/// <summary>
/// XsvSparse formatter generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="nodename">Xml node Name.</param>
/// <param name="additionalParam">Additional parameter
/// based on which the validation of test case is done.</param>
void XsvSparseFormatterGeneralTestCases(string nodename,
AdditionalParameters additionalParam)
{
// Gets the expected sequence from the Xml
string filePathObj = this.utilityObj.xmlUtil.GetTextValue(nodename,
Constants.FilePathNode).TestDir();
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"XsvSparse Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
IEnumerable <ISequence> seqList = null;
SparseSequence sparseSeq = null;
XsvContigParser parserObj = new XsvContigParser(Alphabets.DNA, Constants.CharSeperator, Constants.SequenceIDPrefix);
seqList = parserObj.Parse(filePathObj);
sparseSeq = (SparseSequence)seqList.ElementAt(0);
IReadOnlyList <IndexedItem <byte> > sparseSeqItems = sparseSeq.GetKnownSequenceItems();
string tempFile = Path.GetTempFileName();
XsvSparseFormatter formatterObj = new XsvSparseFormatter(Constants.CharSeperator, Constants.SequenceIDPrefix);
switch (additionalParam)
{
case AdditionalParameters.FormatFilePath:
formatterObj.Format(sparseSeq, tempFile);
break;
default:
break;
case AdditionalParameters.ForamtListWithFilePath:
formatterObj.Format(seqList.ToList(), tempFile);
break;
}
XsvContigParser newParserObj = new XsvContigParser(Alphabets.DNA, Constants.CharSeperator, Constants.SequenceIDPrefix);
// Parse a formatted Xsv file and validate.
seqList = newParserObj.Parse(filePathObj);
SparseSequence expectedSeq = (SparseSequence)seqList.ElementAt(0);
IReadOnlyList <IndexedItem <byte> > expectedSparseSeqItems = expectedSeq.GetKnownSequenceItems();
for (int i = 0; i < sparseSeqItems.Count; i++)
{
IndexedItem <byte> seqItem = sparseSeqItems[i];
IndexedItem <byte> expectedSeqItem = expectedSparseSeqItems[i];
Assert.AreEqual(seqItem.Index, expectedSeqItem.Index);
}
ApplicationLog.WriteLine("Successfully validated the format Xsv file");
}
/// <summary>
/// XsvSparse formatter generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="switchParam">Additional parameter
/// based on which the validation of test case is done.</param>
private void XsvSparseFormatterGeneralTestCases(string switchParam)
{
// Gets the expected sequence from the Xml
string filePathObj = XsvFilename.TestDir();
Assert.IsTrue(File.Exists(filePathObj));
XsvContigParser parserObj = new XsvContigParser(Alphabets.DNA, ',', '#');
IEnumerable <ISequence> seqList = parserObj.Parse(filePathObj);
SparseSequence sparseSeq = (SparseSequence)seqList.FirstOrDefault();
var sparseSeqItems = sparseSeq.GetKnownSequenceItems();
string xsvTempFileName = Path.GetTempFileName();
XsvSparseFormatter formatterObj = new XsvSparseFormatter(',', '#');
using (formatterObj.Open(xsvTempFileName))
{
switch (switchParam)
{
case "FormatFilePath":
formatterObj.Format(sparseSeq);
break;
case "ForamtListWithFilePath":
formatterObj.Format(sparseSeq);
break;
}
}
// Parse a formatted Xsv file and validate.
var parserObj1 = new XsvContigParser(Alphabets.DNA, ',', '#');
using (parserObj1.Open(xsvTempFileName))
{
seqList = parserObj1.Parse();
SparseSequence expectedSeq = (SparseSequence)seqList.FirstOrDefault();
var expectedSparseSeqItems = expectedSeq.GetKnownSequenceItems();
Assert.AreEqual(sparseSeqItems.Count, expectedSparseSeqItems.Count);
for (int i = 0; i < sparseSeqItems.Count; i++)
{
Assert.AreEqual(sparseSeqItems.ElementAt(i).Index, expectedSparseSeqItems.ElementAt(i).Index);
Assert.AreEqual(sparseSeqItems.ElementAt(i).Item, expectedSparseSeqItems.ElementAt(i).Item);
}
}
// Delete the temporary file.
