def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
builder.detach()
leaf_indices_below = suffixtree.calculate_leaf_indices( root = tree.root )
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
leaf_5 = root[ "$" ]
self.assertEqual( leaf_indices_below[ leaf_0 ], [ 0 ] )
self.assertEqual( leaf_indices_below[ leaf_1 ], [ 1 ] )
self.assertEqual( leaf_indices_below[ leaf_2 ], [ 2 ] )
self.assertEqual( leaf_indices_below[ leaf_3 ], [ 3 ] )
self.assertEqual( leaf_indices_below[ leaf_4 ], [ 4 ] )
self.assertEqual( leaf_indices_below[ leaf_5 ], [ 5 ] )
self.assertEqual( sorted( leaf_indices_below[ branch_t ] ), [ 0, 1 ] )
self.assertEqual( sorted( leaf_indices_below[ root ] ), list(range( 6)) )
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
builder.detach()
leaf_indices_below = suffixtree.calculate_leaf_indices( root = tree.root )
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
leaf_5 = root[ "$" ]
self.assertEqual( leaf_indices_below[ leaf_0 ], [ 0 ] )
self.assertEqual( leaf_indices_below[ leaf_1 ], [ 1 ] )
self.assertEqual( leaf_indices_below[ leaf_2 ], [ 2 ] )
self.assertEqual( leaf_indices_below[ leaf_3 ], [ 3 ] )
self.assertEqual( leaf_indices_below[ leaf_4 ], [ 4 ] )
self.assertEqual( leaf_indices_below[ leaf_5 ], [ 5 ] )
self.assertEqual( sorted( leaf_indices_below[ branch_t ] ), [ 0, 1 ] )
self.assertEqual( sorted( leaf_indices_below[ root ] ), range( 6 ) )
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
self.assertRaises( RuntimeError, single.matching_statistics, tree, list() );
builder.detach()
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
result = list( single.matching_statistics( tree, [] ) )
self.assertEqual( result, [] )
result = list( single.matching_statistics( tree, list( "QTTATTATTTAGCQWTTAGFK" ) ) )
self.assertEqual(
result,
[
( 0, ( root, 0 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 2, ( leaf_0, 2 ) ),
( 5, ( leaf_0, 5 ) ),
( 4, ( leaf_1, 5 ) ),
( 3, ( leaf_2, 5 ) ),
( 2, ( leaf_3, 5 ) ),
( 1, ( leaf_4, 5 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
( 4, ( leaf_0, 4 ) ),
( 3, ( leaf_1, 4 ) ),
( 2, ( leaf_2, 4 ) ),
( 1, ( leaf_3, 4 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
]
)
def test(self):
tree = single.tree()
result = list( single.matching_statistics( tree, list( "ABC" ) ) )
self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 )
builder = single.ukkonen( tree = tree )
for c in "TTAGC$":
builder.append( c )
self.assertRaises( RuntimeError, single.matching_statistics, tree, list() );
builder.detach()
root = tree.root
branch_t = root[ "T" ]
leaf_0 = branch_t[ "T" ]
leaf_1 = branch_t[ "A" ]
leaf_2 = root[ "A" ]
leaf_3 = root[ "G" ]
leaf_4 = root[ "C" ]
result = list( single.matching_statistics( tree, [] ) )
self.assertEqual( result, [] )
result = list( single.matching_statistics( tree, list( "QTTATTATTTAGCQWTTAGFK" ) ) )
self.assertEqual(
result,
[
( 0, ( root, 0 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 3, ( leaf_0, 3 ) ),
( 2, ( leaf_1, 3 ) ),
( 1, ( leaf_2, 3 ) ),
( 2, ( leaf_0, 2 ) ),
( 5, ( leaf_0, 5 ) ),
( 4, ( leaf_1, 5 ) ),
( 3, ( leaf_2, 5 ) ),
( 2, ( leaf_3, 5 ) ),
( 1, ( leaf_4, 5 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
( 4, ( leaf_0, 4 ) ),
( 3, ( leaf_1, 4 ) ),
( 2, ( leaf_2, 4 ) ),
( 1, ( leaf_3, 4 ) ),
( 0, ( root, 0 ) ),
( 0, ( root, 0 ) ),
]
)
def test_ukkonen1(self):
tree = single.tree()
self.assertEqual( tree.in_construction, False )
builder = single.ukkonen( tree )
self.assertTrue( tree.in_construction )
self.assertTrue( builder.is_attached )
self.assertTrue( builder.is_valid )
self.assertRaises( RuntimeError, single.ukkonen, tree )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertTrue( builder.is_valid )
self.assertFalse( tree.in_construction )
self.assertRaises( RuntimeError, builder.append, "a" )
