/// <summary>
/// Validate Read characters from curent line
/// </summary>
/// <param name="nodeName">Name of the node used for different test case.</param>
private void ValidateChars(string nodeName)
{
// Get values from xml
string FilePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string startIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.CharsStartIndexNode);
string count = Utility._xmlUtil.GetTextValue(
nodeName, Constants.CharsCountNode);
MBFStreamReader streamReader = new MBFStreamReader(FilePath);
string currentLine = streamReader.Line;
char[] charsArray = streamReader.ReadChars(Int32.Parse(startIndex), Int32.Parse(count));
// Validate array.
for (int i = 0; i < charsArray.Length; i++)
{
Assert.AreEqual(currentLine[i], charsArray[i]);
Console.WriteLine("Validated the char {0} successfully", charsArray[i]);
ApplicationLog.WriteLine("Validated the char successfully");
}
// Dispose stream reader.
streamReader.Close();
streamReader.Dispose();
}
public void ValidateMBFStreamReaderProperties()
{
// Get values from xml
string FilePath = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastAStreamReaderNode, Constants.FilePathNode);
string newLineCharsCount = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastAStreamReaderNode, Constants.NewLineCharacterCountNode);
string pos = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastAStreamReaderNode, Constants.PositionNode);
string startingIndex = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastAStreamReaderNode, Constants.CurrentLineStartingIndexNode);
MBFStreamReader streamReader = new MBFStreamReader(FilePath, true);
// Validate Properties
Assert.IsTrue(streamReader.CanRead);
Assert.IsTrue(streamReader.SkipBlankLines);
Assert.IsTrue(streamReader.HasLines);
Assert.AreEqual(newLineCharsCount,
streamReader.NewLineCharacterCount.ToString());
Assert.AreEqual(pos,
streamReader.Position.ToString());
Assert.AreEqual(newLineCharsCount,
streamReader.NewLineCharacterCount.ToString());
Assert.AreEqual(startingIndex,
streamReader.CurrentLineStartingIndex.ToString());
Console.WriteLine("Validated the StreamReader properties successfully");
ApplicationLog.WriteLine("Validated the StreamReader properties successfully");
// Dispose StreamReader.
streamReader.Close();
streamReader.Dispose();
}
/// <summary>
/// Validate Read Biological sequences using MBFStreamReader
/// </summary>
/// <param name="nodeName">Name of the node used for different test case.</param>
/// <param name="inputType">Different streaming ipnuts used for different test cases</param>
void ValidateMBFStreamReader(string nodeName,
StreamReaderInputType inputType)
{
// Get values from xml
string FilePath = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string[] expectedOutput = _utilityObj._xmlUtil.GetTextValues(
nodeName, Constants.ExpectedLinesNode);
MBFStreamReader streamReader = null;
try
{
// Read Fasta file.
switch (inputType)
{
case StreamReaderInputType.FileName:
streamReader = new MBFStreamReader(FilePath);
break;
case StreamReaderInputType.FileNameWithSkipBlankLines:
streamReader = new MBFStreamReader(FilePath, true);
break;
case StreamReaderInputType.Stream:
using (Stream stream = new FileStream(FilePath, FileMode.Open,
FileAccess.ReadWrite))
{
streamReader = new MBFStreamReader(stream);
}
break;
case StreamReaderInputType.StreamWithSkipBlankLines:
using (Stream stream = new FileStream(FilePath, FileMode.Open,
FileAccess.ReadWrite))
{
streamReader = new MBFStreamReader(stream, true);
}
break;
}
for (int i = 0; i < expectedOutput.Length; i++)
{
Assert.AreEqual(expectedOutput[i], streamReader.Line);
Console.WriteLine("Validated the line {0} successfully", streamReader.Line);
ApplicationLog.WriteLine("Validated the MBF StreamReader successfully");
// Move to next line
streamReader.GoToNextLine();
}
}
finally
{
if (streamReader != null)
{
streamReader.Dispose();
}
}
}
/// <summary>
/// Disposes of all resources held by this object.
/// </summary>
/// <param name="disposing">If disposing equals true, dispose all resources</param>
protected virtual void Dispose(bool disposing)
{
if (disposing)
{
if (_mbfStreamReader != null)
{
_mbfStreamReader.Dispose();
}
}
}
/// <summary>
/// Disposes this object.
/// </summary>
/// <param name="disposing">If true disposes resourses held by this instance.</param>
protected virtual void Dispose(bool disposing)
{
if (disposing)
{
if (_sidecarFileProvider != null)
{
_sidecarFileProvider.Close();
}
if (_mbfStreamReader != null)
{
_mbfStreamReader.Dispose();
}
}
}
public void TestMBFTextReaderCoreFunctionality()
{
string testFileFullName = @"testdata\Fasta\5_sequences.fasta";
using (StreamReader streamReader = new StreamReader(testFileFullName))
{
using (MBFStreamReader mbfReader = new MBFStreamReader(testFileFullName))
{
//Test line access members.
Assert.IsTrue(mbfReader.HasLines);
// Test line reads
string streamLine = streamReader.ReadLine();
Assert.AreEqual(streamLine, mbfReader.Line);
// Test getting of line fields
Assert.AreEqual(streamLine.Substring(26, 10), mbfReader.GetLineField(27, 36));
Assert.AreEqual(streamLine.Substring(14), mbfReader.GetLineField(15));
// Test moving to next line
mbfReader.GoToNextLine();
Assert.AreEqual(streamReader.ReadLine(), mbfReader.Line);
char[] streamBuffer = new char[10];
char[] bioBuffer;
// Test seeking to a position in the stream
streamReader.DiscardBufferedData();
streamReader.BaseStream.Seek(100, SeekOrigin.Begin);
mbfReader.Seek(100, SeekOrigin.Begin);
Assert.AreEqual(streamReader.BaseStream.Position, mbfReader.Position);
// Test character reading
streamReader.ReadBlock(streamBuffer, 0, 10);
bioBuffer = mbfReader.ReadChars(100, 10);
Assert.AreEqual(streamBuffer, bioBuffer);
// Test disposal
mbfReader.Dispose();
Assert.IsFalse(mbfReader.CanRead);
}
}
}
/// <summary>
/// Validate Read Biological sequences using MBFStreamReader
/// </summary>
/// <param name="nodeName">Name of the node used for different test case.</param>
/// <param name="IsStartAndEndIndex">True if validating from start to end index substring,
/// else false</param>
private void ValidateSubString(string nodeName,
bool IsStartAndEndIndex)
{
// Get values from xml
string FilePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedString = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedString);
string startIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartIndexNode);
string endIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndIndexNode);
string subString = string.Empty;
MBFStreamReader streamReader = new MBFStreamReader(FilePath);
if (IsStartAndEndIndex)
{
subString = streamReader.GetLineField(Int32.Parse(startIndex),
Int32.Parse(endIndex));
}
else
{
subString = streamReader.GetLineField(Int32.Parse(startIndex));
}
// Validate sub string of a line.
Assert.AreEqual(expectedString, subString);
Console.WriteLine("The expected substring is {0}", subString);
ApplicationLog.WriteLine("Validated the substring successfully");
// Dispose stream reader.
streamReader.Close();
streamReader.Dispose();
}
