public void ValidateCompoundNucleotideToAminoAcid()
{
ISequenceItem seqItem1 = new Sequence(Alphabets.Protein, "KIET")[0];
ISequenceItem seqItem2 = new Sequence(Alphabets.DNA, "AGC")[0];
List <ISequenceItem> seqItemList = new List <ISequenceItem>();
seqItemList.Add(seqItem1);
seqItemList.Add(seqItem2);
double weightItem1 = 35;
double weightItem2 = 33;
List <double> weightList = new List <double>();
weightList.Add(weightItem1);
weightList.Add(weightItem2);
try
{
ICompoundSequenceItem seqItemObj =
new CompoundAminoAcid('B', "CompoundSeq'", seqItemList, weightList);
Assert.IsTrue(null != seqItemObj);
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the Nucleotide for AminoAcid exception");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the Nucleotide for AminoAcid exception");
}
}
public void InvalidateAminoAcidObjectData()
{
try
{
AminoAcid acidObj = new CompoundAminoAcid('A', "Item");
acidObj.GetObjectData(null as SerializationInfo, new StreamingContext());
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AminoAcid : Successfully validated the exception");
Console.WriteLine(
"AminoAcid : Successfully validated the exception");
}
try
{
CompoundAminoAcid compAcidObj = new CompoundAminoAcid('A', "Item");
compAcidObj.GetObjectData(null as SerializationInfo, new StreamingContext());
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
Console.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
}
}
public void InvalidateCompoundAminoAcidAdd()
{
CompoundAminoAcid aminoAcid = null;
try
{
aminoAcid = new CompoundAminoAcid('A', "Item");
aminoAcid.Add(null as ISequenceItem, 35);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
Console.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
}
finally
{
if (aminoAcid != null)
{
((IDisposable)aminoAcid).Dispose();
}
}
try
{
List <ISequenceItem> seq = new List <ISequenceItem>();
seq.Add(new Sequence(Alphabets.Protein, "a")[0]);
seq.Add(new Sequence(Alphabets.Protein, "a")[0]);
List <double> weight = new List <double>();
weight.Add(80);
weight.Add(78);
aminoAcid = new CompoundAminoAcid(
1, 'B', Constants.CompoundItemName,
false, false, seq, weight);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
Console.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
}
finally
{
if (aminoAcid != null)
{
((IDisposable)aminoAcid).Dispose();
}
}
}
public void ValidateCompoundAminoAcidNegWeight()
{
ICompoundSequenceItem seqItem =
new CompoundAminoAcid('B', "NegativeWeight");
seqItem.Add(new Sequence(Alphabets.Protein, "KIET")[0], -35);
Assert.AreEqual("Lysine", seqItem.SequenceItems[0].Name);
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the negative weight expression");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the negative weight expression");
}
public void ValidateCompoundAminoAcidNonGap()
{
ICompoundSequenceItem seqItemObj =
new CompoundAminoAcid('X', "CompoundSeq", false, false);
Assert.IsFalse(seqItemObj.IsGap);
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the Gap property");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the Gap property");
}
public void InvalidateCompoundAminoAcidListAdd()
{
CompoundAminoAcid cAminoAcid = null;
try
{
List <ISequenceItem> seq = new List <ISequenceItem>();
seq.Add(null);
List <double> weight = new List <double>();
cAminoAcid = new CompoundAminoAcid(
1, 'B', Constants.CompoundItemName,
false, false, seq, weight);;
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
Console.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
}
try
{
List <ISequenceItem> seq = new List <ISequenceItem>();
seq.Add(new Sequence(Alphabets.DNA, "a")[0]);
List <double> weight = new List <double>();
cAminoAcid = new CompoundAminoAcid(
1, 'B', Constants.CompoundItemName,
false, false, seq, weight);;
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
Console.WriteLine(
"CompoundAminoAcid : Successfully validated the exception");
}
finally
{
if (cAminoAcid != null)
{
((IDisposable)cAminoAcid).Dispose();
}
}
}
public void ValidateCompoundAminoAcidInValidSymbol()
{
try
{
ICompoundSequenceItem seqItemObj = new CompoundAminoAcid('Ñ', "CompoundSeq");
ISequence seq = new Sequence(Alphabets.Protein);
seq.Add(seqItemObj);
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the invalid sequence Symbol");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the invalid sequence Symbol");
}
}
public void ValidateCompoundAminoAcidInValidRemove()
{
List <ISequenceItem> seqItemList = null;
List <double> weightList = null;
GetSequenceItemWithWeight(out seqItemList, out weightList, false);
ICompoundSequenceItem seqItem =
new CompoundAminoAcid('B', "CompoundSeq", seqItemList, weightList);
seqItem.Remove(new Sequence(Alphabets.DNA, "T")[0]);
Assert.AreEqual(2, seqItem.SequenceItems.Count);
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the invalid remove");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the invalid remove");
}
public void ValidateCompoundAminoAcidDuplicateSequence()
{
List <ISequenceItem> seqItemList = null;
List <double> weightList = null;
GetSequenceItemWithWeight(out seqItemList, out weightList, false);
ICompoundSequenceItem seqItemObj1 =
new CompoundAminoAcid('B', "CompoundSeq", seqItemList, weightList);
ICompoundSequenceItem seqItemObj2 =
new CompoundAminoAcid('B', "CompoundSeq", seqItemList, weightList);
Assert.AreEqual(seqItemObj1, seqItemObj2);
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the duplicate item");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the duplicate item");
}
public void ValidateCompoundAminoAcidSequenceListNull()
{
List <ISequenceItem> seqItemList = null;
List <double> weightList = null;
GetSequenceItemWithWeight(out seqItemList, out weightList, false);
try
{
ICompoundSequenceItem seqItemObj =
new CompoundAminoAcid('B', "CompoundSeq", null, weightList);
Assert.IsTrue(null != seqItemObj);
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the sequence list null exception");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the sequence list null exception");
}
}
public void ValidateCompoundAminoAcidDuplicateSequenceItemSymbol()
{
List <ISequenceItem> seqItemList = null;
List <double> weightList = null;
GetSequenceItemWithWeight(out seqItemList, out weightList, false);
ICompoundSequenceItem seqItemObj1 =
new CompoundAminoAcid('B', "CompoundSeq", seqItemList, weightList);
ICompoundSequenceItem seqItemObj2 =
new CompoundAminoAcid('B', "CompoundSeq", seqItemList, weightList);
Sequence originalSeq = new Sequence(Alphabets.DNA);
originalSeq.Add(seqItemObj1);
originalSeq.Add(seqItemObj2);
Assert.AreEqual("BB", originalSeq.ToString());
ApplicationLog.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the duplicate item & symbol");
Console.WriteLine(
"CompoundSequenceP2TestCases : Successfully validated the duplicate item & symbol");
}