/// <summary>
/// Creates a dna derived sequence after removing few items using RemoveAt() from original sequence.
/// Validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceRemoveAt(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange1);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveDerivedSequence2);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
string[] removals = removeRange.Split(',');
int position = int.Parse(removals[0], null);
int length = int.Parse(removals[1], null);
// Remove items
for (int index = position; index <= length; index++)
{
derSequence.RemoveAt(index);
}
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of RemoveAt() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of RemoveAt() of derived sequence completed successfully");
}
public void DerivedSequenceClone()
{
Sequence seq = new Sequence(Alphabets.RNA, "ACUGA");
DerivedSequence derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(0);
Assert.AreEqual(derSeq.ToString(), "CUGA");
derSeq.RemoveAt(2);
Assert.AreEqual(derSeq.ToString(), "CUA");
derSeq.Insert(2, Alphabets.RNA.C);
Assert.AreEqual(derSeq.ToString(), "CUCA");
DerivedSequence cloneCopy = derSeq.Clone();
Assert.AreNotSame(derSeq, cloneCopy);
Assert.AreNotSame(derSeq.Source, cloneCopy.Source);
Assert.AreEqual(derSeq.ToString(), cloneCopy.ToString());
}
public void TestDerivedSequenceWithBinaryFormatter()
{
Stream stream = null;
try
{
stream = File.Open("DerivedSequence.data", FileMode.Create);
BinaryFormatter formatter = new BinaryFormatter();
Sequence seq = new Sequence(Alphabets.RNA, "ACUGA");
DerivedSequence derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(0);
Assert.AreEqual(derSeq.ToString(), "CUGA");
derSeq.RemoveAt(2);
Assert.AreEqual(derSeq.ToString(), "CUA");
derSeq.Insert(2, Alphabets.RNA.C);
Assert.AreEqual(derSeq.ToString(), "CUCA");
derSeq.Insert(2, new Nucleotide('C', "Rna"));
Assert.AreEqual(derSeq.ToString(), "CUCCA");
formatter.Serialize(stream, derSeq);
stream.Seek(0, SeekOrigin.Begin);
DerivedSequence deserializedDerSeq = (DerivedSequence)formatter.Deserialize(stream);
Assert.AreEqual(deserializedDerSeq.ToString(), derSeq.ToString());
Assert.AreEqual(deserializedDerSeq[2], derSeq[2]);
Assert.AreEqual(deserializedDerSeq[2].Symbol, derSeq[2].Symbol);
Assert.AreEqual(deserializedDerSeq[2].Name, derSeq[2].Name);
}
catch (Exception)
{
Assert.Fail();
}
finally
{
if (stream != null)
{
stream.Close();
stream = null;
}
}
}
public void ValidateDerivedInvalidRemoveAt()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "AAGGTT");
DerivedSequence deriSeqObj = new DerivedSequence(seqObj);
// Pass invalid index value and get the exception required
try
{
deriSeqObj.RemoveAt(-1);
Assert.IsTrue(false);
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveAt() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveAt() method");
}
}
public void TestDerivedSequence()
{
Sequence seq = new Sequence(Alphabets.RNA, "ACUGUA");
DerivedSequence derSeq = new DerivedSequence(seq);
derSeq.Insert(3, Alphabets.DNA.A);
derSeq.RemoveAt(2);
Assert.AreEqual(derSeq.ToString(), "ACAGUA");
derSeq.Insert(3, Alphabets.DNA.A);
Assert.AreEqual(derSeq.ToString(), "ACAAGUA");
derSeq.RemoveAt(2);
derSeq.RemoveAt(1);
Assert.AreEqual(derSeq.ToString(), "AAGUA");
derSeq.Insert(1, 'C');
Assert.AreEqual(derSeq.ToString(), "ACAGUA");
derSeq.Replace(0, 'C');
Assert.AreEqual(derSeq.ToString(), "CCAGUA");
derSeq.ReplaceRange(1, "UA");
Assert.AreEqual(derSeq.ToString(), "CUAGUA");
derSeq.InsertRange(derSeq.Count, "UUAA");
Assert.AreEqual(derSeq.ToString(), "CUAGUAUUAA");
derSeq.InsertRange(0, "UUAA");
Assert.AreEqual(derSeq.ToString(), "UUAACUAGUAUUAA");
seq = new Sequence(Alphabets.DNA, "ACTGTA");
derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(3);
derSeq.Insert(3, Alphabets.DNA.A);
Assert.AreEqual(derSeq.ToString(), "ACTATA");
derSeq.InsertRange(derSeq.Count, "TTTT");
derSeq.RemoveRange(6, 4);
Assert.AreEqual(derSeq.ToString(), "ACTATA");
derSeq.Insert(derSeq.Count, 'T');
Assert.AreEqual(derSeq.ToString(), "ACTATAT");
derSeq.Add(Alphabets.DNA.G);
Assert.AreEqual(derSeq.ToString(), "ACTATATG");
