public void TestSparseSequenceEnumerator()
{
int i = 0;
ISequence seq = new Sequence(Alphabets.DNA, "ATGC");
var sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
foreach (byte item in sparseSeq)
{
Assert.AreEqual(sparseSeq[i++], item);
}
}
/// <summary>
/// Validate the SparseSequence constructor.
/// </summary>
private static void ValidateSparseSequenceCtor()
{
SparseSequence sparseSeq = null;
// Test for index 0.
sparseSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.DNA.A);
Assert.AreEqual(1, sparseSeq.Count);
Assert.AreEqual(Alphabets.DNA, sparseSeq.Alphabet);
Assert.IsNotNull(sparseSeq.Statistics);
// Test for non zero index.
sparseSeq = new SparseSequence(Alphabets.DNA, 3, Alphabets.DNA.A);
Assert.AreEqual(4, sparseSeq.Count);
// Test for size.
sparseSeq = new SparseSequence(Alphabets.DNA, 10);
Assert.AreEqual(10, sparseSeq.Count);
Assert.AreEqual(Alphabets.DNA, sparseSeq.Alphabet);
Assert.IsNotNull(sparseSeq.Statistics);
// Sequence constructor tests.
ISequence seq = new Sequence(Alphabets.RNA, "AUGC");
sparseSeq = new SparseSequence(Alphabets.RNA, 0, seq);
Assert.AreEqual(4, sparseSeq.Count);
Assert.AreEqual(Alphabets.RNA, sparseSeq.Alphabet);
Assert.IsNotNull(sparseSeq.Statistics);
sparseSeq = new SparseSequence(Alphabets.RNA, 2, seq);
Assert.AreEqual(2 + seq.Count, sparseSeq.Count);
Assert.AreEqual(Alphabets.RNA, sparseSeq.Alphabet);
Assert.IsNotNull(sparseSeq.Statistics);
}
public void TestSparseSequenceIndexers()
{
SparseSequence sparseSeq = null;
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.DNA.A);
byte sequence = sparseSeq[-1];
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
// Zero index.
sparseSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.DNA.A);
Assert.AreEqual(Alphabets.DNA.A, sparseSeq[0]);
// Non Zero index.
sparseSeq = new SparseSequence(Alphabets.DNA, 2, Alphabets.DNA.A);
Assert.AreEqual(Alphabets.DNA.A, sparseSeq[2]);
Assert.AreEqual(0, sparseSeq[0]);
sparseSeq = new SparseSequence(Alphabets.DNA, 2);
Assert.AreEqual(0, sparseSeq[0]);
// Zero index.
ISequence seq = new Sequence(Alphabets.DNA, "ATGC");
sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
Assert.AreEqual(Alphabets.DNA.A, sparseSeq[0]);
Assert.AreEqual(Alphabets.DNA.T, sparseSeq[1]);
Assert.AreEqual(Alphabets.DNA.G, sparseSeq[2]);
Assert.AreEqual(Alphabets.DNA.C, sparseSeq[3]);
// Non Zero index.
sparseSeq = new SparseSequence(Alphabets.DNA, 2, seq);
Assert.AreEqual(0, sparseSeq[0]);
Assert.AreEqual(0, sparseSeq[1]);
Assert.AreEqual(Alphabets.DNA.A, sparseSeq[2]);
Assert.AreEqual(Alphabets.DNA.T, sparseSeq[3]);
Assert.AreEqual(Alphabets.DNA.G, sparseSeq[4]);
Assert.AreEqual(Alphabets.DNA.C, sparseSeq[5]);
sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
sparseSeq[0] = Alphabets.DNA.C;
Assert.AreEqual(Alphabets.DNA.C, sparseSeq[0]);
Assert.AreEqual(4, sparseSeq.Count);
sparseSeq = new SparseSequence(Alphabets.DNA, 10);
sparseSeq[6] = Alphabets.DNA.C;
Assert.AreEqual(Alphabets.DNA.C, sparseSeq[6]);
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 10);
sparseSeq[6] = Alphabets.RNA.U;
Assert.Fail();
}
catch (ArgumentException)
{
}
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 1);
sparseSeq[6] = Alphabets.DNA.C;
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
}
/// <summary>
/// Invalidate Sparse sequence constructor
/// </summary>
private static void ValidateSparseSequenceCtorInvalidParameters()
{
SparseSequence sparseSeq = null;
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.RNA.U);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(Alphabets.RNA, 0, Alphabets.DNA.T);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(sparseSeq);
}
try
{
ISequence seq = new Sequence(Alphabets.RNA, "AUGC");
sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, -1, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, int.MaxValue, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 0, byte.MinValue);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(Alphabets.DNA, 0, null as ISequence);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(
Alphabets.DNA,
-1,
new List<byte>() {
Alphabets.DNA.A,
Alphabets.DNA.C });
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(
Alphabets.DNA,
int.MaxValue,
new List<byte>() {
Alphabets.DNA.A,
Alphabets.DNA.C });
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(
null,
0);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(sparseSeq);
}
try
{
sparseSeq = new SparseSequence(
Alphabets.DNA,
-1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(sparseSeq);
}
}
public void TestSparseSequenceGetSubsequence()
{
List<byte> byteList = new List<byte>();
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.G);
byteList.Add(Alphabets.DNA.A);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.T);
byteList.Add(Alphabets.DNA.C);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.Gap);
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA, 0, byteList);
ISequence result = sparseSeq.GetSubSequence(0, 3);
Assert.AreEqual(3, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.G, result[1]);
Assert.AreEqual(Alphabets.DNA.A, result[2]);
result = sparseSeq.GetSubSequence(0, 0);
Assert.AreEqual(0, result.Count);
result = sparseSeq.GetSubSequence(3, 2);
Assert.AreEqual(2, result.Count);
Assert.AreEqual(Alphabets.DNA.Gap, result[0]);
Assert.AreEqual(Alphabets.DNA.T, result[1]);
// Invalid Argument tests.
