public void TestProcess()
{
var peaks = new PeakList<Peak>();
peaks.Add(new Peak(1.0, 1.0));
peaks.Add(new Peak(2.0, 1.0));
var processor = new PeakListMinIonCountProcessor<Peak>(3);
Assert.AreSame(null, processor.Process(peaks));
peaks.Add(new Peak(3.0, 1.0));
Assert.AreSame(peaks, processor.Process(peaks));
}
public void TestProcess()
{
var peaks = new PeakList<Peak>();
peaks.Add(new Peak(1.0, 10.0));
peaks.Add(new Peak(2.0, 100.0));
var processor1 = new PeakListMinTotalIonIntensityProcessor<Peak>(50.0);
Assert.AreSame(peaks, processor1.Process(peaks));
var processor2 = new PeakListMinIonIntensityProcessor<Peak>(150.0);
Assert.AreSame(null, processor2.Process(peaks));
}
public void TestProcess()
{
var peaks = new PeakList <Peak>();
peaks.Add(new Peak(1.0, 1.0));
peaks.Add(new Peak(2.0, 1.0));
var processor = new PeakListMinIonCountProcessor <Peak>(3);
Assert.AreSame(null, processor.Process(peaks));
peaks.Add(new Peak(3.0, 1.0));
Assert.AreSame(peaks, processor.Process(peaks));
}
public void TestProcess()
{
var peaks = new PeakList <Peak>();
peaks.Add(new Peak(1.0, 10.0));
peaks.Add(new Peak(2.0, 100.0));
var processor1 = new PeakListMinTotalIonIntensityProcessor <Peak>(50.0);
Assert.AreSame(peaks, processor1.Process(peaks));
var processor2 = new PeakListMinIonIntensityProcessor <Peak>(150.0);
Assert.AreSame(null, processor2.Process(peaks));
}
public static PeakList <Peak> ReadElementPeakList(XElement ions, bool isPeakInWindow)
{
var result = new PeakList <Peak>();
foreach (var p in ions.FindElements("Peak"))
{
var mz = double.Parse(p.FindAttribute("mz").Value);
var intensity = double.Parse(p.FindAttribute("intensity").Value);
var charge = int.Parse(p.FindAttribute("charge").Value);
var peak = new Peak(mz, intensity, charge);
if (isPeakInWindow)
{
peak.Tag = int.Parse(p.FindAttribute("tag").Value);
}
result.Add(peak);
}
if (isPeakInWindow)
{
var precursor = ions.FindElement("Precursor");
var dic = precursor.ToDictionary();
result.Precursor.MasterScan = int.Parse(dic["MasterScan"].Value);
result.Precursor.MonoIsotopicMass = double.Parse(dic["MonoIsotopicMass"].Value);
result.Precursor.IsolationMass = double.Parse(dic["IsolationMass"].Value);
result.Precursor.IsolationWidth = double.Parse(dic["IsolationWidth"].Value);
result.Precursor.Charge = int.Parse(dic["Charge"].Value);
result.Precursor.Intensity = double.Parse(dic["Intensity"].Value);
}
return(result);
}
public static PeakList <Peak> ReadElementPeakList(XmlReader reader, string pklName, bool isPeakInWindow)
{
var result = new PeakList <Peak>();
reader.MoveToElement(pklName);
reader.ReadStartElement();
while (reader.LocalName.Equals("Peak"))
{
Peak p = new Peak();
p.Mz = reader.ReadAttributeAsDouble("mz");
p.Intensity = reader.ReadAttributeAsDouble("intensity");
p.Charge = reader.ReadAttributeAsInt("charge");
if (isPeakInWindow)
{
p.Tag = reader.ReadAttributeAsInt("tag");
}
result.Add(p);
reader.Read();
}
if (isPeakInWindow)
{
reader.MoveToElement("Precursor");
reader.ReadStartElement("Precursor");
result.Precursor.MasterScan = reader.ReadElementAsInt("MasterScan");
