public TurnoverCalculator GetTurnoverCalculator()
{
var turnoverCalculator = _turnoverCalculator;
if (turnoverCalculator != null)
{
return(turnoverCalculator);
}
_turnoverCalculator = turnoverCalculator = new TurnoverCalculator(Workspace, Peptide.Sequence);
return(turnoverCalculator);
}
public TurnoverCalculator GetTurnoverCalculator(string peptideSequence)
{
peptideSequence = Peptide.TrimSequence(peptideSequence);
TurnoverCalculator turnoverCalculator;
if (_turnoverCalculators.TryGetValue(peptideSequence, out turnoverCalculator))
{
return(turnoverCalculator);
}
turnoverCalculator = new TurnoverCalculator(Workspace, peptideSequence);
_turnoverCalculators.Add(peptideSequence, turnoverCalculator);
return(turnoverCalculator);
}
public void Init(Workspace workspace)
{
Chromatograms = new List <ChromatogramGenerator.Chromatogram>();
var turnoverCalculator = new TurnoverCalculator(workspace, Sequence);
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
for (int massIndex = 0; massIndex < mzs.Count; massIndex++)
{
Chromatograms.Add(new ChromatogramGenerator.Chromatogram(new MzKey(charge, massIndex), mzs[massIndex]));
}
}
ScanIndexes = new List <int>();
Times = new List <double>();
}
public void Test58Percent()
{
var path = Path.Combine(TestContext.TestDir, Guid.NewGuid().ToString() + ".tpg");
var workspace = CreateWorkspace(path, TracerDef.GetD3LeuEnrichment());
var turnoverCalculator = new TurnoverCalculator(workspace, "LL");
var dict = new Dictionary<TracerFormula, double>();
// initialize the dictionary with 70% newly synthesized from 58% precursor pool
dict.Add(TracerFormula.Parse("Tracer2"), Math.Pow(.58, 2) * .7);
dict.Add(TracerFormula.Parse("Tracer1"), 2 * .58 * .42 * .7);
dict.Add(TracerFormula.Empty, 1- dict.Values.Sum());
double turnover;
double turnoverScore;
IDictionary<TracerFormula, double> bestMatch;
var precursorEnrichment = turnoverCalculator.ComputePrecursorEnrichmentAndTurnover(dict, out turnover, out turnoverScore, out bestMatch);
Assert.AreEqual(.7, turnover);
Assert.AreEqual(58, precursorEnrichment["Tracer"]);
}
public void Test58Percent()
{
var path = Path.Combine(TestContext.TestDir, Guid.NewGuid().ToString() + ".tpg");
var workspace = CreateWorkspace(path, TracerDef.GetD3LeuEnrichment());
var turnoverCalculator = new TurnoverCalculator(workspace, "LL");
var dict = new Dictionary <TracerFormula, double>();
// initialize the dictionary with 70% newly synthesized from 58% precursor pool
dict.Add(TracerFormula.Parse("Tracer2"), Math.Pow(.58, 2) * .7);
dict.Add(TracerFormula.Parse("Tracer1"), 2 * .58 * .42 * .7);
dict.Add(TracerFormula.Empty, 1 - dict.Values.Sum());
double turnover;
double turnoverScore;
IDictionary <TracerFormula, double> bestMatch;
var precursorEnrichment = turnoverCalculator.ComputePrecursorEnrichmentAndTurnover(dict, out turnover, out turnoverScore, out bestMatch);
Assert.AreEqual(.7, turnover);
Assert.AreEqual(58, precursorEnrichment["Tracer"]);
}
public void Redisplay()
{
if (!IsHandleCreated)
{
return;
}
if (_inRedisplay)
{
return;
}
try
{
_inRedisplay = true;
tbxMinCharge.Text = MinCharge.ToString();
tbxMaxCharge.Text = MaxCharge.ToString();
tbxPeptideSequence.Text = PeptideSequence;
