/// <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>
/// Define of Specified option.
/// (This function is not called normally. Please reference design document Page 37.)
/// </summary>
/// <param name="clrParams"></param>
/// <returns></returns>
public ClrVariant BatPitchSpecified(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;
return(ret);
}
/// <summary>
/// Display Remove Contaminant Peak Dialog
/// </summary>
public static void DisplayDlgRemovContamiPeak(ClrVariant clrVar)
{
if (_manager._dlgRemovContamiPeak == null)
{
_manager._dlgRemovContamiPeak = new RemoveContaminantPeakDialog(clrVar);
_manager._dlgRemovContamiPeak.DisplayClosed += _manager.RemoveContaminantPeakDialog_DisplayClosed;
_manager._dlgRemovContamiPeak.Show();
}
else
{
_manager._dlgRemovContamiPeak.UpdateParam(clrVar);
_manager._dlgRemovContamiPeak.Activate();
}
}
/// <summary>
/// Display Spectrum Calculation Dialog
/// </summary>
public static void DisplayDlgSpecCalc(ClrVariant clrVar)
{
if (_manager._dlgSpecCalc == null)
{
_manager._dlgSpecCalc = new SpectrumCalculationDialog(clrVar);
_manager._dlgSpecCalc.DisplayClosed += _manager.SpectrumCalculationDialog_DisplayClosed;
_manager._dlgSpecCalc.Show();
}
else
{
_manager._dlgSpecCalc.UpdateParam(clrVar);
_manager._dlgSpecCalc.Activate();
}
}
/// <summary>
/// Initializes a new instance of the SpectrumCalculationDialog class
/// </summary>
/// <param name="clrVar">Parameter</param>
public RemoveContaminantPeakDialog(ClrVariant clrVar)
: this()
{
// Set parent window
var current = Process.GetCurrentProcess();
IntPtr hwnd = current.MainWindowHandle;
SetWindowLong(this.Handle, GWL_HWNDPARENT, (UInt32)hwnd);
_clrVar = clrVar;
_baselineParam = new BaselineSubtractionParameter();
_resamplingParam = new ResamplingParameter();
_calculate = new RemoveContaminantPeakCalculation(_clrVar, _baselineParam, _resamplingParam);
}
/**
* @fn kome.clr.ClrVariant SimcaDisplayPluginFunction(kome.clr.ClrParameters* clrParams)
* @brief write this function's brief.
* @param[in] clrParams ClrParameters object
* @return If true, it succeeded (boolean)
*/
/// <summary>
/// Mass++ menu(SimcaDisplay...) execute function
/// </summary>
/// <param name="clrParams">parameters object</param>
/// <returns>This value has no meanings.</returns>
public ClrVariant SimcaDisplayPluginFunction(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;
// Method write Here
SimcaDisplayManager.DisplayMainForm();
ret.obj = true;
return(ret);
}
/// <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);
}
/// <summary>
/// Initializes a new instance of the SpectrumCalculationManager class
/// </summary>
/// <param name="clrVariant">Target of operation</param>
/// <exception cref="ArgumentNullException"></exception>
public RemoveContaminantPeakCalculation(ClrVariant clrVariant,
BaselineSubtractionParameter baselineParam,
ResamplingParameter resamplingParam)
{
//Each arguments validation.
if (clrVariant == null)
{
throw new ArgumentNullException("clrVariant");
}
if (baselineParam == null)
{
throw new ArgumentNullException("baselineParam");
}
if (resamplingParam == null)
{
throw new ArgumentNullException("resamplingParam");
}
_clrVariant = clrVariant;
_resamplingParam = resamplingParam;
_resampling = new ResamplingCalculation(_resamplingParam);
_baselineParam = baselineParam;
}
/// <summary>
/// Batch Resampling Entry Function.
/// </summary>
/// <param name="clrParams"></param>
/// <returns></returns>
public ClrVariant BatResample(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;
// Call Manager
int retValue = SpectrumCalculationManager.CommandlineSpecCalc(clrParams);
if (retValue == 0)
{
ret.obj = true; // Success.
}
else
{
ret.obj = false; // Failure.
}
return(ret);
}
/// <summary>
/// Update parameters.
/// </summary>
/// <param name="plotData">plot data</param>
public void UpdateParam(ClrVariant clrVar)
{
}
/// <summary>
/// Create Baseline subtracted xic.
/// </summary>
/// <param name="pfiw">PluginFunctionItemWrapper</param>
/// <param name="resamplingList">Resampling List</param>
/// <param name="ms1List">MS1 List</param>
/// <param name="spvw">SettingParameterValuesWrapper</param>
/// <param name="subtractLowerXICList">output Subtracted lower XIC List</param>
/// <param name="subtractHigherXICList">output Subtracted Highter XIC List</param>
/// <param name="subtractHighestXICList">output Subtracted Highest XIC List</param>
/// <returns>Result</returns>
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);
ClrVariant baselineResult = pfiw.getCall().invoke(param);
//Cancel.
if (StopFlag)
{
param.Dispose();
baseline.clearPoints();
baseline.Dispose();
break;
}
//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);
}