result.Precursor.MonoIsotopicMass = reader.ReadElementAsDouble("MonoIsotopicMass");
result.Precursor.IsolationMass = reader.ReadElementAsDouble("IsolationMass");
result.Precursor.IsolationWidth = reader.ReadElementAsDouble("IsolationWidth");
result.Precursor.Charge = reader.ReadElementAsInt("Charge");
result.Precursor.Intensity = reader.ReadElementAsDouble("Intensity");
}
return(result);
}
public PeakList <Peak> GetMassListFromScanNum(int scan, bool centroid)
{
var result = new PeakList <Peak>();
if (IsBadDataScan(scan))
{
return(result);
}
object varMassList = null;
object varFlags = null;
int curScan = scan;
int arraySize = 0;
int centroidResult = centroid ? 1 : 0;
if (IsCentroidScanForScanNum(scan))
{
centroidResult = 0;
}
double centroidWidth = 0.0;
try
{
this.rawFile.GetMassListFromScanNum(
ref curScan,
null,
0,
0,
0,
centroidResult,
ref centroidWidth,
ref varMassList,
ref varFlags,
ref arraySize);
}
catch
{
Console.WriteLine("reading from scan {0} of {1} error, skipped.", scan, FileName);
WriteIgnoreScan(curScan);
return(result);
}
CheckErrorCode("GetMassListFromScanNum of " + scan.ToString() + " Error");
if (varMassList == null)
{
return(result);
}
var datas = (double[, ])varMassList;
for (int inx = 0; inx < arraySize; inx++)
{
result.Add(new Peak(datas[0, inx], datas[1, inx], 0));
}
return(result);
}
public void TestFindEnvelope()
{
var peaks = new PeakList <Peak>();
peaks.Add(new Peak(301, 1, 1));
peaks.Add(new Peak(302, 2, 1));
peaks.Add(new Peak(303, 1, 1));
peaks.Add(new Peak(304, 2, 1));
var env = this.FindEnvelope(peaks, peaks[0], 0.1);
Assert.AreEqual(3, env.Count);
Assert.IsTrue(!env.Contains(peaks[3]));
peaks.RemoveAt(0);
env = this.FindEnvelope(peaks, peaks[0], 0.1);
Assert.AreEqual(2, env.Count);
Assert.IsTrue(!env.Contains(peaks[2]));
}
private PeakList <T> ReadNextPeakList(StreamReader filein, ref string lastline)
{
//Find the scan/retentionTime line (start with '>')
if (lastline == null || lastline.Length == 0 || lastline[0] != '>')
{
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Length > 0 && lastline[0] == '>')
{
break;
}
}
if (lastline == null)
{
return(null);
}
}
string[] parts = Regex.Split(lastline.Substring(1), @"\s");
var result = new PeakList <T>();
result.ScanTimes.Add(new ScanTime(int.Parse(parts[0]), MyConvert.ToDouble(parts[1])));
if (parts.Length > 2)
{
result.MsLevel = int.Parse(parts[2]);
}
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Length == 0)
{
continue;
}
if (lastline[0] == '>')
{
break;
}
string[] peakParts = Regex.Split(lastline, @"\s");
var peak = new T();
peak.Mz = MyConvert.ToDouble(peakParts[0]);
peak.Intensity = MyConvert.ToDouble(peakParts[1]);
if (peakParts.Length > 2)
{
peak.Charge = int.Parse(peakParts[2]);
}
result.Add(peak);
}
return(result);
}
private void ReadPeakList(XElement pkl, string elementName, PeakList <Peak> peakList)
{
var pklNode = pkl.Element(elementName);
foreach (var peak in pklNode.Elements())
{
double mz = MyConvert.ToDouble(peak.Attribute("Mz").Value);
double intensity = MyConvert.ToDouble(peak.Attribute("Intensity").Value);
