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 MobilityData(SpectrumList spectrumList, double scanTime, int startIndex, int endIndex) : this()
{
SpectrumList = spectrumList;
ScanTime = scanTime;
StartIndex = startIndex;
EndIndex = endIndex;
}
public SpectrumList GetProcessingSpectrumList( SpectrumList spectrumList )
{
foreach( IProcessing item in ProcessingList )
{
if( item.Enabled )
spectrumList = item.ProcessList( spectrumList );
}
return spectrumList;
}
public SpectrumList_ECD_ETD_PrecursorFilter(SpectrumList inner)
: base(inner)
{
ProcessingMethod method = new ProcessingMethod();
method.order = this.dataProcessing().processingMethods.Count;
method.set(CVID.MS_charge_stripping);
this.dataProcessing().processingMethods.Add(method);
}
public MassSpectrum GetMassSpectrum(MassSpectrum metaSpectrum, SpectrumList spectrumList)
{
MassSpectrum spectrum = new MassSpectrum(metaSpectrum, spectrumList.spectrum(metaSpectrum.Index, true));
//MassSpectrum realMetaSpectrum = ( metaSpectrum.Tag as DataGridViewRow ).Tag as MassSpectrum;
//realMetaSpectrum.Element.dataProcessing = spectrum.Element.dataProcessing;
//realMetaSpectrum.Element.defaultArrayLength = spectrum.Element.defaultArrayLength;
return(spectrum);
}
public MassSpectrum(ManagedDataSource source, int index, SpectrumList spectrumList)
{
this.source = source;
this.spectrumList = spectrumList;
this.index = index;
//element = spectrum;
//using( Spectrum element = Element )
{
id = Element.id;
}
}
public SpectrumList GetProcessingSpectrumList(SpectrumList spectrumList)
{
foreach (IProcessing item in ProcessingList)
{
if (item.Enabled)
{
spectrumList = item.ProcessList(spectrumList);
}
}
return(spectrumList);
}
public MassSpectrum(ManagedDataSource source, int index, SpectrumList spectrumList)
{
this.source = source;
this.spectrumList = spectrumList;
this.index = index;
//element = spectrum;
//using( Spectrum element = Element )
{
id = Element.id;
AbbreviatedId = pwiz.CLI.msdata.id.abbreviate(id);
}
}
public TextureExportPreview(SpectrumList specList_)
{
InitializeComponent();
pGridExport.PropertyValueChanged += new PropertyValueChangedEventHandler(pGridExport_PropertyValueChanged);
specList = specList_;
export = new SpectraTextureIO(specList);
sfDlg.Filter = export.Extensions;
pGridExport.SelectedObject = export;
RefreshPropertyGrid();
}
protected void readVendorFile()
{
jobInfo.log("Prepare to Parse Vendor File", "Prepare");
msd = new MSDataFile(jobInfo.inputFilePath);
jobInfo.log("Adapting Vendor File API", "Adapting");
List <string> filter = new List <string>();
SpectrumListFactory.wrap(msd, filter); //这一步操作可以帮助加快Wiff文件的初始化速度
spectrumList = msd.run.spectrumList;
if (spectrumList == null || spectrumList.empty())
{
jobInfo.logError("No Spectrums Found");
}
else
{
jobInfo.log("Adapting Finished");
}
if (jobInfo.format.Equals("WIFF"))
{
FileInfo file1 = new FileInfo(jobInfo.inputFilePath);
if (file1.Exists)
{
fileSize += file1.Length;
}
FileInfo file2 = new FileInfo(jobInfo.inputFilePath + ".mtd");
if (file2.Exists)
{
fileSize += file2.Length;
}
FileInfo file3 = new FileInfo(jobInfo.inputFilePath + ".scan");
if (file3.Exists)
{
fileSize += file3.Length;
}
}
if (jobInfo.format.Equals("RAW"))
{
FileInfo file1 = new FileInfo(jobInfo.inputFilePath);
if (file1.Exists)
{
fileSize += file1.Length;
}
}
}
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 MassSpectrum GetMassSpectrum(object idOrIndex)
{
int index = -1;
if (idOrIndex is int)
{
index = (int)idOrIndex;
}
else if (idOrIndex is string)
{
SpectrumList sl = source.MSDataFile.run.spectrumList;
int findIndex = sl.find(idOrIndex as string);
if (findIndex != sl.size())
{
index = findIndex;
}
}
return(GetMassSpectrum(index, source.MSDataFile.run.spectrumList));
}
