public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\Lewy\aligned\promex_crosstab_temp.tsv";
//CPTAC_Intact_CR32A_24Aug15_Bane_15-02-06-RZ
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));
for (var i = 0; i < NdataSet; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, GetDataSetNames(i));
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, GetDataSetNames(i));
var mspFile2 = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder2, GetDataSetNames(i));
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, GetDataSetNames(i));
Console.WriteLine(rawFile);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var prsmList1 = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
var prsmList2 = prsmReader.LoadIdentificationResult(mspFile2, ProteinSpectrumMatch.SearchTool.MsPathFinder);
prsmList1.AddRange(prsmList2);
var prsmList = MergePrsm(prsmList1);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < NdataSet; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", GetDataSetNames(i));
}
OutputCrossTabWithId(outFilePath, alignment);
}
public void ScorePSM(int scan, string sequenceStr)
{
// Set input file paths.
const string specFilePath =
@"\\protoapps\userdata\Wilkins\UIMF Files\9 pep mix 365 mTorr with ims 45V CID\9 pep mix 365 mTorr with ims 45V CID.pbf";
var lcmsRun = PbfLcMsRun.GetLcMsRun(specFilePath);
var productSpectrum = lcmsRun.GetSpectrum(scan) as ProductSpectrum;
Assert.NotNull(productSpectrum);
var modification = Modification.RegisterAndGetModification("oh->nh2", new Composition(0, 1, 1, -1, 0));
Assert.NotNull(modification);
var searchModifications = new List <SearchModification>
{
new SearchModification(Modification.Get("oh->nh2"), 'M', SequenceLocation.ProteinCTerm, true),
new SearchModification(Modification.Get("oh->nh2"), 'Q', SequenceLocation.ProteinCTerm, true),
new SearchModification(Modification.PyroGluE, 'R', SequenceLocation.ProteinNTerm, true)
};
var aminoAcidSet = new AminoAcidSet(searchModifications, 1);
var sequence = this.LoadSequence(sequenceStr, aminoAcidSet);
//var scorerFactory = new ScorerFactory(new Tolerance(30, ToleranceUnit.Ppm), 1, 5);
//var scorer = scorerFactory.GetScorer(productSpectrum);
//var score = IonUtils.ScoreSequence(scorer, sequence);
//Console.WriteLine(score);
}
public void TestDeconvolution()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
const int minScanNum = 46454; // 635.43
const int maxScanNum = 46661; // 638.90
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
summedSpec.FilterNoise(50.0);
// summedSpec.Display(MAX_POINTS);
var deconvoluted = ProductScorerBasedOnDeconvolutedSpectra.GetDeconvolutedSpectrum(summedSpec, 2, 45, new Tolerance(10), 0.9, 2);
deconvoluted.Display(MAX_POINTS);
}
/// <summary>
/// Shows or hides instrument Precursor m/z and mass from the instrument
/// Reads data from LCMSRun if necessary
/// </summary>
/// <param name="value">Should the instrument data be shown?</param>
/// <param name="pbfLcmsRun">LCMSRun for this data set.</param>
/// <returns>Asynchronous task.</returns>
public async Task ToggleShowInstrumentDataAsync(bool value, PbfLcMsRun pbfLcmsRun)
{
if (value)
{
if (pbfLcmsRun != null)
{
var scans = this.Data;
foreach (var scan in scans.Where(scan => scan.Sequence.Count == 0))
{
PrSm scan1 = scan;
IsolationWindow isolationWindow = await Task.Run(() => pbfLcmsRun.GetIsolationWindow(scan1.Scan));
scan.PrecursorMz = isolationWindow.MonoisotopicMz ?? double.NaN;
scan.Charge = isolationWindow.Charge ?? 0;
scan.Mass = isolationWindow.MonoisotopicMass ?? double.NaN;
}
}
}
else
{
var scans = this.Data;
foreach (var scan in scans.Where(scan => scan.Sequence.Count == 0))
{
scan.PrecursorMz = double.NaN;
scan.Charge = 0;
scan.Mass = double.NaN;
}
}
}
public static string ConvertToPbf(string specFilePath, IMassSpecDataReader specReader,
double precursorSignalToNoiseRatioThreshold, double productSignalToNoiseRatioThreshold, string pbfFilePath = null,
IProgress <ProgressData> progress = null)