if (File.Exists(xsvTempFileName))
{
File.Delete(xsvTempFileName);
}
}
public void XsvSparseBvtFormatterProperties()
{
XsvSparseFormatter formatterObj = new XsvSparseFormatter(Constants.CharSeperator,
Constants.SequenceIDPrefix);
Assert.AreEqual(Constants.XsvSparseFormatterDescription, formatterObj.Description);
Assert.AreEqual(Constants.XsvSparseFileTypes, formatterObj.SupportedFileTypes);
Assert.AreEqual(Constants.XsvSparseFormatterNode, formatterObj.Name);
Assert.AreEqual(Constants.XsvSeperator, formatterObj.Separator);
Assert.AreEqual(Constants.XsvSeqIdPrefix, formatterObj.SequenceIDPrefix);
ApplicationLog.WriteLine
("Successfully validated all the properties of XsvSparse Formatter class.");
}
public void XsvSparseFormatterProperties()
{
string XsvTempFileName = Path.GetTempFileName();
using (XsvSparseFormatter formatterObj = new XsvSparseFormatter(XsvTempFileName, ',', '#'))
{
Assert.AreEqual("Sparse Sequence formatter to character separated value file", formatterObj.Description);
Assert.AreEqual("csv,tsv", formatterObj.SupportedFileTypes);
Assert.AreEqual("XsvSparseFormatter", formatterObj.Name);
Assert.AreEqual(',', formatterObj.Separator);
Assert.AreEqual('#', formatterObj.SequenceIDPrefix);
}
if (File.Exists(XsvTempFileName))
{
File.Delete(XsvTempFileName);
}
}
public void XsvSparseBvtFormatterFormatString()
{
// Gets the expected sequence from the Xml
string filePathObj = Utility._xmlUtil.GetTextValue(Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode);
string expectedString = Utility._xmlUtil.GetTextValue(Constants.SimpleXsvSparseNodeName,
Constants.expectedString);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"XsvSparse Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
IList <ISequence> seqList = null;
SparseSequence sparseSeq = null;
XsvContigParser parserObj = new XsvContigParser(Encodings.IupacNA, Alphabets.DNA,
Constants.CharSeperator, Constants.SequenceIDPrefix);
seqList = parserObj.Parse(filePathObj);
sparseSeq = (SparseSequence)seqList[0];
XsvSparseFormatter formatterObj = new XsvSparseFormatter(Constants.CharSeperator,
Constants.SequenceIDPrefix);
string formattedString = formatterObj.FormatString(sparseSeq);
formattedString = formattedString.Replace("\r", "").Replace("\n", "");
Assert.AreEqual(expectedString, formattedString);
// Log to Nunit GUI.
