#!/usr/bin/env python

__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"

def pog_traceback(pogs, aligned_positions):
    upto = [0, 0]
    full_aligned_positions = []
    align_builder = POGBuilder(pogs)
    for posn in aligned_positions:
        assert len(posn) == 2
        for (dim, pos) in enumerate(posn):
            if pos is not None:
                align_builder.addSkipped(dim, upto[dim], pos)
                upto[dim] = pos+1
        
        align_builder.addAligned(posn)
    
    for dim in [0,1]:
        align_builder.addSkipped(dim, upto[dim], len(pogs[dim]))
    
    result_pog = align_builder.getPOG()
    
    return result_pog

class POGBuilder(object):
    def __init__(self, children):
        self.children = children
        self.remap = [{} for child in children]
        self.started = [False, False]
        self.last = [None, None]
        self.result = [[]]
        self.origins = [[]]
        self.aligned_positions = []
        self.states = []
    
    def addSkipped(self, dim, start, end, old_gap=True):
        for p in range(start, end):
            fp = [None, None]
            fp[dim] = p
            fp = tuple(fp)
            self.addAligned(fp, old_gap=old_gap)
    
    def addAligned(self, posn, old_gap=False):
        pre_merged = set()
        assert len(posn) == 2
        for (dim, pos) in enumerate(posn):
            if pos is None:
                continue
            self.remap[dim][pos] = len(self.aligned_positions)
            self.last[dim] = pos
        self.result.append(pre_merged)
        self.aligned_positions.append(posn)
        if None not in posn:
            state = 'm'
        elif posn[0] is None:
            state = 'x'
        else:
            state = 'y'
        if not old_gap:
            state = state.upper()
        self.states.append(state)
    
    def getPOG(self):
        jumps = []
        gapmap = {}
        ingap = False
        # Build a list of gaps (ie: segments of X or Y state) in
        # the alignment and a dict which maps from seq posn to the
        # start of the surrounding gap.
        for (i, state) in enumerate(self.states):
            gap = state in 'XYxy'
            if gap and not ingap:
                start = i
                ingap = True
            elif ingap and not gap:
                jumps.append((start, i))
                ingap = False
            if ingap:
                gapmap[i] = start
        
        # Keep only those child gaps which sit entirely within a gap
        # in this alignment
        child_jumps = []
        for (dim,pog) in enumerate(self.children):
            r = self.remap[dim]
            l = len(pog)
            for (i, j) in pog.jumps:
                (i, j) = (r[i], r[j])
                if i in gapmap and j in gapmap and gapmap[i] == gapmap[j]:
                    child_jumps.append((i,j))
        
        pog = POG(len(self.aligned_positions), jumps, child_jumps)
        pog.aligned_positions = self.aligned_positions
        pog.states = ''.join(self.states)
        return pog
    

class POG(object):
    """A representation of the indel positions in a sequence, ie:
    those segments of the sequence which may be inserts and so not
    present in the parent sequence.
    
    Indels are represented as tuples of
        (1st posn in indel, 1st posn after indel)
    """
    
    def __init__(self, length, jumps, child_jumps):
        self.jumps = jumps
        self.child_jumps = child_jumps
        self.all_jumps = self.jumps + self.child_jumps
        self.all_jumps.sort(key=lambda (i,j):j)
        self.length = length
        for (i, j) in self.all_jumps:
            assert i <= j, (length, jumps, child_jumps)
            assert 0 <= i <= length, (length, jumps, child_jumps)
            assert 0 <= j <= length, (length, jumps, child_jumps)
    
    def traceback(self, other, aligned_positions):
        return pog_traceback([self, other], aligned_positions)
    
    def asListOfPredLists(self):
        """A representation of the POG as a list of predecessor positions,
        a simple way to represent DAGs eg: [], [0], [1] would be a simple
        sequence of length 3.  Extra start and end positions are added, so
        the length is len(self)+2 and the positions are all offset by 1"""
        result = [[]]
        # First the regular, linear sequence relationships
        for i in range(self.length+1):
            pre = [i]
            result.append(pre)
        # Then add in the indel jumps.  Given an indel from i to j
        # j could have been ajacent to one of i's predecessors in
        # the ancestral sequence. This depends on all_jumps being sorted
        # by j.
        for (i,j) in self.all_jumps:
            if i == j:
                continue
            assert i < j
            result[j+1].extend(result[i+1])
        return result
    
    def getAlignedPositions(self):
        return self.aligned_positions
    
    def getFullAlignedPositions(self):
        return self.aligned_positions
    
    def __len__(self):
        return self.length
    
    def __getitem__(self, index):
        # POGs need to be sliceable for the hirchberg algorithm.
        if index.start is None:
            start = 0
        else:
            start = index.start
        if index.stop is None:
            end = self.length
        else:
            end = index.stop
        assert end >= start, (start, end, index, self.length)
        def moved(i):
            return max(min(i, end), start)-start
        jumps = [(moved(i), moved(j)) for (i,j) in self.jumps if i<end or j>start]
        cjumps = [(moved(i), moved(j)) for (i,j) in self.child_jumps if i<end or j>start]
        return POG(end-start, jumps, cjumps)
    
    def backward(self):
        # Switches predecessors / successors
        # POGs need to be reversable for the hirchberg algorithm.
        length = self.length
        jumps = [(length-j, length-i) for (i,j) in self.jumps]
        cjumps = [(length-j, length-i) for (i,j) in self.child_jumps]
        return POG(length, jumps, cjumps)
    

class LeafPOG(POG):
    """The POG for a known sequence contains no indels."""
    
    def __init__(self, length):
        self.length = length
        self.all_jumps = []
        self.jumps = []
    
    def asListOfPredLists(self):
        pog = [ [[i]] for i in range(length)]
        return [[]] + pog + [[len(pog)]]
    
    def __len__(self):
        return self.length
    
    def backward(self):
        return LeafPOG(self.length)


def leaf2pog(leaf):
    return LeafPOG(len(leaf))
