/// <summary>
/// General method to validate default score for different FastQ
/// format with different sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="parameters">Different Qualitative Score method parameter.</param>
/// </summary>
void ValidateFastQDefaultScores(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 inputSequence = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string expectedMaxScore = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefualtMaxScore);
string expectedMinScore = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefaultMinScore);
QualitativeSequence createdQualitativeSequence = null;
string qualityScoresString = Utility.GetDefaultEncodedQualityScores(expectedFormatType, inputSequence.Length);
byte[] expectedMaxScores = Utility.GetEncodedQualityScores((byte)int.Parse(expectedMaxScore, null as IFormatProvider), inputSequence.Length);
byte[] expectedMinScores = Utility.GetEncodedQualityScores((byte)int.Parse(expectedMinScore, null as IFormatProvider), inputSequence.Length);
int i = 0;
switch (parameters)
{
case QualitativeSequenceParameters.DefaultScoreWithAlphabets:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, inputSequence,
qualityScoresString);
// Validate default score.
i = 0;
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
(byte)(qualityScoresString[i]));
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
qualityScoresString[0]));
break;
case QualitativeSequenceParameters.DefaultScoreWithSequence:
createdQualitativeSequence = new QualitativeSequence(alphabet,
expectedFormatType, inputSequence,
qualityScoresString);
i = 0;
// Validate default score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
(byte)(qualityScoresString[i]));
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
qualityScoresString[0]));
break;
case QualitativeSequenceParameters.MaxDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, Encoding.UTF8.GetBytes(inputSequence),
expectedMaxScores);
i = 0;
// Validate default maximum score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
expectedMaxScores[i]);
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Maximum score {0} is as expected.",
QualitativeSequence.GetMaxEncodedQualScore(expectedFormatType)));
break;
case QualitativeSequenceParameters.MinDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, Encoding.UTF8.GetBytes(inputSequence),
expectedMinScores);
i = 0;
// Validate default minimum score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
expectedMinScores[i]);
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence Minimum score {0} is as expected.",
QualitativeSequence.GetMinEncodedQualScore(expectedFormatType)));
break;
default:
break;
}
}
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));
}
/// <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 Index of Qualitative Sequence Items.
/// <param name="nodeName">xml node name.</param>
/// <param name="indexParam">Different Qualitative Sequence parameters.</param>
/// </summary>
void ValidateGeneralQualitativeSeqItemIndices(string nodeName, QualitativeSequenceParameters indexParam)
{
// 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 expectedFirstItemIdex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstItemIndex);
string expectedLastItemIdex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LastItemIndex);
string expectedGapIndex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IndexOfGap);
long lastItemIndex;
long index;
// Create a qualitative Sequence.
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, inputSequence,
Utility.GetDefaultEncodedQualityScores(expectedFormatType, inputSequence.Length));
// Get a Index of qualitative sequence items
switch (indexParam)
{
case QualitativeSequenceParameters.IndexOfNonGap:
index = createdQualitativeSequence.IndexOfNonGap();
// Validate Qualitative sequence item indices.
Assert.AreEqual(index, Convert.ToInt32(expectedFirstItemIdex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.IndexOfNonGapWithParam:
index = createdQualitativeSequence.IndexOfNonGap(5);
// Validate Qualitative sequence item indices.
Assert.AreEqual(index, Convert.ToInt32(expectedGapIndex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.LastIndexOf:
lastItemIndex = createdQualitativeSequence.LastIndexOfNonGap();
// Validate Qualitative sequence item indices.
Assert.AreEqual(lastItemIndex, Convert.ToInt32(expectedLastItemIdex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.LastIndexOfWithPam:
lastItemIndex = createdQualitativeSequence.LastIndexOfNonGap(5);
// Validate Qualitative sequence item indices.
Assert.AreEqual(lastItemIndex, Convert.ToInt32(expectedGapIndex, (IFormatProvider)null));
break;
default:
break;
}
// Logs to the VSTest GUI window
ApplicationLog.WriteLine("Qualitative Sequence P1 : Qualitative SequenceItems indices validation completed successfully.");
}
/// <summary>
/// General method to validate Index of Qualitative Sequence Items.
/// <param name="nodeName">xml node name.</param>
/// <param name="indexParam">Different Qualitative Sequence parameters.</param>
/// </summary>
void ValidateGeneralQualitativeSeqItemIndices(
string nodeName, QualitativeSequenceParameters indexParam)
{
// 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 expectedFirstItemIdex = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstItemIndex);
string expectedLastItemIdex = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LastItemIndex);
string expectedGapIndex = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IndexOfGap);
long lastItemIndex;
long index;
// Create a qualitative Sequence.
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, inputSequence,
((char)QualitativeSequence.GetDefaultQualScore(expectedFormatType)).ToString());
// Get a Index of qualitative sequence items
switch (indexParam)
{
case QualitativeSequenceParameters.IndexOfNonGap:
index = createdQualitativeSequence.IndexOfNonGap();
// Validate Qualitative sequence item indices.
