public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = new Xic();
foreach (var isolationWindow in GetIsoWindows(precursorIonMz))
{
var peakList = _isoWindowToChromPeaks[isolationWindow];
xic.AddRange(GetXicPointsWithin(minMz, maxMz, peakList));
}
xic.Sort();
return Xic.GetSelectedXic(xic);
}
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = new Xic();
foreach (var isolationWindow in GetIsoWindows(precursorIonMz))
{
var peakList = _isoWindowToChromPeaks[isolationWindow];
xic.AddRange(GetXicPointsWithin(minMz, maxMz, peakList));
}
xic.Sort();
return(Xic.GetSelectedXic(xic));
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0) index = ~index;
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return xicSegment;
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0)
{
index = ~index;
}
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return(xicSegment);
}
