public void GffParserValidateParseWithOneLineFeatures()
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SimpleGffFeaturesNode,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
IList <ISequence> seqs = null;
BasicSequenceParser parserObj = new GffParser(Encodings.Ncbi4NA);
seqs = parserObj.Parse(filePath);
Sequence originalSequence = (Sequence)seqs[0];
bool val = ValidateFeatures(originalSequence,
Constants.OneLineSeqGffNodeName);
Assert.IsTrue(val);
filePath = Utility._xmlUtil.GetTextValue(
Constants.SimpleGffFeaturesReaderNode,
Constants.FilePathNode);
using (StreamReader reader = File.OpenText(filePath))
{
seqs.Add(parserObj.ParseOne(reader));
}
originalSequence = (Sequence)seqs[0];
val = ValidateFeatures(originalSequence,
Constants.OneLineSeqGffNodeName);
Assert.IsTrue(val);
ApplicationLog.WriteLine(
"GFF Parser BVT : All the features validated successfully.");
Console.WriteLine(
"GFF Parser BVT : All the features validated successfully.");
}
/// <summary>
/// Parses all test cases related to ParseOne() method based on the
/// parameters passed and validates the same.
/// </summary>
/// <param name="nodeName">Xml Node name to be read.</param>
/// <param name="isFilePath">Is file path passed as parameter?</param>
static void ValidateParseOneGeneralTestCases(string nodeName,
bool isFilePath)
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"Gff Parser BVT : File Exists in the Path '{0}'.", filePath));
ISequence originalSeq = null;
GffParser parserObj = new GffParser();
if (isFilePath)
{
originalSeq = parserObj.ParseOne(filePath);
}
else
{
using (StreamReader reader = File.OpenText(filePath))
{
originalSeq = parserObj.ParseOne(reader);
}
}
Assert.IsNotNull(originalSeq);
Assert.IsTrue(ValidateFeatures(originalSeq, nodeName));
ApplicationLog.WriteLine(
"Gff Parser BVT : Successfully validated all the Features for a give Sequence in GFF File.");
Console.WriteLine(
"Gff Parser BVT : Successfully validated all the Features for a give Sequence in GFF File.");
string expectedSequence = Utility._xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode);
Sequence seq = (Sequence)originalSeq;
Assert.IsNotNull(seq);
Assert.AreEqual(expectedSequence, seq.ToString());
ApplicationLog.WriteLine(string.Format(null,
"Gff Parser BVT: The Gff sequence '{0}' validation after ParseOne() is found to be as expected.",
seq.ToString()));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format(null,
"Gff Parser BVT: The Gff sequence '{0}' validation after ParseOne() is found to be as expected.",
seq.ToString()));
Assert.AreEqual(expectedSequence.Length, seq.EncodedValues.Length);
ApplicationLog.WriteLine(string.Format(null,
"Gff Parser BVT: The Gff Length sequence '{0}' is as expected.",
expectedSequence.Length));
string expectedAlphabet = Utility._xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture);
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
expectedAlphabet);
ApplicationLog.WriteLine(string.Format(null,
"Gff Parser BVT: The Sequence Alphabet is '{0}' and is as expected.",
seq.Alphabet.Name));
string expectedSequenceId = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SequenceIdNode);
Assert.AreEqual(expectedSequenceId, seq.DisplayID);
ApplicationLog.WriteLine(string.Format(null,
"Gff Parser BVT: The Sequence ID is '{0}' and is as expected.",
seq.DisplayID));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format(null,
"Gff Parser BVT: The Sequence ID is '{0}' and is as expected.",
seq.DisplayID));
}
