public void Add(MassSpectrum spectrum)
{
SpectrumDataSet.SpectrumTableRow row = spectrumDataSet.SpectrumTable.NewSpectrumTableRow();
row.Id = spectrum.Id;
if (nativeIdFormat != CVID.CVID_Unknown)
{
gridView.Columns["Id"].Visible = false;
string[] nameValuePairs = spectrum.Id.Split(" ".ToCharArray());
foreach (string nvp in nameValuePairs)
{
string[] nameValuePair = nvp.Split("=".ToCharArray());
row[nameValuePair[0]] = nameValuePair[1];
}
}
row.Index = spectrum.Index;
updateRow(row, spectrum);
spectrumDataSet.SpectrumTable.AddSpectrumTableRow(row);
//int rowIndex = gridView.Rows.Add();
//gridView.Rows[rowIndex].Tag = spectrum;
spectrum.Tag = this;
if (spectrum.Element.spotID.Length > 0)
{
gridView.Columns["SpotId"].Visible = true;
}
//UpdateRow( rowIndex );
}
public void Add(MassSpectrum spectrum)
{
SpectrumDataSet.SpectrumTableRow row = spectrumDataSet.SpectrumTable.NewSpectrumTableRow();
row.Id = spectrum.Id;
if (nativeIdFormat != CVID.CVID_Unknown)
{
gridView.Columns["Id"].Visible = false;
// guard against case where input is mzXML which
// is identified as, say, Agilent-derived, but
// which uses "scan" (as mzXML must) instead
// of the Agilent "scanID" (as this mzML-centric code expects)
bool foundit = false;
string[] nameValuePairs = spectrum.Id.Split(' ');
foreach (string nvp in nameValuePairs)
{
string[] nameValuePair = nvp.Split('=');
if (row.Table.Columns.Contains(nameValuePair[0]))
{
row[nameValuePair[0]] = nameValuePair[1];
foundit = true;
}
}
if (!foundit)
{
// mismatch between nativeID format and actual (probably mzXML) format
// better to show an ill-fit match - eg "scan" (mzXML) and "scanID" (Agilent)
// than no info at all
string nativeIdDefinition = new CVTermInfo(nativeIdFormat).def;
string[] idPair = nativeIdDefinition.Split('=');
if (row.Table.Columns.Contains(idPair[0]))
{
string[] valPair = spectrum.Id.Split('=');
row[idPair[0]] = (valPair.Length > 1) ? valPair[1] : spectrum.Id;
foundit = true;
}
}
}
row.Index = spectrum.Index;
updateRow(row, spectrum);
spectrumDataSet.SpectrumTable.AddSpectrumTableRow(row);
//int rowIndex = gridView.Rows.Add();
//gridView.Rows[rowIndex].Tag = spectrum;
spectrum.Tag = this;
if (spectrum.Element.spotID.Length > 0)
{
gridView.Columns["SpotId"].Visible = true;
}
//UpdateRow( rowIndex );
}
public void UpdateRow(int rowIndex, SpectrumList spectrumList)
{
SpectrumDataSet.SpectrumTableRow row = (spectraSource[rowIndex] as DataRowView).Row as SpectrumDataSet.SpectrumTableRow;
if (spectrumList != null)
{
this.spectrumList[row.Index].SpectrumList = spectrumList;
updateRow(row, this.spectrumList[row.Index]);
//dp = rowSpectrum.DataProcessing;
//row.Tag = rowSpectrum = new MassSpectrum( rowSpectrum, s );
//rowSpectrum.DataProcessing = dp;
}
else
{
updateRow(row, this.spectrumList[row.Index]);
//s = rowSpectrum.Element;
//dp = rowSpectrum.DataProcessing;
}
}
public void updateRow(SpectrumDataSet.SpectrumTableRow row, MassSpectrum spectrum)
{
spectrumList[spectrum.Index] = spectrum;
Spectrum s = spectrum.Element; //GetElement(false);
DataProcessing dp = spectrum.DataProcessing;
Scan scan = null;
InstrumentConfiguration ic = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
ic = scan.instrumentConfiguration;
}
if (dp == null)
{
dp = s.dataProcessing;
}
CVParam param;
param = s.cvParam(CVID.MS_ms_level);
row.MsLevel = !param.empty() ? (int)param.value : 0;
param = scan != null?scan.cvParam(CVID.MS_scan_start_time) : new CVParam();
row.ScanTime = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_m_z);
row.BasePeakMz = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_intensity);
row.BasePeakIntensity = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_total_ion_current);
row.TotalIonCurrent = !param.empty() ? (double)param.value : 0;
var precursorInfo = new StringBuilder();
var isolationWindows = new StringBuilder();
if (row.MsLevel == 1 || s.precursors.Count == 0)
{
precursorInfo.Append("n/a");
isolationWindows.Append("n/a");
}
else
{
foreach (Precursor p in s.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
if (precursorInfo.Length > 0)
{
precursorInfo.Append(",");
}
precursorInfo.AppendFormat("{0:G8}", (double)si.cvParam(CVID.MS_selected_ion_m_z).value);