Assert.AreEqual(index, Convert.ToInt32(expectedFirstItemIdex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.IndexOfNonGapWithParam:
index = createdQualitativeSequence.IndexOfNonGap(5);
// Validate Qualitative sequence item indices.
Assert.AreEqual(index, Convert.ToInt32(expectedGapIndex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.LastIndexOf:
lastItemIndex = createdQualitativeSequence.LastIndexOfNonGap();
// Validate Qualitative sequence item indices.
Assert.AreEqual(lastItemIndex, Convert.ToInt32(expectedLastItemIdex, (IFormatProvider)null));
break;
case QualitativeSequenceParameters.LastIndexOfWithPam:
lastItemIndex = createdQualitativeSequence.LastIndexOfNonGap(5);
// Validate Qualitative sequence item indices.
Assert.AreEqual(lastItemIndex, Convert.ToInt32(expectedGapIndex, (IFormatProvider)null));
break;
default:
break;
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine("Qualitative Sequence P1 : Qualitative SequenceItems indices validation completed successfully.");
}
/// <summary>
/// General method to validate default score for different FastQ
/// format with different sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="parameters">Different Qualitative Score method parameter.</param>
/// </summary>
void ValidateFastQDefaultScores(
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 inputSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string expectedMaxScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefualtMaxScore);
string expectedMinScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefaultMinScore);
QualitativeSequence createdQualitativeSequence = null;
switch (parameters)
{
case QualitativeSequenceParameters.DefaultScoreWithAlphabets:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, inputSequence,
((char)QualitativeSequence.GetDefaultQualScore(expectedFormatType)).ToString());
// Validate default score.
foreach (byte qualitativeScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualitativeScore,
QualitativeSequence.GetDefaultQualScore(expectedFormatType));
}
// Log Nunit GUI.
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
QualitativeSequence.GetDefaultQualScore(expectedFormatType)));
break;
case QualitativeSequenceParameters.DefaultScoreWithSequence:
createdQualitativeSequence = new QualitativeSequence(alphabet,
expectedFormatType, inputSequence,
((char)QualitativeSequence.GetDefaultQualScore(expectedFormatType)).ToString());
// Validate default score.
foreach (byte qualitativeScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualitativeScore,
QualitativeSequence.GetDefaultQualScore(expectedFormatType));
}
// Log Nunit GUI.
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
QualitativeSequence.GetDefaultQualScore(expectedFormatType)));
break;
case QualitativeSequenceParameters.MaxDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, encodingObj.GetBytes(inputSequence),
new byte[] { byte.Parse(expectedMaxScore, (IFormatProvider)null) });
// Validate default maximum score.
foreach (byte qualitativeScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualitativeScore,
QualitativeSequence.GetMaxQualScore(expectedFormatType));
}
// Log Nunit GUI.
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Maximum score {0} is as expected.",
QualitativeSequence.GetMaxQualScore(expectedFormatType)));
break;
case QualitativeSequenceParameters.MinDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, encodingObj.GetBytes(inputSequence),
new byte[] { byte.Parse(expectedMinScore, (IFormatProvider)null) });
// Validate default minimum score.
foreach (byte qualitativeScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualitativeScore,
QualitativeSequence.GetMinQualScore(expectedFormatType));
}
// Log Nunit GUI.
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Minimum score {0} is as expected.",
QualitativeSequence.GetMinQualScore(expectedFormatType)));
break;
default:
break;
}
}
/// <summary>
/// General method to validate default score for different FastQ
/// format with different sequence.
/// <param name="nodeName">xml node name.</param>
/// <param name="parameters">Different Qualitative Score method parameter.</param>
/// </summary>
void ValidateFastQDefaultScores(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 inputSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string expectedMaxScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefualtMaxScore);
string expectedMinScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DefaultMinScore);
QualitativeSequence createdQualitativeSequence = null;
string qualityScoresString = Utility.GetDefaultEncodedQualityScores(expectedFormatType, inputSequence.Length);
byte[] expectedMaxScores = Utility.GetEncodedQualityScores((byte)int.Parse(expectedMaxScore, null as IFormatProvider), inputSequence.Length);
byte[] expectedMinScores = Utility.GetEncodedQualityScores((byte)int.Parse(expectedMinScore, null as IFormatProvider), inputSequence.Length);
int i = 0;
switch (parameters)
{
case QualitativeSequenceParameters.DefaultScoreWithAlphabets:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, inputSequence,
qualityScoresString);
// Validate default score.
i = 0;
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
(byte)(qualityScoresString[i]));
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
qualityScoresString[0]));
break;
case QualitativeSequenceParameters.DefaultScoreWithSequence:
createdQualitativeSequence = new QualitativeSequence(alphabet,
expectedFormatType, inputSequence,
qualityScoresString);
i = 0;
// Validate default score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
(byte)(qualityScoresString[i]));
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Default score {0} is as expected.",
qualityScoresString[0]));
break;
case QualitativeSequenceParameters.MaxDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, Encoding.UTF8.GetBytes(inputSequence),
expectedMaxScores);
i = 0;
// Validate default maximum score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
expectedMaxScores[i]);
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Maximum score {0} is as expected.",
QualitativeSequence.GetMaxEncodedQualScore(expectedFormatType)));
break;
case QualitativeSequenceParameters.MinDefaultScore:
createdQualitativeSequence = new QualitativeSequence(
alphabet, expectedFormatType, Encoding.UTF8.GetBytes(inputSequence),
expectedMinScores);
i = 0;
// Validate default minimum score.
foreach (byte qualitativeScore in createdQualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualitativeScore,
expectedMinScores[i]);
i++;
}
// Log VSTest GUI.