cbxShowPeptideMzs.Enabled = !string.IsNullOrEmpty(PeptideSequence);
tbxMassAccuracy.Text = MassAccuracy.ToString();
TurnoverCalculator turnoverCalculator = null;
if (!string.IsNullOrEmpty(PeptideSequence))
{
turnoverCalculator = new TurnoverCalculator(Workspace, PeptideSequence);
}
msGraphControlEx1.GraphPane.GraphObjList.Clear();
msGraphControlEx1.GraphPane.CurveList.Clear();
if (_spectrumData == null || comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
if (comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
string chromatogramName;
float[] timeArray;
float[] intensityArray;
msDataFileImpl.GetChromatogram(comboChromatogram.SelectedIndex, out chromatogramName, out timeArray, out intensityArray);
_chromatogramDatas[comboChromatogram.SelectedIndex] = new ChromatogramData(chromatogramName, timeArray, intensityArray);
}
_spectrumData = _spectrumData ?? new SpectrumData(msDataFileImpl, ScanIndex);
}
}
ChromatogramData chromatogram = null;
if (comboChromatogram.SelectedIndex >= 0)
{
chromatogram = _chromatogramDatas[comboChromatogram.SelectedIndex];
}
tbxMsLevel.Text = _spectrumData.MsLevel.ToString();
tbxTime.Text = _spectrumData.Time.ToString();
if (chromatogram != null && ScanIndex < chromatogram.TimeArray.Length)
{
tbxChromatogramRetentionTime.Text = chromatogram.TimeArray[ScanIndex].ToString();
tbxChromatogramIonCurrent.Text = chromatogram.IntensityArray[ScanIndex].ToString(NumberFormat);
}
else
{
tbxChromatogramRetentionTime.Text = tbxChromatogramIonCurrent.Text = @"N/A";
}
if (cbxShowProfile.Checked && _spectrumData.ProfileMzs != null)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, new SpectrumGraphItem()
{
Points =
new PointPairList(_spectrumData.ProfileMzs,
_spectrumData.ProfileIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.line,
Color = Color.Blue,
});
}
if (_spectrumData.ProfileIntensities != null)
{
tbxSumOfProfileIntensities.Text = _spectrumData.ProfileIntensities.Sum().ToString(NumberFormat);
}
else
{
tbxSumOfProfileIntensities.Text = "";
}
tbxCentroidIntensitySum.Text = _spectrumData.CentroidIntensities.Sum().ToString(NumberFormat);
var spectrum = new SpectrumGraphItem
{
Points = new PointPairList(_spectrumData.CentroidMzs, _spectrumData.CentroidIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.stick,
Color = Color.Black
};
if (turnoverCalculator != null)
{
var mzRanges = new Dictionary <MzRange, String>();
double monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideSequence);
double peptideIntensity = 0.0;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
foreach (var mzRange in turnoverCalculator.GetMzs(charge))
{
double mass = (mzRange.Center - AminoAcidFormulas.ProtonMass) * charge;
double massDifference = mass - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
mzRanges.Add(mzRange, label);
var chromatogramPoint = MsDataFileUtil.GetPoint(mzRange, _spectrumData.CentroidMzs, _spectrumData.CentroidIntensities);
peptideIntensity += chromatogramPoint.GetIntensity(mzRange, MassAccuracy);
}
}
spectrum.MassAccuracy = MassAccuracy;
spectrum.MzRanges = mzRanges;
tbxPeptideIntensity.Text = peptideIntensity.ToString(NumberFormat);
}
if (cbxShowCentroids.Checked)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, spectrum);
