private ChromatogramRequestDocument GetChromatogramRequestDocument(SpectrumFilter spectrumFilter)
{
ChromatogramRequestDocument chromatogramRequestDocument = spectrumFilter.ToChromatogramRequestDocument();
if (null == _retentionTimePredictor)
{
return(chromatogramRequestDocument);
}
var peptidesBySequence = new Dictionary <string, PeptideDocNode>();
foreach (var peptide in _srmDocument.Molecules)
{
peptidesBySequence[peptide.RawTextId] = peptide;
}
var chromatogramGroups = new List <ChromatogramRequestDocumentChromatogramGroup>();
foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup)
{
PeptideDocNode peptideDocNode = null;
if (!string.IsNullOrEmpty(chromatogramGroup.ModifiedSequence))
{
peptidesBySequence.TryGetValue(chromatogramGroup.ModifiedSequence, out peptideDocNode);
}
bool isFirstPassPeptide = peptideDocNode != null &&
_retentionTimePredictor.IsFirstPassPeptide(peptideDocNode);
if (_firstPass == isFirstPassPeptide)
{
chromatogramGroups.Add(chromatogramGroup);
}
}
chromatogramRequestDocument.ChromatogramGroup = chromatogramGroups.ToArray();
return(chromatogramRequestDocument);
}
public ChromatogramRequestProvider(SrmDocument srmDocument, ChorusUrl chorusUrl, IRetentionTimePredictor retentionTimePredictor, bool firstPass)
{
_srmDocument = srmDocument;
_chorusUrl = chorusUrl;
_retentionTimePredictor = retentionTimePredictor;
_firstPass = firstPass;
// Create a SpectrumFilter without an IRetentionTimeProvider in order to get the list of ChromKeys that we will eventually provide.
SpectrumFilter spectrumFilter = new SpectrumFilter(_srmDocument, _chorusUrl, null);
_chromKeys = ImmutableList.ValueOf(ListChromKeys(GetChromatogramRequestDocument(spectrumFilter)));
}
public ChromatogramRequestProvider(SrmDocument srmDocument, ChorusUrl chorusUrl, IRetentionTimePredictor retentionTimePredictor, bool firstPass)
{
_srmDocument = srmDocument;
_chorusUrl = chorusUrl;
_retentionTimePredictor = retentionTimePredictor;
_firstPass = firstPass;
// Create a SpectrumFilter without an IRetentionTimeProvider in order to get the list of ChromKeys that we will eventually provide.
SpectrumFilter spectrumFilter = new SpectrumFilter(_srmDocument, _chorusUrl, null);
_chromKeys = ImmutableList.ValueOf(ListChromKeys(GetChromatogramRequestDocument(spectrumFilter)));
}
public void TestMsx(SrmDocument doc, string dataPath)
{
// Load the file and check MsDataFileImpl
using (var file = new MsDataFileImpl(dataPath))
{
var filter = new SpectrumFilter(doc, null, null);
Assert.IsTrue(filter.EnabledMsMs);
var demultiplexer = new MsxDemultiplexer(file, filter);
demultiplexer.ForceInitializeFile();
// Check that the demultiplexer found the correct multiplexing parameters
Assert.AreEqual(5, demultiplexer.IsoWindowsPerScan);
Assert.AreEqual(100, demultiplexer.NumIsoWindows);
Assert.AreEqual(20, demultiplexer.DutyCycleLength);
var isoMapper = demultiplexer.IsoMapperTest;
Assert.AreEqual(100, isoMapper.NumWindows);
// Check the isolation window mapper responsible for mapping each unique isolation
// window detected in the file to a unique index
TestIsolationWindowMapper(isoMapper, file, 4.00182);
var transBinner = new TransitionBinner(filter, isoMapper);
// Test creation of a transition binner from a spectrum filter
TestTransitionBinnerFromFilter(transBinner, isoMapper);
var testSpectrum = file.GetSpectrum(TEST_SPECTRUM);
// Generate a transition binner containing a lot of tough cases with
// overlapping transitions and test
double[] binnedExpected =
{
0.0, 25160.11261, 18254.06375, 18254.06375, 18254.06375,
11090.00577, 19780.18628, 19780.18628
};
var transBinnerOverlap = TestTransitionBinnerOverlap(testSpectrum, isoMapper, binnedExpected);
TestSpectrumProcessor(transBinnerOverlap, isoMapper, file, TEST_SPECTRUM);
TestPeakIntensityCorrection(testSpectrum, isoMapper,
demultiplexer);
int[] intensityIndices = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 290, 291, 292, 293, 294, 295, 296 };
double[] intensityValues =
{
0.0, 0.0, 0.0, 0.0, 142.95, 349.75,
542.87, 511.77, 248.4, 0.0, 49.28,
1033.65, 278.56, 0.0, 0.0, 0.0,
0.0, 0.0
};
// Test demultiplexing of a real spectrum
TestSpectrumDemultiplex(demultiplexer, TEST_SPECTRUM, testSpectrum, intensityIndices, intensityValues, 0);
}
}
protected override void DoTest()
{
string chorusRequestOutputDirectory;
if (null != TestContext.TestResultsDirectory)
{
chorusRequestOutputDirectory = Path.Combine(TestContext.TestResultsDirectory, "chorusrequests");
Directory.CreateDirectory(chorusRequestOutputDirectory);
}
else
{
// When running unit tests under resharper, we have no TestResultsDirectory, so we only send
// the output to Console.Out.