def test_ukkonen1(self):
tree = single.tree()
self.assertEqual( tree.in_construction, False )
builder = single.ukkonen( tree )
self.assertTrue( tree.in_construction )
self.assertTrue( builder.is_attached )
self.assertTrue( builder.is_valid )
self.assertRaises( RuntimeError, single.ukkonen, tree )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertTrue( builder.is_valid )
self.assertFalse( tree.in_construction )
self.assertRaises( RuntimeError, builder.append, "a" )
def test_ukkonen2(self):
tree = single.tree()
builder = single.ukkonen( tree )
builder.append( glyph = "a" )
self.assertTrue( builder.is_valid )
builder.append( glyph = "n" )
self.assertTrue( builder.is_valid )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertFalse( tree.in_construction )
builder = single.ukkonen( tree )
self.assertTrue( builder.is_valid )
self.assertTrue( builder.is_attached )
self.assertTrue( tree.in_construction )
builder.append( glyph = "a" )
self.assertFalse( builder.is_valid )
self.assertRaises( RuntimeError, builder.detach )
builder.append( glyph = "n" )
self.assertFalse( builder.is_valid )
self.assertRaises( RuntimeError, builder.detach )
builder.append( glyph = "a" )
self.assertFalse( builder.is_valid )
self.assertRaises( RuntimeError, builder.detach )
builder.append( glyph = "s" )
self.assertTrue( builder.is_valid )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertFalse( tree.in_construction )
builder = single.ukkonen( tree )
self.assertTrue( builder.is_valid )
self.assertTrue( builder.is_attached )
self.assertTrue( tree.in_construction )
builder.append( glyph = "$" )
self.assertTrue( builder.is_valid )
builder.detach()
root = tree.root
self.assertTrue( root.is_root() )
self.assertEqual( set( root.keys() ), set( [ "a", "n", "s", "$" ] ) )
b_a = root[ "a" ]
self.assertFalse( b_a.is_root() )
self.assertFalse( b_a.is_leaf() )
self.assertEqual( b_a.start, 0 )
self.assertEqual( b_a.stop, 1 )
self.assertEqual( set( b_a.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_a.parent, root )
b_a_n = b_a[ "n" ]
self.assertFalse( b_a_n.is_root() )
self.assertFalse( b_a_n.is_leaf() )
self.assertEqual( b_a_n.start, 1 )
self.assertEqual( b_a_n.stop, 3 )
self.assertEqual( set( b_a_n.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_a_n.parent, b_a )
b_a_n_n = b_a_n[ "n" ]
self.assertTrue( b_a_n_n.is_leaf() )
self.assertEqual( b_a_n_n.start, 3 )
self.assertEqual( b_a_n_n.stop, 7 )
self.assertEqual( b_a_n_n.label, 0 )
self.assertEqual( b_a_n_n.parent, b_a_n )
b_a_n_s = b_a_n[ "s" ]
self.assertTrue( b_a_n_s.is_leaf() )
self.assertEqual( b_a_n_s.start, 5 )
self.assertEqual( b_a_n_s.stop, 7 )
self.assertEqual( b_a_n_s.label, 2 )
self.assertEqual( b_a_n_s.parent, b_a_n )
b_a_s = b_a[ "s" ]
self.assertTrue( b_a_s.is_leaf() )
self.assertEqual( b_a_s.start, 5 )
self.assertEqual( b_a_s.stop, 7 )
self.assertEqual( b_a_s.label, 4 )
self.assertEqual( b_a_s.parent, b_a )
b_n = root[ "n" ]
self.assertFalse( b_n.is_root() )
self.assertFalse( b_n.is_leaf() )
self.assertEqual( b_n.start, 1 )
self.assertEqual( b_n.stop, 3 )
self.assertEqual( set( b_n.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_n.parent, root )
b_n_n = b_n[ "n" ]
self.assertTrue( b_n_n.is_leaf() )
self.assertEqual( b_n_n.start, 3 )
self.assertEqual( b_n_n.stop, 7 )
self.assertEqual( b_n_n.label, 1 )
self.assertEqual( b_n_n.parent, b_n )
b_n_s = b_n[ "s" ]
self.assertTrue( b_n_s.is_leaf() )
self.assertEqual( b_n_s.start, 5 )
self.assertEqual( b_n_s.stop, 7 )
self.assertEqual( b_n_s.label, 3 )
self.assertEqual( b_n_s.parent, b_n )
b_s = root[ "s" ]
self.assertTrue( b_s.is_leaf() )
self.assertEqual( b_s.start, 5 )
self.assertEqual( b_s.stop, 7 )
self.assertEqual( b_s.label, 5 )
self.assertEqual( b_s.parent, root )
b_dl = root[ "$" ]
self.assertTrue( b_dl.is_leaf() )
