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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
from . import pathmap
from dendropy.datamodel import basemodel
from dendropy.datamodel import charmatrixmodel
from dendropy.utility.textprocessing import StringIO
class ValidateWriteable(object):
def write_out_validate_equal_and_return(self,
writeable,
schema,
kwargs):
self.maxDiff = None
sio = StringIO()
writeable.write(file=sio, schema=schema, **kwargs)
s0 = sio.getvalue()
s1 = writeable.as_string(schema=schema, **kwargs)
self.assertEqual(s0, s1)
with pathmap.SandboxedFile() as tempf:
writeable.write(path=tempf.name, schema=schema, **kwargs)
tempf.flush()
tempf.close()
with open(tempf.name, "r") as src:
s2 = src.read()
self.assertEqual(s0, s2)
return s0
class ValidateReadable(object):
def get_from(self,
object_type,
source_path,
schema,
kwargs):
results = []
with open(source_path, "r") as s0:
obj0 = object_type.get(stream=s0, schema=schema, **kwargs)
results.append(obj0)
obj1 = object_type.get(path=source_path, schema=schema, **kwargs)
results.append(obj1)
with open(source_path, "r") as s0:
s = s0.read()
obj2 = object_type.get(data=s, schema=schema, **kwargs)
results.append(obj2)
return results
def read_from(self,
object_factory,
source_path,
schema,
kwargs):
results = []
obj0 = object_factory()
with open(source_path, "r") as s0:
obj0.read(stream=s0, schema=schema, **kwargs)
results.append(obj0)
obj1 = object_factory()
obj1.read(path=source_path, schema=schema, **kwargs)
results.append(obj1)
obj2 = object_factory()
with open(source_path, "r") as s0:
s = s0.read()
obj2.read(value=s, schema=schema, **kwargs)
results.append(obj2)
return results
class Comparator(object):
def compare_distinct_taxon(self,
x1, x2,
taxon_namespace_scoped=True,
compare_annotations=True):
if taxon_namespace_scoped:
self.assertIs(x1, x2)
else:
if x1 is None or x2 is None:
self.assertIs(x1, None)
self.assertIs(x2, None)
else:
self.assertIsNot(x1, x2)
self.assertEqual(x1.label, x2.label)
if compare_annotations:
self.compare_distinct_annotables(x1, x2)
def compare_distinct_taxon_namespace(self,
x1, x2,
taxon_namespace_scoped=True,
compare_annotations=True,):
if taxon_namespace_scoped:
self.assertIs(x1, x2)
else:
if x1 is None or x2 is None:
self.assertIs(x1, None)
self.assertIs(x2, None)
else:
self.assertIsNot(x1, x2)
self.assertEqual(x1.label, x2.label)
self.assertEqual(len(x1._taxa), len(x2._taxa))
for t1, t2 in zip(x1._taxa, x2._taxa):
self.compare_distinct_taxon(t1, t2,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_annotations=compare_annotations)
if compare_annotations:
self.compare_distinct_annotables(x1, x2)
def compare_distinct_sequences(self,
x1, x2,
compare_annotations=True):
self.assertIsNot(x1, x2)
self.assertEqual(len(x1), len(x2))
for c1, c2 in zip(x1, x2):
self.assertEqual(c1, c2)
if compare_annotations:
self.compare_distinct_annotables(x1, x2)
def compare_distinct_char_matrix(self,
x1, x2,
taxon_namespace_scoped=True,
compare_matrix_annotations=True,
compare_sequence_annotations=True,
compare_taxon_annotations=True):
self.assertIsNot(x1, x2)
self.assertEqual(len(x1), len(x2))
self.compare_distinct_taxon_namespace(x1.taxon_namespace, x2.taxon_namespace,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_annotations=compare_taxon_annotations,
)
self.assertEqual(x1.label, x2.label)
self.assertEqual(x1.data_type, x2.data_type)
if isinstance(x1, charmatrixmodel.DiscreteCharacterMatrix):
# print(x1.data_type, x1.datatype_alphabet)
self.assertEqual(len(x1.state_alphabets), len(x2.state_alphabets))
for sa1, sa2 in zip(x1.state_alphabets, x2.state_alphabets):
self.assertIs(sa1, sa2)
self.assertIs(x1._default_state_alphabet, x2._default_state_alphabet)
for t1, t2 in zip(x1, x2):
if taxon_namespace_scoped:
self.assertIs(t1, t2)
else:
self.assertIsNot(t1, t2)
s1 = x1[t1]
s2 = x2[t2]
self.compare_distinct_sequences(s1, s2,
compare_annotations=compare_sequence_annotations)
if compare_matrix_annotations:
self.compare_distinct_annotables(x1, x2)
def compare_distinct_tree_list(self,
x1, x2,
taxon_namespace_scoped=True,
compare_tree_annotations=True,
compare_taxon_annotations=True):
self.assertIsNot(x1, x2)
self.assertEqual(len(x1), len(x2))