var p = new Peak(mz, intensity);
peakList.Add(p);
}
}
private void ReadPeakList(XmlHelper xmlHelper, XmlNode pkl, string elementName, PeakList <Peak> peakList)
{
XmlNode pklNode = xmlHelper.GetValidChild(pkl, elementName);
foreach (XmlNode peak in pklNode.ChildNodes)
{
double mz = MyConvert.ToDouble(peak.Attributes["Mz"].InnerText);
double intensity = MyConvert.ToDouble(peak.Attributes["Intensity"].InnerText);
var p = new Peak(mz, intensity);
peakList.Add(p);
}
}
public void TestDeisotopic()
{
var peaks = new PeakList <Peak>();
peaks.Add(new Peak(101.0000, 10, 1));
peaks.Add(new Peak(101.2000, 3, 0));
peaks.Add(new Peak(102.0034, 20, 1));
peaks.Add(new Peak(103.0067, 10, 1));
peaks.Add(new Peak(104.0101, 20, 1));
peaks.Add(new Peak(105.0134, 10, 1));
//peaks.ForEach(m => Console.WriteLine(m));
var cur = this.Process(peaks);
Assert.AreEqual(4, cur.Count);
//no charge
Assert.AreEqual(101.2000, peaks[1].Mz, 0.1);
//first envelope
Assert.AreEqual(101.0000, peaks[0].Mz, 0.1);
Assert.AreEqual(102.0034, peaks[2].Mz, 0.1);
//second envelope
Assert.AreEqual(104.0101, peaks[3].Mz, 0.1);
}
public PeakList <Peak> GetLabelData(int scan, double minMz, double maxMz)
{
var result = new PeakList <Peak>();
if (IsBadDataScan(scan))
{
return(result);
}
object varLabels = null;
object varFlags = null;
int curScan = scan;
try
{
this.rawFile.GetLabelData(ref varLabels, ref varFlags, ref curScan);
}
catch
{
Console.WriteLine("reading from scan {0} of {1} error, skipped.", scan, FileName);
WriteIgnoreScan(curScan);
return(result);
}
CheckErrorCode("GetLabelData " + scan + " Error");
var labels = (double[, ])varLabels;
int dim = labels.GetLength(1);
for (int inx = 0; inx < dim; inx++)
{
double mz = labels[0, inx];
if (mz < minMz)
{
continue;
}
if (mz > maxMz)
{
break;
}
var charge = (int)labels[5, inx];
double intensity = labels[1, inx];
result.Add(new Peak(mz, intensity, charge));
}
return(result);
}
public override PeakList <Peak> GetPeakList(int scan)
{
double[][] pkl = GetPeakArray(scan);
PeakList <Peak> result = new PeakList <Peak>();
for (int i = 0; i < pkl[0].Length; i++)
{
result.Add(new Peak(pkl[0][i], pkl[1][i]));
}
return(result);
}
public override PeakList <Peak> GetPeakList(int scan)
{
double[] mzAndIntensity = GetMzAndIntensities(scan);
PeakList <Peak> result = new PeakList <Peak>();
for (int i = 0; i < mzAndIntensity.Length; i += 2)
{
result.Add(new Peak(mzAndIntensity[i], mzAndIntensity[i + 1]));
}
return(result);
}
private static PeakList <Peak> ElementToPeakList(XElement ele, string peakname, bool isPeakInWindow)
{
PeakList <Peak> result = new PeakList <Peak>();
var rawpeaks = ele.Element(peakname);
if (rawpeaks != null)
{
foreach (var peakEle in rawpeaks.Elements("Peak"))
{
var peak = new Peak()
{
Mz = MyConvert.ToDouble(peakEle.Attribute("mz").Value),
Intensity = MyConvert.ToDouble(peakEle.Attribute("intensity").Value)
};
var chargeTag = peakEle.Attribute("charge");
if (chargeTag != null)
{
peak.Charge = int.Parse(chargeTag.Value);
}
if (isPeakInWindow)
{
var attrTag = peakEle.Attribute("tag");
