"""
CS146 Example with sequence alignment using recursion and memoization
"""
from functools import wraps
import urllib.request

# Python has rejected the certificate used for the CS dept. server so we bypass some of those checks
import ssl
ssl._create_default_https_context = ssl._create_unverified_context

# Edge scores
MATCH = 1
MISMATCH = -1
GAP = -1

# Record source of incoming best edge
DIAG = 0
LEFT = 1
UPWD = 2
TAXI = 3

def countcalls(func):
    """Decorator to track the number of times a function is called. Provides `calls` attribute."""
    countcalls.calls = 0

    @wraps(func)
    def wrapper(*args, **kwargs):
        initial_calls = countcalls.calls
        countcalls.calls += 1
        result = func(*args, **kwargs)
        wrapper.calls = countcalls.calls - initial_calls
        return result

    return wrapper

@countcalls
def global_align(lft_seq, top_seq, lft, top):
    """Perform Needleman-Wunsch global alignment of two sequences

    Args:
        lft_seq: String sequence on "left side" of the alignment grid
        top_seq: String sequence on "top" of the alignment grid
        lft: Index to align through, i.e., left_seq[lft-1] with top_seq[top-1]
        top: Index to align through, i.e., left_seq[lft-1] with top_seq[top-1]

    Returns:
        Score of global alignment of left_seq[lft-1] with top_seq[top-1]
    """
    if lft == 0 and top == 0:
        return 0
    elif lft == 0:
        return global_align(lft_seq, top_seq, lft, top-1) + GAP
    elif top == 0:
        return global_align(lft_seq, top_seq, lft-1, top) + GAP
    else:
        if lft_seq[lft-1] == top_seq[top-1]:
            diag = MATCH
        else:
            diag = MISMATCH
        return max(
            global_align(lft_seq, top_seq, lft, top-1) + GAP,
            global_align(lft_seq, top_seq, lft-1, top) + GAP,
            global_align(lft_seq, top_seq, lft-1, top-1) + diag
        )

# Test example    
# global_align("TGTCC", "TGATC", 5, 5)
# print("Number of recursive calls:", global_align.calls) # Report number of recursive calls

@countcalls
def global_align_memo(lft_seq, top_seq, lft, top, scores):
    """Perform memoized Needleman-Wunsch global alignment of two sequences

    Args:
        lft_seq: String sequence on "left side" of the alignment grid
        top_seq: String sequence on "top" of the alignment grid
        lft: Index to align through, i.e., left_seq[lft-1] with top_seq[top-1]
        top: Index to align through, i.e., left_seq[lft-1] with top_seq[top-1]
        scores: Dictionary of memoized scores for each (lft, top) pair

    Returns:
        Score of global alignment of left_seq[lft-1] with top_seq[top-1]
    """
    #TODO: Have we already solved this problem? Return solution if so.

    if lft == 0 and top == 0:
        edge = 0
    elif lft == 0:
        edge = global_align_memo(lft_seq, top_seq, lft, top-1, scores) + GAP
    elif top == 0:
        edge = global_align_memo(lft_seq, top_seq, lft-1, top, scores) + GAP
    else:
        if lft_seq[lft-1] == top_seq[top-1]:
            diag = MATCH
        else:
            diag = MISMATCH
        edge = max(
            global_align_memo(lft_seq, top_seq, lft, top-1, scores) + GAP,
            global_align_memo(lft_seq, top_seq, lft-1, top, scores) + GAP,
            global_align_memo(lft_seq, top_seq, lft-1, top-1, scores) + diag
        )
    
    #TODO: Save solution to this problem for future reference
    return edge

# Test example
# scores = {}
# global_align_memo("TGTCC", "TGATC", 5, 5, scores)
# print("Number of recursive calls:", global_align_memo.calls) # Report number of recursive calls