}
var iw = p.isolationWindow;
CVParam isolationTarget = iw.cvParam(CVID.MS_isolation_window_target_m_z);
if (!isolationTarget.empty())
{
double iwMz = (double)isolationTarget.value;
if (isolationWindows.Length > 0)
{
isolationWindows.Append(",");
}
CVParam lowerOffset = iw.cvParam(CVID.MS_isolation_window_lower_offset);
CVParam upperOffset = iw.cvParam(CVID.MS_isolation_window_upper_offset);
if (lowerOffset.empty() || upperOffset.empty())
{
isolationWindows.AppendFormat("{0:G8}", iwMz);
}
else
{
isolationWindows.AppendFormat("[{0:G8}-{1:G8}]", iwMz - (double)lowerOffset.value, iwMz + (double)upperOffset.value);
}
}
}
}
if (precursorInfo.Length == 0)
{
precursorInfo.Append("unknown");
}
row.PrecursorInfo = precursorInfo.ToString();
if (isolationWindows.Length == 0)
{
isolationWindows.Append("unknown");
}
row.IsolationWindows = isolationWindows.ToString();
StringBuilder scanInfo = new StringBuilder();
foreach (Scan scan2 in s.scanList.scans)
{
if (scan2.scanWindows.Count > 0)
{
foreach (ScanWindow sw in scan2.scanWindows)
{
if (scanInfo.Length > 0)
{
scanInfo.Append(",");
}
scanInfo.AppendFormat("[{0:G8}-{1:G8}]",
(double)sw.cvParam(CVID.MS_scan_window_lower_limit).value,
(double)sw.cvParam(CVID.MS_scan_window_upper_limit).value);
}
}
}
if (scanInfo.Length == 0)
{
scanInfo.Append("unknown");
}
row.ScanInfo = scanInfo.ToString();
row.IonMobility = scan != null ? (double)scan.cvParam(CVID.MS_ion_mobility_drift_time).value : 0;
if (row.IonMobility == 0 && scan != null)
{
row.IonMobility = (double)scan.cvParam(CVID.MS_inverse_reduced_ion_mobility).value;
if (row.IonMobility == 0)
{
// Early version of drift time info, before official CV params
var userparam = scan.userParam("drift time");
if (!userparam.empty())
{
row.IonMobility = userparam.timeInSeconds() * 1000.0;
}
}
}
row.SpotId = s.spotID;
row.SpectrumType = s.cvParamChild(CVID.MS_spectrum_type).name;
row.DataPoints = s.defaultArrayLength;
row.IcId = (ic == null || ic.id.Length == 0 ? "unknown" : ic.id);
row.DpId = (dp == null || dp.id.Length == 0 ? "unknown" : dp.id);
}
public void updateRow(SpectrumDataSet.SpectrumTableRow row, MassSpectrum spectrum)
{
spectrumList[spectrum.Index] = spectrum;
Spectrum s = spectrum.Element; //GetElement(false);
DataProcessing dp = spectrum.DataProcessing;
Scan scan = null;
InstrumentConfiguration ic = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
ic = scan.instrumentConfiguration;
}
if (dp == null)
{
dp = s.dataProcessing;
}
CVParam param;
param = s.cvParam(CVID.MS_ms_level);
row.MsLevel = !param.empty() ? (int)param.value : 0;
param = scan != null?scan.cvParam(CVID.MS_scan_start_time) : new CVParam();
row.ScanTime = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_m_z);
row.BasePeakMz = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_intensity);
row.BasePeakIntensity = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_total_ion_current);
row.TotalIonCurrent = !param.empty() ? (double)param.value : 0;
StringBuilder precursorInfo = new StringBuilder();
if (row.MsLevel == 1 || s.precursors.Count == 0)
{
precursorInfo.Append("n/a");
}
else
{
foreach (Precursor p in s.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
if (precursorInfo.Length > 0)
{
precursorInfo.Append(",");
}
precursorInfo.Append((double)si.cvParam(CVID.MS_selected_ion_m_z).value);
}
}
}
if (precursorInfo.Length == 0)
{
precursorInfo.Append("unknown");
}
row.PrecursorInfo = precursorInfo.ToString();
StringBuilder scanInfo = new StringBuilder();
foreach (Scan scan2 in s.scanList.scans)
{
if (scan2.scanWindows.Count > 0)
{
foreach (ScanWindow sw in scan2.scanWindows)
{
if (scanInfo.Length > 0)
{
scanInfo.Append(",");
}
scanInfo.AppendFormat("[{0}-{1}]",
(double)sw.cvParam(CVID.MS_scan_window_lower_limit).value,
(double)sw.cvParam(CVID.MS_scan_window_upper_limit).value);
}
}
}
if (scanInfo.Length == 0)
{
scanInfo.Append("unknown");
}
row.ScanInfo = scanInfo.ToString();
row.SpotId = s.spotID;
row.SpectrumType = s.cvParamChild(CVID.MS_spectrum_type).name;
row.DataPoints = s.defaultArrayLength;
row.IcId = (ic == null || ic.id.Length == 0 ? "unknown" : ic.id);
row.DpId = (dp == null || dp.id.Length == 0 ? "unknown" : dp.id);
}