Assert.AreEqual(0, derSeq.IndexOf(Alphabets.DNA.A));
Assert.IsTrue(derSeq.Contains(Alphabets.DNA.G));
Assert.IsTrue(derSeq.Remove(Alphabets.DNA.C));
Assert.AreEqual(derSeq.ToString(), "ATATATG");
Assert.IsFalse(derSeq.Contains(Alphabets.DNA.C));
Assert.IsFalse(derSeq.Remove(Alphabets.DNA.C));
Assert.AreEqual(derSeq.Source.ToString(), "ACTGTA");
derSeq.Clear();
Assert.AreEqual(derSeq.Source.ToString(), derSeq.ToString());
Assert.AreEqual(derSeq.Source.ToString(), "ACTGTA");
seq = new Sequence(Alphabets.DNA, "ACTGTA");
derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(3);
derSeq.Insert(3, Alphabets.DNA.A);
IList <IndexedItem <UpdatedSequenceItem> > updatedItems = derSeq.GetUpdatedItems();
Assert.AreEqual(updatedItems.Count, 2);
Assert.AreEqual(updatedItems[0].Index, 3);
Assert.AreEqual(updatedItems[0].Item.Type, UpdateType.Removed);
Assert.AreEqual(updatedItems[1].Index, 4);
Assert.AreEqual(updatedItems[1].Item.Type, UpdateType.Inserted);
seq = new Sequence(Alphabets.DNA, "ACGTATAT");
derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(5);
derSeq.RemoveAt(4);
derSeq.RemoveAt(3);
derSeq.RemoveAt(1);
Assert.AreEqual(derSeq.ToString(), "AGAT");
updatedItems = derSeq.GetUpdatedItems();
Assert.AreEqual(updatedItems.Count, 4);
Assert.AreEqual(updatedItems[0].Index, 1);
Assert.AreEqual(updatedItems[0].Item.Type, UpdateType.Removed);
Assert.AreSame(updatedItems[0].Item.SequenceItem, seq[1]);
Assert.AreEqual(updatedItems[1].Index, 3);
Assert.AreEqual(updatedItems[1].Item.Type, UpdateType.Removed);
Assert.AreSame(updatedItems[1].Item.SequenceItem, seq[3]);
Assert.AreEqual(updatedItems[2].Index, 4);
Assert.AreEqual(updatedItems[2].Item.Type, UpdateType.Removed);
Assert.AreSame(updatedItems[2].Item.SequenceItem, seq[4]);
Assert.AreEqual(updatedItems[3].Index, 5);
Assert.AreEqual(updatedItems[3].Item.Type, UpdateType.Removed);
Assert.AreSame(updatedItems[3].Item.SequenceItem, seq[5]);
seq = new Sequence(Alphabets.DNA, "ACGTATAT");
derSeq = new DerivedSequence(seq);
derSeq.RemoveRange(1, 4);
Assert.AreEqual(derSeq.ToString(), "ATAT");
seq = new Sequence(Alphabets.DNA, "ACGTATAT");
derSeq = new DerivedSequence(seq);
derSeq.RemoveAt(1);
derSeq.RemoveAt(2);
derSeq.RemoveAt(5);
derSeq.Insert(3, 'A');
updatedItems = derSeq.GetUpdatedItems();
Assert.AreEqual(updatedItems.Count, 4);
Assert.AreEqual(updatedItems.Where(R => R.Item.Type == UpdateType.Removed).Count(), 3);
Assert.AreEqual(updatedItems.Where(R => R.Item.Type == UpdateType.Inserted).Count(), 1);
#region Test - IndexOfNonGap and LastIndexOfNonGap
seq = new Sequence(Alphabets.RNA, "--ACUGUA-");
derSeq = new DerivedSequence(seq);
Assert.AreEqual(seq.IndexOfNonGap(), 2);
Assert.AreEqual(seq.IndexOfNonGap(1), 2);
Assert.AreEqual(seq.IndexOfNonGap(4), 4);
Assert.AreEqual(seq.IndexOfNonGap(8), -1);
Assert.AreEqual(seq.LastIndexOfNonGap(), 7);
Assert.AreEqual(seq.LastIndexOfNonGap(seq.Count - 1), 7);
Assert.AreEqual(seq.LastIndexOfNonGap(7), 7);
Assert.AreEqual(seq.LastIndexOfNonGap(5), 5);
Assert.AreEqual(seq.IndexOfNonGap(), derSeq.IndexOfNonGap());
Assert.AreEqual(seq.IndexOfNonGap(1), derSeq.IndexOfNonGap(1));
Assert.AreEqual(seq.IndexOfNonGap(4), derSeq.IndexOfNonGap(4));
Assert.AreEqual(seq.IndexOfNonGap(8), derSeq.IndexOfNonGap(8));
Assert.AreEqual(seq.LastIndexOfNonGap(), derSeq.LastIndexOfNonGap());
Assert.AreEqual(seq.LastIndexOfNonGap(seq.Count - 1), derSeq.LastIndexOfNonGap(derSeq.Count - 1));
Assert.AreEqual(seq.LastIndexOfNonGap(7), derSeq.LastIndexOfNonGap(7));
Assert.AreEqual(seq.LastIndexOfNonGap(5), derSeq.LastIndexOfNonGap(5));
#endregion Test - IndexOfNonGap and LastIndexOfNonGap
seq = new Sequence(Alphabets.RNA, "ACUGUA");
derSeq = new DerivedSequence(seq);
derSeq.Insert(3, new Nucleotide('A', "RNACHAR"));
derSeq.RemoveAt(2);
Assert.AreEqual(derSeq.ToString(), "ACAGUA");
CompoundNucleotide cn = new CompoundNucleotide('M', "Compound");
cn.Add(new Nucleotide('A', "Item A"), 30);
cn.Add(new Nucleotide('C', "Item C"), 20);
derSeq.Insert(3, cn);
Assert.AreEqual(derSeq[2].Symbol, 'A');
Assert.AreEqual(derSeq[2].Name, "RNACHAR");
Assert.AreEqual(derSeq[3].Symbol, 'M');
}