if (attrTag != null)
{
peak.Tag = int.Parse(attrTag.Value);
}
}
result.Add(peak);
}
if (isPeakInWindow)
{
var precursor = rawpeaks.Element("Precursor");
if (precursor != null)
{
result.Precursor.MasterScan = int.Parse(precursor.Element("MasterScan").Value);
result.Precursor.MonoIsotopicMass = MyConvert.ToDouble(precursor.Element("MonoIsotopicMass").Value);
result.Precursor.IsolationMass = MyConvert.ToDouble(precursor.Element("IsolationMass").Value);
result.Precursor.IsolationWidth = MyConvert.ToDouble(precursor.Element("IsolationWidth").Value);
result.Precursor.Charge = int.Parse(precursor.Element("Charge").Value);
result.Precursor.Intensity = MyConvert.ToDouble(precursor.Element("Intensity").Value);
}
}
}
return(result);
}
public PeakList <Peak> GetLabelData(int scan)
{
var result = new PeakList <Peak>();
if (IsBadDataScan(scan))
{
Console.WriteLine("scan {0} of {1} is defined as ignore.", scan, FileName);
return(result);
}
object varLabels = null;
object varFlags = null;
int curScan = scan;
try
{
this.rawFile.GetLabelData(ref varLabels, ref varFlags, ref curScan);
}
catch
{
Console.WriteLine("reading from scan {0} of {1} error, skipped.", scan, FileName);
WriteIgnoreScan(curScan);
this.Open(this.FileName);
return(result);
//throw new RawReadException(scan);
}
CheckErrorCode("GetLabelData " + scan + " Error");
var labels = (double[, ])varLabels;
int dim = labels.GetLength(1);
for (int inx = 0; inx < dim; inx++)
{
double mz = labels[0, inx];
double intensity = labels[1, inx];
double noise = labels[4, inx];
var charge = (int)labels[5, inx];
result.Add(new Peak(mz, intensity, charge)
{
Noise = noise
});
}
return(result);
}
public PeakList <T> Process(PeakList <T> t)
{
List <PeakList <T> > envelopes = t.GetEnvelopes(this.ppmTolerance);
((List <T>)t).Clear();
foreach (var envelope in envelopes)
{
t.Add(envelope[0]);
}
t.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
return(t);
}
public static PeakList <Peak> GetPeakList(this IMsdrDataReader reader, double retentionTime, IMsdrPeakFilter peakFilter)
{
PeakList <Peak> result = new PeakList <Peak>();
IBDASpecData s = reader.GetSpectrum(retentionTime, MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, peakFilter, true);
for (int i = 0; i < s.XArray.Length; i++)
{
result.Add(new Peak(s.XArray[i], s.YArray[i]));
}
if (s.MZOfInterest.Length > 0)
{
result.PrecursorMZ = s.MZOfInterest[0].Start;
}
result.ScanTimes.Add(new ScanTime(0, retentionTime));
return(result);
}
public static PeakList <Peak> Base64ToPeakList(string peaksStr)
{
var result = new PeakList <Peak>();
byte[] bytes = Convert.FromBase64String(peaksStr);
for (int index = 0; index < bytes.Length; index += 8)
{
var mzBytes = new byte[4];
var intensityBytes = new byte[4];
for (int i = 0; i < 4; i++)
{
mzBytes[i] = bytes[index + i];
intensityBytes[i] = bytes[index + 4 + i];
}
double mz = GetDoubleFromGetNetworkModeBytes(mzBytes);
double intensity = GetDoubleFromGetNetworkModeBytes(intensityBytes);
var p = new Peak(mz, intensity);
result.Add(p);
}
return(result);
}
