internal void IncrementalBatchSearch(MSParser.MSFull ms, List <PathCandidate> pathCandidates, RegexGeneration.RegexGenerationParams regexParams)
{
//Handle the precursor stuff
double precursor = -1;
double precursorCharge = -1;
double lowerSearchBound = -1;
double upperSearchBound = -1;
if (ms.ZLines.Count > 0 && regexParams.UsePrecursorInformation)
{
string[] zLine = tabSplitterRegex.Split(ms.ZLines[0]);
precursorCharge = double.Parse(zLine[1]);
precursor = PatternTools.pTools.DechargeMSPeakToPlus1(ms.ChargedPrecursor, precursorCharge);
if (precursorCharge <= regexParams.MinTrustedCharge)
{
lowerSearchBound = precursor - regexParams.PrecursorLowerBound;
upperSearchBound = precursor + regexParams.PrecursorUpperBound;
}
else
{
lowerSearchBound = PatternTools.pTools.DechargeMSPeakToPlus1(ms.ChargedPrecursor, regexParams.MinTrustedCharge);
upperSearchBound = -1;
}
}
else if (regexParams.UsePrecursorInformation && ms.ZLines.Count == 0)
{
lowerSearchBound = (regexParams.MinTrustedCharge * ms.ChargedPrecursor) - 500;
upperSearchBound = -1;
}
else if (!regexParams.UsePrecursorInformation)
{
lowerSearchBound = ms.MSData[(int)(ms.MSData.Count * 0.8)].MZ;
upperSearchBound = -1;
}
SearchResult sr = Search(lowerSearchBound, upperSearchBound, pathCandidates, regexParams.MaxRegexes, ms.ScanNumber, ms.ChargedPrecursor, precursorCharge);
sr.TheResults.Sort((a, b) => b.Score.CompareTo(a.Score));
if (sr.TheResults.Count > 0)
{
if (sr.DeltaCN > 0)
{
mySearchResults.Add(sr);
}
}
}
public List <MSFull> GetNext(int noSpectra)
{
List <MSFull> myScans = new List <MSFull>(noSpectra);
string thisLine = "";
MSFull thisScan;
if (cycleCounter == 0)
{
thisScan = new MSParser.MSFull();
}
else
{
thisScan = bufferScan;
}
while (true)
{
thisLine = sr.ReadLine();
if (thisLine == null)
{
break;
}
if (thisLine.Length == 0)
{
continue;
}
if (isNumber.Match(thisLine, 0, 1).Success)
{
//We are dealing with MS ion data
string[] ionData = mzSeparator.Split(thisLine);
Ion ion = new Ion(double.Parse(ionData[0]), double.Parse(ionData[1]), thisScan.CromatographyRetentionTime, thisScan.ScanNumber);
//Save our data
thisScan.MSData.Add(ion);
}
else if (thisLine.StartsWith("Z"))
{
string[] theStrings3 = tabSeparator.Split(thisLine);
if (thisScan.Charges == null)
{
thisScan.Charges = new List <int> {
int.Parse(theStrings3[1])
};
thisScan.Precursors = new List <double> {
double.Parse(theStrings3[2])
};
}
else
{
thisScan.Charges.Add(int.Parse(theStrings3[1]));
if (thisScan.Precursors == null)
{
thisScan.Precursors = new List <double>();
}
thisScan.Precursors.Add(double.Parse(theStrings3[2]));
}
}
else if (thisLine.Contains("ActivationType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.ActivationType = theStrings2[2];
}
else if (thisLine.Contains("InstrumentType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.InstrumentType = theStrings2[2];
}
else if (thisLine.Contains("RetTime"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
if (theStrings2.Length == 2)
{
//The retention time is separated with a space so we need to further break it up
string[] s = Regex.Split(theStrings2[1], @" ");
thisScan.CromatographyRetentionTime = double.Parse(s[1]);
}
else if (theStrings2.Length == 3)
{
thisScan.CromatographyRetentionTime = double.Parse(theStrings2[2]);
}
else
{
throw new Exception("Problems parsing Retention time Line.\n" + thisLine);
}
}
else if (thisLine.StartsWith("S"))
{
//Step 1:Save the Old One
if (thisScan.MSData.Count > 0) //Make sure we dont have an empty scan!
