/// <summary>
/// General method to validate creation of Qualitative sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="parameters">Different Qualitative Sequence parameters.</param>
/// </summary>
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));
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 inputScoreforIUPAC = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxScoreNode);
string inputQuality = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputByteArrayNode);
byte[] byteArray = Encoding.UTF8.GetBytes(inputQuality);
int index = 0;
// Create and validate Qualitative Sequence.
switch (parameters)
{
case QualitativeSequenceParameters.Score:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, Utility.GetDefaultEncodedQualityScores(expectedFormatType, inputSequence.Length));
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, Convert.ToInt32(inputScoreforIUPAC, (IFormatProvider)null));
}
break;
case QualitativeSequenceParameters.ByteArray:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
Encoding.UTF8.GetBytes(inputSequence), byteArray);
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, Convert.ToInt32(byteArray[index], (IFormatProvider)null));
index++;
}
break;
default:
break;
}
// Validate createdSequence qualitative sequence.
Assert.IsNotNull(createdQualitativeSequence);
Assert.AreEqual(createdQualitativeSequence.Alphabet, alphabet);
Assert.AreEqual(createdQualitativeSequence.ConvertToString(), expectedSequence);
Assert.AreEqual(createdQualitativeSequence.Count.ToString((IFormatProvider)null), expectedSequenceCount);
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence {0} is as expected.", createdQualitativeSequence));
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence Score {0} is as expected.", createdQualitativeSequence.GetEncodedQualityScores()));
Assert.AreEqual(createdQualitativeSequence.FormatType, expectedFormatType);
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative format type {0} is as expected.", createdQualitativeSequence.FormatType));
}
/// <summary>
/// General method to validate creation of Qualitative sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="parameters">Different Qualitative Sequence parameters.</param>
/// </summary>
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));
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 inputScoreforIUPAC = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxScoreNode);
string inputQuality = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputByteArrayNode);
byte[] byteArray = Encoding.UTF8.GetBytes(inputQuality);
int index = 0;
// Create and validate Qualitative Sequence.
switch (parameters)
{
case QualitativeSequenceParameters.Score:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, Utility.GetDefaultEncodedQualityScores(expectedFormatType, inputSequence.Length));
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, Convert.ToInt32(inputScoreforIUPAC, (IFormatProvider)null));
}
break;
case QualitativeSequenceParameters.ByteArray:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
Encoding.UTF8.GetBytes(inputSequence), byteArray);
// Validate score
foreach (byte qualScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualScore, Convert.ToInt32(byteArray[index], (IFormatProvider)null));
index++;
}
break;
default:
break;
}
// Validate createdSequence qualitative sequence.
Assert.IsNotNull(createdQualitativeSequence);
Assert.AreEqual(createdQualitativeSequence.Alphabet, alphabet);
Assert.AreEqual(createdQualitativeSequence.ConvertToString(), expectedSequence);
Assert.AreEqual(createdQualitativeSequence.Count.ToString((IFormatProvider)null), expectedSequenceCount);
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence {0} is as expected.", createdQualitativeSequence));
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence Score {0} is as expected.", createdQualitativeSequence.GetEncodedQualityScores()));
Assert.AreEqual(createdQualitativeSequence.FormatType, expectedFormatType);
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative format type {0} is as expected.", createdQualitativeSequence.FormatType));
}
