public void UpdateProcessing(MassSpectrum spectrum)
{
int newVirtualSize = spectrum.ProcessingList.Count;
if (globalOverrideMode == OverrideMode.Replace)
{
newVirtualSize = globalProcessingListOverride.Count;
}
else
{
newVirtualSize += globalProcessingListOverride.Count;
}
if (processingListView.VirtualListSize != newVirtualSize)
{
processingListView.VirtualListSize = newVirtualSize;
selectIndex(newVirtualSize - 1);
}
if (currentSpectrum != spectrum)
{
currentSpectrum = spectrum;
Text = TabText = "Processing for spectrum " + spectrum.Id;
runOverrideToolStripButton.Text = "Override " + spectrum.Source.Source.Name + " Processing";
processingListView_SelectedIndexChanged(this, EventArgs.Empty);
}
processingListView.Refresh();
}
public void UpdateAnnotations(MassSpectrum spectrum)
{
if (currentSpectrum != spectrum)
{
currentSpectrum = spectrum;
Text = TabText = "Annotations for spectrum " + spectrum.Title;
runOverrideToolStripButton.Text = "Override " + spectrum.Source.Source.Name + " Annotations";
annotationsListView.VirtualListSize = spectrum.AnnotationList.Count;
if (spectrum.AnnotationList.Count > 0)
{
selectIndex(spectrum.AnnotationList.Count - 1);
}
else
{
splitContainer.Panel2.Controls.Clear();
lastSelectedAnnotation = null;
clearing = true;
annotationsListView.SelectedIndices.Clear();
clearing = false;
}
}
annotationsListView.Refresh();
}
public SpectrumList GetProcessingSpectrumList(MassSpectrum spectrum, SpectrumList spectrumList)
{
IList <IProcessing> usedProcessingList = spectrum.ProcessingList.ToList();
if (globalProcessingListOverride.Any())
{
if (replaceToolStripMenuItem.Checked)
{
usedProcessingList = globalProcessingListOverride;
}
else if (beforeToolStripMenuItem.Checked)
{
usedProcessingList.InsertRange(0, globalProcessingListOverride);
}
else if (afterToolStripMenuItem.Checked)
{
usedProcessingList.AddRange(globalProcessingListOverride);
}
}
else if (processingListOverrideBySource.ContainsKey(spectrum.Source))
{
usedProcessingList = processingListOverrideBySource[spectrum.Source];
}
foreach (IProcessing item in usedProcessingList)
{
if (item.Enabled)
{
spectrumList = item.ProcessList(spectrumList);
}
}
return(spectrumList);
}
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 );
}
internal SpectrumListCellDoubleClickEventArgs(SpectrumListForm sender, DataGridViewCellMouseEventArgs e)
: base(e.ColumnIndex, e.RowIndex, e.X, e.Y, e)
{
if (e.RowIndex > -1 && e.RowIndex < sender.GridView.RowCount)
{
spectrum = sender.GetSpectrum(e.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 MassSpectrum(MassSpectrum metaSpectrum, pwiz.CLI.msdata.Spectrum spectrum)
{
source = metaSpectrum.source;
spectrumList = metaSpectrum.spectrumList;
index = metaSpectrum.index;
Tag = metaSpectrum.Tag;
AnnotationSettings = metaSpectrum.AnnotationSettings;
//element = spectrum;
id = metaSpectrum.id;
}
public DataPointTableForm(GraphItem graphItem)
{
InitializeComponent();
item = graphItem;
spectrum = item as MassSpectrum;
dataGridView.VirtualMode = true;
//dataGridView.Rows.Insert( 0, pointList.Count );
Refresh();
if (mobilityArray != null)
{
dataGridView.Columns.Add("mobility", "Ion Mobility");
}
}
public void UpdateAnnotations(MassSpectrum spectrum)
{
if (currentSpectrum != spectrum)
{
currentSpectrum = spectrum;
Text = TabText = "Annotations for spectrum " + spectrum.Id;
runOverrideToolStripButton.Text = "Override " + spectrum.Source.Source.Name + " Annotations";
annotationsListView.VirtualListSize = spectrum.AnnotationList.Count;
if (spectrum.AnnotationList.Count > 0)
{
selectIndex(spectrum.AnnotationList.Count - 1);
}
}
annotationsListView.Refresh();
}
public void UpdateProcessing(MassSpectrum spectrum)
{
if (processingListView.VirtualListSize != spectrum.ProcessingList.Count)
{
processingListView.VirtualListSize = spectrum.ProcessingList.Count;
selectIndex(spectrum.ProcessingList.Count - 1);
}
if (currentSpectrum != spectrum)
{
currentSpectrum = spectrum;
Text = TabText = "Processing for spectrum " + spectrum.Id;
runOverrideToolStripButton.Text = "Override " + spectrum.Source.Source.Name + " Processing";
processingListView_SelectedIndexChanged(this, EventArgs.Empty);
}
processingListView.Refresh();
}
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 int IndexOf(MassSpectrum spectrum)
{
return(spectraSource.Find("Id", spectrum.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;
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);
}
public ProcessingChangedEventArgs(Scope scope, MassSpectrum spectrum)
{
ChangeScope = scope;
Spectrum = spectrum;
}
