void GeneralQualitativeSequence(
string nodeName, QualitativeSequenceParameters parameters)
{
// Gets the actual sequence and the alphabet from the Xml
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode));
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FastQFormatType));
string expectedScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedScore);
QualitativeSequence createdQualitativeSequence = null;
string inputSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QSequenceCount);
string expectedMaxScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxScoreNode);
string inputScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputScoreNode);
string expectedOuptutScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputScoreNode);
string inputQuality = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputByteArrayNode);
byte[] byteArray = ASCIIEncoding.ASCII.GetBytes(inputQuality);
Byte[] inputScoreArray = encodingObj.GetBytes(inputQuality);
// Create and validate Qualitative Sequence.
switch (parameters)
{
case QualitativeSequenceParameters.Score:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, inputQuality);
int count = 0;
// Validate score
foreach (byte qualScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualScore, inputScoreArray[count]);
count++;
}
break;
case QualitativeSequenceParameters.ByteArray:
byte[] scoreValue = ASCIIEncoding.ASCII.GetBytes(inputSequence);
int index = 0;
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
scoreValue, inputScoreArray);
// Validate score
foreach (byte qualScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualScore, inputScoreArray[index]);
index++;
}
break;
default:
break;
}
string qualitativeSequence = new string(createdQualitativeSequence.Select(a => (char)a).ToArray());
// Validate createdSequence qualitative sequence.
Assert.IsNotNull(createdQualitativeSequence);
Assert.AreEqual(alphabet, createdQualitativeSequence.Alphabet);
Assert.AreEqual(expectedSequence, qualitativeSequence);
Assert.AreEqual(expectedSequenceCount, createdQualitativeSequence.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedScore, createdQualitativeSequence.QualityScores.Count().ToString((IFormatProvider)null));
Assert.AreEqual(expectedFormatType, createdQualitativeSequence.FormatType);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sequence {0} is as expected.",
qualitativeSequence));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sequence Score {0} is as expected.",
createdQualitativeSequence.Count().ToString((IFormatProvider)null)));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative format type {0} is as expected.",
createdQualitativeSequence.FormatType));
}
void GeneralQualitativeSequence(
string nodeName, QualitativeSequenceParameters parameters)
{
//// Gets the actual sequence and the alphabet from the Xml
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode));
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FastQFormatType));
string expectedScore = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedScore);
QualitativeSequence createdQualitativeSequence = null;
string inputSequence = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QSequenceCount);
string inputQuality = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputByteArrayNode);
Byte[] inputScoreArray = Encoding.UTF8.GetBytes(inputQuality);
// Create and validate Qualitative Sequence.
switch (parameters)
{
case QualitativeSequenceParameters.Score:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, inputQuality);
int count = 0;
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, inputScoreArray[count]);
count++;
}
break;
case QualitativeSequenceParameters.ByteArray:
byte[] scoreValue = Encoding.UTF8.GetBytes(inputSequence);
int index = 0;
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
scoreValue, inputScoreArray);
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, inputScoreArray[index]);
index++;
}
break;
default:
break;
}
string qualitativeSequence = new string(createdQualitativeSequence.Select(a => (char)a).ToArray());
// Validate createdSequence qualitative sequence.
Assert.IsNotNull(createdQualitativeSequence);
Assert.AreEqual(alphabet, createdQualitativeSequence.Alphabet);
Assert.AreEqual(expectedSequence, qualitativeSequence);
Assert.AreEqual(expectedSequenceCount, createdQualitativeSequence.Count.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence BVT:Qualitative Sequence {0} is as expected.", qualitativeSequence));
Assert.AreEqual(expectedScore, createdQualitativeSequence.GetEncodedQualityScores().Count().ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence BVT:Qualitative Sequence Score {0} is as expected.", createdQualitativeSequence.Count().ToString((IFormatProvider)null)));
Assert.AreEqual(expectedFormatType, createdQualitativeSequence.FormatType);
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence BVT:Qualitative format type {0} is as expected.", createdQualitativeSequence.FormatType));
}
