// Grouping the scans in the file
/// <summary>
/// Given a file, reads through the scans and groups them into SetOfScans objects, each containing one or more full ms1 scans and the corresponding boxcar scans.
/// Discards all ms2 scans (although the SetOfScans object also has a list to hold these, if you wanted to include them).
/// This method includes many comments which can be uncommented for debugging to write information to the console.
/// </summary>
/// <param name="file"></param>
/// <returns></returns> list of SetOfScans objects, each SetOfScans contains one full ms1 scan and its corresponding boxcar scans.
public static List <SetOfScans> SeparateScans(MsDataFile file)
{
List <SetOfScans> sorted = new List <SetOfScans>();
// Get only the ms1 and boxcar scans (discard ms2):
var ms1scans = file.GetMS1Scans().ToList();
//Console.WriteLine("Number of ms1scans (full ms and boxcar method): " + ms1scans.Count);
// Initialize variables:
MsDataScan current = ms1scans.ElementAt(0);
string currentFilter = current.ScanFilter;
//Console.WriteLine("first scan filter: " + currentFilter);
MsDataScan next = ms1scans.ElementAt(1);
string nextFilter = next.ScanFilter;
//Console.WriteLine("next scan filter: " + nextFilter);
SetOfScans set = new SetOfScans();
// Loop through to group the scans. This should create as many SetOfScans objects as there are boxes (specified in the setup of the scan).
for (int i = 0; i < ms1scans.Count; i++)
{
if (current.ScanFilter.Contains("Full ms ")) // the space is important! Otherwise this will be recorded as a boxcar scan instead of an ms1
{
set.AddToMs1Scans(current);
// Console.WriteLine("Found full ms, added to set");
}
// if this boxcar scan has boxcar scans after it
else if (current.ScanFilter.Contains("Full msx ms") && next.ScanFilter.Contains("Full msx ms"))
{
set.AddToBoxcarScans(current);
//Console.WriteLine("Found msx ms, added to set");
}
// if this boxcar scan is the last boxcar scan in the set, start a new set
else if (current.ScanFilter.Contains("Full msx ms") && !next.ScanFilter.Contains("Full msx ms"))
{
set.AddToBoxcarScans(current);
//Console.WriteLine("Found last msx ms in set, added to set");
sorted.Add(set);
//Console.WriteLine("Added set to Sorted");
set = new SetOfScans();
}
current = next;
currentFilter = current.ScanFilter;
if ((i + 1) < ms1scans.Count) // if there is a next MsDataScan in the file
{
next = ms1scans.ElementAt(i + 1);
nextFilter = next.ScanFilter;
}
}
return(sorted);
}
/// <summary>
/// Helper method for CombineScans
/// Identifies which scan in the set has the most points in the boxcar range
/// </summary>
/// <param name="set"></param>
/// <param name="boxcar"></param> BestScan object with first index, last index, total intensity, and scan
public static BestScan FindBoxcarScan(SetOfScans set, BoxcarRange range, int count)
{
double bestIntensity = 0;
MsDataScan bestScan = set.BoxcarScans[0];
int bestFirstIndex = 0;
int bestLastIndex = 0;
int bestLen = 0;
List <MsDataScan> boxcarScans = set.BoxcarScans;
// Check each scan to find the one that corresponds best to the boxcar scan range
foreach (var scan in boxcarScans)
{
BestScan bestrange = FindScanRange(scan, range);
// the scan is better than the previous scan if:
// it has more m/z values in the range, and if
// the total intensity is higher
int firstIndex = bestrange.FirstIndex;
int lastIndex = bestrange.LastIndex;
int currentLen = lastIndex - firstIndex;
if (currentLen > bestLen)
{
if (bestrange.TotalIntensity < bestIntensity)
{
Console.WriteLine("ACK! scan#: " + count + " has a lot of very low intensity scans and may have been incorrectly counted in a boxcar range!");
}
// if the scan has more m/z points in the boxcar range than the previously best scan, update variables.
bestLen = currentLen;
bestLastIndex = lastIndex;
bestFirstIndex = firstIndex;
bestScan = scan;
}
}
return(new BestScan(bestFirstIndex, bestLastIndex, bestIntensity, bestScan));
}
/// <summary>
/// Helper method for MergeScans
/// Combines the 3 scans in a set into one MsDataScan.
/// </summary>
/// <param name="set"></param>
/// <param name="boxcarRanges"></param>
/// <returns></returns> MsDataScan combined scans
public static MsDataScan CombineScans(SetOfScans set, SetOfBoxcarRanges[] boxcarTypes)
{
List <double[]> bestPoints = new List <double[]>();
var count = 1;
foreach (var boxcarRanges in boxcarTypes)
{
foreach (var boxcarRange in boxcarRanges)
{
BestScan bestScan = FindBoxcarScan(set, boxcarRange, count);
// find the m/z values and intensities in that scan's x and y arrays between the first and last index, add to the lists
for (int i = bestScan.FirstIndex; i <= bestScan.LastIndex; i++)
{
double x = bestScan.Scan.MassSpectrum.XArray[i];
double y = bestScan.Scan.MassSpectrum.YArray[i];
bestPoints.Add(new double[] { x, y });
}
}
}
// recast bestPoints (List<Double[]>) into double[,]
double[,] mzIntensities = new double[bestPoints[0].Length, bestPoints.Count];
for (int i = 0; i < bestPoints[0].Length; i++)
{
for (int j = 0; j < bestPoints.Count; j++)
{
mzIntensities[i, j] = bestPoints[j][i];
}
}
// create and return the new MsDataScan
MzSpectrum newMassSpectrum = new MzSpectrum(mzIntensities);
MsDataScan newScan = new MsDataScan(newMassSpectrum, count, 1, true, set.BoxcarScans[0].Polarity, set.BoxcarScans[0].RetentionTime, set.BoxcarScans[0].ScanWindowRange, set.BoxcarScans[0].ScanFilter, set.BoxcarScans[0].MzAnalyzer, set.BoxcarScans[0].TotalIonCurrent, set.BoxcarScans[0].InjectionTime, set.BoxcarScans[0].NoiseData, set.BoxcarScans[0].NativeId);
count++;
return(newScan);
}
