def edit_distance(seq1, seq2): while len(seq1[0]) > 1 and len(seq2[0]) > 1: seq1 = seq1[0] seq2 = seq2[0] matrix = {} for x in range(len(seq1) + 1): matrix[x, 0] = x for y in range(len(seq2) + 1): matrix[0, y] = y for x in range(1, len(seq1) + 1): for y in range(1, len(seq2) + 1): if seq1[x - 1] == seq2[y - 1]: mismatch = 0 else: mismatch = 1 matrix[x, y] = min(matrix[x, y - 1] + 1, matrix[x - 1, y] + 1, matrix[x - 1, y - 1] + mismatch) return matrix[x, y] def joined_distance(sib1, sib2, node): return (edit_distance(sib1, node) + edit_distance(sib2, node) - edit_distance(sib1, sib2))/2 def edit_matrix(genes): distances = [] for x in genes: x_dist = [] for y in genes[:(genes.index(x))] + genes[(genes.index(y))+1:] x_dist += [edit_distance(x,y)] distances += [x_dist] return distances class node: def __init__(self, ltree, top, rtree): self.top = top self.ltree = ltree self.rtree = rtree def __repr__(self): return str(self.top) class BT(node): def __init__(self, left=None, top=None, right=None): if top == None: # primitive self.rep = None else: # extending self.rep = node(left, top, right) def withEntry(self, key, value): return node([], [(key, value)], []) def empty(self): return self.rep == None def root(self): precondition(not self.empty()) return self.rep.top def left(self): precondition(not self.empty()) return self.rep.ltree def right(self): precondition(not self.empty()) return self.rep.rtree def size(self): if self.empty(): return 0 else: return self.left().size() + self.right().size() + 1 def __repr__(self): #inorder traversal a =[] if not self.empty(): if not self.left().empty(): a += self.left().__repr__() if not self.empty(): a += [(self.root()[0][0], self.root()[0][1])] if not self.right().empty(): a += self.right().__repr__() return a ############# class BSTD(BT): """ def rep_invariant(self): if self.empty(): return True elif not self.left().empty(): if self.left().root()[0][0] >= self.root()[0][0]: return False elif not self.right().empty(): if self.right().root()[0][0] <= self.root()[0][0]: return False if self.left().rep_invariant() and self.left().rep_invariant(): return True """ # insert mutator without allowing duplicates def generate(genes): best = len(max(genes, key=len)) distances = edit_matrix(genes) for x in distances: for y in x: if y < best: best = y pair = (genes[distances.index(x)], genes[x.index(y)]) spots = (genes[distances.index(x)],genes[x.index(y)]) distances = distances[:spots[0]] + distances[spots[0]+1:] distances = distances[:spots[1]] + distances[spots[1]+1:] while len(distances) > 0:
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