public override PeakList <Peak> GetPeakList(int scan, double minMz, double maxMz)
{
double[] mzAndIntensity = GetMzAndIntensities(scan);
PeakList <Peak> result = new PeakList <Peak>();
for (int i = 0; i < mzAndIntensity.Length; i += 2)
{
if (mzAndIntensity[i] < minMz)
{
continue;
}
if (mzAndIntensity[i] > maxMz)
{
break;
}
result.Add(new Peak(mzAndIntensity[i], mzAndIntensity[i + 1]));
}
return(result);
}
/// <summary>
/// 将可用的PeakList的强度合并为一个总的PeakList，用于线性回归计算。
/// </summary>
/// <returns>合并后的PeakList</returns>
private PeakList <Peak> MergeEnvelopes()
{
var mergedPeaks = new PeakList <Peak>();
var initPeaks = this.ObservedEnvelopes.Where(m => m.Enabled).ToList();
foreach (var envelope in initPeaks)
{
int maxCount = Math.Min(6, envelope.Count);
for (int i = 0; i < maxCount; i++)
{
if (i >= mergedPeaks.Count)
{
mergedPeaks.Add(new Peak(envelope[i].Mz, envelope[i].Intensity));
}
else
{
mergedPeaks[i].Intensity = mergedPeaks[i].Intensity + envelope[i].Intensity;
}
}
}
return(mergedPeaks);
}
public override PeakList <Peak> GetPeakList(int scan, double minMz, double maxMz)
{
double[][] pkl = GetPeakArray(scan);
PeakList <Peak> result = new PeakList <Peak>();
for (int i = 0; i < pkl[0].Length; i++)
{
if (pkl[0][i] < minMz)
{
continue;
}
if (pkl[0][i] > maxMz)
{
break;
}
result.Add(new Peak(pkl[0][i], pkl[1][i]));
}
return(result);
}
private int FindPeak <T>(List <T> peaks, int nextPeakIndex, Pair <double, double> nextMzRange, int charge) where T : IPeak
{
var candidates = new PeakList <T>();
for (int i = nextPeakIndex; i < peaks.Count; i++)
{
if (peaks[i].Mz > nextMzRange.Second)
{
break;
}
if (peaks[i].Mz < nextMzRange.First)
{
continue;
}
//if peaks[i] has been assigned charge and the charge is not
//equals the assumed charge, just ignore it.
if (0 != peaks[i].Charge && charge != peaks[i].Charge)
{
continue;
}
candidates.Add(peaks[i]);
}
if (candidates.Count > 0)
{
T peak = candidates.FindMaxIntensityPeak();
return(peaks.IndexOf(peak));
}
else
{
return(-1);
}
}
protected override PeakList <T> DoReadNextPeakList(out bool hasNext)
{
var result = new PeakList <T>();
string lastLine = "";
List <string> headers = ReadHeader(ref lastLine);
Dictionary <string, string> annotations = ReadAnnotation(ref lastLine);
List <string> peaks = ReadPeak(ref lastLine);
hasNext = CheckHasNext(this.reader);
foreach (string line in headers)
{
if (line.StartsWith(MascotGenericFormatConstants.MS_SCAN_TAG))
{
ParseScan(result, line);
}
else if (line.StartsWith(MascotGenericFormatConstants.MSMS_SCAN_TAG))
{
ParseScan(result, line);
}
else if (line.StartsWith(MascotGenericFormatConstants.FILENAME_TAG))
{
result.Experimental = line.Substring(line.IndexOf(':') + 1).Trim();
}
}
foreach (var de in annotations)
{
if (de.Key.Equals(MascotGenericFormatConstants.PEPMASS_TAG))
{
string[] values = Regex.Split(de.Value, "\\s");
result.PrecursorMZ = MyConvert.ToDouble(values[0]);
if (values.Length > 1)
{
result.PrecursorIntensity = MyConvert.ToDouble(values[1]);
}
}
else if (de.Key.Equals(MascotGenericFormatConstants.CHARGE_TAG))
{
string charge = de.Value;
