public void TestDistanceMatrix()
{
int dimension = 4;
IDistanceMatrix distanceMatrix = new SymmetricDistanceMatrix(dimension);
for (int i = 0; i < distanceMatrix.Dimension - 1; ++i)
{
for (int j = i + 1; j < distanceMatrix.Dimension; ++j)
{
distanceMatrix[i, j] = i + j;
distanceMatrix[j, i] = i + j;
}
}
IHierarchicalClustering hierarchicalClustering = new HierarchicalClusteringSerial(distanceMatrix);
Assert.AreEqual(7, hierarchicalClustering.Nodes.Count);
for (int i = 0; i < dimension * 2 - 1; ++i)
{
Assert.AreEqual(i, hierarchicalClustering.Nodes[i].ID);
}
for (int i = dimension; i < hierarchicalClustering.Nodes.Count; ++i)
{
Console.WriteLine(hierarchicalClustering.Nodes[i].LeftChildren.ID);
Console.WriteLine(hierarchicalClustering.Nodes[i].RightChildren.ID);
}
//Assert.AreEqual(0, hierarchicalClustering.Nodes[4].LeftChildren.ID);
//Assert.AreEqual(1, hierarchicalClustering.Nodes[4].RightChildren.ID);
//Assert.AreEqual(2, hierarchicalClustering.Nodes[5].LeftChildren.ID);
//Assert.AreEqual(4, hierarchicalClustering.Nodes[5].RightChildren.ID);
//Assert.AreEqual(3, hierarchicalClustering.Nodes[6].LeftChildren.ID);
//Assert.AreEqual(5, hierarchicalClustering.Nodes[6].RightChildren.ID);
}
public void TestProgressiveAligner()
{
ISequence templateSequence = new Sequence(Alphabets.DNA, "ATGCSWRYKMBVHDN-");
Dictionary <ISequenceItem, int> itemSet = new Dictionary <ISequenceItem, int>();
for (int i = 0; i < templateSequence.Count; ++i)
{
itemSet.Add(templateSequence[i], i);
}
Profiles.ItemSet = itemSet;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrices.AmbiguousDna);
int gapOpenPenalty = -8;
int gapExtendPenalty = -1;
int kmerLength = 3;
ISequence seqA = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
ISequence seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG");
ISequence seqC = new Sequence(Alphabets.DNA, "GGGACAAAATCAG");
List <ISequence> sequences = new List <ISequence>();
sequences.Add(seqA);
sequences.Add(seqB);
sequences.Add(seqC);
KmerDistanceMatrixGenerator kmerDistanceMatrixGenerator =
new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA);
kmerDistanceMatrixGenerator.GenerateDistanceMatrix(sequences);
IHierarchicalClustering hierarchicalClustering = new HierarchicalClusteringSerial(kmerDistanceMatrixGenerator.DistanceMatrix);
BinaryGuideTree tree = new BinaryGuideTree(hierarchicalClustering);
IProgressiveAligner progressiveAligner = new ProgressiveAligner(ProfileAlignerNames.NeedlemanWunschProfileAligner, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
progressiveAligner.Align(sequences, tree);
ISequence expectedSeqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
ISequence expectedSeqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
ISequence expectedSeqC = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
Assert.AreEqual(expectedSeqA.ToString(), progressiveAligner.AlignedSequences[0].ToString());