chorusRequestOutputDirectory = null;
}
var xmlSerializer = new XmlSerializer(typeof(pwiz.Skyline.Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
foreach (var chorusDataSet in ChorusDataSets)
{
TestFilesDir testFilesDir = TestFilesDirForUrl(chorusDataSet.SkyZipUrl);
string skyFileName = Path.GetFileName(testFilesDir.FullPath);
Assert.IsNotNull(skyFileName, "skyFileName != null");
StringAssert.EndsWith(skyFileName, ".sky");
skyFileName = Uri.UnescapeDataString(skyFileName);
string skyFilePath = Path.Combine(testFilesDir.FullPath, skyFileName);
RunUI(() => SkylineWindow.OpenFile(skyFilePath));
WaitForDocumentLoaded();
SrmDocument document = null;
RunUI(() => { document = SkylineWindow.DocumentUI; });
Assert.IsNotNull(document);
SpectrumFilter spectrumFilterData = new SpectrumFilter(document, MsDataFileUri.Parse(""), null);
var chorusRequestDocument = spectrumFilterData.ToChromatogramRequestDocument();
Console.Out.WriteLine("***BEGIN {0}.chorusrequest.xml***", chorusDataSet.Name);
using (var xmlWriter = XmlWriter.Create(Console.Out, new XmlWriterSettings {
Encoding = Encoding.UTF8
}))
{
xmlSerializer.Serialize(xmlWriter, chorusRequestDocument);
}
Console.Out.WriteLine("***END {0}.chorusrequest.xml***", chorusDataSet.Name);
if (null != chorusRequestOutputDirectory)
{
string outputFile = Path.Combine(chorusRequestOutputDirectory,
chorusDataSet.Name + ".chorusrequest.xml");
using (var stream = new FileStream(outputFile, FileMode.Create))
{
xmlSerializer.Serialize(stream, chorusRequestDocument);
}
}
}
}
public void TestOverlap(SrmDocument doc, string dataPath)
{
// Load the file and check MsDataFileImpl
using (var file = new MsDataFileImpl(dataPath))
{
var filter = new SpectrumFilter(doc, null, null);
Assert.IsTrue(filter.EnabledMsMs);
var demultiplexer = new OverlapDemultiplexer(file, filter);
demultiplexer.ForceInitializeFile();
// Check that the demultiplexer found the correct multiplexing parameters
Assert.AreEqual(1, demultiplexer.IsoWindowsPerScan);
Assert.AreEqual(40, demultiplexer.NumIsoWindows);
Assert.AreEqual(41, demultiplexer.NumDeconvRegions);
var isoMapper = demultiplexer.IsoMapperTest;
// Basic checks of IsolationWindowMapper
TestIsolationWindowMapper(isoMapper, file, 20.009);
// Checks of overlap-specific functionality in IsolationWindowMapper
TestOverlapIsolationWindowMapper(isoMapper, file);
var transBinner = new TransitionBinner(filter, isoMapper);
// Test creation of a transition binner from a spectrum filter
TestTransitionBinnerFromFilter(transBinner, isoMapper);
var testSpectrum = file.GetSpectrum(TEST_SPECTRUM_OVERLAP);
// Generate a transition binner containing a lot of tough cases with
// overlapping transitions and test
double[] binnedExpected =
{
0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0
};
var transBinnerOverlap = TestTransitionBinnerOverlap(testSpectrum, isoMapper, binnedExpected);
TestSpectrumProcessor(transBinnerOverlap, isoMapper, file, TEST_SPECTRUM_OVERLAP);
int[] intensityIndices = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 290, 291, 292, 293, 294, 295, 296 };
double[] intensityValues =
{
0.0, 0.0, 0.0, 0.0, 4545.85, 15660.49,
35050.01, 56321.66, 62715.75, 43598.31, 23179.42,