}
if (turnoverCalculator != null && cbxShowPeptideMzs.Checked)
{
double massAccuracy = MassAccuracy;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
var height = int.MaxValue;
foreach (var mzRange in mzs)
{
double min = mzRange.MinWithMassAccuracy(massAccuracy);
double max = mzRange.MaxWithMassAccuracy(massAccuracy);
msGraphControlEx1.GraphPane.GraphObjList.Add(new BoxObj(min, height, max - min, height, Color.Goldenrod, Color.Goldenrod)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
});
}
}
}
msGraphControlEx1.Invalidate();
}
finally
{
_inRedisplay = false;
}
}
public void Redisplay()
{
if (!IsHandleCreated)
{
return;
}
if (_inRedisplay)
{
return;
}
try
{
_inRedisplay = true;
tbxMinCharge.Text = MinCharge.ToString();
tbxMaxCharge.Text = MaxCharge.ToString();
tbxPeptideSequence.Text = PeptideSequence;
cbxShowPeptideMzs.Enabled = !string.IsNullOrEmpty(PeptideSequence);
tbxMassAccuracy.Text = MassAccuracy.ToString();
TurnoverCalculator turnoverCalculator = null;
if (!string.IsNullOrEmpty(PeptideSequence))
{
turnoverCalculator = new TurnoverCalculator(Workspace, PeptideSequence);
}
msGraphControlEx1.GraphPane.GraphObjList.Clear();
msGraphControlEx1.GraphPane.CurveList.Clear();
if (_spectrumData == null || comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
if (comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
string chromatogramName;
float[] timeArray;
float[] intensityArray;
msDataFileImpl.GetChromatogram(comboChromatogram.SelectedIndex, out chromatogramName, out timeArray, out intensityArray);
_chromatogramDatas[comboChromatogram.SelectedIndex] = new ChromatogramData(chromatogramName, timeArray, intensityArray);
}
_spectrumData = _spectrumData ?? new SpectrumData(msDataFileImpl, ScanIndex);
}
}
ChromatogramData chromatogram = null;
if (comboChromatogram.SelectedIndex >= 0)
{
chromatogram = _chromatogramDatas[comboChromatogram.SelectedIndex];
}
tbxMsLevel.Text = _spectrumData.MsLevel.ToString();
tbxTime.Text = _spectrumData.Time.ToString();
if (chromatogram != null && ScanIndex < chromatogram.TimeArray.Length)
{
tbxChromatogramRetentionTime.Text = chromatogram.TimeArray[ScanIndex].ToString();
tbxChromatogramIonCurrent.Text = chromatogram.IntensityArray[ScanIndex].ToString(NumberFormat);
}
else
{
tbxChromatogramRetentionTime.Text = tbxChromatogramIonCurrent.Text = @"N/A";
}
if (cbxShowProfile.Checked && _spectrumData.ProfileMzs != null)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, new SpectrumGraphItem()
{
Points =
new PointPairList(_spectrumData.ProfileMzs,
_spectrumData.ProfileIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.line,
Color = Color.Blue,
});
}
if (_spectrumData.ProfileIntensities != null)
{
tbxSumOfProfileIntensities.Text = _spectrumData.ProfileIntensities.Sum().ToString(NumberFormat);
}
else
{
tbxSumOfProfileIntensities.Text = "";
}
tbxCentroidIntensitySum.Text = _spectrumData.CentroidIntensities.Sum().ToString(NumberFormat);
var spectrum = new SpectrumGraphItem
{
Points = new PointPairList(_spectrumData.CentroidMzs, _spectrumData.CentroidIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.stick,
Color = Color.Black
};
if (turnoverCalculator != null)
{
var mzRanges = new Dictionary<MzRange, String>();
double monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideSequence);
double peptideIntensity = 0.0;
for (int charge = MinCharge; charge <= MaxCharge; charge ++)
{
foreach (var mzRange in turnoverCalculator.GetMzs(charge))
{
double mass = (mzRange.Center - AminoAcidFormulas.ProtonMass)* charge;
double massDifference = mass - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
mzRanges.Add(mzRange, label);
var chromatogramPoint = MsDataFileUtil.GetPoint(mzRange, _spectrumData.CentroidMzs, _spectrumData.CentroidIntensities);
peptideIntensity += chromatogramPoint.GetIntensity(mzRange, MassAccuracy);
}
}
spectrum.MassAccuracy = MassAccuracy;
spectrum.MzRanges = mzRanges;
tbxPeptideIntensity.Text = peptideIntensity.ToString(NumberFormat);
}
if (cbxShowCentroids.Checked)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, spectrum);
}
if (turnoverCalculator != null && cbxShowPeptideMzs.Checked)
{
double massAccuracy = MassAccuracy;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
var height = int.MaxValue;
foreach (var mzRange in mzs)
{
double min = mzRange.MinWithMassAccuracy(massAccuracy);
double max = mzRange.MaxWithMassAccuracy(massAccuracy);
msGraphControlEx1.GraphPane.GraphObjList.Add(new BoxObj(min, height, max - min, height, Color.Goldenrod, Color.Goldenrod)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
});
}
}
}
msGraphControlEx1.Invalidate();
}
finally
{
_inRedisplay = false;
}
}
} // CreateLogicalOffer
private int GetLogicalProposedAmount(GradeRangeSubproduct grsp)
{
decimal annualTurnover = 0;
decimal freeCashFlow = 0;
decimal valueAdded = 0;
try {
var turnoverCalc = new TurnoverCalculator(this.customerID, DateTime.UtcNow, DB, Log).LoadInputData();
if (turnoverCalc.OutOfDate)
{
Log.Debug("Out of date marketplaces detected for {0}.", OuterContextDescription);
}
else
{
turnoverCalc.Execute();
if (turnoverCalc.HasOnline)
{
Log.Debug("Online turnover for {0}.", OuterContextDescription);
turnoverCalc.ExecuteOnline();
}
else
{
Log.Debug("Offline turnover for {0}.", OuterContextDescription);
}
annualTurnover = turnoverCalc.Model.AnnualTurnover;
freeCashFlow = turnoverCalc.Model.UseHmrc ? turnoverCalc.Model.FreeCashFlowValue : 0;
valueAdded = turnoverCalc.Model.UseHmrc ? turnoverCalc.Model.ValueAdded : 0;
} // if
} catch (Exception e) {
Log.Alert(e, "Failed to load turnover for {0}.", OuterContextDescription);
} // try
Log.Debug(
"Turnover = {0}, FCF = {1}, VA = {2} for {3}.",
annualTurnover,
freeCashFlow,
valueAdded,
OuterContextDescription
);
decimal[] allOffers =
{
annualTurnover *(grsp.TurnoverShare ?? 0),
freeCashFlow *(grsp.FreeCashFlowShare ?? 0),
valueAdded *(grsp.ValueAddedShare ?? 0),
};
List <int> validOffers = allOffers.Where(v => v > 0).Select(grsp.LoanAmount).Where(v => v > 0).ToList();
Log.Debug(
"Proposed amounts for {0}:\n\tAll offer amounts: {1}\n\tValid offer amounts: {2}",
OuterContextDescription,
string.Join(", ", allOffers),
string.Join(", ", validOffers)
);
if (validOffers.Count > 0)
{
int minOffer = validOffers.Min();
Log.Debug("Proposed offer amount for {0} is {1}.", OuterContextDescription, minOffer);
return(minOffer);
} // if
Log.Debug("No valid offers found for {0}.", OuterContextDescription);
