protected float parseRT(Scan scan)
{
CVParam cv = scan.cvParamChild(CVID.MS_scan_start_time);
float time = float.Parse(cv.value.ToString());
rtUnit = cv.unitsName;
return(Convert.ToSingle(Math.Round(time, 5)));
}
public CV(CVParam param)
{
this.cvid = ((int)param.cvid) + ":" + param.name;
this.value = param.value.ToString();
int unitsId = (int)param.units;
if (unitsId != -1)
{
this.units = (int)param.units + ":" + param.unitsName;
}
}
/// <summary>
/// add precursor and non-matched annotations
/// </summary>
public override void AddAnnotations(pwiz.MSGraph.MSGraphPane graphPane, Graphics g, pwiz.MSGraph.MSPointList pointList, ZedGraph.GraphObjList annotations)
{
base.AddAnnotations(graphPane, g, pointList, annotations);
//using( Spectrum element = Element )
{
foreach (Precursor p in Element.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
double precursorMz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
int precursorCharge = 0;
CVParam precursorChargeParam = si.cvParam(CVID.MS_charge_state);
if (precursorChargeParam.empty())
{
precursorChargeParam = si.cvParam(CVID.MS_possible_charge_state);
}
if (!precursorChargeParam.empty())
{
precursorCharge = (int)precursorChargeParam.value;
}
double stickLength = 0.1;
ZedGraph.LineObj stickOverlay = new ZedGraph.LineObj(precursorMz, 1, precursorMz, stickLength);
stickOverlay.Location.CoordinateFrame = ZedGraph.CoordType.XScaleYChartFraction;
stickOverlay.Line.Width = 3;
stickOverlay.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
stickOverlay.Line.Color = Color.Green;
annotations.Add(stickOverlay);
// Create a text label from the X data value
string precursorLabel;
if (precursorCharge > 0)
{
precursorLabel = String.Format("{0}\n(+{1} precursor)", precursorMz.ToString("f3"), precursorCharge);
}
else
{
precursorLabel = String.Format("{0}\n(precursor of unknown charge)", precursorMz.ToString("f3"));
}
ZedGraph.TextObj text = new ZedGraph.TextObj(precursorLabel, precursorMz, stickLength,
ZedGraph.CoordType.XScaleYChartFraction, ZedGraph.AlignH.Center, ZedGraph.AlignV.Bottom);
text.ZOrder = ZedGraph.ZOrder.A_InFront;
text.FontSpec.FontColor = stickOverlay.Line.Color;
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
//text.FontSpec.Fill = new Fill( Color.FromArgb( 100, Color.White ) );
text.FontSpec.Angle = 0;
annotations.Add(text);
}
}
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Charge;
hashCode = (hashCode * 397) ^ (FragmentArrays != null ? FragmentArrays.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Index != null ? Index.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParam != null ? CVParam.GetHashCode() : 0);
return(hashCode);
}
}
public override Spectrum spectrum(int index, bool getBinaryData)
{
Spectrum s = base.spectrum(index, true);
if (s.cvParam(CVID.MS_MSn_spectrum).empty() ||
(int)s.cvParam(CVID.MS_ms_level).value == 1)
{
if (!getBinaryData)
{
s.binaryDataArrays.Clear();
}
return(s);
}
PrecursorList pl = s.precursors;
BinaryData mzArray = s.getMZArray().data;
BinaryData intensityArray = s.getIntensityArray().data;
PointDataMap <double> mziMap = new PointDataMap <double>();
for (int i = 0; i < (int)s.defaultArrayLength; ++i)
{
mziMap.Insert(mzArray[i], intensityArray[i]);
}
Set <double> pointsToRemove = new Set <double>();
foreach (Precursor p in pl)
{
foreach (SelectedIon si in p.selectedIons)
{
double mz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
PointDataMap <double> .Enumerator itr = mziMap.LowerBound(mz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - mz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
CVParam chargeParam = si.cvParam(CVID.MS_charge_state);
if (!chargeParam.empty())
{
int z = (int)chargeParam.value;
for (int i = 1; i < z; ++i)
{
double strippedMz = (mz * z) / (z - i);
itr = mziMap.LowerBound(strippedMz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - strippedMz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
}
}
}
}
if (getBinaryData)
{
mzArray.Clear();
intensityArray.Clear();
foreach (PointDataMap <double> .MapPair pair in mziMap)
{
if (pointsToRemove.Contains(pair.Key))
{
continue;
}
mzArray.Add(pair.Key);
intensityArray.Add(pair.Value);
}
s.defaultArrayLength = (ulong)mzArray.Count;
}
else
{
s.binaryDataArrays.Clear();
s.defaultArrayLength -= (ulong)pointsToRemove.Count;
}
return(s);
}
public SpectrumList_Preexisting_ListViewItem(ProcessingMethod method)
: base(method.cvParamChild(CVID.MS_data_processing_action).name)
{
methodParam = method.cvParamChild(CVID.MS_data_processing_action);
}
private void gridView_ShowCellToolTip(DataGridViewCell cell)
{
MassSpectrum spectrum = cell.OwningRow.Tag as MassSpectrum;
Spectrum s = spectrum.Element;
TreeViewForm treeViewForm = new TreeViewForm(spectrum);
TreeView tv = treeViewForm.TreeView;
if (gridView.Columns[cell.ColumnIndex].Name == "PrecursorInfo")
{
treeViewForm.Text = "Precursor Details";