Console.WriteLine("Successfully validated the formatString Xsv file");
ApplicationLog.WriteLine("Successfully validated the formatString Xsv file");
}
/// <summary>
/// XsvSparse parser generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
private void XsvSparseParserGeneralTestCases()
{
// Gets the expected sequence from the Xml
string filePathObj = XsvFilename.TestDir();
Assert.IsTrue(File.Exists(filePathObj));
XsvContigParser parserObj = new XsvContigParser(Alphabets.DNA, ',', '#');
string expectedSeqIds = "Chr22+Chr22+Chr22+Chr22,m;Chr22;16,m;Chr22;17,m;Chr22;29,m;Chr22;32,m;Chr22;39,m;Chr22;54,m;Chr22;72,m;Chr22;82,m;Chr22;85,m;Chr22;96,m;Chr22;99,m;Chr22;118,m;Chr22;119,m;Chr22;129,m;Chr22;136,m;Chr22;146,m;Chr22;153,m;Chr22;161,m;Chr22;162,m;Chr22;174,m;Chr22;183,m;Chr22;209,m;Chr22;210,m;Chr22;224,m;Chr22;241,m;Chr22;243,m;Chr22;253,m;Chr22;267,m;Chr22;309,m;Chr22;310,m;Chr22;313,m;Chr22;331,m;Chr22;333,m;Chr22;338,m;Chr22;348,m;Chr22;352,m;Chr22;355,m;Chr22;357,m;Chr22;368,m;Chr22;370,m;Chr22;380,m;Chr22;382,m;Chr22;402,m;Chr22;418,m;Chr22;419,m;Chr22;429,m;Chr22;432,m;Chr22;450,m;Chr22;462,m;Chr22;482,m;Chr22;484,m;Chr22;485,m;Chr22;494,m;Chr22;508,m;Chr22;509,m;Chr22;512,";
IEnumerable <ISequence> seqList = parserObj.Parse(filePathObj);
SparseSequence sparseSeq = (SparseSequence)seqList.FirstOrDefault();
if (null == sparseSeq)
{
string expCount = "57";
Assert.IsNotNull(seqList);
Assert.AreEqual(expCount, seqList.ToList().Count);
StringBuilder actualId = new StringBuilder();
foreach (ISequence seq in seqList)
{
SparseSequence sps = (SparseSequence)seq;
actualId.Append(sps.ID);
actualId.Append(",");
}
Assert.AreEqual(expectedSeqIds, actualId.ToString());
}
else
{
string[] idArray = expectedSeqIds.Split(',');
Assert.AreEqual(sparseSeq.ID, idArray[0]);
}
string XsvTempFileName = Path.GetTempFileName();
XsvSparseFormatter formatter = new XsvSparseFormatter(',', '#');
using (formatter.Open(XsvTempFileName))
{
formatter.Format(seqList.ToList());
}
string expectedOutput = string.Empty;
using (StreamReader readerSource = new StreamReader(filePathObj))
{
expectedOutput = readerSource.ReadToEnd();
}
string actualOutput = string.Empty;
using (StreamReader readerDest = new StreamReader(XsvTempFileName))
{
actualOutput = readerDest.ReadToEnd();
}
Assert.AreEqual(Utility.CleanupWhiteSpace(expectedOutput),
Utility.CleanupWhiteSpace(actualOutput));
Assert.IsNotNull(sparseSeq.Alphabet);
// Delete the temporary file.
if (File.Exists(XsvTempFileName))
{
File.Delete(XsvTempFileName);
}
}
/// <summary>
/// XsvSparse formatter generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="nodename">Xml node Name.</param>
/// <param name="additionalParam">Additional parameter
/// based on which the validation of test case is done.</param>
static void XsvSparseFormatterGeneralTestCases(string nodename,
AdditionalParameters additionalParam)
{
// Gets the expected sequence from the Xml
string filePathObj = Utility._xmlUtil.GetTextValue(nodename,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"XsvSparse Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
IList <ISequence> seqList = null;
SparseSequence sparseSeq = null;
XsvContigParser parserObj = new XsvContigParser(Encodings.IupacNA, Alphabets.DNA,
Constants.CharSeperator, Constants.SequenceIDPrefix);
seqList = parserObj.Parse(filePathObj);
sparseSeq = (SparseSequence)seqList[0];
IList <IndexedItem <ISequenceItem> > sparseSeqItems =
sparseSeq.GetKnownSequenceItems();
XsvSparseFormatter formatterObj = new XsvSparseFormatter(Constants.CharSeperator,
Constants.SequenceIDPrefix);
switch (additionalParam)
{
case AdditionalParameters.FormatFilePath:
formatterObj.Format(sparseSeq, Constants.XsvTempFileName);
break;
default:
break;
case AdditionalParameters.ForamtListWithFilePath:
formatterObj.Format(seqList, Constants.XsvTempFileName);
break;
case AdditionalParameters.FormatTextWriter:
using (TextWriter writer = new StreamWriter(Constants.XsvTempFileName))
{
formatterObj.Format(sparseSeq, writer);
}
break;
case AdditionalParameters.FormatTextWriterWithOffset:
using (TextWriter writer = new StreamWriter(Constants.XsvTempFileName))
{
formatterObj.Format(sparseSeq, 0, writer);
}
break;
case AdditionalParameters.FormatListTextWriter:
using (TextWriter writer = new StreamWriter(Constants.XsvTempFileName))
{
formatterObj.Format(seqList, writer);
}
break;
}
// Parse a formatted Xsv file and validate.
