/// <summary>
/// Use binary search to find all Isotopic Peaks we want to consider when looking for the cross-links shifts.
/// </summary>
/// <param name="completePeakList">The complete list of Isotopic Peaks that we will use for searching.</param>
/// <param name="minimumMz">The minimum m/z value to consider.</param>
/// <param name="scanLc">The LC Scan to consider.</param>
/// <param name="scanIms">The IMS Scan to consider.</param>
/// <returns>All peaks that are in the given LC Scan and IMS Scan and m/z >= thegiven m/z of the Feature.</returns>
public static List<IPeak> FindCandidatePeaks(List<IsotopicPeak> completePeakList, double minimumMz, int scanLc, int scanIms)
{
// Set up Peak Comparer to use for binary search later on
AnonymousComparer<IsotopicPeak> peakComparer = new AnonymousComparer<IsotopicPeak>((x, y) => x.ScanLc != y.ScanLc ? x.ScanLc.CompareTo(y.ScanLc) : x.ScanIms != y.ScanIms ? x.ScanIms.CompareTo(y.ScanIms) : x.Mz.CompareTo(y.Mz));
IsotopicPeak lowPeak = new IsotopicPeak {ScanLc = scanLc, ScanIms = scanIms, Mz = minimumMz, Intensity = 1};
IsotopicPeak highPeak = new IsotopicPeak { ScanLc = scanLc, ScanIms = scanIms + 1, Mz = 0, Intensity = 1 };
int lowPeakPosition = completePeakList.BinarySearch(lowPeak, peakComparer);
int highPeakPosition = completePeakList.BinarySearch(highPeak, peakComparer);
lowPeakPosition = lowPeakPosition < 0 ? ~lowPeakPosition : lowPeakPosition;
highPeakPosition = highPeakPosition < 0 ? ~highPeakPosition : highPeakPosition;
List<IPeak> candidatePeaks = new List<IPeak>();
for (int j = lowPeakPosition; j < highPeakPosition; j++)
{
IsotopicPeak peak = completePeakList[j];
MSPeak msPeak = new MSPeak(peak.Mz, peak.Intensity, 0.05f, 1);
candidatePeaks.Add(msPeak);
}
return candidatePeaks;
}
/// <summary>
/// Parses a single line of the input file and returns a single Isotopic Peak.
/// </summary>
/// <param name="line">The line to read, as a string.</param>
/// <param name="columnMapping">The column mapping for the input file.</param>
/// <returns>A single IsotopicPeak object created by using the information from the parsed line.</returns>
private static IsotopicPeak ParseLine(string line, IDictionary<string, int> columnMapping)
{
var columnName = "unknown";
try
{
var columns = line.Split('\t', ',', '\n');
var peak = new IsotopicPeak();
columnName = "FrameNum";
if (columnMapping.ContainsKey(FRAME_NUM))
peak.ScanLc = int.Parse(columns[columnMapping[FRAME_NUM]]);
columnName = "ScanNum";
if (columnMapping.ContainsKey(SCAN_NUM))
peak.ScanIms = int.Parse(columns[columnMapping[SCAN_NUM]]);
columnName = "MZ";
if (columnMapping.ContainsKey(MZ))
peak.Mz = double.Parse(columns[columnMapping[MZ]]);
columnName = "Intensity";
if (columnMapping.ContainsKey(INTENSITY))
peak.Intensity = (int)Math.Round(double.Parse(columns[columnMapping[INTENSITY]]));
return peak;
}
catch (Exception)
{
Console.WriteLine("Error parsing column " + columnName + " in line: " + line);
throw;
}
}