{
return(PbfLcMsRun.ConvertToPbf(specFilePath, MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath),
precursorSignalToNoiseRatioThreshold, productSignalToNoiseRatioThreshold, pbfFilePath, progress));
}
public void WriteAsPbf(string outputFilePath, IProgress <ProgressData> progress = null)
{
using (var writer = new BinaryWriter(File.Open(outputFilePath, FileMode.Create)))
{
PbfLcMsRun.WriteAsPbf(this, writer, progress);
}
}
/// <summary>
/// Returns InformedProteomics LcMsRun object from mass spec data types including .raw and .mzml
/// </summary>
/// <param name="rawFilePath"></param>
/// <returns></returns>
public LcMsRun GetLcMsData(string rawFilePath)
{
var progress = new Progress <ProgressData>();
progress.ProgressChanged += Progress_ProgressChanged;
var run = PbfLcMsRun.GetLcMsRun(rawFilePath, progress);
/*
* string ext = Path.GetExtension(rawFilePath);
* switch (ext.ToLower())
* {
* case ".raw":
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.XCaliburRun);
* break;
* case ".mzml":
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.MzMLFile);
* break;
* case ".gz":
* if (rawFilePath.ToLower().EndsWith(".mzml.gz"))
* {
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.MzMLFile);
* }
* break;
* }*/
return(run);
}
public void TestGeneratingProductXic()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath);
// const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping raf portion of test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
const double precursorIonMz = 815.16;
const double productIonMz = 902.445;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic1.Display();
var xic2 = rafRun.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic2.Display();
Assert.True(xic1.Equals(xic2));
Console.WriteLine(@"Done");
}
public void TestProMexFilter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
const string ms1FtPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft";
if (!File.Exists(ms1FtPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, ms1FtPath);
}
var filter = new Ms1FtFilter(run, new Tolerance(10), ms1FtPath);
// Console.WriteLine("ScanNums: {0}", string.Join("\t",filter.GetMatchingMs2ScanNums(8480.327609)));
Assert.IsTrue(filter.GetMatchingMs2ScanNums(8480.327609).Contains(5255));
}
public void TestIsosFilter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string isosFilePath = @"H:\Research\QCShew_TopDown\Production\ICRTools\QC_Shew_Intact_26Sep14_Bane_C2Column3_Isos.csv";
if (!File.Exists(isosFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, isosFilePath);
}
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var filter = new IsosFilter(run, new Tolerance(10), isosFilePath);
Console.WriteLine(string.Join("\t", filter.GetMatchingMs2ScanNums(30261.68374)));
}
public void TestSumMs1Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
const int minScanNum = 46454;
const int maxScanNum = 46661;
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
summedSpec.Display(MAX_POINTS);
}
public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\CompRef\aligned\promex_crosstab_temp.tsv";
var runLabels = new[] { "32A", "32B", "32C", "32D", "32E", "32F", "32G", "33A", "33B", "33C", "33D", "33E", "33F", "33G" };
var nDataset = runLabels.Length;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.pbf", RawFolder, runLabels[i]);
var mspFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ_IcTda.tsv", MsPfFolder, runLabels[i]);
var ms1FtFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.ms1ft", Ms1FtFolder, runLabels[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
if (File.Exists(mspFile))
{
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsMz(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < nDataset; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", runLabels[i]);
}
OutputCrossTabWithId(outFilePath, alignment, runLabels);
}
public void DoAnalysis()
{
InitilizeMatrix(_spectrumMatchesMatrix);
InitilizeMatrix(_tagsGeneratedMatrix);