ApplicationLog.WriteLine(string.Format(null, "Qualitative Sequence P1:Qualitative Sequence Minimum score {0} is as expected.",
QualitativeSequence.GetMinEncodedQualScore(expectedFormatType)));
break;
default:
break;
}
}
/// <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));
}
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));
}
/// <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 expectedOuptutScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputScoreNode);
string inputQuality = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InputByteArrayNode);
byte[] byteArray = UTF8Encoding.UTF8.GetBytes(inputQuality);
int index = 0;
// Create and validate Qualitative Sequence.
switch (parameters)
{
case QualitativeSequenceParameters.Score:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, ((char)QualitativeSequence.GetDefaultQualScore(expectedFormatType)).ToString());
// Validate score
foreach (byte qualScore in createdQualitativeSequence.QualityScores)
{
Assert.AreEqual(qualScore, Convert.ToInt32(inputScoreforIUPAC, (IFormatProvider)null));
}
break;
case QualitativeSequenceParameters.ByteArray:
createdQualitativeSequence = new QualitativeSequence(alphabet, expectedFormatType,
UTF8Encoding.UTF8.GetBytes(inputSequence), new byte[] { byte.Parse(expectedOuptutScore, (IFormatProvider)null) });
// Validate score
foreach (byte qualScore in createdQualitativeSequence.QualityScores)
{
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(new string(createdQualitativeSequence.Select(a => (char)a).ToArray()), expectedSequence);
Assert.AreEqual(createdQualitativeSequence.Count.ToString((IFormatProvider)null), expectedSequenceCount);
Assert.AreEqual(createdQualitativeSequence.FormatType, expectedFormatType);
// Logs to the VSTest GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence {0} is as expected.",
createdQualitativeSequence.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative Sequence Score {0} is as expected.",
createdQualitativeSequence.QualityScores.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P1:Qualitative format type {0} is as expected.",
createdQualitativeSequence.FormatType));
}
/// <summary>
/// General method to invalidate creation of Qualitative sequence
/// with invalid qual score..
/// <param name="nodeName">Name of the Format type xml node.</param>
/// <param name="errorMessage">Error message xml node name.</param>
/// <param name="qualPam">Qualitative sequence constructor paramter.</param>
/// </summary>
void InValidateQualSequence(string nodeName, string errorMessage,
QualitativeSequenceParameters qualPam)
{
// Get values from xml.
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FastQFormatType));
string expectedErrorMessage = this.utilityObj.xmlUtil.GetTextValue(
nodeName, errorMessage).Replace("FORMATTYPE", expectedFormatType.ToString());
string inputSequence = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.inputSequenceNode);
string actualError = string.Empty;
string updatedActualError = string.Empty;
QualitativeSequence qualSeq = null;
byte[] scoreArray = { 65, 64, 66, 68, 69, 67, 65, 65, 65, 65, 65,
200, 3, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 4 };
switch (qualPam)
{
case QualitativeSequenceParameters.FormatType:
//Try to create Qualitative sequence by invalid Quality score
try
{
qualSeq = new QualitativeSequence(Alphabets.DNA, expectedFormatType,
Encoding.UTF8.GetBytes(inputSequence), (byte[])null);
Assert.Fail();
}
catch (ArgumentException ex)
{
actualError = ex.Message;
// Validate an expected exception.
updatedActualError = actualError.Replace("\r", "").Replace("\n", "");
Assert.AreEqual(expectedErrorMessage.ToLower(CultureInfo.CurrentCulture),
updatedActualError.ToLower(CultureInfo.CurrentCulture));
}
break;
case QualitativeSequenceParameters.ByteArray:
//Try to create Qualitative sequence by invalid Quality score
try
{
qualSeq = new QualitativeSequence(Alphabets.DNA, expectedFormatType,
Encoding.UTF8.GetBytes(inputSequence), scoreArray);
Assert.Fail();
}
catch (ArgumentException ex)
{
actualError = ex.Message;
// Validate an expected exception.
updatedActualError = actualError.Replace("\r", "").Replace("\n", "");
Assert.AreEqual(expectedErrorMessage.ToLower(CultureInfo.CurrentCulture),
updatedActualError.ToLower(CultureInfo.CurrentCulture));
}
break;
default:
break;
}
// Log to VSTest GUI.
Assert.IsNull(qualSeq);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence P2: Qualitative Sequence Invalid score exception was validated successfully {0}",
updatedActualError));
}
