public void LinearRegression(string jobDirectory, string jobList, int numJobs)
{
var jobDirectoryPath = GetPath(jobDirectory);
var jobListPath = GetPath(jobList);
var num = 0;
var options = new Options();
PeptideCache.Clear();
var dataSets = new List <LcmsDataSet>();
using (var sr = new StreamReader(jobListPath))
{
var pathName = sr.ReadLine();
while (pathName != null && num < numJobs)
{
pathName = Path.Combine(jobDirectoryPath, pathName);
var reader = PhrpReaderFactory.Create(pathName, options);
dataSets.Add(reader.Read(pathName));
pathName = sr.ReadLine();
num++;
}
}
var processor = new MtdbProcessor(options);
processor.Process(dataSets, new BackgroundWorker());
foreach (var set in dataSets)
{
Assert.AreNotEqual(set.RegressionResult.RSquared, 0);
// Set to 1.000001 due to (for some reason) RSquared occasionally
// being calculated as 1.00000000000044
Assert.Less(set.RegressionResult.RSquared, 1.000001);
}
}
public void TestLoadingSingleFile(string jobPath, int expectedEvidences)
{
PeptideCache.Clear();
var options = new Options();
var jobDirectoryPath = GetPath(jobPath);
var pathName = jobDirectoryPath;
var reader = PhrpReaderFactory.Create(pathName, options);
var data = reader.Read(pathName);
Assert.AreEqual(expectedEvidences, data.Evidences.Count);
}
public void TestLoadScans(string path)
{
var filePath = GetPath(path);
var options = new Options();
var reader = PhrpReaderFactory.Create(filePath, options);
var data = reader.Read(filePath);
foreach (var e in data.Evidences)
{
Assert.GreaterOrEqual(e.ObservedNet, 0.0);
Assert.LessOrEqual(e.ObservedNet, 1.0);
}
}
public void TrypticEnds(string jobDirectory, string jobList, int numJobs)
{
var jobDirectoryPath = GetPath(jobDirectory);
var jobListPath = GetPath(jobList);
var num = 0;
var options = new Options();
PeptideCache.Clear();
using (var sr = new StreamReader(jobListPath))
{
var pathName = sr.ReadLine();
while (pathName != null && num < numJobs)
{
pathName = Path.Combine(jobDirectoryPath, pathName);
var reader = PhrpReaderFactory.Create(pathName, options);
var data = reader.Read(pathName);
var resultType = clsPHRPReader.AutoDetermineResultType(pathName);
switch (resultType)
{
case clsPHRPReader.ePeptideHitResultType.XTandem:
foreach (XTandemResult evidence in data.Evidences)
{
Debug.Assert(evidence.NumTrypticEnds >= 0);
Debug.Assert(evidence.NumTrypticEnds < 3);
}
break;
case clsPHRPReader.ePeptideHitResultType.Sequest:
foreach (SequestResult evidence in data.Evidences)
{
Debug.Assert(evidence.NumTrypticEnds >= 0);
Debug.Assert(evidence.NumTrypticEnds < 3);
}
break;
case clsPHRPReader.ePeptideHitResultType.MSGFDB:
foreach (MsgfPlusResult evidence in data.Evidences)
{
Debug.Assert(evidence.NumTrypticEnds >= 0);
Debug.Assert(evidence.NumTrypticEnds < 3);
}
break;
}
pathName = sr.ReadLine();
num++;
}
}
}
public void TestLoadingGZippedFile(string txtPath, string gZipPath)
{
PeptideCache.Clear();
var options = new Options();
var gZipDirectoryPath = GetPath(gZipPath);
var txtDirectoryPath = GetPath(txtPath);
var gPathName = gZipDirectoryPath;
var gReader = PhrpReaderFactory.Create(gPathName, options);
var timeStart = DateTime.Now;
var gData = gReader.Read(gPathName);
var timeEnd = DateTime.Now;
Console.WriteLine(string.Format("Reading .gz took {0} seconds", timeEnd - timeStart));
var tPathName = txtDirectoryPath;
var tReader = PhrpReaderFactory.Create(tPathName, options);
timeStart = DateTime.Now;
var tData = tReader.Read(tPathName);
timeEnd = DateTime.Now;
Console.WriteLine(string.Format("Reading .mzid took {0} seconds", timeEnd - timeStart));
// To ensure that reading the same data gets the same number of evidences
Assert.AreEqual(gData.Evidences.Count, tData.Evidences.Count);
for (var i = 0; i < gData.Evidences.Count; i++)
{
var gEv = gData.Evidences[i];
var tEv = tData.Evidences[i];
//Test for each portion of the evidence being identical
Assert.AreEqual(gEv.MonoisotopicMass, tEv.MonoisotopicMass);
Assert.AreEqual(gEv.Charge, tEv.Charge);
Assert.AreEqual(gEv.DelM, tEv.DelM);
Assert.AreEqual(gEv.DelMPpm, tEv.DelMPpm);
Assert.AreEqual(gEv.ModificationCount, tEv.ModificationCount);
Assert.AreEqual(gEv.ModificationDescription, tEv.ModificationDescription);
Assert.AreEqual(gEv.Mz, tEv.Mz);
Assert.AreEqual(gEv.ObservedMonoisotopicMass, tEv.ObservedMonoisotopicMass);
Assert.AreEqual(gEv.ObservedNet, tEv.ObservedNet);
Assert.AreEqual(gEv.Scan, tEv.Scan);
Assert.AreEqual(gEv.Sequence, tEv.Sequence);
Assert.AreEqual(gEv.SpecProb, tEv.SpecProb);
}
}
public void TestLoadingFiles(string jobDirectory, string jobList, int numJobs, params int[] expectedEvidences)
{
PeptideCache.Clear();
var options = new Options();
var jobDirectoryPath = GetPath(jobDirectory);
var jobListPath = GetPath(jobList);
var num = 0;
using (var sr = new StreamReader(jobListPath))
{
var pathName = sr.ReadLine();
while (pathName != null && num < numJobs)
{
pathName = Path.Combine(jobDirectoryPath, pathName);
var reader = PhrpReaderFactory.Create(pathName, options);
var data = reader.Read(pathName);
Assert.AreEqual(expectedEvidences[num], data.Evidences.Count);
pathName = sr.ReadLine();
num++;
}
}
}