self.assertEqual( b_dl.start, 6 )
self.assertEqual( b_dl.stop, 7 )
self.assertEqual( b_dl.label, 6 )
self.assertEqual( b_dl.parent, root )
self.assertEqual( b_a.suffix, root )
self.assertEqual( b_n.suffix, b_a )
self.assertEqual( b_a_n.suffix, b_n )
def test_ukkonen2(self):
tree = single.tree()
builder = single.ukkonen( tree )
builder.append( glyph = "a" )
self.assertTrue( builder.is_valid )
builder.append( glyph = "n" )
self.assertTrue( builder.is_valid )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertFalse( tree.in_construction )
builder = single.ukkonen( tree )
self.assertTrue( builder.is_valid )
self.assertTrue( builder.is_attached )
self.assertTrue( tree.in_construction )
builder.append( glyph = "a" )
self.assertFalse( builder.is_valid )
self.assertRaises( builder.detach )
builder.append( glyph = "n" )
self.assertFalse( builder.is_valid )
self.assertRaises( builder.detach )
builder.append( glyph = "a" )
self.assertFalse( builder.is_valid )
self.assertRaises( builder.detach )
builder.append( glyph = "s" )
self.assertTrue( builder.is_valid )
builder.detach()
self.assertFalse( builder.is_attached )
self.assertFalse( tree.in_construction )
builder = single.ukkonen( tree )
self.assertTrue( builder.is_valid )
self.assertTrue( builder.is_attached )
self.assertTrue( tree.in_construction )
builder.append( glyph = "$" )
self.assertTrue( builder.is_valid )
builder.detach()
root = tree.root
self.assertTrue( root.is_root() )
self.assertEqual( set( root.keys() ), set( [ "a", "n", "s", "$" ] ) )
b_a = root[ "a" ]
self.assertFalse( b_a.is_root() )
self.assertFalse( b_a.is_leaf() )
self.assertEqual( b_a.start, 0 )
self.assertEqual( b_a.stop, 1 )
self.assertEqual( set( b_a.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_a.parent, root )
b_a_n = b_a[ "n" ]
self.assertFalse( b_a_n.is_root() )
self.assertFalse( b_a_n.is_leaf() )
self.assertEqual( b_a_n.start, 1 )
self.assertEqual( b_a_n.stop, 3 )
self.assertEqual( set( b_a_n.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_a_n.parent, b_a )
b_a_n_n = b_a_n[ "n" ]
self.assertTrue( b_a_n_n.is_leaf() )
self.assertEqual( b_a_n_n.start, 3 )
self.assertEqual( b_a_n_n.stop, 7 )
self.assertEqual( b_a_n_n.label, 0 )
self.assertEqual( b_a_n_n.parent, b_a_n )
b_a_n_s = b_a_n[ "s" ]
self.assertTrue( b_a_n_s.is_leaf() )
self.assertEqual( b_a_n_s.start, 5 )
self.assertEqual( b_a_n_s.stop, 7 )
self.assertEqual( b_a_n_s.label, 2 )
self.assertEqual( b_a_n_s.parent, b_a_n )
b_a_s = b_a[ "s" ]
self.assertTrue( b_a_s.is_leaf() )
self.assertEqual( b_a_s.start, 5 )
self.assertEqual( b_a_s.stop, 7 )
self.assertEqual( b_a_s.label, 4 )
self.assertEqual( b_a_s.parent, b_a )
b_n = root[ "n" ]
self.assertFalse( b_n.is_root() )
self.assertFalse( b_n.is_leaf() )
self.assertEqual( b_n.start, 1 )
self.assertEqual( b_n.stop, 3 )
self.assertEqual( set( b_n.keys() ), set( [ "n", "s" ] ) )
self.assertEqual( b_n.parent, root )
b_n_n = b_n[ "n" ]
self.assertTrue( b_n_n.is_leaf() )
self.assertEqual( b_n_n.start, 3 )
self.assertEqual( b_n_n.stop, 7 )
self.assertEqual( b_n_n.label, 1 )
self.assertEqual( b_n_n.parent, b_n )
b_n_s = b_n[ "s" ]
self.assertTrue( b_n_s.is_leaf() )
self.assertEqual( b_n_s.start, 5 )
self.assertEqual( b_n_s.stop, 7 )
self.assertEqual( b_n_s.label, 3 )
self.assertEqual( b_n_s.parent, b_n )
b_s = root[ "s" ]
self.assertTrue( b_s.is_leaf() )
self.assertEqual( b_s.start, 5 )
self.assertEqual( b_s.stop, 7 )
self.assertEqual( b_s.label, 5 )
self.assertEqual( b_s.parent, root )
b_dl = root[ "$" ]
self.assertTrue( b_dl.is_leaf() )
self.assertEqual( b_dl.start, 6 )
self.assertEqual( b_dl.stop, 7 )
self.assertEqual( b_dl.label, 6 )
self.assertEqual( b_dl.parent, root )
self.assertEqual( b_a.suffix, root )
self.assertEqual( b_n.suffix, b_a )
self.assertEqual( b_a_n.suffix, b_n )
