//建立Ms1Scan的索引
new private TempIndex parseMS1(Spectrum spectrum, int index)
{
TempIndex ms1 = new TempIndex();
ms1.level = 1;
ms1.num = index;
if (spectrum.scanList.scans.Count != 1)
{
return(ms1);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms1.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms1.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms1.rt = parseRT(scan);
ms1.tic = parseTIC(spectrum);
if (msType == null)
{
parseMsType(spectrum);
}
if (polarity == null)
{
parsePolarity(spectrum);
}
return(ms1);
}
protected TempIndex parseMS2(Spectrum spectrum, int index, int parentIndex)
{
TempIndex ms2 = new TempIndex();
ms2.level = 2;
ms2.pNum = parentIndex;
ms2.num = index;
try
{
double mz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
double lowerOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_lower_offset);
double upperOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_upper_offset);
int charge = getPrecursorCharge(spectrum);
ms2.charge = charge;
ms2.mz = mz;
ms2.mzStart = mz - lowerOffset;
ms2.mzEnd = mz + upperOffset;
ms2.wid = lowerOffset + upperOffset;
}
catch (Exception e)
{
jobInfo.log("ERROR:SpectrumIndex:" + spectrum.index)
.log("ERROR:SpectrumId:" + spectrum.id)
.log("ERROR: mz:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value)
.log("ERROR: lowerOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value)
.log("ERROR: upperOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value);
throw e;
}
if (activator == null)
{
parseActivator(spectrum.precursors[0].activation);
}
if (spectrum.scanList.scans.Count != 1)
{
return(ms2);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms2.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms2.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms2.rt = parseRT(scan);
ms2.tic = parseTIC(spectrum);
return(ms2);
}
private void scan(int i)
{
Spectrum spectrum = spectrumList.spectrum(i, true);
//忽略所有MS1的谱图
if (spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
return;
}
double targetMz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
ArrayList ms2List = null;
if (rangeMap.Contains(targetMz))
{
ms2List = (ArrayList)ms2Map[targetMz];
}
else
{
double mz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
double lowerOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_lower_offset);
double upperOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_upper_offset);
WindowRange range = new WindowRange(mz - lowerOffset, mz + upperOffset, mz);
BlockIndex addIndex = new BlockIndex();
addIndex.setWindowRange(range);
rangeMap.Add(targetMz, addIndex);
ms2Map.Add(targetMz, ArrayList.Synchronized(new ArrayList()));
ms2List = (ArrayList)ms2Map[targetMz];
}
if (spectrum.scanList.scans.Count != 1)
{
return;
}
try
{
TempScan ts = new TempScan(i, parseRT(spectrum.scanList.scans[0]), parseTIC(spectrum));
if (jobInfo.jobParams.includeCV)
{
ts.cvs = CV.trans(spectrum);
}
compress(spectrum, ts);
ms2List.Add(ts);
}
catch (Exception exception)
{
jobInfo.log(exception.Message);
return;
}
}
//建立Ms2Scan的索引
new private TempIndex parseMS2(Spectrum spectrum, int index, int parentIndex)
{
TempIndex ms2 = new TempIndex();
ms2.level = 2;
ms2.pNum = parentIndex;
ms2.num = index;
try
{
float mz = (float)double.Parse(spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value.ToString());
//兼容Agilent的DDA数据格式中可能出现的lower offset和upper offset为空的情况
string lowerOffsetStr = spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value.ToString();
string upperOffsetStr = spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value.ToString();
float lowerOffset = 0f;
if (!lowerOffsetStr.IsNullOrEmpty())
{
lowerOffset = (float)double.Parse(lowerOffsetStr);
}
float upperOffset = 0f;
if (!upperOffsetStr.IsNullOrEmpty())
{
upperOffset = (float)double.Parse(upperOffsetStr);
}
ms2.charge = getPrecursorCharge(spectrum);
ms2.mz = mz;
ms2.mzStart = mz - lowerOffset;
ms2.mzEnd = mz + upperOffset;
ms2.wid = lowerOffset + upperOffset;
}
catch (Exception e)
{
jobInfo.log("ERROR:SpectrumIndex:" + spectrum.index)
.log("ERROR:SpectrumId:" + spectrum.id)
.log("ERROR: mz:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_target_m_z).value)
.log("ERROR: lowerOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_lower_offset).value)
.log("ERROR: upperOffset:" + spectrum.precursors[0].isolationWindow
.cvParamChild(CVID.MS_isolation_window_upper_offset).value);
throw e;
}
if (spectrum.scanList.scans.Count != 1)
{
return(ms2);
}
Scan scan = spectrum.scanList.scans[0];
if (jobInfo.jobParams.includeCV)
{
ms2.cvList = CV.trans(spectrum);
if (scan.cvParams != null)
{
ms2.cvList.AddRange(CV.trans(scan.cvParams));
}
}
ms2.rt = parseRT(scan);
ms2.tic = parseTIC(spectrum);
if (activator == null)
{
parseActivator(spectrum.precursors[0].activation);
}
return(ms2);
}