2745.94, 3870.54, 4060.16, 3148.17, 1656.38,
0.0, 0.0
};
// Test demultiplexing of a real spectrum
TestSpectrumDemultiplex(demultiplexer, TEST_SPECTRUM_OVERLAP, testSpectrum, intensityIndices,
intensityValues, 0);
}
}
public double GetScore(Sequence sequence, int charge, int scan, LcMsRun lcmsRun)
{
var mass = sequence.Composition.Mass + Composition.H2O.Mass;
var spectrum = lcmsRun.GetSpectrum(scan);
var ionTypes = _rankScore.GetIonTypes(charge, mass);
var filteredSpectrum = SpectrumFilter.FilterIonPeaks(sequence, spectrum, ionTypes, _tolerance);
var match = new SpectrumMatch(sequence, filteredSpectrum, charge);
var score = 0.0;
var rankedPeaks = new RankedPeaks(filteredSpectrum);
foreach (var ionType in ionTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = rankedPeaks.RankIon(ion, _tolerance);
score += _rankScore.GetScore(ionType, rank, charge, mass);
}
}
return(score);
}
private void btnExport_Click(object sender, EventArgs e)
{
string strReferenceFile = (string)comboBoxReferenceFile.SelectedItem;
string strSaveFileName = string.Empty;
if (!string.IsNullOrEmpty(_documentFilePath))
{
strSaveFileName = Path.GetFileNameWithoutExtension(_documentFilePath);
}
if (!string.IsNullOrEmpty(strReferenceFile))
{
strSaveFileName += Path.GetFileNameWithoutExtension(strReferenceFile);
}
strSaveFileName += ".ChorusRequest.xml"; // Not L10N
strSaveFileName = strSaveFileName.Replace(' ', '_');
using (var saveFileDialog = new SaveFileDialog {
FileName = strSaveFileName
})
{
if (saveFileDialog.ShowDialog(this) != DialogResult.OK || string.IsNullOrEmpty(saveFileDialog.FileName))
{
return;
}
SpectrumFilter spectrumFilterData = new SpectrumFilter(Document, MsDataFileUri.Parse(strReferenceFile), null);
using (var saver = new FileSaver(saveFileDialog.FileName))
{
if (!saver.CanSave(this))
{
return;
}
using (var stream = new StreamWriter(saver.SafeName))
{
var xmlSerializer = new XmlSerializer(typeof(Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
xmlSerializer.Serialize(stream, spectrumFilterData.ToChromatogramRequestDocument());
}
saver.Commit();
}
}
Close();
}
private void ComputeMatch(SpectrumMatch match, int charge, int massIndex)
{
var isDecoy = match.Decoy;
var massErrors = _massErrors[charge][massIndex];
var rankTable = (isDecoy ? _drankTables[charge][massIndex] : _rankTables[charge][massIndex]);
var ionFrequencies = _ionProbabilities[charge][massIndex];
var acMatch = match;
if (Config.AcquisitionMethod == AcquisitionMethod.Dia)
{
// filter out all peaks except ion peaks
var ionPeakSpectrum = SpectrumFilter.FilterIonPeaks(match.Sequence, match.Spectrum,
Config.IonTypes, Config.Tolerance);
acMatch = new SpectrumMatch(acMatch.Sequence, ionPeakSpectrum, acMatch.ScanNum, acMatch.PrecursorCharge, acMatch.Decoy);
}
else
{
_precursorOffsets[charge][massIndex].AddMatch(match);
// filter precursor peaks
var precursorFilter = new PrecursorFilter(_precursorOffsets[charge][massIndex],
Config.MassErrorTolerance);
acMatch = precursorFilter.Filter(acMatch);
}
rankTable.AddMatch(acMatch);
if (isDecoy)
{
return;
}
massErrors.AddMatch(match);
var filteredSpectrum = SpectrumFilter.GetFilteredSpectrum(match.Spectrum, Config.WindowWidth,
Config.RetentionCount);