Assert.AreEqual(expectedSeqB.ToString(), progressiveAligner.AlignedSequences[1].ToString());
Assert.AreEqual(expectedSeqC.ToString(), progressiveAligner.AlignedSequences[2].ToString());
}
public void TestBinaryGuideTree()
{
int numberOfNodes = 5;
List <BinaryGuideTreeNode> nodes = new List <BinaryGuideTreeNode>(numberOfNodes);
for (int i = 0; i < numberOfNodes; ++i)
{
nodes.Add(new BinaryGuideTreeNode(i));
}
nodes[3].LeftChildren = nodes[0];
nodes[3].RightChildren = nodes[1];
nodes[4].LeftChildren = nodes[3];
nodes[4].RightChildren = nodes[2];
nodes[0].Parent = nodes[3];
nodes[1].Parent = nodes[3];
nodes[2].Parent = nodes[4];
nodes[3].Parent = nodes[4];
Assert.IsFalse(nodes[0].IsRoot);
Assert.IsTrue(nodes[0].IsLeaf);
Assert.IsFalse(nodes[1].IsRoot);
Assert.IsTrue(nodes[1].IsLeaf);
Assert.IsFalse(nodes[2].IsRoot);
Assert.IsTrue(nodes[2].IsLeaf);
Assert.IsFalse(nodes[3].IsRoot);
Assert.IsFalse(nodes[3].IsLeaf);
Assert.IsTrue(nodes[4].IsRoot);
Assert.IsFalse(nodes[4].IsLeaf);
Assert.AreEqual(nodes[3], nodes[0].Parent);
int numberOfEdges = 4;
List <BinaryGuideTreeEdge> edges = new List <BinaryGuideTreeEdge>(numberOfEdges);
for (int i = 0; i < numberOfEdges; ++i)
{
edges.Add(new BinaryGuideTreeEdge(i));
}
edges[0].ParentNode = nodes[3];
edges[0].ChildNode = nodes[0];
edges[1].ParentNode = nodes[3];
edges[1].ChildNode = nodes[1];
edges[2].ParentNode = nodes[4];
edges[2].ChildNode = nodes[2];
edges[3].ParentNode = nodes[4];
edges[3].ChildNode = nodes[3];
int dimension = 4;
IDistanceMatrix distanceMatrix = new SymmetricDistanceMatrix(dimension);
for (int i = 0; i < distanceMatrix.Dimension - 1; ++i)
{
for (int j = i + 1; j < distanceMatrix.Dimension; ++j)
{
distanceMatrix[i, j] = i + j;
distanceMatrix[j, i] = i + j;
}
}
IHierarchicalClustering hierarchicalClustering = new HierarchicalClusteringSerial(distanceMatrix);
BinaryGuideTree binaryGuideTree = new BinaryGuideTree(hierarchicalClustering);
Assert.AreEqual(7, binaryGuideTree.NumberOfNodes);
Assert.AreEqual(6, binaryGuideTree.NumberOfEdges);
Assert.AreEqual(4, binaryGuideTree.NumberOfLeaves);
Assert.IsTrue(binaryGuideTree.Nodes[binaryGuideTree.Nodes.Count - 1].IsRoot);
for (int i = 0; i < binaryGuideTree.Nodes.Count; ++i)
{
Console.WriteLine(binaryGuideTree.Nodes[i].ID);
}
// Test ExtractSubTreeNodes
Assert.AreEqual(3, binaryGuideTree.ExtractSubTreeNodes(binaryGuideTree.Nodes[4]).Count);
Assert.AreEqual(7, binaryGuideTree.ExtractSubTreeNodes(binaryGuideTree.Nodes[binaryGuideTree.Nodes.Count - 1]).Count);
Assert.AreEqual(1, binaryGuideTree.ExtractSubTreeNodes(binaryGuideTree.Nodes[0]).Count);
// Test ExtractSubTreeLeafNodes
Assert.AreEqual(2, binaryGuideTree.ExtractSubTreeLeafNodes(binaryGuideTree.Nodes[4]).Count);
Assert.AreEqual(4, binaryGuideTree.ExtractSubTreeLeafNodes(binaryGuideTree.Nodes[binaryGuideTree.Nodes.Count - 1]).Count);
Assert.AreEqual(1, binaryGuideTree.ExtractSubTreeLeafNodes(binaryGuideTree.Nodes[0]).Count);
