public void ValidateSparseSequenceLastIndexOfNonGap()
{
var sparseSeqObj = new SparseSequence(Alphabets.DNA, 10);
sparseSeqObj[2] = Alphabets.DNA.Gap;
sparseSeqObj[1] = Alphabets.DNA.A;
Assert.AreEqual(1, sparseSeqObj.LastIndexOfNonGap(2));
Assert.AreEqual(1, sparseSeqObj.LastIndexOfNonGap(1));
ApplicationLog.WriteLine("SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
}
/// <summary>
/// Invalidate Sparse sequence IndexOfNonGap
/// </summary>
/// <param name="sparseSeq">Sparse Sequence</param>
private static void InvalidateSparseSequenceIndexOfNonGap(SparseSequence sparseSeq)
{
sparseSeq.Count = 1000;
sparseSeq[9] = null;
sparseSeq[10] = Alphabets.DNA.Gap;
sparseSeq[20] = Alphabets.DNA.GA;
sparseSeq[501] = Alphabets.DNA.A;
sparseSeq[905] = Alphabets.DNA.Gap;
sparseSeq[906] = null;
Assert.AreEqual(20, sparseSeq.IndexOfNonGap());
Assert.AreEqual(20, sparseSeq.IndexOfNonGap(10));
Assert.AreEqual(20, sparseSeq.IndexOfNonGap(20));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap());
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(910));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(905));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(501));
}
public void ValidateSparseSequenceLastIndexOfNonGap()
{
SparseSequence sparseSeqObj = new SparseSequence(Alphabets.DNA);
sparseSeqObj.Count = 1000;
sparseSeqObj[9] = null;
sparseSeqObj[10] = Alphabets.DNA.ACT;
sparseSeqObj[20] = Alphabets.DNA.GA;
sparseSeqObj[501] = Alphabets.DNA.A;
sparseSeqObj[905] = Alphabets.DNA.Gap;
sparseSeqObj[906] = null;
Assert.AreEqual(501, sparseSeqObj.LastIndexOfNonGap());
Assert.AreEqual(501, sparseSeqObj.LastIndexOfNonGap(910));
Assert.AreEqual(501, sparseSeqObj.LastIndexOfNonGap(905));
Assert.AreEqual(501, sparseSeqObj.LastIndexOfNonGap(501));
Console.WriteLine(
"SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
ApplicationLog.WriteLine(
"SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
}
public void ValidateSparseSequenceLastIndexOfNonGapNull()
{
SparseSequence sparseSeqObj = new SparseSequence(Alphabets.DNA, 2);
sparseSeqObj[1] = Alphabets.DNA.Gap;
sparseSeqObj[0] = Alphabets.DNA.A;
Assert.AreEqual(0, sparseSeqObj.LastIndexOfNonGap());
Console.WriteLine(
"SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
ApplicationLog.WriteLine(
"SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
}
public void TestSparseSequence()
{
SparseSequence tempSeq = null;
#region Test constructors by passing invalid parameters.
try
{
tempSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.RNA.U);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(Alphabets.RNA, 0, Alphabets.DNA.T);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(tempSeq);
}
try
{
ISequence seq = new Sequence(Alphabets.RNA, "AUGC");
tempSeq = new SparseSequence(Alphabets.DNA, 0, seq);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(Alphabets.DNA, -1, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(Alphabets.DNA, int.MaxValue, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(Alphabets.DNA, 0, null as ISequenceItem);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(Alphabets.DNA, 0, null as ISequence);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(
Alphabets.DNA,
-1,
new List <ISequenceItem>()
{
Alphabets.DNA.A,
Alphabets.DNA.C
});
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(tempSeq);
}
try
{
tempSeq = new SparseSequence(
Alphabets.DNA,
int.MaxValue,
new List <ISequenceItem>()
{
Alphabets.DNA.A,
Alphabets.DNA.C
});
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.IsNull(tempSeq);
}
#endregion Test constructors by passing invalid parameters.
// Test constructor which takes only Alphabet for the IsReadOnly property.
