public void FastAFormatterValidateWrite1()
{
var formatter = new FastAFormatter();
using (formatter.Open(Constants.FastaTempFileName))
{
// Gets the actual sequence and the alphabet from the Xml
string actualSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
string alpName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
// Logs information to the log file
ApplicationLog.WriteLine(string.Format("FastA Formatter BVT: Validating with Sequence '{0}' and Alphabet '{1}'.",
actualSequence, alpName));
var seqOriginal = new Sequence(Utility.GetAlphabet(alpName),
actualSequence) { ID = "" };
Assert.IsNotNull(seqOriginal);
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format("FastA Formatter BVT: Creating the Temp file '{0}'.",
Constants.FastaTempFileName));
var seqList = new List<ISequence> { seqOriginal, seqOriginal, seqOriginal };
formatter.Format(seqList);
formatter.Close();
IEnumerable<ISequence> seqsNew = null;
// Read the new file, then compare the sequences
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
seqsNew = parser.Parse(Constants.FastaTempFileName);
char[] seqString = seqsNew.ElementAt(0).Select(a => (char) a).ToArray();
var newSequence = new string(seqString);
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: New Sequence is '{0}'.",
newSequence));
// Now compare the sequences.
int countNew = seqsNew.Count();
Assert.AreEqual(3, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(seqOriginal.ID, seqsNew.ElementAt(0).ID);
Assert.AreEqual(new string(seqsNew.ElementAt(0).Select(a => (char) a).ToArray()), newSequence);
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method.",
newSequence));
// 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.
File.Delete(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
}
}
public void FastAFormatterValidateWriteWithStream()
{
string actualSequence = string.Empty;
var formatter = new FastAFormatter();
{
using (formatter.Open(Constants.FastaTempFileName))
{
// Gets the actual sequence and the alphabet from the Xml
actualSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
string alpName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
// Logs information to the log file
ApplicationLog.WriteLine(string.Format("FastA Formatter BVT: Validating with Sequence '{0}' and Alphabet '{1}'.",
actualSequence, alpName));
var seqOriginal = new Sequence(Utility.GetAlphabet(alpName), actualSequence);
seqOriginal.ID = "";
Assert.IsNotNull(seqOriginal);
// Use the formatter to write the original sequences to a stream.
ApplicationLog.WriteLine(string.Format("FastA Formatter BVT: Creating the Temp file '{0}'.",
Constants.FastaTempFileName));
formatter.Format(seqOriginal);
formatter.Close();
}
IEnumerable<ISequence> seq = null;
using (var reader = File.OpenRead(Constants.FastaTempFileName))
{
// Read the new file, then compare the sequences
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
seq = parser.Parse(reader);
//Create a list of sequences.
List<ISequence> seqsList = seq.ToList();
Assert.IsNotNull(seqsList);
var seqString = new string(seqsList[0].Select(a => (char) a).ToArray());
Assert.AreEqual(actualSequence, seqString);
}
}
// 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.
File.Delete(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
}
public void FastAFormatterInvalidateClose()
{
FastAFormatter formatter = new FastAFormatter();
formatter.Close();
}
