public void TestAlignmentScore()
{
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.StandardSimilarityMatrix.AmbiguousDna);
int gapOpenPenalty = -8;
int gapExtendPenalty = -1;
// Test PairWiseScoreFunction
ISequence seqA = new Sequence(Alphabets.DNA, "ACG");
ISequence seqB = new Sequence(Alphabets.DNA, "ACG");
float score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(15, score);
seqA = new Sequence(Alphabets.DNA, "ACG");
seqB = new Sequence(Alphabets.DNA, "ACC");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(6, score);
seqA = new Sequence(Alphabets.DNA, "AC-");
seqB = new Sequence(Alphabets.DNA, "ACC");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(2, score);
seqA = new Sequence(Alphabets.DNA, "AC--");
seqB = new Sequence(Alphabets.DNA, "ACCG");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(1, score);
seqA = new Sequence(Alphabets.DNA, "A---");
seqB = new Sequence(Alphabets.DNA, "A--C");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(-3, score);
seqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
seqB = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(42, score);
seqA = new Sequence(Alphabets.DNA, "GGG---AAAAATCAGATT");
seqB = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(33, score);
seqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(40, score);
seqA = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
score = MsaUtils.PairWiseScoreFunction(seqA, seqB, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
//Assert.AreEqual(56, score);
// Test MultipleAlignmentScoreFunction
List <ISequence> sequences = new List <ISequence>();
seqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
seqB = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
sequences.Add(seqA);
sequences.Add(seqB);
score = MsaUtils.MultipleAlignmentScoreFunction(sequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
Console.WriteLine("alignment score is: {0}", score);
for (int i = 0; i < sequences.Count; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
//Assert.AreEqual(42, score);
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---"));
score = MsaUtils.MultipleAlignmentScoreFunction(sequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
Console.WriteLine("alignment score is: {0}", score);
for (int i = 0; i < sequences.Count; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
//Assert.AreEqual(46, score);
sequences[0] = new Sequence(Alphabets.DNA, "GGG---AAAAATCAGATT");
score = MsaUtils.MultipleAlignmentScoreFunction(sequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
for (int i = 0; i < sequences.Count; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
Console.WriteLine("alignment score is: {0}", score);
for (int i = 0; i < sequences.Count; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
//Assert.AreEqual(40, score);
// Test CalculateOffset
seqA = new Sequence(Alphabets.DNA, "ABCD");
seqB = new Sequence(Alphabets.DNA, "ABCD");
List <int> offset = MsaUtils.CalculateOffset(seqA, seqB);
Console.WriteLine("offsets are:");
for (int i = 0; i < offset.Count; ++i)
{
Console.Write("{0}\t", offset[i]);
}
seqA = new Sequence(Alphabets.DNA, "A-BCD");
seqB = new Sequence(Alphabets.DNA, "AB-CD");
offset = MsaUtils.CalculateOffset(seqA, seqB);
Console.WriteLine("\noffsets are:");
for (int i = 0; i < offset.Count; ++i)
{
Console.Write("{0}\t", offset[i]);
}
seqA = new Sequence(Alphabets.DNA, "A-BCD");
seqB = new Sequence(Alphabets.DNA, "----AB-CD");
offset = MsaUtils.CalculateOffset(seqA, seqB);
Console.WriteLine("\noffsets are:");
for (int i = 0; i < offset.Count; ++i)
{
Console.Write("{0}\t", offset[i]);
}
sequences.Clear();
sequences.Add(seqA);
sequences.Add(new Sequence(Alphabets.DNA, "ABBCG"));
List <ISequence> sequencesRef = new List <ISequence>();
sequencesRef.Add(seqA);
sequencesRef.Add(new Sequence(Alphabets.DNA, "ABBCG"));
for (int i = 0; i < sequences.Count; ++i)
{
offset = MsaUtils.CalculateOffset(sequences[i], sequencesRef[i]);
Console.WriteLine("\noffsets are:");
for (int j = 0; j < offset.Count; ++j)
{
Console.Write("{0}\t", offset[j]);
}
}
Console.WriteLine("Q score is: {0}", MsaUtils.CalculateAlignmentScoreQ(sequences, sequencesRef));
Console.WriteLine("TC score is: {0}", MsaUtils.CalculateAlignmentScoreTC(sequences, sequencesRef));
// Test on one example
sequences.Clear();
sequences.Add(new Sequence(Alphabets.DNA, "GGGA---A-AAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCA-AAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCA-AAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA---A-A--TC-G---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCA-A--TCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTA--TCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA--CA-AAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA---A-AAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCA-AAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA--CA-AAATCAG---"));
gapOpenPenalty = -4;
gapExtendPenalty = -1;
Console.WriteLine("score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(sequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
sequences.Clear();
sequences.Add(new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA-----AATC-G---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATC--AATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTA-TCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---"));
Console.WriteLine("score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(sequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
// Test Quick Sort
float[] a = new float[5] {
0, 2, 1, 5, 4
};
int[] aIndex = new int[5] {
0, 1, 2, 3, 4
};
MsaUtils.QuickSort(a, aIndex, 0, a.Length - 1);
Console.WriteLine("quicksort");
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(a[i]);
}
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(aIndex[i]);
}
Console.WriteLine("quicksortM");
a = new float[5] {
0, 2, 1, 5, 4
};
int[] aIndexB = null;
MsaUtils.QuickSortM(a, out aIndexB, 0, 4);
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(a[i]);
}
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(aIndexB[i]);
}
Console.WriteLine("quicksort");
a = new float[5] {
0, 2, 1, 5, 4
};
int[] aIndexC = MsaUtils.CreateIndexArray(a.Length);
MsaUtils.QuickSort(a, aIndexC, 0, a.Length - 1);
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(aIndexC[i]);
}
a = new float[5] {
1, 0, 0, 0, 0
};
aIndex = new int[5] {
0, 1, 2, 3, 4
};
MsaUtils.QuickSort(a, aIndex, 0, a.Length - 1);
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(a[i]);
}
for (int i = 0; i < a.Length; ++i)
{
Console.WriteLine(aIndex[i]);
}
}