var filteredMatch = new SpectrumMatch(match.Sequence, filteredSpectrum, match.PrecursorCharge);
ionFrequencies.AddMatch(filteredMatch);
}
public ChromatogramRequestDocument GetChromatogramRequest()
{
SpectrumFilter spectrumFilter = new SpectrumFilter(_srmDocument, _chorusUrl, null, _firstPass ? null : _retentionTimePredictor);
return GetChromatogramRequestDocument(spectrumFilter);
}
private ChromatogramRequestDocument GetChromatogramRequestDocument(SpectrumFilter spectrumFilter)
{
ChromatogramRequestDocument chromatogramRequestDocument = spectrumFilter.ToChromatogramRequestDocument();
if (null == _retentionTimePredictor)
{
return chromatogramRequestDocument;
}
var peptidesBySequence = new Dictionary<string, PeptideDocNode>();
foreach (var peptide in _srmDocument.Molecules)
{
peptidesBySequence[peptide.RawTextId] = peptide;
}
var chromatogramGroups = new List<ChromatogramRequestDocumentChromatogramGroup>();
foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup)
{
PeptideDocNode peptideDocNode = null;
if (!string.IsNullOrEmpty(chromatogramGroup.ModifiedSequence))
{
peptidesBySequence.TryGetValue(chromatogramGroup.ModifiedSequence, out peptideDocNode);
}
bool isFirstPassPeptide = peptideDocNode == null ||
_retentionTimePredictor.IsFirstPassPeptide(peptideDocNode);
if (_firstPass == isFirstPassPeptide)
{
chromatogramGroups.Add(chromatogramGroup);
}
}
chromatogramRequestDocument.ChromatogramGroup = chromatogramGroups.ToArray();
return chromatogramRequestDocument;
}
public ChromatogramRequestDocument GetChromatogramRequest()
{
SpectrumFilter spectrumFilter = new SpectrumFilter(_srmDocument, _chorusUrl, null, _firstPass ? null : _retentionTimePredictor);
return(GetChromatogramRequestDocument(spectrumFilter));
}
static public float SpectrumField(SpectrumFilter spectrumFilter, float linearizedFrequency, float levelBeat)
{
float peakInverse;
EditorGUILayout.Space();
Rect rect = GUILayoutUtility.GetRect(120, 1000, 64, 64);
bool insideRect = rect.Contains(Event.current.mousePosition);
if (rect.Contains(Event.current.mousePosition))
{
mousePosition = Event.current.mousePosition - rect.min;
GUI.changed = true;
}
#if UNITY_2017_2_OR_NEWER
if (Event.current.type == EventType.MouseDown && insideRect)
#else
if (Event.current.type == EventType.mouseDown && insideRect)
#endif
{
markerPos = Event.current.mousePosition - rect.min;
linearizedFrequency = markerPos.x / rect.width;
mouseDown = true;
GUI.changed = true;
}
#if UNITY_2017_2_OR_NEWER
else if (Event.current.type == EventType.MouseUp)
#else
else if (Event.current.type == EventType.mouseUp)
#endif
{
mouseDown = false;
}
#if UNITY_2017_2_OR_NEWER
if ((Event.current.type == EventType.MouseDrag && mouseDown))
#else
if ((Event.current.type == EventType.mouseDrag && mouseDown))
#endif
{
markerPos = Event.current.mousePosition - rect.min;
linearizedFrequency = markerPos.x / rect.width;
GUI.changed = true;
}
linearizedFrequency = Mathf.Clamp01(linearizedFrequency);
GUI.BeginGroup(rect);
#if UNITY_2017_2_OR_NEWER
if (Event.current.type == EventType.Repaint)
#else
if (Event.current.type == EventType.repaint)
#endif
{
GL.Clear(true, false, Color.grey);
if (mat == null)
{
var shader = Shader.Find("Hidden/LDG/UI");
mat = new Material(shader);