InitilizeMatrix(_dataBaseHitMatrix);
GetFilteredFeatures(_filteredFile);
for (var i = 0; i < _rawFiles.Length; i++)
{
Console.WriteLine("Processing File {0}...............", i);
var run = PbfLcMsRun.GetLcMsRun(_rawFiles[i]);
var ms2List = run.GetScanNumbers(2);
Console.WriteLine("# of scans {0}", ms2List.Count);
for (var j = 0; j < _filteredFeatures.Count; j++)
{
var matchedSpecList = GetMatchedSpectrums(run, ms2List, _filteredFeatures[j], i);
_spectrumMatchesMatrix[j][i] = matchedSpecList.Count;
var tags = GetTags(matchedSpecList);
_tagsGeneratedMatrix[j][i] = tags.Count;
var hitCount = TagsInDatabase(tags);
_dataBaseHitMatrix[j][i] = hitCount;
}
}
}
public void TestDisplaySpectrum(string rawFile, string tsvFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(tsvFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
// init SpectrumPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumPlotViewModel = new SpectrumPlotViewModel(dialogService, new FragmentationSequenceViewModel(), 1.05, false);
// init test data
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init test ions
var ions = new ReactiveList <LabeledIonViewModel>();
spectrumPlotViewModel.Spectrum = prsm.Ms2Spectrum;
////spectrumPlotViewModel.Ions = ions;
// plot should not be null
Assert.NotNull(spectrumPlotViewModel.PlotModel);
// plot should contain 1 stem series (the spectrum stem series)
Assert.True(spectrumPlotViewModel.PlotModel.Series.Count == 1);
}
private void AlignFeatures(List <string> datasets, string mspfFolder, string ms1ftFolder, string outFilePath)
{
var nDataset = datasets.Count;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(12);
var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, datasets[i]);
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", mspfFolder, datasets[i]);
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", ms1ftFolder, datasets[i]);
var ms1FtFile2 = string.Format(@"{0}\{1}.seqtag.ms1ft", ms1ftFolder, datasets[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
var features2 = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile2, run);
features.AddRange(features2);
if (File.Exists(mspFile))
{
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
//var prsmFeatureMatch = new bool[prsmList.Count];
foreach (var match in prsmList)
{
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
foreach (var feature in features)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsMz(feature.Mass);
foreach (var match in prsmList)
{
if (feature.MinScanNum < match.ScanNum && match.ScanNum < feature.MaxScanNum && Math.Abs(feature.Mass - match.Mass) < massTol)
{
feature.ProteinSpectrumMatches.Add(match);
//prsmFeatureMatch[k] = true;
}
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < nDataset; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", datasets[i]);
}
AnalysisCompRef.OutputCrossTabWithId(outFilePath, alignment, datasets);
}
public void TestMaxEntDeconvoluter()
{
const string rawFileFolder = @"\\proto-11\MSXML_Cache\PBF_Gen_1_214\2015_4";
const string fname = "WHIM2_LoHi_T2DD_HCD_GF07_02";
var rawFile = string.Format(@"{0}\{1}.pbf", rawFileFolder, fname);
var ms1ft = string.Format(@"\\protoapps\UserData\Jungkap\CompRef\lowRes\{0}.ms1ft", fname);
var run = PbfLcMsRun.GetLcMsRun(rawFile, 1.4826, 0);
var ms1ScanNums = run.GetMs1ScanVector();
var featureFinder = new LcMsPeakMatrixLowResolution(run);
foreach (var scan in ms1ScanNums)
{
var fts = featureFinder.DetectMs1Features(scan);
//Console.WriteLine("{0}\t{1}",scan, fts.Count);
}
var features = featureFinder.GetLcMsFeatures();
var writer = new StreamWriter(ms1ft);
var id = 1;
writer.WriteLine("FeatureID\tMinScan\tMaxScan\tMinCharge\tMaxCharge\tMonoMass\tAbundance\tRepScan\tMaxElutionTime\tElutionLength\tLikelihoodRatio");
foreach (var feature in features.OrderBy(f => f.Mass))
{
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}", id, feature.MinScanNum, feature.MaxScanNum, feature.MinCharge,