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA);
Assert.IsFalse(sparseSeq.IsReadOnly);
sparseSeq.Insert(0, 'C');
Assert.AreEqual(sparseSeq.Count, 1);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
sparseSeq = new SparseSequence(Alphabets.DNA, 0, Alphabets.DNA.A);
string id = Guid.NewGuid().ToString(string.Empty);
sparseSeq.ID = id;
sparseSeq.DisplayID = "SparseSeq1";
#region Test parameters
Assert.AreSame(Alphabets.DNA, sparseSeq.Alphabet);
Assert.IsTrue(sparseSeq.IsReadOnly);
Assert.AreSame(sparseSeq.Complement[0], Alphabets.DNA.T);
Assert.AreEqual(sparseSeq.Count, 1);
Assert.AreEqual(sparseSeq.DisplayID, "SparseSeq1");
Assert.AreEqual(sparseSeq.ID, id);
#endregion Test parameters
#region Test editing with IsReadOnly set to true.
try
{
sparseSeq.Add(Alphabets.DNA.A);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.Clear();
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.Insert(0, 'C');
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.Insert(0, Alphabets.DNA.A);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.InsertRange(0, "CGA");
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.Remove(Alphabets.DNA.A);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.RemoveAt(0);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.RemoveRange(0, 2);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
}
try
{
sparseSeq.Replace(0, 'C');
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
}
try
{
sparseSeq.Replace(0, Alphabets.DNA.C);
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
}
try
{
sparseSeq.ReplaceRange(0, "G");
Assert.Fail();
}
catch (InvalidOperationException)
{
Assert.AreEqual(sparseSeq.Count, 1);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
}
#endregion Test editing with IsReadOnly set to true.
#region Test not supported members
string sequencedata = string.Empty;
try
{
sequencedata = sparseSeq.ToString();
Assert.Fail();
}
catch (NotSupportedException)
{
Assert.IsTrue(string.IsNullOrEmpty(sequencedata));
}
#endregion Test not supported members
Assert.AreEqual(sparseSeq.IndexOf(Alphabets.DNA.A), 0);
Assert.AreSame(sparseSeq.Range(0, 1)[0], Alphabets.DNA.A);
Assert.AreSame(sparseSeq.Reverse[0], Alphabets.DNA.A);
Assert.AreSame(sparseSeq.ReverseComplement[0], Alphabets.DNA.T);
Assert.IsTrue(sparseSeq.Contains(Alphabets.DNA.A));
ISequenceItem[] seqItemArray = new Nucleotide[10];
seqItemArray[0] = Alphabets.DNA.G;
sparseSeq.CopyTo(seqItemArray, 1);
Assert.AreSame(seqItemArray[0], Alphabets.DNA.G);
Assert.AreSame(seqItemArray[1], Alphabets.DNA.A);
try
{
sparseSeq.CopyTo(null, 1);
Assert.Fail();
}
catch (ArgumentNullException)
{
}
Assert.IsTrue(sparseSeq.IsReadOnly);
sparseSeq.IsReadOnly = false;
#region Test editing with IsReadOnly set to false.
#region Test - void Add(ISequenceItem)
sparseSeq.Add(Alphabets.DNA.G);
Assert.AreEqual(sparseSeq.Count, 2);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
try
{
sparseSeq.Add(Alphabets.RNA.U);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 2);
}
#endregion Test - void Add(ISequenceItem)
#region Test - void Clear()
sparseSeq.Clear();
Assert.AreEqual(sparseSeq.Count, 0);
#endregion Test - void Clear()
#region Test - void Insert(int position, char character)
sparseSeq.Insert(0, 'C');
Assert.AreEqual(sparseSeq.Count, 1);
sparseSeq.Insert(sparseSeq.Count, 'A');
Assert.AreEqual(sparseSeq.Count, 2);
try
{
sparseSeq.Insert(-1, 'A');
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 2);
}
try
{
sparseSeq.Insert(sparseSeq.Count + 1, 'A');
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 2);
}
try
{
sparseSeq.Insert(0, 'U');
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 2);
}
#endregion Test - void Insert(int position, char character)
#region Test - void Insert(int index, ISequenceItem item)
sparseSeq.Insert(0, Alphabets.DNA.G);
Assert.AreEqual(sparseSeq.Count, 3);
sparseSeq.Insert(sparseSeq.Count, Alphabets.DNA.G);
Assert.AreEqual(sparseSeq.Count, 4);
try
{
sparseSeq.Insert(-1, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 4);
}
try
{
sparseSeq.Insert(sparseSeq.Count + 1, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 4);
}
try
{
sparseSeq.Insert(0, Alphabets.RNA.U);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 4);
}
#endregion Test - void Insert(int index, ISequenceItem item)
#region Test - Count
sparseSeq.Clear();
Assert.AreEqual(sparseSeq.Count, 0);
sparseSeq.Count = 5;
Assert.IsNull(sparseSeq[0]);
