/// <summary>
/// Add result data points(added data is clone).
/// </summary>
/// <param name="points"></param>
public void AddResult(ClrDataPoints points, SpectrumWrapper baseSpectrum, string name)
{
SpectrumResampling spectrum = new SpectrumResampling(baseSpectrum.getSample(), name);
spectrum.SetData(points);
_list.Add(spectrum);
}
SpectrumWrapper InitChannel(int channel, int spectrumSize, Transform parent)
{
SpectrumWrapper result = new SpectrumWrapper();
result.channel = channel;
result.spectrumBuff = new float[spectrumSize];
result.transforms = new Transform[spectrumSize];
result.currentSpectrums = new NativeArray <float>(spectrumSize, Allocator.Persistent);
result.prevSpectrums = new NativeArray <float>(spectrumSize, Allocator.Persistent);
result.origins = new NativeArray <Vector3>(spectrumSize, Allocator.Persistent);
for (int index = 0;
index < spectrumSize;
++index)
{
GameObject obj = Object.Instantiate(cubePrefab);
SpiralPos pos = Utils.GetSpiralPos(index);
obj.transform.parent = parent;
obj.transform.localPosition = new Vector3(pos.x, 0, pos.z);
result.transforms[index] = obj.transform;
result.origins[index] = obj.transform.localPosition;
}
result.transformsAccess = new TransformAccessArray(result.transforms);
return(result);
}
/// <summary>
/// Read Spectrum
/// </summary>
/// <param name="node">DataGroupNodeWrapper</param>
/// <param name="descendant">descendant of node(child or grandchild.....</param>
/// <param name="childNum">child number</param>
/// <param name="listReadSpec">ReadSpectrumData List</param>
/// <param name="descendantList">descendant List</param>
private void ReadSpectrum(DataGroupNodeWrapper node, uint descendant,
uint childNum, ref List <ReadSpectrumData> listReadSpec, List <uint> descendantList)
{
uint numSpec = node.getNumberOfSpectra();
for (uint n = 0; n < numSpec; n++)
{
SpectrumWrapper spec = node.getSpectrum(n);
ReadSpectrumData tmpData = new ReadSpectrumData(spec, descendantList, descendant, childNum, n);
listReadSpec.Add(tmpData);
}
uint numChild = node.getNumberOfChildren();
for (uint n = 0; n < numChild; n++)
{
DataGroupNodeWrapper child = node.getChild(n);
if (child != null)
{
List <uint> tmpDescendant = new List <uint>();
for (int cnt = 0; cnt < descendantList.Count; cnt++)
{
tmpDescendant.Add(descendantList[cnt]);
}
tmpDescendant.Add(n);
ReadSpectrum(child, descendant + 1, n, ref listReadSpec, tmpDescendant);
}
else
{
Debug.Assert(false);
}
}
}
void Start()
{
int spectrumSize = settings.spectrumSize;
left = InitChannel(0, spectrumSize, parentLeft);
right = InitChannel(1, spectrumSize, parentRight);
}
/// <summary>
/// Initialize ReadSpectrumData structure.
/// </summary>
/// <param name="spec">Spectrum is read from file</param>
/// <param name="descendantList">Descendant List</param>
/// <param name="descendant">Descendant</param>
/// <param name="childNum">Child number</param>
/// <param name="specNum">Spectrum number</param>
internal ReadSpectrumData(SpectrumWrapper spec, List <uint> descendantList, uint descendant, uint childNum, uint specNum)
{
Spec = spec;
DescendantList = descendantList;
Descendant = descendant;
ChildNum = childNum;
SpecNum = specNum;
}
/// <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>
/// 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>
/// Read Spectrum(only ms1)
/// </summary>
/// <param name="node">DataGroupNodeWrapper</param>
/// <param name="listReadSpec">SpectrumWrapper List</param>
private void ReadSpectrum(DataGroupNodeWrapper node, ref List <SpectrumWrapper> listReadSpec)
{
uint numSpec = node.getNumberOfSpectra();
for (uint n = 0; n < numSpec; n++)
{
SpectrumWrapper spec = node.getSpectrum(n);
if (spec.getMsStage() == 1)
{
listReadSpec.Add(spec);
}
}
uint numChild = node.getNumberOfChildren();
for (uint n = 0; n < numChild; n++)
{
DataGroupNodeWrapper child = node.getChild(n);
if (child != null)
{
ReadSpectrum(child, ref listReadSpec);
}
}
}
/// <summary>
/// Add result data points.
/// </summary>
/// <param name="points"></param>
public void AddResult(ClrDataPoints points, SpectrumWrapper baseSpectrum)
{
_ptsList.Add(points);
_specList.Add(baseSpectrum);
}
/// <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);
}
/// <summary>
/// add spec to SpectrumWrapper list
/// </summary>
/// <param name="spec">SpectrumWrapper</param>
public void AddSpecData(SpectrumWrapper spec)
{
_specList.Add(spec);
}