return(0);
} // GetLogicalProposedAmount
public void Init(Workspace workspace)
{
Chromatograms = new List<ChromatogramGenerator.Chromatogram>();
var turnoverCalculator = new TurnoverCalculator(workspace, Sequence);
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
for (int massIndex = 0; massIndex < mzs.Count; massIndex++)
{
Chromatograms.Add(new ChromatogramGenerator.Chromatogram(new MzKey(charge, massIndex), mzs[massIndex]));
}
}
ScanIndexes = new List<int>();
Times = new List<double>();
}
private void BtnGoOnClick(object sender, EventArgs e)
{
graphDetails.GraphPane.CurveList.Clear();
int pointCount = PointCount;
double precursorPool = PrecursorPool;
double turnover = Turnover;
int labelCount = LabelCount;
double noise = Noise;
var points = new PointPairList();
var tracerDef = Workspace.GetTracerDefs().FirstOrDefault(td => td.AminoAcidSymbol.HasValue);
if (tracerDef == null)
{
MessageBox.Show(
"The simulation cannot be run because there is no amino acid tracer defined in this workspace");
return;
}
Debug.Assert(tracerDef.AminoAcidSymbol.HasValue);
string peptide = new string(tracerDef.AminoAcidSymbol.Value, labelCount);
var turnoverCalculator = new TurnoverCalculator(Workspace, peptide);
var initialTracerPercents = TracerPercentFormula.Parse("").SetElementCount(tracerDef.Name, tracerDef.InitialApe);
var newTracerPercents = TracerPercentFormula.Parse("").SetElementCount(tracerDef.Name, precursorPool);
var initialDistribution = turnoverCalculator.GetDistribution(initialTracerPercents);
var newDistribution = turnoverCalculator.GetDistribution(newTracerPercents);
var currentMixture = Mix(initialDistribution, (100.0 - turnover) / 100, newDistribution, turnover / 100);
var keys = new List <TracerFormula>();
for (int i = 0; i <= labelCount; i++)
{
keys.Add(TracerFormula.Parse("").SetElementCount(tracerDef.Name, i));
}
var bestMatches = new List <IDictionary <TracerFormula, double> >();
var precursorEnrichments = new List <TracerPercentFormula>();
var observedResults = new List <IDictionary <TracerFormula, double> >();
while (points.Count < pointCount)
{
var noisyMixture = Perturb(keys, currentMixture, noise / 100);
double calcTurnover;
double calcTurnoverScore;
double calcPrecursorPool;
IDictionary <TracerFormula, double> bestMatch;
var calcMixture = turnoverCalculator.ComputePrecursorEnrichmentAndTurnover(noisyMixture, out calcTurnover, out calcTurnoverScore, out bestMatch);
if (calcMixture == null)
{
continue;
}
calcMixture.TryGetValue(tracerDef.Name, out calcPrecursorPool);
points.Add(new PointPair(calcTurnover * 100, calcPrecursorPool));
bestMatches.Add(bestMatch);
precursorEnrichments.Add(calcMixture);
observedResults.Add(noisyMixture);
}
graphResults.GraphPane.CurveList.Clear();
graphResults.GraphPane.GraphObjList.Clear();
var lineItem = graphResults.GraphPane.AddCurve(null, points, Color.Black);
lineItem.Line.IsVisible = false;
graphResults.GraphPane.XAxis.Title.Text = "% newly synthesized";
graphResults.GraphPane.YAxis.Title.Text = "Precursor pool";
graphResults.GraphPane.AxisChange();
graphResults.Invalidate();
dataGridView.Rows.Clear();
var row = dataGridView.Rows[dataGridView.Rows.Add()];
