public void GffFormatterValidateOpen()
{
using (GffFormatter formatter = new GffFormatter())
{
try
{
formatter.Open(Constants.GffTempFileName);
}
catch (System.IO.IOException exception)
{
Assert.Fail("Exception thrown on opening a file " + exception.Message);
}
}
ApplicationLog.WriteLine("Opened the file successfully");
}
public void GffFormatterValidateStreams()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleGffNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
IList <ISequence> seqs = null;
Sequence originalSequence = null;
using (GffParser parserObj = new GffParser(filePath))
{
seqs = parserObj.Parse().ToList();
originalSequence = (Sequence)seqs[0];
}
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: Creating the Temp file '{0}'.",
Constants.GffTempFileName));
using (StreamWriter writer = new StreamWriter(Constants.GffTempFileName))
{
using (GffFormatter formatter = new GffFormatter())
{
formatter.ShouldWriteSequenceData = true;
formatter.Open(writer);
formatter.Write(originalSequence);
}
}
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
using (GffParser newParser = new GffParser(Constants.GffTempFileName))
{
seqsNew = newParser.Parse().ToList();
}
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
bool val = ValidateFeatures(seqsNew[0], Constants.SimpleGffNodeName);
Assert.IsTrue(val);
ApplicationLog.WriteLine(
"GFF Formatter BVT : All the features validated successfully.");
// Now compare the sequences.
int countNew = seqsNew.Count();
int expectedCount = 1;
Assert.AreEqual(expectedCount, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(originalSequence.ID, seqsNew[0].ID);
ISequence newSeq = seqsNew.FirstOrDefault();
Assert.AreEqual(new string(originalSequence.Select(x => (char)x).ToArray()),
new string(newSeq.Select(x => (char)x).ToArray()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: The Gff sequences '{0}' are matching with Write() method.",
seqsNew[0].ToString()));
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
if (File.Exists(Constants.GffTempFileName))
{
File.Delete(Constants.GffTempFileName);
}
ApplicationLog.WriteLine("Deleted the temp file created.");
}
