def sameCoordinates(self, pairwiseAlignment):
return self.contig1 == pairwiseAlignment.contig1 and \
self.start1 == pairwiseAlignment.start1 and \
self.end1 == pairwiseAlignment.end1 and \
self.strand1 == pairwiseAlignment.strand1 and \
self.contig2 == pairwiseAlignment.contig2 and \
self.start2 == pairwiseAlignment.start2 and \
self.end2 == pairwiseAlignment.end2 and \
self.strand2 == pairwiseAlignment.strand2 and \
close(self.score, pairwiseAlignment.score, 0.001)
def __eq__(self, pairwiseAlignment):
if pairwiseAlignment is None:
return False
return self.contig1 == pairwiseAlignment.contig1 and \
self.start1 == pairwiseAlignment.start1 and \
self.end1 == pairwiseAlignment.end1 and \
self.strand1 == pairwiseAlignment.strand1 and \
self.contig2 == pairwiseAlignment.contig2 and \
self.start2 == pairwiseAlignment.start2 and \
self.end2 == pairwiseAlignment.end2 and \
self.strand2 == pairwiseAlignment.strand2 and \
close(self.score, pairwiseAlignment.score, 0.001) and \
self.operationList == pairwiseAlignment.operationList
def __eq__(self, pairwiseAlignment):
if pairwiseAlignment is None:
return False
return self.contig1 == pairwiseAlignment.contig1 and \
self.start1 == pairwiseAlignment.start1 and \
self.end1 == pairwiseAlignment.end1 and \
self.strand1 == pairwiseAlignment.strand1 and \
self.contig2 == pairwiseAlignment.contig2 and \
self.start2 == pairwiseAlignment.start2 and \
self.end2 == pairwiseAlignment.end2 and \
self.strand2 == pairwiseAlignment.strand2 and \
close(self.score, pairwiseAlignment.score, 0.001) and \
self.operationList == pairwiseAlignment.operationList
def testRemodelTreeRemovingRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomLeafNode(binaryTree)
remodTree = remodelTreeRemovingRoot(binaryTree, node.traversalID.mid)
print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
d = getDistancesBetweenLeaves(binaryTree)
d2 = getDistancesBetweenLeaves(remodTree)
print d
print d2
for key in d2:
assert close(d2[key], d[key], 0.0001)
def testRemodelTreeRemovingRoot(self):
for test in xrange(0, self.testNo):
binaryTree = getRandomTree()
binaryTree_depthFirstNumbers(binaryTree)
node = getRandomLeafNode(binaryTree)
remodTree = remodelTreeRemovingRoot(binaryTree,
node.traversalID.mid)
print "test", test, printBinaryTree(
binaryTree,
True), printBinaryTree(node,
True), printBinaryTree(remodTree, True)
binaryTree_depthFirstNumbers(remodTree)
distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
d = getDistancesBetweenLeaves(binaryTree)
d2 = getDistancesBetweenLeaves(remodTree)
print d
print d2
for key in d2:
assert close(d2[key], d[key], 0.0001)
def __eq__(self, op):
if op is None:
return False
return self.type == op.type and self.length == op.length and close(self.score, op.score, 0.0001)