Assert.IsNull(sparseSeq[1]);
Assert.IsNull(sparseSeq[2]);
Assert.IsNull(sparseSeq[3]);
Assert.IsNull(sparseSeq[4]);
sparseSeq[2] = Alphabets.DNA.G;
Assert.AreEqual(sparseSeq.Count, 5);
Assert.IsNull(sparseSeq[0]);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.G);
Assert.IsNull(sparseSeq[3]);
Assert.IsNull(sparseSeq[4]);
sparseSeq.Insert(2, 'A');
Assert.AreEqual(sparseSeq.Count, 6);
Assert.IsNull(sparseSeq[0]);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.IsNull(sparseSeq[4]);
Assert.IsNull(sparseSeq[5]);
sparseSeq.Insert(4, Alphabets.DNA.C);
Assert.AreEqual(sparseSeq.Count, 7);
Assert.IsNull(sparseSeq[0]);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[5]);
Assert.IsNull(sparseSeq[6]);
#endregion Test - Count
#region Test - void InsertRange(int position, string sequence)
sparseSeq.InsertRange(0, "CGA");
Assert.AreEqual(sparseSeq.Count, 10);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[3]);
Assert.IsNull(sparseSeq[4]);
Assert.AreSame(sparseSeq[5], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[6], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[7], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[8]);
Assert.IsNull(sparseSeq[9]);
try
{
sparseSeq.InsertRange(-1, "CGA");
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 10);
}
try
{
sparseSeq.InsertRange(sparseSeq.Count + 1, "CGA");
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 10);
}
try
{
sparseSeq.InsertRange(0, string.Empty);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.AreEqual(sparseSeq.Count, 10);
}
try
{
sparseSeq.InsertRange(0, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.AreEqual(sparseSeq.Count, 10);
}
#endregion Test - void InsertRange(int position, string sequence)
#region Test - bool Remove(ISequenceItem item)
Assert.IsTrue(sparseSeq.Remove(Alphabets.DNA.A));
Assert.AreEqual(sparseSeq.Count, 9);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.IsNull(sparseSeq[2]);
Assert.IsNull(sparseSeq[3]);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[5], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[6], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[7]);
Assert.IsNull(sparseSeq[8]);
Assert.IsFalse(sparseSeq.Remove(Alphabets.DNA.T));
Assert.IsFalse(sparseSeq.Remove(Alphabets.RNA.U));
Assert.AreEqual(sparseSeq.Count, 9);
#endregion Test - bool Remove(ISequenceItem item)
#region Test - void RemoveAt(int index)
sparseSeq.RemoveAt(2);
Assert.AreEqual(sparseSeq.Count, 8);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.IsNull(sparseSeq[2]);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[5], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[6]);
Assert.IsNull(sparseSeq[7]);
try
{
sparseSeq.RemoveAt(-1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 8);
}
try
{
sparseSeq.RemoveAt(sparseSeq.Count);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 8);
}
#endregion Test - void RemoveAt(int index)
#region Test - void RemoveRange(int position, int length)
sparseSeq.RemoveRange(1, 3);
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[3]);
Assert.IsNull(sparseSeq[4]);
try
{
sparseSeq.RemoveRange(-1, 1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
}
try
{
sparseSeq.RemoveRange(sparseSeq.Count, 1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
}
try
{
sparseSeq.RemoveRange(0, -1);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
}
try
{
sparseSeq.RemoveRange(2, 4);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 5);
}
#endregion Test - void RemoveRange(int position, int length)
#region Test - void Replace(int position, char character)
sparseSeq.Replace(3, 'A');
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
sparseSeq.Replace(2, 'T');
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
try
{
sparseSeq.Replace(-1, 'C');
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.Replace(sparseSeq.Count, 'C');
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.Replace(2, 'U');
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
}
#endregion Test - void Replace(int position, char character)
#region Test - void Replace(int position, ISequenceItem item)
sparseSeq.Replace(1, null);
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[4]);
sparseSeq.Replace(3, Alphabets.DNA.T);
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
sparseSeq.Replace(1, Alphabets.DNA.C);
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
// try replacing null with null.