if (s.precursors.Count == 0)
{
tv.Nodes.Add("No precursor information available.");
}
else
{
foreach (Precursor p in s.precursors)
{
string pNodeText = "Precursor scan";
if (p.sourceFile != null && p.externalSpectrumID.Length > 0)
{
pNodeText += String.Format(": {0}:{1}", p.sourceFile.name, p.externalSpectrumID);
}
else if (p.spectrumID.Length > 0)
{
pNodeText += String.Format(": {0}", p.spectrumID);
}
TreeNode pNode = tv.Nodes.Add(pNodeText);
addParamsToTreeNode(p as ParamContainer, pNode);
if (p.selectedIons.Count == 0)
{
pNode.Nodes.Add("No selected ion list available.");
}
else
{
foreach (SelectedIon si in p.selectedIons)
{
TreeNode siNode = pNode.Nodes.Add("Selected ion");
//siNode.ToolTipText = new CVTermInfo(CVID.MS_selected_ion); // not yet in CV
addParamsToTreeNode(si as ParamContainer, siNode);
}
}
if (p.activation.empty())
{
pNode.Nodes.Add("No activation details available.");
}
else
{
TreeNode actNode = pNode.Nodes.Add("Activation");
addParamsToTreeNode(p.activation as ParamContainer, actNode);
}
if (p.isolationWindow.empty())
{
pNode.Nodes.Add("No isolation window details available.");
}
else
{
TreeNode iwNode = pNode.Nodes.Add("Isolation Window");
addParamsToTreeNode(p.isolationWindow as ParamContainer, iwNode);
}
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "ScanInfo")
{
treeViewForm.Text = "Scan Configuration Details";
if (s.scanList.empty())
{
tv.Nodes.Add("No scan details available.");
}
else
{
TreeNode slNode = tv.Nodes.Add("Scan List");
addParamsToTreeNode(s.scanList as ParamContainer, slNode);
foreach (Scan scan in s.scanList.scans)
{
TreeNode scanNode = slNode.Nodes.Add("Acquisition");
addParamsToTreeNode(scan as ParamContainer, scanNode);
foreach (ScanWindow sw in scan.scanWindows)
{
TreeNode swNode = scanNode.Nodes.Add("Scan Window");
addParamsToTreeNode(sw as ParamContainer, swNode);
}
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "InstrumentConfigurationID")
{
treeViewForm.Text = "Instrument Configuration Details";
InstrumentConfiguration ic = s.scanList.scans[0].instrumentConfiguration;
if (ic == null || ic.empty())
{
tv.Nodes.Add("No instrument configuration details available.");
}
else
{
TreeNode icNode = tv.Nodes.Add(String.Format("Instrument Configuration ({0})", ic.id));
addParamsToTreeNode(ic as ParamContainer, icNode);
if (ic.componentList.Count == 0)
{
icNode.Nodes.Add("No component list available.");
}
else
{
TreeNode clNode = icNode.Nodes.Add("Component List");
foreach (pwiz.CLI.msdata.Component c in ic.componentList)
{
string cNodeText;
switch (c.type)
{
case ComponentType.ComponentType_Source:
cNodeText = "Source";
break;
case ComponentType.ComponentType_Analyzer:
cNodeText = "Analyzer";
break;
default:
case ComponentType.ComponentType_Detector:
cNodeText = "Detector";
break;
}
TreeNode cNode = clNode.Nodes.Add(cNodeText);
addParamsToTreeNode(c as ParamContainer, cNode);
}
}
Software sw = ic.software;
if (sw == null || sw.empty())
{
icNode.Nodes.Add("No software details available.");
}
else
{
TreeNode swNode = icNode.Nodes.Add(String.Format("Software ({0})", sw.id));
CVParam softwareParam = sw.cvParamChild(CVID.MS_software);
TreeNode swNameNode = swNode.Nodes.Add("Name: " + softwareParam.name);
swNameNode.ToolTipText = new CVTermInfo(softwareParam.cvid).def;
swNode.Nodes.Add("Version: " + sw.version);
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "DataProcessing")
{
treeViewForm.Text = "Data Processing Details";
DataProcessing dp = s.dataProcessing;
if (dp == null || dp.empty())
{
tv.Nodes.Add("No data processing details available.");
}
else
{
TreeNode dpNode = tv.Nodes.Add(String.Format("Data Processing ({0})", dp.id));
if (dp.processingMethods.Count == 0)
{
dpNode.Nodes.Add("No component list available.");
}
else
{
TreeNode pmNode = dpNode.Nodes.Add("Processing Methods");
foreach (ProcessingMethod pm in dp.processingMethods)
{
addParamsToTreeNode(pm as ParamContainer, pmNode);
}
}
}
}
else
{
return;
}
tv.ExpandAll();
treeViewForm.StartPosition = FormStartPosition.CenterParent;
treeViewForm.AutoSize = true;
//treeViewForm.DoAutoSize();
treeViewForm.Show(this.DockPanel);
//leaveTimer.Start();
this.Focus();
}
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);
}
/// <summary>
/// Handle the cvParam element
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single "cvParam" element</param>
private CVParam ReadCvParam(XmlReader reader)
{
reader.MoveToContent();
CVParam cvParam = new CVParam();
cvParam.Accession = reader.GetAttribute("accession");
cvParam.CVRef = reader.GetAttribute("cvRef");
cvParam.Name = reader.GetAttribute("name");
cvParam.Value = reader.GetAttribute("value");
cvParam.UnitAccession = reader.GetAttribute("unitAccession");
cvParam.UnitCVRef = reader.GetAttribute("unitCVRef");
cvParam.UnitName = reader.GetAttribute("unitName");
reader.Close();
return cvParam;
}