if (charge.Contains("and"))
{
result.Annotations.Add(de.Key, de.Value);
continue;
}
if (charge.EndsWith("+"))
{
charge = charge.Substring(0, charge.Length - 1);
}
result.PrecursorCharge = int.Parse(charge);
}
else if (de.Key.Equals(MascotGenericFormatConstants.SCAN_TAG))
{
ParseScan(result, de.Value);
}
else if (de.Key.Equals(MascotGenericFormatConstants.RETENTION_TIME_TAG))
{
double rtInSecond = 0.0;
if (MyConvert.TryParse(de.Value, out rtInSecond))
{
var rtInMin = rtInSecond / 60.0;
if (result.ScanTimes.Count == 0)
{
result.ScanTimes.Add(new ScanTime(0, rtInMin));
}
else
{
result.ScanTimes[0].RetentionTime = rtInMin;
}
}
}
else
{
result.Annotations.Add(de.Key, de.Value);
}
}
foreach (string line in peaks)
{
string[] values = Regex.Split(line, "\\s");
try
{
var peak = new T()
{
Mz = MyConvert.ToDouble(values[0]),
Intensity = MyConvert.ToDouble(values[1])
};
result.Add(peak);
}
catch (Exception)
{
throw new Exception(string.Format("Format error, cannot read peak info from {0}", line));
}
}
return(result);
}
public override IEnumerable <string> Process(string fileName)
{
var result = new FileInfo(targetDir + "\\" + Path.ChangeExtension(new FileInfo(fileName).Name, ".mgf")).FullName;
int charge = 1;
PeakList <Peak> ms1 = new PeakList <Peak>();
//读取ms1
List <string> comments = new List <string>();
comments.Add("COM=" + software);
using (StreamReader sr = new StreamReader(fileName))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("COM="))
{
comments.Add(line);
continue;
}
if (line.StartsWith("BEGIN IONS"))
{
break;
}
comments.Add(line);
var parts = line.Split('\t');
if (parts.Length == 2)
{
try
{
ms1.Add(new Peak(double.Parse(parts[0]), double.Parse(parts[1])));
}
catch (Exception) { }
}
}
}
MascotGenericFormatReader <Peak> reader = new MascotGenericFormatReader <Peak>();
var pkls = reader.ReadFromFile(fileName);
foreach (var pkl in pkls)
{
var mzTolerance = PrecursorUtils.ppm2mz(pkl.PrecursorMZ, precursorTolerance);
var peak = ms1.FindPeak(pkl.PrecursorMZ, mzTolerance).FindMaxIntensityPeak();
if (peak == null)
{
pkl.PrecursorIntensity = ms1.Min(m => m.Intensity);
}
else
{
pkl.PrecursorIntensity = peak.Intensity;
}
}
pkls.Sort((m1, m2) => m2.PrecursorIntensity.CompareTo(m1.PrecursorIntensity));
for (int i = 0; i < pkls.Count; i++)
{
var line = pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] as string;
var m = reg.Match(line);
string experimental;
if (m.Success)
{
experimental = m.Groups[1].Value;
var m2 = nameReg.Match(experimental);
if (m2.Success)
{
if (m2.Groups[2].Value.Length == 1)
{
experimental = m2.Groups[1].Value + "0" + m2.Groups[2].Value;
}
}
}
else
{
experimental = pkls[i].Experimental;
}
pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] = string.Format("{0}.{1}.{2:0}.{3}.dta", experimental, i + 1, pkls[i].PrecursorIntensity, charge);
}
var writer = new MascotGenericFormatWriter <Peak>();
writer.Comments.AddRange(comments);
writer.WriteToFile(result, pkls);
return(new string[] { result });
}
public void SetUp()
{
pl = new PeakList<Peak>();
pl.Add(new Peak(430.0884, 43875.5, 1));
