public void SparseSequenceClone()
{
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA);
sparseSeq.Count = 50;
sparseSeq[0] = Alphabets.DNA.C;
sparseSeq[5] = Alphabets.DNA.G;
sparseSeq[30] = Alphabets.DNA.C;
sparseSeq[44] = Alphabets.DNA.A;
sparseSeq[45] = new Nucleotide('A', "Nucleotide A");
CompoundNucleotide cn = new CompoundNucleotide('M', "Compound");
cn.Add(new Nucleotide('A', "Item A"), 30);
cn.Add(new Nucleotide('C', "Item C"), 20);
sparseSeq[46] = cn;
Assert.AreEqual(sparseSeq.Count, 50);
Assert.AreEqual(sparseSeq.Alphabet, Alphabets.DNA);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[5], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[30], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[44], Alphabets.DNA.A);
Assert.AreEqual(sparseSeq[45].Symbol, 'A');
Assert.AreSame(sparseSeq[46], cn);
Assert.AreNotSame(sparseSeq[46], Alphabets.DNA.AC);
for (int i = 0; i < sparseSeq.Count; i++)
{
if (i != 0 && i != 5 && i != 30 && i != 44 && i != 45 && i != 46)
{
Assert.IsNull(sparseSeq[i]);
}
}
SparseSequence sparseSeqClone = sparseSeq.Clone();
Assert.AreEqual(sparseSeqClone.Count, 50);
Assert.AreEqual(sparseSeqClone.Alphabet, Alphabets.DNA);
Assert.AreSame(sparseSeqClone[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeqClone[5], Alphabets.DNA.G);
Assert.AreSame(sparseSeqClone[30], Alphabets.DNA.C);
Assert.AreSame(sparseSeqClone[44], Alphabets.DNA.A);
Assert.AreNotSame(sparseSeqClone[46], cn);
Assert.AreNotSame(sparseSeqClone[46], Alphabets.DNA.AC);
Assert.AreEqual(sparseSeqClone[46].Symbol, 'M');
cn = sparseSeqClone[46] as CompoundNucleotide;
IList <ISequenceItem> sequenceItems = cn.SequenceItems;
Assert.AreEqual(sequenceItems.Count, 2);
Assert.IsTrue(sequenceItems.First(I => I.Symbol == 'A') != null);
Assert.IsTrue(sequenceItems.First(I => I.Symbol == 'C') != null);
for (int i = 0; i < sparseSeqClone.Count; i++)
{
if (i != 0 && i != 5 && i != 30 && i != 44 && i != 45 && i != 46)
{
Assert.IsNull(sparseSeqClone[i]);
}
}
}
/// <summary>
/// Creates a sparse sequence and inserts sequence items of alphabet.
/// Creates copy of sparse sequence object using clone() method.
/// and Validates if copy of sparse sequence is as expected.
/// </summary>
/// <param name="alphabet">alphabet instance.</param>
private void ValidateSparseSequenceCopy(IAlphabet alphabet)
{
SparseSequence sparseSequence = CreateSparseSequence(alphabet, 15);
SparseSequence sparseSeqCopy = sparseSequence.Clone();
// Retrieve all stored sequence items and validate Sparse Sequence
int retrieveIndex = 15;
foreach (ISequenceItem item in alphabet)
{
// Validate new added items
Assert.IsTrue(sparseSeqCopy.Contains(item));
Assert.AreEqual(sparseSeqCopy.IndexOf(item), retrieveIndex);
Assert.AreEqual(item, sparseSeqCopy[retrieveIndex]);
Assert.AreEqual(item.Symbol, sparseSeqCopy[retrieveIndex].Symbol);
retrieveIndex++;
}
Console.WriteLine(
"SparseSequenceBVT: Validation of copy of sparse sequence object is completed");
ApplicationLog.WriteLine(
"SparseSequenceBVT: Validation of copy of sparse sequence object is completed");
}
