWindows]


def parseReferenceWindow(s, refInfoLookup):
    if s is None:
        return None
    m = re.match("(.*):(.*)-(.*)", s)
    if m:
        refContigInfo = refInfoLookup(m.group(1))
        refId = refContigInfo.ID
        refName = refContigInfo.Name
        refStart = int(m.group(2))
        refEnd = min(int(m.group(3)), refContigInfo.Length)
    else:
        refContigInfo = refInfoLookup(s)
        refId = refContigInfo.ID
        refName = refContigInfo.Name
        refStart = 0
        refEnd = refContigInfo.Length
    return ReferenceWindow(refId=refId, refName=refName, start=refStart,
                           end=refEnd)


def createReferenceWindows(refInfo):
    return [ReferenceWindow(refId=r.ID,
                            refName=r.Name,
                            start=0,
                            end=r.Length) for r in refInfo]


def enumerateChunks(referenceStride, referenceWindow):
    """
    Enumerate all work chunks on this reference contig (restricted to
    the windows, if provided).
    """
    def intersection(int1, int2):
        s1, e1 = int1
        s2, e2 = int2
        si, ei = max(s1, s2), min(e1, e2)
        if si < ei:
            return (si, ei)
        else:
            return None

    def enumerateIntervals(bounds, stride):
        """
        Enumerate windows of size "stride", attempting to align window
        boundaries on multiple of stride.
        """
        def alignDown(chunk, x):
            return (x // chunk) * chunk

        def alignUp(chunk, x):
            return int(math.ceil(float(x) / chunk) * chunk)

        start, end = bounds
        roundStart = alignDown(stride, start)
        roundEnd = alignUp(stride, end)

        for s in range(roundStart, roundEnd, stride):
            roundWin = (s, s + stride)
            yield intersection(bounds, roundWin)

    for (s, e) in enumerateIntervals((referenceWindow.start,
                                      referenceWindow.end), referenceStride):
        yield ReferenceWindow(refId=referenceWindow.refId,
                              refName=referenceWindow.refName,
                              start=s, end=e)


def loadAlignmentChemistry(alignmentSet):
    chems = alignmentSet.sequencingChemistry
    chemCounts = {k: len(list(v)) for k, v in itertools.groupby(chems)}
    majorityChem = max(chemCounts, key=chemCounts.get)
    return majorityChem