SparseSequence expectedSeq;
seqList = parserObj.Parse(Constants.XsvTempFileName);
expectedSeq = (SparseSequence)seqList[0];
IList <IndexedItem <ISequenceItem> > expectedSparseSeqItems =
expectedSeq.GetKnownSequenceItems();
for (int i = 0; i < sparseSeqItems.Count; i++)
{
IndexedItem <ISequenceItem> seqItem = sparseSeqItems[i];
IndexedItem <ISequenceItem> expectedSeqItem = expectedSparseSeqItems[i];
Assert.AreEqual(seqItem.Index, expectedSeqItem.Index);
}
// Log to Nunit GUI.
Console.WriteLine("Successfully validated the format Xsv file");
ApplicationLog.WriteLine("Successfully validated the format Xsv file");
// Delete the temporary file.
if (File.Exists(Constants.XsvTempFileName))
{
File.Delete(Constants.XsvTempFileName);
}
}
/// <summary>
/// XsvSparse formatter generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="switchParam">Additional parameter
/// based on which the validation of test case is done.</param>
private void XsvSparseFormatterGeneralTestCases(string switchParam)
{
// Gets the expected sequence from the Xml
string filePathObj = Directory.GetCurrentDirectory() + XsvFilename;
Assert.IsTrue(File.Exists(filePathObj));
IEnumerable <ISequence> seqList = null;
SparseSequence sparseSeq = null;
XsvContigParser parserObj = new XsvContigParser(filePathObj, Alphabets.DNA, ',', '#');
seqList = parserObj.Parse();
sparseSeq = (SparseSequence)seqList.FirstOrDefault();
IList <IndexedItem <byte> > sparseSeqItems =
sparseSeq.GetKnownSequenceItems();
string XsvTempFileName = Path.GetTempFileName();
using (XsvSparseFormatter formatterObj = new XsvSparseFormatter(XsvTempFileName, ',', '#'))
{
switch (switchParam)
{
case "FormatFilePath":
formatterObj.Write(sparseSeq);
break;
default:
break;
case "ForamtListWithFilePath":
formatterObj.Write(sparseSeq);
break;
}
}
// Parse a formatted Xsv file and validate.
using (XsvContigParser parserObj1 = new XsvContigParser(XsvTempFileName, Alphabets.DNA, ',', '#'))
{
SparseSequence expectedSeq;
seqList = parserObj1.Parse();
expectedSeq = (SparseSequence)seqList.FirstOrDefault();
IList <IndexedItem <byte> > expectedSparseSeqItems =
expectedSeq.GetKnownSequenceItems();
Assert.AreEqual(sparseSeqItems.Count, expectedSparseSeqItems.Count);
for (int i = 0; i < sparseSeqItems.Count; i++)
{
Assert.AreEqual(sparseSeqItems.ElementAt(i).Index, expectedSparseSeqItems.ElementAt(i).Index);
Assert.AreEqual(sparseSeqItems.ElementAt(i).Item, expectedSparseSeqItems.ElementAt(i).Item);
}
}
// Delete the temporary file.
if (File.Exists(XsvTempFileName))
{
File.Delete(XsvTempFileName);
}
}