public override void ReadFromDisk()
{
SpectrumList lSpectra = null;
TextReader tr = new StreamReader(fname);
try
{
XmlSerializer xs = new XmlSerializer(typeof(SpectrumList));
lSpectra = (SpectrumList)xs.Deserialize(tr);
spectra = new SpectrumList(lSpectra);
}
catch (Exception e)
{
Console.WriteLine("Failed to deserialize. Reason: " + e.Message);
}
finally
{
tr.Close();
}
}
public override void ReadFromDisk()
{
SpectrumList lSpectra = null;
FileStream fs = new FileStream(fname, FileMode.Open);
try
{
BinaryFormatter b = new BinaryFormatter();
lSpectra = (SpectrumList)b.Deserialize(fs);
spectra = new SpectrumList(lSpectra);
}
catch (SerializationException e)
{
Console.WriteLine("Failed to deserialize. Reason: " + e.Message);
throw;
}
finally
{
fs.Close();
}
}
public ParseSpectraFile(string mzmlPath, HashSet <int> scanNumSet, string ext)
{
int currentScanNum = -1;
try
{
MSDataFile msd = new MSDataFile(mzmlPath);
SpectrumList spectrumList = msd.run.spectrumList;
for (int i = 0; i < spectrumList.size(); ++i)
{
Spectrum spectrum = spectrumList.spectrum(i, true);
if (int.Parse(spectrum.cvParams[0].value) == 2)
{
Match match = scanNumPattern.Match(spectrum.id);
currentScanNum = int.Parse(match.Groups[1].Value);
if (scanNumSet.Contains(currentScanNum))
{
MZIntensityPairList mzIntensityPairs = new MZIntensityPairList();
spectrum.getMZIntensityPairs(ref mzIntensityPairs);
Dictionary <float, int> originalPeakList = new Dictionary <float, int>(mzIntensityPairs.Count);
foreach (MZIntensityPair mzIntensity in mzIntensityPairs)
{
originalPeakList[(float)mzIntensity.mz] = (int)mzIntensity.intensity;
}
spectraMap[currentScanNum] = originalPeakList;
}
}
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message + ": " + currentScanNum, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
Application.Exit();
}
}
public MassSpectrum GetMassSpectrum( int index, SpectrumList spectrumList )
{
return new MassSpectrum( this, index, spectrumList );
}
public Tuple <List <Point3D>, BoundingBox> Get3dSpectrum()
{
var result = new Tuple <List <Point3D>, BoundingBox>(new List <Point3D>(),
new BoundingBox
{
MinX = Double.MaxValue, MaxX = Double.MinValue, MinY = Double.MaxValue, MaxY = Double.MinValue
});
var bounds = result.Item2;
if (StartIndex == EndIndex)
{
var s = SpectrumList.spectrum(StartIndex, true);
var mzArray = s.getMZArray().data.Storage();
var intensityArray = s.getIntensityArray().data.Storage();
var mobilityArray = s.GetIonMobilityArray();
if (mobilityArray == null)
{
throw new NullReferenceException("mobilityBDA");
}
for (int j = 0, end = mzArray.Length; j < end; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
double mobility = mobilityArray[j];
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, mobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, mobility);
result.Item1.Add(new Point3D(mz, mobility, intensity));
}
}
else
{
for (int i = StartIndex, end = EndIndex; i <= end; ++i)
{
var s = SpectrumList.spectrum(i, true);
var mzArray = s.getMZArray().data.Storage();
var intensityArray = s.getIntensityArray().data.Storage();
var mobilityArray = s.GetIonMobilityArray();
for (int j = 0; j < mzArray.Length; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
double mobility = mobilityArray?.ElementAt(j) ?? (double)s.scanList.scans[0].cvParamChild(CVID.MS_ion_mobility_attribute).value;
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, mobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, mobility);
result.Item1.Add(new Point3D(mz, mobility, intensity));
}
}
}
return(result);
}
public MassSpectrum GetMassSpectrum(int index, SpectrumList spectrumList)
{
return(new MassSpectrum(this, index, spectrumList));
}
private static bool HasSrmSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// If the first spectrum is not SRM, the others will not be either