self.compare_distinct_taxon_namespace(x1.taxon_namespace, x2.taxon_namespace,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_annotations=compare_taxon_annotations,
)
self.assertEqual(x1.label, x2.label)
for t1, t2 in zip(x1, x2):
self.assertIsNot(t1, t2)
self.compare_distinct_trees(t1, t2,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_tree_annotations=compare_tree_annotations,
compare_taxon_annotations=compare_taxon_annotations)
def compare_distinct_trees(self,
x1, x2,
taxon_namespace_scoped=True,
compare_tree_annotations=True,
compare_taxon_annotations=True):
self.assertIsNot(x1, x2)
self.assertEqual(x1.label, x2.label)
self.compare_distinct_taxon_namespace(x1.taxon_namespace, x2.taxon_namespace,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_annotations=compare_taxon_annotations,
)
self.compare_distinct_nodes(x1.seed_node, x2.seed_node,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_tree_annotations=compare_tree_annotations,
compare_taxon_annotations=compare_taxon_annotations)
def compare_distinct_nodes(self,
x1, x2,
taxon_namespace_scoped=True,
compare_tree_annotations=True,
compare_taxon_annotations=True,
check_children=True):
self.assertIsNot(x1, x2)
self.assertEqual(x1.label, x2.label)
taxon1 = x1.taxon
taxon2 = x2.taxon
self.compare_distinct_taxon(x1.taxon, x2.taxon,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_annotations=compare_taxon_annotations)
self.assertIsNot(x1.edge, x2.edge)
self.assertEqual(x1.edge.label, x2.edge.label)
self.assertEqual(x1.edge.length, x2.edge.length)
self.assertIs(x1.edge.head_node, x1)
self.assertIs(x2.edge.head_node, x2)
if x1._parent_node is None or x2._parent_node is None:
self.assertIs(x1._parent_node, None)
self.assertIs(x2._parent_node, None)
self.assertIs(x1.edge.tail_node, None)
self.assertIs(x2.edge.tail_node, None)
else:
self.compare_distinct_nodes(x1._parent_node, x2._parent_node,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_tree_annotations=compare_tree_annotations,
compare_taxon_annotations=compare_taxon_annotations,
check_children=False)
self.assertIn(x1, x1._parent_node._child_nodes)
self.assertNotIn(x1, x2._parent_node._child_nodes)
self.assertIn(x2, x2._parent_node._child_nodes)
self.assertNotIn(x2, x1._parent_node._child_nodes)
if check_children:
self.assertEqual(len(x1._child_nodes), len(x2._child_nodes))
for c1, c2 in zip(x1._child_nodes, x2._child_nodes):
self.compare_distinct_nodes(c1, c2,
taxon_namespace_scoped=taxon_namespace_scoped,
compare_tree_annotations=compare_tree_annotations,
compare_taxon_annotations=compare_taxon_annotations,
check_children=True)
if compare_tree_annotations:
self.compare_distinct_annotables(x1, x2)
self.compare_distinct_annotables(x1.edge, x2.edge)
def compare_distinct_annotables(self, x1, x2):
self.assertIsNot(x1, x2)
if not x1.has_annotations:
self.assertTrue( (not hasattr(x1, "_annotations")) or len(x1._annotations) == 0 )
self.assertFalse(x2.has_annotations)
self.assertTrue( (not hasattr(x2, "_annotations")) or len(x2._annotations) == 0 )
return
self.assertTrue( hasattr(x1, "_annotations") and len(x1._annotations) > 0 )
self.assertTrue(x2.has_annotations)
self.assertTrue( hasattr(x2, "_annotations") and len(x2._annotations) > 0 )
self.assertIs(x1._annotations.target, x1)
self.assertIs(x2._annotations.target, x2)
self.assertIsNot(x1._annotations, x2._annotations)
self.assertEqual(len(x1._annotations), len(x2._annotations))
for a1, a2 in zip(x1._annotations, x2._annotations):
self.assertIsNot(a1, a2)
if a1.is_attribute:
self.assertTrue(a2.is_attribute)
self.assertEqual(a1._value[1], a2._value[1])
else:
self.assertEqual(a1._value, a2._value)
for k in a1.__dict__:
if k == "_value":
continue
self.assertIn(k, a2.__dict__)
v1 = a1.__dict__[k]
v2 = a2.__dict__[k]
if isinstance(v1, basemodel.DataObject):
self.assertTrue(isinstance(v2, basemodel.DataObject))
self.assertIsNot(v1, v2)
elif isinstance(v1, basemodel.AnnotationSet):
self.assertTrue(isinstance(v2, basemodel.AnnotationSet))
self.assertIs(v1.target, a1)
self.assertIs(v2.target, a2)
for s1, s2 in zip(v1, v2):
self.compare_distinct_annotables(s1, s2)
else:
self.assertEqual(v1, v2)
self.compare_distinct_annotables(a1, a2)
|