feature.MaxCharge, feature.Mass, feature.Abundance, feature.RepresentativeScanNum, feature.MinElutionTime, feature.MaxElutionTime, 0);
id++;
}
writer.Close();
}
public void TestReadingBrukerDaltonDataSet()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\MassSpecFiles\ICR\20141212FGWT1_F5_1_01_3230.mzML";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Test start");
var pbf = new PbfLcMsRun(specFilePath, null, null, 1.4826, 1.4826);
//var pbf = new PbfLcMsRun(specFilePath, null, null, 3, 1.4826);
/*
* foreach (var spec in reader.ReadAllSpectra())
* {
* if (spec != null)
* {
* Console.WriteLine(spec.ScanNum);
* }
* }*/
Console.WriteLine(@"Test end");
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return reader;
}
public void TestMatchedPeakPostScorer()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Parameters
var productIonTolerance = new Tolerance(10);
var scorer = new MatchedPeakPostScorer(productIonTolerance, 1, 10);
var sw = new System.Diagnostics.Stopwatch();
const int ms2ScanNum = 4658;
var sequence = new Sequence("GYSIKDIIYQGEKSGVHNWQTLSGQNFYWHPDWLHIAEDLTGHKATASIQAEGTKATQNEAEQTIVKHLNKS", new AminoAcidSet());
var specFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
sw.Start();
var score = scorer.ComputeScore(spec, sequence);
Console.WriteLine("{0}\t{1}\t{2}", sequence, ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestAbpSumMs1Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var specFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TestYufengData\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + specFilePath);
}
const int minScanNum = 5657;
const int maxScanNum = 5699;
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
var peakList = summedSpec.GetPeakListWithin(1180.0, 1192.0);
var filteredPeakList = new List <Peak>();
PeakListUtils.FilterNoise(peakList, ref filteredPeakList);
new Spectrum(filteredPeakList, 0).Display(MAX_POINTS);
}
public void TestSumMs2Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var specFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TestYufengData\NewQC_LongSep_29Sep14_141001104925.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + specFilePath);
}
const int minScanNum = 1289;
//const int maxScanNum = 1389;
const int minCharge = 6;
//const int maxCharge = 6;
const string sequence = "EIRGYRPPEPYKGKGVRYDDEEVRRKEAKKK";
var aaSet = new AminoAcidSet();
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
var scorer = new InformedTopDownScorer(run, aaSet, 1, minCharge - 1, new Tolerance(10));
scorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm,
Composition.Parse("C(166) H(270) N(52) O(49) S(0)"), minCharge, minScanNum);
}
public void TestRunningTimeSummingSpectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 1.4826, 1.4826) as PbfLcMsRun;
var sw = new Stopwatch();
sw.Start();
const int windowSize = 5;
foreach (var scanNum in run.GetScanNumbers(1))
{
//var spec = run.GetSpectrum(scanNum);
var spec = run.GetSummedMs1Spectrum(Math.Max(scanNum - windowSize, run.MinLcScan),
Math.Min(scanNum + windowSize, run.MaxLcScan));
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf");
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var pbfRun = new PbfLcMsRun(rafFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return(reader);
}
public void TestDisplaySpectra(string rawFile, string idFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init XicPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumViewModel = new SpectrumViewModel(dialogService, lcms);
// init test ions
var baseIonTypes = new List <BaseIonType> {
BaseIonType.B, BaseIonType.Y
};
var neutralLosses = new List <NeutralLoss> {
NeutralLoss.NoLoss
};
const int charge = 1;
const int minCharge = 1, maxCharge = 2;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = IonUtils.GetIonTypes(ionTypeFactory, baseIonTypes, neutralLosses, minCharge, maxCharge);
var ions = IonUtils.GetFragmentIonLabels(prsm.Sequence, charge, ionTypes);
