public void FindMSPeaksTest1()
{
ParameterLoader loader = new ParameterLoader();
loader.LoadParametersFromFile(parameterFilename);
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(1, 1, 100000);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
DeconToolsPeakDetector peakfinder = new DeconToolsPeakDetector(loader.PeakParameters);
peakfinder.Execute(resultcollection);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < resultcollection.Run.PeakList.Count; i++)
{
MSPeak mspeak = (MSPeak)resultcollection.Run.PeakList[i];
sb.Append(resultcollection.Run.PeakList[i].XValue);
sb.Append("\t");
sb.Append(resultcollection.Run.PeakList[i].Height);
sb.Append("\t");
sb.Append(mspeak.SN);
sb.Append("\t");
sb.Append(resultcollection.Run.PeakList[i].Width);
sb.Append("\t");
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
Assert.AreEqual(2438, resultcollection.Run.PeakList.Count);
Assert.AreEqual(547.316411323136, Convert.ToDecimal(resultcollection.Run.PeakList[982].XValue));
Assert.AreEqual(100385, resultcollection.Run.PeakList[982].Height);
}
public void IMFcompareToCanonicalResults_noSumming()
{
//generate results using new framework
int numScansSummed = 1;
Run run = new IMFRun(imfFilepath);
ResultCollection results = new ResultCollection(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 231, 233, numScansSummed, 1, false);
sscc.Create();
ParameterLoader loader = new ParameterLoader();
loader.LoadParametersFromFile(qtParameterfile1);
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
Task peakDetector = new DeconToolsPeakDetector(loader.PeakParameters);
peakDetector.Execute(results);
Task horndecon = new HornDeconvolutor(loader.TransformParameters);
horndecon.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
//read in results from canonical _isos
List <IsosResult> canonIsos = readInIsos(canonIMFIsosFilename, Globals.MSFileType.PNNL_IMS);
Assert.AreEqual(canonIsos.Count, results.ResultList.Count);
//compare numbers
StringBuilder sb = new StringBuilder();
for (int i = 0; i < results.ResultList.Count; i++)
{
sb.Append("scanmass\t");
sb.Append(results.ResultList[i].ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(canonIsos[i].ScanSet.PrimaryScanNumber);
sb.Append("\n");
sb.Append("monoMass\t");
sb.Append(results.ResultList[i].IsotopicProfile.MonoIsotopicMass.ToString("0.0000"));
sb.Append("\t");
sb.Append(canonIsos[i].IsotopicProfile.MonoIsotopicMass);
sb.Append("\n");
sb.Append("intens\t");
sb.Append(results.ResultList[i].IsotopicProfile.IntensityAggregate);
sb.Append("\t");
sb.Append(canonIsos[i].IsotopicProfile.IntensityAggregate);
sb.Append("\n");
sb.Append("score\t");
sb.Append(results.ResultList[i].IsotopicProfile.Score.ToString("0.0000"));
sb.Append("\t");
sb.Append(canonIsos[i].IsotopicProfile.Score);
sb.Append("\n");
sb.Append("FWHM\t");
sb.Append(results.ResultList[i].IsotopicProfile.GetFWHM().ToString("0.0000"));
sb.Append("\t");
sb.Append(canonIsos[i].IsotopicProfile.GetFWHM());
sb.Append("\n");
sb.Append("s/n\t");
sb.Append(results.ResultList[i].IsotopicProfile.GetSignalToNoise().ToString("0.0000"));
sb.Append("\t");
sb.Append(canonIsos[i].IsotopicProfile.GetSignalToNoise());
sb.Append("\n");
sb.Append("\n");
}
Console.Write(sb.ToString());
}