sparseSeq[4] = null;
try
{
sparseSeq.Replace(-1, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.Replace(sparseSeq.Count, Alphabets.DNA.A);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.Replace(2, Alphabets.RNA.U);
Assert.Fail();
}
catch (ArgumentException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
#endregion Test - void Replace(int position, ISequenceItem item)
#region Test - void ReplaceRange(int position, string sequence)
try
{
sparseSeq.ReplaceRange(-1, "GC");
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.ReplaceRange(sparseSeq.Count, "GC");
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.ReplaceRange(0, string.Empty);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
try
{
sparseSeq.ReplaceRange(0, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.T);
Assert.IsNull(sparseSeq[4]);
}
sparseSeq.ReplaceRange(3, "GC");
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[1], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.C);
#endregion Test - void ReplaceRange(int position, string sequence)
#region Test - ISequenceItem this[int index]
sparseSeq[1] = null;
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.C);
sparseSeq[0] = Alphabets.DNA.A;
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.C);
try
{
sparseSeq[-1] = Alphabets.DNA.A;
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
try
{
sparseSeq[sparseSeq.Count] = Alphabets.DNA.A;
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
}
Assert.AreEqual(sparseSeq.Count, 5);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.A);
Assert.IsNull(sparseSeq[1]);
Assert.AreSame(sparseSeq[2], Alphabets.DNA.T);
Assert.AreSame(sparseSeq[3], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[4], Alphabets.DNA.C);
#endregion Test - ISequenceItem this[int index]
#region Test - IList<IndexedSequenceItem> GetKnownSequenceItems
IList <IndexedItem <ISequenceItem> > knownItems = sparseSeq.GetKnownSequenceItems();
Assert.AreEqual(knownItems.Count, 4);
Assert.AreEqual(knownItems[0].Index, 0);
Assert.AreSame(knownItems[0].Item, Alphabets.DNA.A);
Assert.AreEqual(knownItems[1].Index, 2);
Assert.AreSame(knownItems[1].Item, Alphabets.DNA.T);
Assert.AreEqual(knownItems[2].Index, 3);
Assert.AreSame(knownItems[2].Item, Alphabets.DNA.G);
Assert.AreEqual(knownItems[3].Index, 4);
Assert.AreSame(knownItems[3].Item, Alphabets.DNA.C);
#endregion Test - IList<IndexedSequenceItem> GetKnownSequenceItems
#region Test - IEnumerator<ISequenceItem> GetEnumerator()
int i = 0;
foreach (ISequenceItem item in sparseSeq)
{
Assert.AreSame(sparseSeq[i++], item);
}
#endregion Test - IEnumerator<ISequenceItem> GetEnumerator()
#endregion Test editing with IsReadOnly set to false.
#region Test - Constructor by passing a sparse sequence.
// Create new sparse sequence from a sparse sequence by adding sequence item from index 1.
tempSeq = new SparseSequence(sparseSeq.Alphabet, 1, sparseSeq);
Assert.AreEqual(tempSeq.Count, 6);
Assert.IsNull(tempSeq[0]);
Assert.AreSame(tempSeq[1], Alphabets.DNA.A);
Assert.IsNull(tempSeq[2]);
Assert.AreSame(tempSeq[3], Alphabets.DNA.T);
Assert.AreSame(tempSeq[4], Alphabets.DNA.G);
Assert.AreSame(tempSeq[5], Alphabets.DNA.C);
#endregion Test - Constructor by passing a sparse sequence.