var ionVms = ions.Select(label => new LabeledIonViewModel(label.Composition, label.IonType, label.IsFragmentIon, lcms, label.PrecursorIon, label.IsChargeState, label.Index)).ToList();
}
public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\Quant\aligned\promex_crosstab.tsv";
//const string outFolder = @"\\protoapps\UserData\Jungkap\CompRef\aligned";
var runLabels = new string[] { "1x1", "1x2", "1x3", "1x4", "1x5", "5x1", "5x2", "5x3", "5x4", "5x5", "10x1", "10x2", "10x3", "10x4", "10x5", };
var nDataset = runLabels.Length;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new SpikeInFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", RawFolder, datasets[i]);
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, datasets[i]);
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, datasets[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
/*
* for (var i = 0; i < nDataset; i++)
* {
* alignment.FillMissingFeatures(i);
* Console.WriteLine("{0} has been processed", runLabels[i]);
* }
*/
OutputCrossTabWithId(outFilePath, alignment, runLabels);
}
private void FeatureMapGeneration()
{
var resultsFilePath = Path.Combine(Path.GetTempPath(), Path.GetFileNameWithoutExtension(mFeatureMapPbfFile) + "_FeatureMap.png");
var map = new LcMsFeatureMap(PbfLcMsRun.GetLcMsRun(mFeatureMapPbfFile), mFeatureMapResultsFile, 2000, 50000);
map.SaveImage(resultsFilePath);
Console.WriteLine("Image saved to " + resultsFilePath);
}
public void TestSumIsoProfilesAcrossDifferentCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
//var spec = run.GetSpectrum(46452); // 635.37
var spec = run.GetSummedMs1Spectrum(46437, 46466);
var tolerance = new Tolerance(10);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O();
var theoProfile = neutral.GetIsotopomerEnvelopeRelativeIntensities();
var expProfile = new double[theoProfile.Length];
for (var charge = 22; charge <= 45; charge++)
{
var ion = new Ion(neutral, charge);
var isotopePeaks = spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null)
{
continue;
}
Assert.True(isotopePeaks.Length == theoProfile.Length);
for (var i = 0; i < isotopePeaks.Length; i++)
{
if (isotopePeaks[i] != null)
{
expProfile[i] += isotopePeaks[i].Intensity;
}
}
}
for (var i = 0; i < theoProfile.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", neutral.GetIsotopeMass(i), theoProfile[i], expProfile[i] / expProfile.Max());
}
Console.WriteLine("Corr: " + FitScoreCalculator.GetPearsonCorrelation(theoProfile, expProfile));
}
public void TestFitMinusOneScore(int precursor, string adduct, string commonName, string id, string rawFilePath)
{
var lipid = new Lipid()
{
AdductFull = adduct, CommonName = commonName
};
var lipidTarget = lipid.CreateLipidTarget();
var composition = lipidTarget.Composition;
var compMinus1 = new Composition(composition.C, composition.H - 1, composition.N, composition.O, composition.S, composition.P); //Subtract one hydrogen to make this a minus1 fit score
var lcmsRun = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcmsRun.GetSpectrum(precursor);
var relativeIntensityThreshold = 0.1;
var tolerance = new Tolerance(30, ToleranceUnit.Ppm);
//Get the values to use to calculate pearson correlation
var observedPeaks = LipidUtil.GetAllIsotopePeaks(spectrum, compMinus1, tolerance,
relativeIntensityThreshold);
if (observedPeaks == null)
{
Console.WriteLine("Observed peaks is null for scan " + id);
}
var isotopomerEnvelope = IsoProfilePredictor.GetIsotopomerEnvelop(
compMinus1.C,
compMinus1.H,
compMinus1.N,
compMinus1.O,
compMinus1.S);
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
Console.WriteLine("The theoretical y values are: ");
foreach (var value in isotopomerEnvelope.Envolope)
{
Console.WriteLine(value + ", ");
}
Console.WriteLine("The observed peak intensity x values are: ");
foreach (var value in observedIntensities)
{
Console.WriteLine(value + ", ");
}
}
public void CountTagMatches()
{
for (var i = 1; i < 52; i++)
{
var dataName = "Lewy_intact_" + i.ToString("D2");
