/// <summary>
/// Return Remove contaminant peak is Enabled.
/// </summary>
/// <param name="clrParams"></param>
/// <returns></returns>
public ClrVariant RemoveContaminantPeakIsEnabled(ClrParameters clrParams)
{
ClrVariant ret = new ClrVariant();
ret.type = ClrVariant.DataType.BOOL;
ret.obj = false;
try
{
ClrMsDataVariant msObj = new ClrMsDataVariant(ClrPluginCallTool.getActiveObject(clrParams));
SampleWrapper sw = msObj.getSample();
if (sw != null)
{
DataGroupNodeWrapper dgnw = sw.getRootDataGroupNode();
if (1 < dgnw.getNumberOfSpectra())
{
ret.obj = true;
}
}
}
catch
{
ret.obj = false;
}
return(ret);
}
/// <summary>
/// Submit latest result to sample tree.
/// </summary>
public void SubmitResultToTree()
{
// No Result
if (Result == null)
{
return;
}
ClrMsDataVariant msObj = new ClrMsDataVariant(_clrVariant);
DataGroupNodeWrapper dgnw = msObj.getSample().getRootDataGroupNode();
//Add result to sample tree.
SampleSetResampling sampleSet = new SampleSetResampling();
SampleResampling sample = new SampleResampling(sampleSet);
sample.openSample();
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
sample.setName("Contaminant peak removed " + msObj.getSample().getName());
root.setName("Contaminant peak removed " + dgnw.getName());
int cnt = 0;
for (int i = 0; i < Result.Spectrums.Count(); i++)
{
ClrDataPoints pts = Result.DataPoints[i];
SpectrumWrapper sw = Result.Spectrums[i];
XYDataWrapper xyd;
SpectrumResampling spec;
if (Result.Spectrums.Count == 1)
{
spec = new SpectrumResampling(sample, sw.getName());
}
else
{
cnt++;
spec = new SpectrumResampling(sample, Result.Spectrums[i].getName() + " (" + cnt.ToString() + ")");
}
xyd = spec.getXYData();
spec.SetData(pts);
spec.onGetXYData(xyd, -1.0, -1.0);
spec.setMinX(pts.getMinX());
spec.setMaxX(pts.getMaxX());
spec.setMaxIntensity(pts.getMaxY());
spec.setMsStage((int)sw.getMsStage());
sample.setSampleIndex((int)0);
root.addSpectrum(spec);
}
sampleSet.addSample(sample);
ClrPluginCallTool.onOpenSample(sample);
}
/// <summary>
/// Display Calculation Results on tree view
/// </summary>
public void DisplayCalculationResult()
{
// No Result
if (_resultSpecCal == null)
{
return;
}
//Add result to sample tree.
SampleSetResampling sampleSet = new SampleSetResampling();
SampleResampling sample = new SampleResampling(sampleSet);
sample.openSample();
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
sample.setName(_resultSpecCal.Spectrums[0].getName() + " Sample");
root.setName(_resultSpecCal.Spectrums[0].getName() + " Sample");
int cnt = 0;
foreach (SpectrumResampling sr in _resultSpecCal.Spectrums)
{
ClrDataPoints xyd = new ClrDataPoints();
SpectrumResampling spec;
if (_resultSpecCal.Spectrums.Count == 1)
{
spec = new SpectrumResampling(sample, sr.getName() + " Spectrum");
}
else
{
cnt++;
spec = new SpectrumResampling(sample, sr.getName() + " Spectrum_" + cnt.ToString());
}
ClrDataPoints pts = new ClrDataPoints();
sr.getXYData(pts, false);
spec.getXYData(xyd, false);
spec.SetData(pts);
spec.setMinX(pts.getMinX());
spec.setMaxX(pts.getMaxX());
spec.setMaxIntensity(pts.getMaxY());
spec.onGetXYData(xyd, -1.0, -1.0);
spec.setMsStage((int)sr.getMsStage());
sample.setSampleIndex((int)0);
root.addSpectrum(spec);
}
sampleSet.addSample(sample);
ClrPluginCallTool.onOpenSample(sample);
}
/// <summary>
/// Remove contaminant peak is Enabled.
/// </summary>
/// <param name="clrParams">parameters for C# plug-in from Mass++</param>
/// <returns></returns>
public ClrVariant RemoveContaminantPeak(ClrParameters clrParams)
{
// Return value (Success: true, Failure: false)
ClrVariant ret = new ClrVariant();
// We initially set ret.prim.boolVal to false so that we can return a false
// result easily using "return ret" if a failure condition occurs.
ret.type = ClrVariant.DataType.BOOL;
ret.obj = false;
// Convert clrParams to ActiveObject
ClrVariant clrVar = ClrPluginCallTool.getActiveObject(clrParams);
// Display main window.