using (var spectrum = spectrumList.spectrum(0, false))
{
return IsSrmSpectrum(spectrum);
}
}
public MassSpectrum GetMassSpectrum( MassSpectrum metaSpectrum, SpectrumList spectrumList )
{
MassSpectrum spectrum = new MassSpectrum( this, spectrumList.spectrum( metaSpectrum.Index, true ) );
spectrum.Tag = metaSpectrum.Tag;
return spectrum;
}
public MassSpectrum GetMassSpectrum( int index, bool getBinaryData, SpectrumList spectrumList )
{
return new MassSpectrum( this, spectrumList.spectrum( index, getBinaryData ) );
}
public SpectraDiskIO(SpectrumList specList)
{
spectra = specList;
}
public SpectraDiskIO()
{
spectra = new SpectrumList();
}
private void init()
{
spectra = new SpectrumList();
categories = new Hashtable();
keywords = new Hashtable();
imagesSmall = new ImageList();
imagesSmall.ImageSize = imageSizeSmall;
imagesLarge = new ImageList();
imagesLarge.ImageSize = imageSizeLarge;
specDrawer = new SpectrumPainter();
}
public SpectrumList Category(String category)
{
SpectrumList sl = null;
if (categories.ContainsKey(category))
{
sl = new SpectrumList();
sl.Category = category;
foreach (int idx in ((ArrayList) categories[category]))
{
sl.Add(spectra[idx]);
}
}
return sl;
}
public SpectraBinIO(SpectrumList specList)
: base(specList)
{
}
private static bool HasDriftTimeSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// Assume that if any spectra have drift times, all do
using (var spectrum = spectrumList.spectrum(0, false))
{
return GetDriftTimeMsec(spectrum).HasValue;
}
}
public void Dispose()
{
if (_spectrumList != null)
_spectrumList.Dispose();
_spectrumList = null;
if (_chromatogramList != null)
_chromatogramList.Dispose();
_chromatogramList = null;
if (_msDataFile != null)
_msDataFile.Dispose();
_msDataFile = null;
}
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 SpectraXMLIO(SpectrumList specList)
: base(specList)
{
}
private void init()
{
collection = new SpectrumList();
specPainter = new SpectrumPainter();
View = View.LargeIcon;
Columns.Add("Name");
Columns.Add("Minlambda");
Columns.Add("MaxLambda");
Columns.Add("Points");
Columns.Add("Interpolation");
Columns.Add("BaseIntensity");
Columns.Add("MinIntensity");
Columns.Add("MaxIntensity");
SmallImageList = new ImageList();
LargeImageList = new ImageList();
initImageLists();
AllowDrop = true;
}
private void CollectionOpen()
{
ofDlg.Filter = spectraXMLIO.Extensions + "|" + spectraBinIO.Extensions;
SpectraDiskIO Reader = null;
if (ofDlg.ShowDialog() == DialogResult.OK)
{
if (ofDlg.FilterIndex == 1)
Reader = spectraXMLIO;
if (ofDlg.FilterIndex == 2)
Reader = spectraBinIO;
if (Reader != null)
{
Reader.FileName = ofDlg.FileName;
Reader.ReadFromDisk();
Collection = Reader.Spectra;
collectionFileName = sfDlg.FileName;
}
}
}
//TODO
private void SetCollection(SpectrumList specList)
{
collection = specList;
if (collection != null)
{
collection.OnSpectrumAdded += new SpectrumList.SpectrumAdded(collection_OnSpectrumAdded);
collection.OnSpectrumDeleted += new SpectrumList.SpectrumDeleted(collection_OnSpectrumDeleted);
}
InvalidateCollection();
}
public SpectraTextureIO(SpectrumList specList)
: base(specList)
{
init();
}
public MassSpectrum GetMassSpectrum( MassSpectrum metaSpectrum, SpectrumList spectrumList )
{
MassSpectrum spectrum = new MassSpectrum( metaSpectrum, spectrumList.spectrum( metaSpectrum.Index, true ) );
//MassSpectrum realMetaSpectrum = ( metaSpectrum.Tag as DataGridViewRow ).Tag as MassSpectrum;
//realMetaSpectrum.Element.dataProcessing = spectrum.Element.dataProcessing;
//realMetaSpectrum.Element.defaultArrayLength = spectrum.Element.defaultArrayLength;
return spectrum;
}
private void CollectionNew()
{
Collection = new SpectrumList();
}