try
{
sparseSeq.GetSubSequence(10, 10);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
sparseSeq.GetSubSequence(0, 9);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
sparseSeq.GetSubSequence(1, 8);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
}
public void TestSparseSequenceIndexOfNonGap()
{
List<byte> byteList = new List<byte>();
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.G);
byteList.Add(Alphabets.DNA.A);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.T);
byteList.Add(Alphabets.DNA.C);
byteList.Add(Alphabets.DNA.Gap);
byteList.Add(Alphabets.DNA.Gap);
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA, 0, byteList);
long result = sparseSeq.IndexOfNonGap();
Assert.AreEqual(1, result);
result = sparseSeq.IndexOfNonGap(1);
Assert.AreEqual(1, result);
result = sparseSeq.IndexOfNonGap(6);
Assert.AreEqual(-1, result);
result = sparseSeq.LastIndexOfNonGap();
Assert.AreEqual(5, result);
result = sparseSeq.LastIndexOfNonGap(6);
Assert.AreEqual(5, result);
result = sparseSeq.LastIndexOfNonGap(1);
Assert.AreEqual(1, result);
result = sparseSeq.LastIndexOfNonGap(0);
Assert.AreEqual(-1, result);
// Alphabet with no gaps.
SparseSequence tempSeq = new SparseSequence(NoGapAlphabet.Instance, 0, byteList);
result = tempSeq.IndexOfNonGap(3);
Assert.AreEqual(3, result);
result = tempSeq.IndexOfNonGap(0);
Assert.AreEqual(0, result);
result = tempSeq.LastIndexOfNonGap(4);
Assert.AreEqual(4, result);
// Zero length sequences
SparseSequence sparseSeqZeroLen = new SparseSequence(Alphabets.DNA);
long zeroResult = sparseSeqZeroLen.IndexOfNonGap();
Assert.AreEqual(-1, zeroResult);
zeroResult = sparseSeqZeroLen.LastIndexOfNonGap();
Assert.AreEqual(-1, zeroResult);
// Invalid argument inputs.
try
{
result = sparseSeq.IndexOfNonGap(-1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
result = sparseSeq.IndexOfNonGap(100);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
result = sparseSeq.LastIndexOfNonGap(-1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
result = sparseSeq.LastIndexOfNonGap(100);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
}
public void TestSparseSequenceComplementMethods()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATGC");
var sparseSeq = new SparseSequence(Alphabets.DNA, 1, seq);
ISequence compSeq = sparseSeq.GetComplementedSequence();
Assert.AreEqual(5, compSeq.Count);
Assert.AreEqual(0, compSeq[0]);
Assert.AreEqual(Alphabets.DNA.T, compSeq[1]);
Assert.AreEqual(Alphabets.DNA.A, compSeq[2]);
Assert.AreEqual(Alphabets.DNA.C, compSeq[3]);
Assert.AreEqual(Alphabets.DNA.G, compSeq[4]);
compSeq = sparseSeq.GetReversedSequence();
Assert.AreEqual(5, compSeq.Count);
Assert.AreEqual(0, compSeq[4]);
Assert.AreEqual(Alphabets.DNA.A, compSeq[3]);
Assert.AreEqual(Alphabets.DNA.T, compSeq[2]);
Assert.AreEqual(Alphabets.DNA.G, compSeq[1]);
Assert.AreEqual(Alphabets.DNA.C, compSeq[0]);
compSeq = sparseSeq.GetReverseComplementedSequence();
Assert.AreEqual(5, compSeq.Count);
Assert.AreEqual(0, compSeq[4]);
Assert.AreEqual(Alphabets.DNA.T, compSeq[3]);
Assert.AreEqual(Alphabets.DNA.A, compSeq[2]);
Assert.AreEqual(Alphabets.DNA.C, compSeq[1]);
Assert.AreEqual(Alphabets.DNA.G, compSeq[0]);
}
public void TestSparseSequenceGetKnownSequenceItems()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATGC");
var sparseSeq = new SparseSequence(Alphabets.DNA, 0, seq);
var knownItems = sparseSeq.GetKnownSequenceItems();
Assert.AreEqual(knownItems.Count, 4);
Assert.AreEqual(0, knownItems[0].Index);
Assert.AreEqual(Alphabets.DNA.A, knownItems[0].Item);
Assert.AreEqual(1, knownItems[1].Index);
Assert.AreEqual(Alphabets.DNA.T, knownItems[1].Item);
Assert.AreEqual(2, knownItems[2].Index);
Assert.AreEqual(Alphabets.DNA.G, knownItems[2].Item);
Assert.AreEqual(3, knownItems[3].Index);
Assert.AreEqual(Alphabets.DNA.C, knownItems[3].Item);
}