row.Cells[colQuantity.Index].Value = "% newly synthesized";
var statsTurnover = new Statistics(points.Select(p => p.X).ToArray());
row.Cells[colMean.Index].Value = statsTurnover.Mean();
row.Cells[colMedian.Index].Value = statsTurnover.Median();
row.Cells[colStdDev.Index].Value = statsTurnover.StdDev();
row = dataGridView.Rows[dataGridView.Rows.Add()];
var statsPrecursorPool = new Statistics(points.Select(p => p.Y).ToArray());
row.Cells[colQuantity.Index].Value = "Precursor Pool";
row.Cells[colMean.Index].Value = statsPrecursorPool.Mean();
row.Cells[colMedian.Index].Value = statsPrecursorPool.Median();
row.Cells[colStdDev.Index].Value = statsPrecursorPool.StdDev();
_precursorEnrichmentsByPoint = points.Select(p => p.Y).ToArray();
_bestMatches = bestMatches;
_observedResults = observedResults;
_scatterPlotCurve = lineItem;
_expected = currentMixture;
_turnovers = points.Select(p => p.X).ToArray();
_tracerFormulas = keys;
ShowResult(-1);
}
private void UpdateGraph()
{
if (_inUpdateGraph)
{
return;
}
try
{
_inUpdateGraph = true;
_msGraphControl.GraphPane.GraphObjList.Clear();
_msGraphControl.GraphPane.CurveList.Clear();
dataGridView1.Rows.Clear();
int charge;
try
{
charge = Convert.ToInt32(tbxCharge.Text);
tbxCharge.BackColor = Color.White;
}
catch
{
charge = 0;
tbxCharge.BackColor = Color.Red;
}
double massResolution;
try
{
massResolution = double.Parse(tbxMassResolution.Text);
tbxMassResolution.BackColor = Color.White;
}
catch
{
tbxMassResolution.BackColor = Color.Red;
massResolution = .01;
}
var sequence = tbxSequence.Text;
MassDistribution spectrum;
if (string.IsNullOrEmpty(sequence))
{
var formula = tbxFormula.Text;
var molecule = Molecule.Parse(formula);
if (molecule.Values.Sum() > 10000000)
{
tbxFormula.BackColor = Color.Red;
return;
}
try
{
spectrum = Workspace.GetAminoAcidFormulas().GetMassDistribution(molecule, charge);
tbxFormula.BackColor = Color.White;
}
catch
{
tbxFormula.BackColor = Color.Red;
return;
}
}
else
{
tbxFormula.Text = Workspace.GetAminoAcidFormulas().GetFormula(sequence).ToString();
var turnoverCalculator = new TurnoverCalculator(Workspace, sequence);
var aminoAcidFormulas = Workspace.GetAminoAcidFormulasWithTracers();
aminoAcidFormulas = aminoAcidFormulas.SetMassResolution(massResolution);
try
{
if (cbxTracerPercents.Checked)
{
var tracerPercentFormula = TracerPercentFormula.Parse(tbxTracerFormula.Text);
spectrum = turnoverCalculator.GetAminoAcidFormulas(tracerPercentFormula)
.GetMassDistribution(sequence, charge);
}
else
{
var tracerFormula = TracerFormula.Parse(tbxTracerFormula.Text);
spectrum = aminoAcidFormulas.GetMassDistribution(
turnoverCalculator.MoleculeFromTracerFormula(tracerFormula), charge);
double massShift = aminoAcidFormulas.GetMassShift(sequence);
if (charge > 0)
{
massShift /= charge;
}
spectrum = spectrum.OffsetAndDivide(massShift, 1);
}
tbxTracerFormula.BackColor = Color.White;
}
catch
{
tbxTracerFormula.BackColor = Color.Red;
spectrum = aminoAcidFormulas.GetMassDistribution(sequence, charge);
}
}
if (spectrum == null)
{
return;
}
var curveItem = _msGraphControl.AddGraphItem(_msGraphControl.GraphPane, new GraphItem
{
Title = "Intensity",
Color = Color.Black,
Points =
new PointPairList(
spectrum.Keys.
ToArray(),
spectrum.Values.