#region Test - Complement
ISequence compSeq = sparseSeq.Complement;
Assert.AreEqual(compSeq.Count, 5);
Assert.AreSame(compSeq[0], Alphabets.DNA.T);
Assert.IsNull(compSeq[1]);
Assert.AreSame(compSeq[2], Alphabets.DNA.A);
Assert.AreSame(compSeq[3], Alphabets.DNA.C);
Assert.AreSame(compSeq[4], Alphabets.DNA.G);
#endregion Test - Complement
#region Test - Reverse
compSeq = sparseSeq.Reverse;
Assert.AreEqual(compSeq.Count, 5);
Assert.AreSame(compSeq[4], Alphabets.DNA.A);
Assert.IsNull(compSeq[3]);
Assert.AreSame(compSeq[2], Alphabets.DNA.T);
Assert.AreSame(compSeq[1], Alphabets.DNA.G);
Assert.AreSame(compSeq[0], Alphabets.DNA.C);
#endregion Test - Reverse
#region Test - ReverseComplement
compSeq = sparseSeq.ReverseComplement;
Assert.AreEqual(compSeq.Count, 5);
Assert.AreSame(compSeq[4], Alphabets.DNA.T);
Assert.IsNull(compSeq[3]);
Assert.AreSame(compSeq[2], Alphabets.DNA.A);
Assert.AreSame(compSeq[1], Alphabets.DNA.C);
Assert.AreSame(compSeq[0], Alphabets.DNA.G);
#endregion Test - ReverseComplement
#region Test - IndexOfNotNull and LastIndexOfNotNull
sparseSeq = new SparseSequence(Alphabets.DNA);
sparseSeq.Count = 1000;
sparseSeq[9] = null;
sparseSeq[10] = Alphabets.DNA.Gap;
sparseSeq[20] = Alphabets.DNA.GA;
sparseSeq[501] = Alphabets.DNA.A;
sparseSeq[905] = Alphabets.DNA.Gap;
sparseSeq[906] = null;
Assert.AreEqual(10, sparseSeq.IndexOfNotNull());
Assert.AreEqual(20, sparseSeq.IndexOfNotNull(10));
Assert.AreEqual(10, sparseSeq.IndexOfNotNull(9));
Assert.AreEqual(10, sparseSeq.IndexOfNotNull(0));
Assert.AreEqual(905, sparseSeq.IndexOfNotNull(501));
Assert.AreEqual(-1, sparseSeq.IndexOfNotNull(sparseSeq.Count));
Assert.AreEqual(905, sparseSeq.LastIndexOfNotNull());
Assert.AreEqual(501, sparseSeq.LastIndexOfNotNull(905));
Assert.AreEqual(905, sparseSeq.LastIndexOfNotNull(906));
Assert.AreEqual(905, sparseSeq.LastIndexOfNotNull(sparseSeq.Count));
Assert.AreEqual(10, sparseSeq.LastIndexOfNotNull(20));
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull(10));
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull(0));
sparseSeq = new SparseSequence(Alphabets.DNA);
sparseSeq.Count = 1000;
Assert.AreEqual(-1, sparseSeq.IndexOfNotNull());
Assert.AreEqual(-1, sparseSeq.IndexOfNotNull(10));
Assert.AreEqual(-1, sparseSeq.IndexOfNotNull(sparseSeq.Count));
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull());
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull(300));
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull(sparseSeq.Count));
Assert.AreEqual(-1, sparseSeq.LastIndexOfNotNull(0));
#endregion Test - IndexOfNotNull and LastIndexOfNotNull
#region Test - IndexOfNonGap and LastIndexOfNonGap
sparseSeq = new SparseSequence(Alphabets.DNA);
sparseSeq.Count = 1000;
sparseSeq[9] = null;
sparseSeq[10] = Alphabets.DNA.Gap;
sparseSeq[20] = Alphabets.DNA.GA;
sparseSeq[501] = Alphabets.DNA.A;
sparseSeq[905] = Alphabets.DNA.Gap;
sparseSeq[906] = null;
Assert.AreEqual(20, sparseSeq.IndexOfNonGap());
Assert.AreEqual(20, sparseSeq.IndexOfNonGap(10));
Assert.AreEqual(20, sparseSeq.IndexOfNonGap(20));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap());
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(910));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(905));
Assert.AreEqual(501, sparseSeq.LastIndexOfNonGap(501));
#endregion Test - IndexOfNonGap and LastIndexOfNonGap
}
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 ValidateSparseSequenceLastIndexOfNonGapNull()
{
var sparseSeqObj = new SparseSequence(Alphabets.DNA, 2);
sparseSeqObj[1] = Alphabets.DNA.Gap;
sparseSeqObj[0] = Alphabets.DNA.A;
Assert.AreEqual(0, sparseSeqObj.LastIndexOfNonGap());
ApplicationLog.WriteLine("SparseSequenceBVT: Validation of LastIndexOfNonGap() method successfully completed");
}