{
myScans.Add(thisScan);
}
//Step 2:Get the new one ready
thisScan = new MSParser.MSFull();
string[] theStrings = tabSeparator.Split(thisLine);
thisScan.ScanNumber = int.Parse(theStrings[1]);
thisScan.MSData = new List <Ion>();
if (theStrings.Length != 3)
{
//we are dealing with MS1 - the precursor shall be 0
//We are dealing with MS and should save precursor information
thisScan.ChargedPrecursor = double.Parse(theStrings[3]);
}
if (myScans.Count == noSpectra)
{
bufferScan = thisScan;
break;
}
}
}
if (thisLine == null)
{
sr.Close();
}
cycleCounter++;
return(myScans);
}
public void ParseFile(FileInfo file, double minimumIonIntensity) {
//Get the file to RAM
myScans.Clear();
headerLines.Clear();
ParsedFileInfo = file;
StreamReader sr = new StreamReader(file.OpenRead());
string thisLine;
MSFile thisFile = new MSFile();
thisFile.FileName = file.Name;
int lineCounter = 0; //Helps to debug.
MSParser.MSFull thisScan = new MSParser.MSFull();
while ((thisLine = sr.ReadLine()) != null)
{
lineCounter++;
if (thisLine.Length == 0) { continue; }
if (isNumber.Match(thisLine, 0, 1).Success)
{
//We are dealing with MS ion data
string[] ionData = mzSeparator.Split(thisLine);
Ion ion = new Ion(double.Parse(ionData[0]), double.Parse(ionData[1]), thisScan.CromatographyRetentionTime, thisScan.ScanNumber);
//Save our data
thisScan.MSData.Add(ion);
}
else if (thisLine.StartsWith("H"))
{
headerLines.Add(thisLine);
}
else if (thisLine.StartsWith("Z"))
{
string[] theStrings3 = tabSeparator.Split(thisLine);
if (thisScan.Charges == null)
{
thisScan.Charges = new List<int> { int.Parse(theStrings3[1]) };
thisScan.Precursors = new List<double> { double.Parse(theStrings3[2]) };
}
else
{
thisScan.Charges.Add(int.Parse(theStrings3[1]));
if (thisScan.Precursors == null)
{
thisScan.Precursors = new List<double>();
}
thisScan.Precursors.Add(double.Parse(theStrings3[2]));
}
}
else if (thisLine.Contains("ActivationType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.ActivationType = theStrings2[2];
}
else if (thisLine.Contains("InstrumentType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.InstrumentType = theStrings2[2];
}
else if (thisLine.Contains("RetTime"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
if (theStrings2.Length == 2)
{
//The retention time is separated with a space so we need to further break it up
string[] s = Regex.Split(theStrings2[1], @" ");
thisScan.CromatographyRetentionTime = double.Parse(s[1]);
}
else if (theStrings2.Length == 3)
{
thisScan.CromatographyRetentionTime = double.Parse(theStrings2[2]);
}
else
{
throw new Exception("Problems parsing Retention time Line.\n" + thisLine);
}
}
else if (thisLine.StartsWith("S"))
{
//We have a new spectra // scan
//Denoise our scan
thisScan.MSData.RemoveAll(p => p.Intensity < minimumIonIntensity);
//Compute the ion intensity
foreach (var scan in thisScan.MSData)
{
thisScan.TotalIonIntensity += scan.Intensity;
}
//Step 1:Save the Old One
if (thisScan.MSData.Count > 0) //Make sure we dont have an empty scan!
{
myScans.Add(thisScan);
}
//Step 2:Get the new one ready
thisScan = new MSParser.MSFull();
thisScan.TotalIonIntensity = 0;
string[] theStrings = tabSeparator.Split(thisLine);
thisScan.ScanNumber = int.Parse(theStrings[1]);
thisScan.MSData = new List<Ion>();
if (theStrings.Length != 3)
{
//we are dealing with MS1 - the precursor shall be 0
//We are dealing with MS and should save precursor information
thisScan.ChargedPrecursor = double.Parse(theStrings[3]);
}
}
}
//Save our last scan
myScans.Add(thisScan);
sr.Close();
}
