public void IonPresent()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(RawFile))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, RawFile);
}
var spectrumMatchList = InitTest();
var ionProbabilityTable = new Dictionary <IonType, Probability <IonType> > [MaxPrecCharge];
for (int i = 0; i < ionProbabilityTable.Count(); i++)
{
ionProbabilityTable[i] = new Dictionary <IonType, Probability <IonType> >();
}
StreamWriter outputFile = File.AppendText(OutputFileName);
foreach (var spectrumMatch in spectrumMatchList)
{
var charge = spectrumMatch.PrecursorCharge - 1;
var offsetFrequencies = new IonFrequencyTable(_ionTypes, _tolerance, RelativeIntensityThreshold);
offsetFrequencies.AddMatches(new List <SpectrumMatch> {
spectrumMatch
});
var probabilities = offsetFrequencies.GetProbabilities();
var testProbabilities = ComputeOffsetFrequencies(spectrumMatch);
Assert.True(probabilities.Length == testProbabilities.Count);
Array.Sort(probabilities, new CompareIonProbabilityByIon());
testProbabilities.Sort(new CompareIonProbabilityByIon());
outputFile.WriteLine("Scan:\t{0}\tPeptide:\t{1}\tCharge:\t{2}", spectrumMatch.Spectrum.ScanNum, spectrumMatch.Peptide, spectrumMatch.PrecursorCharge);
outputFile.WriteLine("Ion\tFound\tTotal\tTestFound\tTestTotal\tEqual?");
for (int i = 0; i < probabilities.Length; i++)
{
Assert.True(probabilities[i].Label.Name == testProbabilities[i].Label.Name);
bool foundEqual = probabilities[i].Found.Equals(testProbabilities[i].Found);
bool totalEqual = probabilities[i].Total.Equals(testProbabilities[i].Total);
var ion = testProbabilities[i].Label;
if (!ionProbabilityTable[charge].ContainsKey(ion))
{
ionProbabilityTable[charge].Add(ion, new Probability <IonType>(ion));
}
ionProbabilityTable[charge][ion] += testProbabilities[i];
outputFile.Write(probabilities[i].Label + "\t");
outputFile.Write("{0}\t{1}\t", probabilities[i].Found, probabilities[i].Total);
outputFile.Write("{0}\t{1}\t", testProbabilities[i].Found, testProbabilities[i].Total);
outputFile.WriteLine(foundEqual && totalEqual);
}
outputFile.WriteLine();
}
outputFile.Close();
for (int i = 0; i < MaxPrecCharge; i++)
{
var chargeOutName = IonProbabilityFileName + "_Charge" + (i + 1) + ".txt";
using (var ionProbOut = new StreamWriter(chargeOutName))
{
ionProbOut.WriteLine("Ion\tProbability");
foreach (var key in ionProbabilityTable[i].Keys)
{
ionProbOut.WriteLine(ionProbabilityTable[i][key].Label.Name + "\t" + ionProbabilityTable[i][key].Prob);
}
}
}
}
public void IonFrequencyFunction()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string configFilePath = @"C:\Users\wilk011\Documents\DataFiles\IonFreqConfig.ini";
if (!File.Exists(configFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, configFilePath);
}
InitTest(new ConfigFileReader(configFilePath));
foreach (var name in _names)
{
var tsvName = _preTsv.Replace("@", name);
var rawName = _preRaw.Replace("@", name);
var txtFiles = Directory.GetFiles(tsvName).ToList();
var rawFilesTemp = Directory.GetFiles(rawName).ToList();
var rawFiles = rawFilesTemp.Where(rawFile => Path.GetExtension(rawFile) == ".raw").ToList();
Assert.True(rawFiles.Count == txtFiles.Count);
int tableCount = 1;
if (_precursorCharge > 0)
{
tableCount = _precursorCharge;
}
var ionFrequencyFunctions = new IonFrequencyTable[tableCount];
var decoyionFrequencyFunctions = new IonFrequencyTable[tableCount];
for (int i = 0; i < tableCount; i++)
{
ionFrequencyFunctions[i] = new IonFrequencyTable(_ionTypes,
_defaultTolerance, _relativeIntensityThreshold, _combineCharges);
decoyionFrequencyFunctions[i] = new IonFrequencyTable(_ionTypes,
_defaultTolerance, _relativeIntensityThreshold, _combineCharges);
}
for (int i = 0; i < txtFiles.Count; i++)
{
string textFile = txtFiles[i];
string rawFile = rawFiles[i];
Console.WriteLine("{0}\t{1}", Path.GetFileName(textFile), Path.GetFileName(rawFile));
var lcms = new LazyLcMsRun(rawFile, NoiseFiltration, NoiseFiltration);
var matchList = new SpectrumMatchList(lcms, txtFiles[i], DataFileFormat.IcBottomUp);
SpectrumMatchList decoyMatchList = null;
if (_useDecoy)
{
decoyMatchList = new SpectrumMatchList(lcms, txtFiles[i], DataFileFormat.IcBottomUp, 0, true);
}
for (int j = 0; j < tableCount; j++)
{
var matches = _precursorCharge > 0 ? matchList.GetCharge(j + 1) : matchList;
matches.FilterSpectra();
ionFrequencyFunctions[j].AddMatches(matches);
if (decoyMatchList != null)
{
var decoyMatches = _precursorCharge > 0 ? decoyMatchList.GetCharge(j + 1) : decoyMatchList;
decoyMatches.FilterSpectra();
decoyionFrequencyFunctions[j].AddMatches(decoyMatches);
}
}
}
// Print Offset Frequency tables to output file
var outFile = _outFileName.Replace("@", name);
for (int i = 0; i < tableCount; i++)
{
string outFileName = outFile.Replace("*", (i + 1).ToString(CultureInfo.InvariantCulture));
var ionFrequencies = ionFrequencyFunctions[i].GetProbabilities();
var decoyionFrequencies = decoyionFrequencyFunctions[i].GetProbabilities();
using (var finalOutputFile = new StreamWriter(outFileName))
{
finalOutputFile.Write("Ion\tTarget");
if (_useDecoy)
{
finalOutputFile.Write("\tDecoy");
}
finalOutputFile.WriteLine();
for (int j = 0; j < ionFrequencies.Length; j++)
{
finalOutputFile.Write("{0}\t{1}", ionFrequencies[j].Label.Name, ionFrequencies[j].Prob);
if (_useDecoy)
{
finalOutputFile.Write("\t{0}", decoyionFrequencies[j]);
}
finalOutputFile.WriteLine();
}
}
}
}
}