pl.Add(new Peak(445.1205, 335180.5, 1));
pl.Add(new Peak(446.1185, 51638.0, 1));
pl.Add(new Peak(446.1255, 129918.6, 1));
pl.Add(new Peak(447.1170, 30164.7, 1));
pl.Add(new Peak(491.9578, 442529.3, 3));
pl.Add(new Peak(492.2919, 206717.3, 3));
pl.Add(new Peak(492.6270, 137434.5, 3));
pl.Add(new Peak(492.9613, 26216.6, 3));
pl.Add(new Peak(531.2642, 129351.8, 4));
pl.Add(new Peak(631.2642, 129351.8, 0));
}
public void TestMergeWith()
{
PeakList<Peak> pl1 = new PeakList<Peak>();
pl1.Add(new Peak(420, 10, 1));
pl1.Add(new Peak(445, 10, 1));
PeakList<Peak> pl2 = new PeakList<Peak>();
pl2.Add(new Peak(420.004, 30, 2));
pl2.Add(new Peak(445.004, 30, 1));
pl1.MergeByMZFirst(pl2, 50);
Assert.AreEqual(3, pl1.Count);
Assert.AreEqual(420, pl1[0].Mz, 0.001);
Assert.AreEqual(1, pl1[0].Charge);
Assert.AreEqual(420.004, pl1[1].Mz, 0.001);
Assert.AreEqual(2, pl1[1].Charge);
Assert.AreEqual(445.003, pl1[2].Mz, 0.001);
Assert.AreEqual(1, pl1[2].Charge);
Assert.AreEqual(10, pl1[0].Intensity);
Assert.AreEqual(30, pl1[1].Intensity);
Assert.AreEqual(40, pl1[2].Intensity);
}
public PeakList <T> ReadFromFile(string dtaFilename)
{
var fi = new FileInfo(dtaFilename);
if (!fi.Exists)
{
throw new FileNotFoundException("Cannot find the file " + dtaFilename);
}
var result = new PeakList <T>();
SequestFilename sf = SequestFilename.Parse(fi.Name);
result.Experimental = sf.Experimental;
result.ScanTimes.Add(new ScanTime(sf.FirstScan, 0.0));
if (sf.FirstScan != sf.LastScan)
{
result.ScanTimes.Add(new ScanTime(sf.LastScan, 0.0));
}
result.PrecursorCharge = sf.Charge;
using (var filein = new StreamReader(new FileStream(dtaFilename, FileMode.Open, FileAccess.Read)))
{
string lastline;
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Trim().Length > 0)
{
break;
}
}
if (lastline == null)
{
return(null);
}
string[] parts = Regex.Split(lastline, @"\s+");
double precursorMass = MyConvert.ToDouble(parts[0]);
result.PrecursorCharge = int.Parse(parts[1]);
result.PrecursorMZ = PrecursorUtils.MHToMz(precursorMass, result.PrecursorCharge, true);
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Length == 0)
{
continue;
}
if (lastline[0] == '>')
{
break;
}
string[] peakParts = Regex.Split(lastline, @"\s+");
var peak = new T();
peak.Mz = MyConvert.ToDouble(peakParts[0]);
peak.Intensity = MyConvert.ToDouble(peakParts[1]);
if (peakParts.Length > 2)
{
peak.Charge = int.Parse(peakParts[2]);
}
result.Add(peak);
}
return(result);
}
}
public void Deconvolute <T>(List <T> peaks) where T : IPeak
{
peaks.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
var peakEnvelopeMap = new Dictionary <T, List <PeakList <T> > >();
var envelopes = new List <PeakList <T> >();
for (int i = 0; i < peaks.Count - 1; i++)
{
double mzTolerance = PrecursorUtils.ppm2mz(peaks[i].Mz, this.ppmTolerance);
if (peaks[i + 1].Mz - peaks[i].Mz > C_GAP + mzTolerance)
{
continue;
}
var envelopeList = new List <PeakList <T> >();
for (int charge = 1; charge <= this.maxCharge; charge++)
{
//if peaks[i] has already been assigned a charge,
//only that charge will be considered