// Test FindSmallestTreeDifference
BinaryGuideTree binaryGuideTreeB = new BinaryGuideTree(hierarchicalClustering);
BinaryGuideTreeNode node = BinaryGuideTree.FindSmallestTreeDifference(binaryGuideTree.Nodes[binaryGuideTree.Nodes.Count - 1], binaryGuideTreeB.Nodes[binaryGuideTreeB.Nodes.Count - 1]);
Assert.IsNull(node);
node = BinaryGuideTree.FindSmallestTreeDifference(binaryGuideTree.Nodes[binaryGuideTree.Nodes.Count - 1], binaryGuideTreeB.Nodes[0]);
Assert.IsNotNull(node);
// Test CompareTwoTrees
for (int i = 0; i < binaryGuideTree.Nodes.Count; ++i)
{
Console.Write(binaryGuideTree.Nodes[i].ID);
}
for (int i = 0; i < binaryGuideTreeB.Nodes.Count; ++i)
{
Console.Write(binaryGuideTreeB.Nodes[i].ID);
}
BinaryGuideTree.CompareTwoTrees(binaryGuideTree, binaryGuideTreeB);
for (int i = 0; i < binaryGuideTree.Nodes.Count; ++i)
{
Console.Write(binaryGuideTree.Nodes[i].ID);
Console.Write(binaryGuideTree.Nodes[i].NeedReAlignment);
binaryGuideTree.Nodes[i].NeedReAlignment = false;
}
for (int i = 0; i < binaryGuideTreeB.Nodes.Count; ++i)
{
Console.Write(binaryGuideTreeB.Nodes[i].ID);
Console.Write(binaryGuideTreeB.Nodes[i].NeedReAlignment);
binaryGuideTreeB.Nodes[i].NeedReAlignment = false;
}
Assert.IsFalse(binaryGuideTree.Nodes[4].NeedReAlignment);
Assert.IsFalse(binaryGuideTree.Nodes[5].NeedReAlignment);
Assert.IsFalse(binaryGuideTree.Nodes[6].NeedReAlignment);
for (int i = binaryGuideTree.NumberOfLeaves; i < binaryGuideTree.NumberOfNodes; ++i)
{
Assert.IsFalse(binaryGuideTree.Nodes[i].NeedReAlignment);
}
binaryGuideTreeB.Root.ID = 7;
BinaryGuideTree.CompareTwoTrees(binaryGuideTree, binaryGuideTreeB);
Assert.IsFalse(binaryGuideTree.Root.NeedReAlignment);
binaryGuideTreeB.Nodes[5].ID = 8;
BinaryGuideTree.CompareTwoTrees(binaryGuideTree, binaryGuideTreeB);
for (int i = 0; i < binaryGuideTree.Nodes.Count; ++i)
{
Console.Write(binaryGuideTree.Nodes[i].ID);
Console.Write(binaryGuideTree.Nodes[i].NeedReAlignment);
}
for (int i = 0; i < binaryGuideTreeB.Nodes.Count; ++i)
{
Console.Write(binaryGuideTreeB.Nodes[i].ID);
Console.Write(binaryGuideTreeB.Nodes[i].NeedReAlignment);
}
Assert.IsFalse(binaryGuideTree.Nodes[5].NeedReAlignment);
Assert.IsFalse(binaryGuideTree.Root.NeedReAlignment);
binaryGuideTreeB.Nodes[5].LeftChildren = binaryGuideTreeB.Nodes[3];
BinaryGuideTree.CompareTwoTrees(binaryGuideTree, binaryGuideTreeB);
Assert.IsTrue(binaryGuideTree.Nodes[5].NeedReAlignment);
Assert.IsTrue(binaryGuideTree.Root.NeedReAlignment);
Assert.IsFalse(binaryGuideTree.Nodes[4].NeedReAlignment);
// Test SeparateSequencesByCuttingTree
List <int>[] newSequences = binaryGuideTree.SeparateSequencesByCuttingTree(3);
Assert.AreEqual(2, newSequences[0].Count);
Assert.AreEqual(2, newSequences[1].Count);
List <int>[] newSequencesB = binaryGuideTree.SeparateSequencesByCuttingTree(2);
Assert.AreEqual(1, newSequencesB[0].Count);
Assert.AreEqual(3, newSequencesB[1].Count);
}
