def test_conversion(self):
fn = self.fn
g = GenomeNode.create_from_ptr(fn.gn, True)
self.assertEqual((100, 500), g.range)
f2 = FeatureNode.create_from_ptr(g.gn, True)
self.assertEqual((100, 500), f2.range)
def test_conversion(self):
fn = self.fn
g = GenomeNode.create_from_ptr(fn.gn, True)
self.assertEqual((100, 500), g.range)
f2 = FeatureNode.create_from_ptr(g.gn, True)
self.assertEqual((100, 500), f2.range)
def setUp(self):
self.fn = FeatureNode.create_new("foo", "gene", 100, 10000, "+")
self.cn = CommentNode.create_new("comment")
self.rn = RegionNode.create_new("foo", 100, 2000)
self.sn = SequenceNode.create_new("foo", "AGATATAGA")
self.tv = TestVisitor()
self.etv = ErrorTestVisitor()
def setUp(self):
self.fn = FeatureNode.create_new("foo", "gene", 100, 10000, "+")
self.cn = CommentNode.create_new("comment")
self.rn = RegionNode.create_new("foo", 100, 2000)
self.sn = SequenceNode.create_new("foo", "AGATATAGA")
self.en = EOFNode.create_new()
self.mn = MetaNode.create_new("foo", "bar")
self.tv = TestVisitor()
self.etv = ErrorTestVisitor()
def test_iterator(self):
fn = self.fn
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn4 = FeatureNode.create_new("test", "type4", 250, 300, "+")
fn.add_child(fn3)
fn.add_child(fn4)
# try object as iterator
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# try iterator method
types = []
for i, f in enumerate(fn.traverse_dfs()):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# try callable object as iterator
types = []
for i, f in enumerate(fn(method="depth_first")):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# direct
types = []
for i, f in enumerate(fn(method="direct")):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
types = []
for i, f in enumerate(fn.traverse_direct()):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
fn.depth_first = False
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
def test_iterator(self):
fn = self.fn
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn4 = FeatureNode.create_new("test", "type4", 250, 300, "+")
fn.add_child(fn3)
fn.add_child(fn4)
# try object as iterator
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# try iterator method
types = []
for i, f in enumerate(fn.traverse_dfs()):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# try callable object as iterator
types = []
for i, f in enumerate(fn(method="depth_first")):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assert_(i == 3, i)
# direct
types = []
for i, f in enumerate(fn(method="direct")):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
types = []
for i, f in enumerate(fn.traverse_direct()):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
fn.depth_first = False
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assert_(i == 2, i)
def test_fni(self):
fn = self.fn
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
tfn = fni.next()
num_features += 1
self.assertEqual(num_features, 2)
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn.add_child(fn3)
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
num_features += 1
tfn = fni.next()
self.assertEqual(num_features, 3)
def test_fni(self):
fn = self.fn
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
tfn = fni.next()
num_features += 1
self.assertEqual(num_features, 2)
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn.add_child(fn3)
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
num_features += 1
tfn = fni.next()
self.assertEqual(num_features, 3)
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
self.fn2 = FeatureNode.create_new("test", "type2", 200, 300, "+")
self.fn.add_child(self.fn2)
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
self.fn2 = FeatureNode.create_new("test", "type2", 200, 300, "+")
self.fn.add_child(self.fn2)
def visit_feature_node(self, fn):
new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000,
"+")
fn.add_child(new_child)
def visit_feature_node(self, fn):
new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000, "+")
fn.add_child(new_child)