if (0 != peaks[i].Charge && charge != peaks[i].Charge)
{
continue;
}
double gap = this.mzGaps[charge - 1];
var curPeaks = new PeakList <T>();
curPeaks.Add(peaks[i]);
//just use precursor charge to record the assumed charge
curPeaks.PrecursorCharge = charge;
int nextPeakIndex = i + 1;
while (true)
{
double currMz = curPeaks[curPeaks.Count - 1].Mz;
var nextMzRange = new Pair <double, double>(currMz + gap - mzTolerance, currMz + gap + mzTolerance);
int findPeakIndex = FindPeak(peaks, nextPeakIndex, nextMzRange, charge);
if (-1 == findPeakIndex)
{
break;
}
curPeaks.Add(peaks[findPeakIndex]);
nextPeakIndex = findPeakIndex + 1;
}
if (charge > MIN_THREE_PEAKS_NEEDED_FOR_CHARGE_LARGER_THAN)
{
if (curPeaks.Count > 2)
{
envelopeList.Add(curPeaks);
}
}
else if (curPeaks.Count > 1)
{
envelopeList.Add(curPeaks);
}
}
if (envelopeList.Count > 0)
{
peakEnvelopeMap.Add(peaks[i], envelopeList);
envelopes.AddRange(envelopeList);
}
}
SortEnvelopesByCountChargeMz(envelopes);
RemoveAllContainedEnvelopes(envelopes);
while (envelopes.Count > 0)
{
SortEnvelopesByCountChargeMz(envelopes);
if (1 >= envelopes[0].Count)
{
break;
}
envelopes[0].SetFragmentIonCharge(envelopes[0].PrecursorCharge);
foreach (T p in envelopes[0])
{
for (int j = 1; j < envelopes.Count; j++)
{
if (envelopes[j].Contains(p))
{
if (envelopes[j].PrecursorCharge != envelopes[0].PrecursorCharge)
{
envelopes[j].Remove(p);
}
}
}
}
envelopes.RemoveAt(0);
for (int iEnv = envelopes.Count - 1; iEnv >= 0; iEnv--)
{
if (1 >= envelopes[iEnv].Count)
{
envelopes.RemoveAt(iEnv);
}
}
}
}
public List <PeakList <Peak> > ReadFromFile(string fileName)
{
List <PeakList <Peak> > result = new List <PeakList <Peak> >();
using (StreamReader sr = new StreamReader(fileName))
{
Progress.SetRange(0, sr.BaseStream.Length);
string line;
Dictionary <string, string> headers = new Dictionary <string, string>();
List <string> peaks = new List <string>();
while ((line = sr.ReadLine()) != null)
{
if (line.Trim().Equals("peaklist start"))
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
headers.Clear();
peaks.Clear();
bool inHeader = true;
while ((line = sr.ReadLine()) != null)
{
var tline = line.Trim();
if (tline.Equals("peaklist end"))
{
break;
}
if (tline.Length == 0)
{
continue;
}
if (!inHeader)
{
peaks.Add(tline);
}
else if (Char.IsLetter(tline[0]))
{
var pos = tline.IndexOf('=');
var key = tline.Substring(0, pos);
var value = tline.Substring(pos + 1);
headers[key] = value;
}
else
{
inHeader = false;
peaks.Add(tline);
}
}
if (headers.Count > 0 && peaks.Count > 0)
{
PeakList <Peak> pkl = new PeakList <Peak>();
pkl.PrecursorMZ = MyConvert.ToDouble(headers["mz"]);
pkl.PrecursorCharge = Convert.ToInt32(headers["charge"]);
pkl.MsLevel = 2;
pkl.ScanMode = headers["fragmentation"];
SequestFilename sf = parser.GetValue(headers["header"]);
pkl.ScanTimes.Add(new ScanTime(sf.FirstScan, 0.0));
pkl.Experimental = sf.Experimental;
result.Add(pkl);
foreach (var l in peaks)
{
var p = l.Split('\t');
if (p.Length > 1)
{
pkl.Add(new Peak(MyConvert.ToDouble(p[0]), MyConvert.ToDouble(p[1])));
}
}
}
}
}
}
return(result);
}