ToArray())
});
curveItem.Label.IsVisible = false;
_msGraphControl.AxisChange();
_msGraphControl.Invalidate();
var entries = spectrum.ToArray();
dataGridView1.Rows.Add(entries.Length);
for (int i = 0; i < entries.Count(); i++)
{
var row = dataGridView1.Rows[i];
row.Cells[colMass.Index].Value = entries[i].Key;
row.Cells[colIntensity.Index].Value = entries[i].Value;
}
}
finally
{
_inUpdateGraph = false;
}
}
private void UpdateGraph()
{
if (_inUpdateGraph)
{
return;
}
try
{
_inUpdateGraph = true;
_msGraphControl.GraphPane.GraphObjList.Clear();
_msGraphControl.GraphPane.CurveList.Clear();
dataGridView1.Rows.Clear();
int charge;
try
{
charge = Convert.ToInt32(tbxCharge.Text);
tbxCharge.BackColor = Color.White;
}
catch
{
charge = 0;
tbxCharge.BackColor = Color.Red;
}
double massResolution;
try
{
massResolution = double.Parse(tbxMassResolution.Text);
tbxMassResolution.BackColor = Color.White;
}
catch
{
tbxMassResolution.BackColor = Color.Red;
massResolution = .01;
}
var sequence = tbxSequence.Text;
MassDistribution spectrum;
if (string.IsNullOrEmpty(sequence))
{
var formula = tbxFormula.Text;
var molecule = Molecule.Parse(formula);
if (molecule.Values.Sum() > 10000000)
{
tbxFormula.BackColor = Color.Red;
return;
}
try
{
spectrum = Workspace.GetAminoAcidFormulas().GetMassDistribution(molecule, charge);
tbxFormula.BackColor = Color.White;
}
catch
{
tbxFormula.BackColor = Color.Red;
return;
}
}
else
{
tbxFormula.Text = Workspace.GetAminoAcidFormulas().GetFormula(sequence).ToString();
var turnoverCalculator = new TurnoverCalculator(Workspace, sequence);
var aminoAcidFormulas = Workspace.GetAminoAcidFormulasWithTracers();
aminoAcidFormulas = aminoAcidFormulas.SetMassResolution(massResolution);
try
{
if (cbxTracerPercents.Checked)
{
var tracerPercentFormula = TracerPercentFormula.Parse(tbxTracerFormula.Text);
spectrum = turnoverCalculator.GetAminoAcidFormulas(tracerPercentFormula)
.GetMassDistribution(sequence, charge);
}
else
{
var tracerFormula = TracerFormula.Parse(tbxTracerFormula.Text);
spectrum = aminoAcidFormulas.GetMassDistribution(
turnoverCalculator.MoleculeFromTracerFormula(tracerFormula), charge);
double massShift = aminoAcidFormulas.GetMassShift(sequence);
if (charge > 0)
{
massShift /= charge;
}
spectrum = spectrum.OffsetAndDivide(massShift, 1);
}
tbxTracerFormula.BackColor = Color.White;
}
catch
{
tbxTracerFormula.BackColor = Color.Red;
spectrum = aminoAcidFormulas.GetMassDistribution(sequence, charge);
}
}
if (spectrum == null)
{
return;
}
var curveItem = _msGraphControl.AddGraphItem(_msGraphControl.GraphPane, new GraphItem
{
Title = "Intensity",
Color = Color.Black,
Points =
new PointPairList(
spectrum.Keys.
ToArray(),
spectrum.Values.
ToArray())
});
curveItem.Label.IsVisible = false;
_msGraphControl.AxisChange();
_msGraphControl.Invalidate();
var entries = spectrum.ToArray();
dataGridView1.Rows.Add(entries.Length);
for (int i = 0; i < entries.Count(); i++)
{
var row = dataGridView1.Rows[i];
row.Cells[colMass.Index].Value = entries[i].Key;
row.Cells[colIntensity.Index].Value = entries[i].Value;
}
}
finally
{
_inUpdateGraph = false;
}
}
public TurnoverCalculator GetTurnoverCalculator(string peptideSequence)
{
peptideSequence = Peptide.TrimSequence(peptideSequence);
TurnoverCalculator turnoverCalculator;
if (_turnoverCalculators.TryGetValue(peptideSequence, out turnoverCalculator))
{
return turnoverCalculator;
}
turnoverCalculator = new TurnoverCalculator(Workspace, peptideSequence);
_turnoverCalculators.Add(peptideSequence, turnoverCalculator);
return turnoverCalculator;
}
