/// <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>
/// Get Spectrum Data(selected by File and Spectrum Name and RT value and Precusor value)
/// </summary>
/// <param name="nameDataListIndex">index number of file name combobox</param>
/// <param name="specName">Spectrum Name(selected combobox or determinded by selected RT and Precusor combobox) </param>
/// <param name="rt">RT value (selected combobox or determinded by selected Spectrum Name combobox) </param>
/// <param name="precusor">Precusor value (selected combobox or determinded by selected Spectrum Name combobox) </param>
/// <returns>SpectrumWrapper</returns>
public SpectrumWrapper GetSpectrumWrapperData(int nameDataListIndex, string specName, string rt, string precusor)
{
string folder = _fileNameDataList[nameDataListIndex].Folder;
string fileName = _fileNameDataList[nameDataListIndex].FileName;
int sampleNum = _fileNameDataList[nameDataListIndex].SampleTabNo;
var pred = new Predicate <SelSpectrum>(x =>
(x.Folder == folder &&
x.FileName == fileName &&
x.SpecName == specName &&
x.RT == rt &&
x.Precusor == precusor &&
x.SampleTabNo == sampleNum));
int find = _selSpectrum.FindIndex(pred);
// error
if (find < 0)
{
return(null);
}
string tfp = Path.Combine(folder, fileName);
FileFactoryWrapper factory = FileFactoryWrapper.getInstance();
SampleSetWrapper set = factory.openFile(tfp);
SampleWrapper sample = set.getSample((uint)_selSpectrum[find].SampleTabNo - 1);
sample.openSample();
DataGroupNodeWrapper targetNode = sample.getRootDataGroupNode();
int listcount = _selSpectrum[find].DescendantList.Count;
for (int cnt = 0; cnt < listcount; cnt++)
{
targetNode = targetNode.getChild(_selSpectrum[find].DescendantList[cnt]);
}
SpectrumWrapper spec = targetNode.getSpectrum(_selSpectrum[find].SpecNum);
var predfn = new Predicate <FileManage>(x => (x.FileName == tfp));
find = _listFileManage.FindIndex(predfn);
if (find < 0)
{
FileManage fmanage;
fmanage.FileFactory = factory;
fmanage.SampleSet = set;
fmanage.FileName = tfp;
_listFileManage.Add(fmanage);
}
// Not closed File,because stocked spectrum data read from file not used when file is closed
return(spec);
}
/// <summary>
/// Read MSB Data File
/// </summary>
/// <param name="filepath">MSB file Path</param>
/// <returns></returns>
public int ReadMSBData(string filepath)
{
string folder = Path.GetDirectoryName(filepath);
string fileName = Path.GetFileName(filepath);
var pred = new Predicate <SelSpectrum>(x => (x.Folder == folder && x.FileName == fileName));
int find = _selSpectrum.FindIndex(pred);
if (find >= 0)
{
return(-1);
}
FileFactoryWrapper factory = FileFactoryWrapper.getInstance();
SampleSetWrapper set = factory.openFile(filepath);
if (set == null)
{
return(-1);
}
for (int num = 0; num < set.getNumberOfSamples(); num++)
{
FileData _tmpFileNameData = new FileData(num + 1, folder, fileName);
SampleWrapper sample = set.getSample((uint)num);
sample.openSample();
Debug.WriteLine(sample.getSampleSet().getFileName());
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
List <ReadSpectrumData> listReadSpec = new List <ReadSpectrumData>();
List <uint> DescendantList = new List <uint>();
ReadSpectrum(root, 0, 0, ref listReadSpec, DescendantList);
for (uint n = 0; n < listReadSpec.Count; n++)
{
SpectrumWrapper spec = listReadSpec[(int)n].Spec;
string precursor = "";
if (spec.getMsStage() == 1)
{
precursor = "-----";
}
else if (spec.getMsStage() == 2)
{
precursor = spec.getPrecursor().ToString();
}
else
{
precursor = "\"" + spec.getPrecursor(1).ToString();
for (int pcnt = 2; pcnt < spec.getMsStage(); pcnt++)
{
precursor += ("," + spec.getPrecursor(pcnt).ToString());
}
precursor += "\"";
}
SelSpectrum selSpec = new SelSpectrum(num + 1,
folder, fileName, spec.getName(), spec.getRt().ToString(), precursor,
n, listReadSpec[(int)n].DescendantList, listReadSpec[(int)n].Descendant,
listReadSpec[(int)n].ChildNum, listReadSpec[(int)n].SpecNum);
selSpec.TotalSpecNum = n;
_selSpectrum.Add(selSpec);
SpectrumData tmpSpectrumNameData = new SpectrumData();
tmpSpectrumNameData.SpectrumName = spec.getName();
tmpSpectrumNameData.RT = spec.getRt();
if (spec.getMsStage() == 1)
{
tmpSpectrumNameData.Precusor = "-----";
}
else if (spec.getMsStage() == 2)
{
tmpSpectrumNameData.Precusor = spec.getPrecursor().ToString();
}
else
{
tmpSpectrumNameData.Precusor = "\"" + spec.getPrecursor(1).ToString();;
for (int pcnt = 2; pcnt < spec.getMsStage(); pcnt++)
{
tmpSpectrumNameData.Precusor = tmpSpectrumNameData.Precusor + "," + spec.getPrecursor(pcnt).ToString();
}
tmpSpectrumNameData.Precusor = tmpSpectrumNameData.Precusor + "\"";
}
_tmpFileNameData.SpectrumNameDataList.Add(tmpSpectrumNameData);
_tmpFileNameData.SpectrumNameList.Add(spec.getName());
}
_fileNameDataList.Add(_tmpFileNameData);
_bindFileName.Add("[" + _tmpFileNameData.SampleTabNo.ToString() + "] " + _tmpFileNameData.FileName);
_bindFileNameLastRow.Insert(_bindFileNameLastRow.Count - 1, "["
+ _tmpFileNameData.SampleTabNo.ToString() + "] " + _tmpFileNameData.FileName);
}
factory.closeFile(set);
return(0);
}