RemoveContaminantPeakManager.DisplayDlgRemovContamiPeak(clrVar);
ret.obj = true;
return(ret);
}
private bool CreateBaselineSubtractedXIC(
PluginFunctionItemWrapper pfiw,
List <ClrDataPoints> resamplingList,
List <SpectrumWrapper> ms1List,
SettingParameterValuesWrapper spvw,
ref ClrDataPoints[] subtractLowerXICList,
ref ClrDataPoints[] subtractHigherXICList,
ref ClrDataPoints subtractHighestXICList
)
{
uint resamplingLength = resamplingList[0].getLength();
int lowerIndex = (resamplingLength < int.MaxValue) ? (int)resamplingLength : int.MaxValue;
int higherIndex = (0 < (int)(resamplingLength - lowerIndex))? (int)(resamplingLength - lowerIndex) : 0;
subtractLowerXICList = new ClrDataPoints[lowerIndex];
subtractHigherXICList = new ClrDataPoints[higherIndex];
for (uint i = 0; i < resamplingLength; i++)
{
//Update message.
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.REMOVE_CONTAMINANT_PEAK,
(int)i, (int)resamplingLength);
}
//Cancel.
if (StopFlag)
{
break;
}
//Create XIC.
ClrDataPoints pts = new ClrDataPoints();
for (int j = 0; j < resamplingList.Count; j++)
{
//Cancel.
if (StopFlag)
{
break;
}
pts.addPoint(ms1List[j].getRt(), resamplingList[j].getY(i));
}
//Cancel.
if (StopFlag)
{
pts.clearPoints();
pts.Dispose();
break;
}
//Baseline Subtraction
ClrParameters param = new ClrParameters();
ClrDataPoints baseline = new ClrDataPoints();
ClrPluginCallTool.setXYData(param, pts);
ClrPluginCallTool.setBaseline(param, baseline);
ClrPluginCallTool.setSettingValues(param, spvw);
pfiw.getCall().invoke(param);
//Cancel.
if (StopFlag)
{
param.Dispose();
baseline.clearPoints();
baseline.Dispose();
}
//Resampling baseline.
ClrDataPoints subtracted = new ClrDataPoints();
ResamplingParameter resamplingParam = new ResamplingParameter();
ResamplingCalculation resamplingCalc = new ResamplingCalculation(resamplingParam);
resamplingParam.ResamplingMode = ResamplingParameter.SamplingMode.FIRST;
resamplingParam.Interpolation = _resamplingParam.Interpolation;
resamplingParam.AddXYData(pts);
resamplingParam.AddXYData(baseline);
resamplingCalc.Execute();
ClrDataPoints resampledBaseline = resamplingCalc.Result.getResultData(1);
for (uint j = 0; j < resampledBaseline.getLength(); j++)
{
double intensity = Math.Max(pts.getY(j) - resampledBaseline.getY(j), 0);
subtracted.addPoint(pts.getX(j), intensity);
}
// Countermeasure to OutOfBoundsException.
if (i < int.MaxValue)
{
subtractLowerXICList[i] = subtracted;
}
else if (int.MaxValue < i && i < (uint)int.MaxValue * 2)
{
subtractHigherXICList[i - int.MaxValue] = subtracted;
}
else
{
subtractHighestXICList = subtracted;
}
resamplingParam.ClearXYDataList();
resamplingCalc.Result.ClearXYDataList();
}
return(!StopFlag);
}
/// <summary>
/// Graph ChangeSelectItem event handler
/// </summary>
/// <param name="sender">sender</param>
/// <param name="e">event args</param>
private void Graph_ChangeSelectItem(object sender, UserControlSimcaGraph.SelectItemEventArgs e)
{
if (!_checkBoxSyncQuant.Checked)
{
return;
}
bool activeTab = false;
switch ((TAB_ID)_tabControlPlot.SelectedIndex)
{
case TAB_ID.SCORE_PLOT:
if ((UserControlSimcaGraph)sender == _graphScore)
{
activeTab = true;
}
break;
case TAB_ID.LOADING_PLOT:
if ((UserControlSimcaGraph)sender == _graphLoading)
{
activeTab = true;
}
break;
case TAB_ID.S_PLOT:
if ((UserControlSimcaGraph)sender == _graphSPlot)
{
activeTab = true;
}
break;
default:
break;
}
if (!activeTab)
{
return;
}
// Renewal of an emphasis display
IdentificationManagerWrapper managerWrapper = IdentificationManagerWrapper.getInstance();
managerWrapper.clearFocusedPeaks(); // clear
if (e.SelectItemArray != null)
{
foreach (int peakId in e.SelectItemArray)
{
managerWrapper.addFocusedPeak(peakId);
if (e.DoubleClick)
{
managerWrapper.activatePeak(peakId);
}
}
}
ClrPluginCallTool.refresh();
}