}
mat.SetPass(0);
// background
DrawGL.Rect(rect, true, new Color(0.33f, 0.33f, 0.33f));
if (spectrumFilter)
{
peakInverse = 1.0f - Mathf.Clamp01(levelBeat);
// peak line
DrawGL.Line(new Vector2(0, peakInverse * rect.height), new Vector2(rect.width, peakInverse * rect.height), new Color(0.15f, 0.15f, 0.15f));
// mouse x pos
if (insideRect)
{
DrawGL.Line(new Vector2(mousePosition.x, 0), new Vector2(mousePosition.x, rect.height), new Color(0.15f, 0.15f, 0.15f));
}
if (EditorApplication.isPlaying && Time.frameCount > 5)
{
//DrawGL.Curve(spectrumFilter.spectrumSource.normalizedPeaks, 1, rect.width, rect.height, new Color(0.2f, 0.2f, 0.2f));
DrawGL.Graph(spectrumFilter.fallingLevels, 1, rect.width, rect.height, new Color(0.0f, 0.5f, 1.0f), spectrumFilter.interpolationMode);
// draw spectrum
#if UNITY_5_6_OR_NEWER
GL.Begin(GL.LINE_STRIP);
for (int i = 0; i < rect.width; i++)
{
float iLevel = spectrumFilter.GetLevel((float)i / rect.width);
GL.Color(new Color(0.0f, 0.75f, 0.0f));
GL.Vertex3(i, Mathf.Clamp01(1.0f - iLevel) * rect.height, 0);
}
#else
GL.Begin(GL.LINES);
Vector2 xy = Vector2.zero;
Vector2 xyPrev = xy;
for (int i = 0; i < rect.width; i++)
{
xy.Set(i, Mathf.Clamp01(1.0f - spectrumFilter.GetLevel((float)i / rect.width)) * rect.height);
if (i > 0)
{
GL.Color(new Color(0.0f, 0.75f, 0.0f));
GL.Vertex3(xyPrev.x, xyPrev.y, 0);
GL.Vertex3(xy.x, xy.y, 0);
}
xyPrev = xy;
}
#endif
GL.End();
}
}
DrawGL.Line(new Vector2(linearizedFrequency * rect.width, 0), new Vector2(linearizedFrequency * rect.width, rect.height), new Color(0.95f, 0.2f, 0.2f));
// background outline
DrawGL.Rect(rect, false, new Color(0.45f, 0.45f, 0.45f));
}
GUI.EndGroup();
statsStyle.normal.textColor = new Color(0.8f, 0.8f, 0.8f);
statsStyle.alignment = TextAnchor.UpperRight;
float freq = Frequency.UnlinearizeFrequency(1.0f - Mathf.Clamp01(mousePosition.x / rect.width));
//GUI.Label(rect, "Freq: " + freq.ToString("n2") + ", Peak: " + levelBeat.ToString("n2") + " ", statsStyle);
if (insideRect)
{
GUI.Label(rect, "Freq: " + freq.ToString("n2") + " ", statsStyle);
}
return(linearizedFrequency);
}
public static List <double> RestoreSignalValues(ISignal signal, bool includeFi = true, SpectrumFilter filter = null)
{
List <double> result = new List <double>();
Dictionary <int, GarmonicSignal> garmonicSignals = new Dictionary <int, GarmonicSignal>();
double includeFiValue = Convert.ToDouble(includeFi);
int N = 0;
if (signal is GarmonicSignal)
{
garmonicSignals.Add(1, signal as GarmonicSignal);
N = (signal as GarmonicSignal).N;
}
else
{
List <GarmonicSignal> filteredSignals = (signal as PoligarmonicSignal).Signals;
if (filter != null)
{
filteredSignals = filter.Filter(filteredSignals);
}
for (int i = 1; i <= filteredSignals.Count; i++)
{
garmonicSignals.Add(filteredSignals[i - 1].GarmonicIndex, filteredSignals[i - 1]);
N = filteredSignals[i - 1].N;
}
}
for (int i = 1; i <= N; i++)
{
double accumulator = 0;
foreach (var innerSignal in garmonicSignals)
{
var temp = innerSignal.Value.AFinder.AmplitudeValue * Math.Cos(((2 * Math.PI * i * innerSignal.Value.GarmonicIndex - 1) / N) - innerSignal.Value.AFinder.StartPhase);
accumulator += temp;
}
result.Add(accumulator);
}
return(result);
}