var filePath = string.Format(@"{0}\{1}.pbf", PbfPath, dataName);
var run = PbfLcMsRun.GetLcMsRun(filePath);
var scans = run.GetScanNumbers(2);
Console.WriteLine(scans.Count);
}
}
public void TestWritingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
Console.WriteLine(@"Writing...");
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var outputFilePath = PbfLcMsRun.GetPbfFileName(TestRawFilePath);
var pbf = new PbfLcMsRun(TestRawFilePath, null, outputFilePath);
Console.WriteLine(@"Done. {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGeneratingProductXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath);
// const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping raf portion of test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
var mzArr = new double[100000];
var precursorMzArr = new double[mzArr.Length];
var rnd = new Random();
for (var i = 0; i < mzArr.Length; i++)
{
mzArr[i] = rnd.NextDouble() * 1450.0 + 50.0;
precursorMzArr[i] = rnd.NextDouble() * (810.0 - 390.0) + 390.0;
}
var sw = new System.Diagnostics.Stopwatch();
//double sec;
// method 1
sw.Start();
for (var i = 0; i < mzArr.Length; i++)
{
var mz = mzArr[i];
var tolTh = tolerance.GetToleranceAsTh(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
var xic1 = run.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
//var xic2 = rafRun.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
//Assert.True(xic1.Equals(xic2));
}
sw.Stop();
Console.WriteLine(@"Method 1: {0:f4} sec", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
for (var i = 0; i < mzArr.Length; i++)
{
var mz = mzArr[i];
var tolTh = tolerance.GetToleranceAsTh(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
rafRun.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
}
sw.Stop();
Console.WriteLine(@"Method 2: {0:f4} sec", sw.Elapsed.TotalSeconds);
Console.WriteLine(@"Done");
}
public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var pbfRun = new PbfLcMsRun(rafFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}
public void TestSpectrumNavigation()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
// var spec = rafRun.GetSpectrum(54531);
var scanNum = rafRun.GetNextScanNum(54530, 1);
Console.WriteLine(scanNum);
}
public void TestReadingBrukerDaltonDataSet()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\MassSpecFiles\ICR\20141212FGWT1_F5_1_01_3230.mzML";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Test start");
var pbf = new PbfLcMsRun(specFilePath, null, null, 1.4826, 1.4826);
//var pbf = new PbfLcMsRun(specFilePath, null, null, 3, 1.4826);
/*
foreach (var spec in reader.ReadAllSpectra())
{
if (spec != null)
{
Console.WriteLine(spec.ScanNum);
}
}*/
Console.WriteLine(@"Test end");
}
public void TestRunningTimeChromGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var numPeptides = 0;
foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin))
{
++numPeptides;
var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length-4), aaSet).Composition + Composition.H2O;
var mz = new Ion(comp, 2).GetMonoIsotopicMz();
//Console.WriteLine(peptide.Annotation + " " + mz);
rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//Assert.True(xic1.Count == xic2.Count);
//for (var i = 0; i < xic1.Count; i++)
//{
// if (!xic1[i].Equals(xic2[i]))
// {
// Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]);
// }
// Assert.True(xic1[i].Equals(xic2[i]));
//}
if (numPeptides == 100000) break;
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGeneratingProductXic()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath);
// const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping raf portion of test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
const double precursorIonMz = 815.16;
const double productIonMz = 902.445;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic1.Display();
var xic2 = rafRun.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic2.Display();
Assert.True(xic1.Equals(xic2));
Console.WriteLine(@"Done");
}
