/// <summary>
/// Constructor
/// </summary>
/// <param name="run">LcMsRun (for determining minimum and maximum elution time</param>
/// <param name="features">List of features</param>
/// <param name="title">Plot title</param>
/// <param name="minMass">Minimum mass</param>
/// <param name="maxMass">Maximum mass</param>
public LcMsFeatureMap(LcMsRun run, IEnumerable<LcMsFeature> features, string title, double minMass, double maxMass) :
this(features, title,
minMass, maxMass,
Math.Max(run.GetElutionTime(run.MinLcScan) - 5, 0),
run.GetElutionTime(run.MaxLcScan) + 5)
{
}
private List<ProductSpectrum> GetMatchedSpectrums(LcMsRun run, IList<int> ms2List ,Tuple<int,double, double, double, double,double> feature, int fileIndex)
{
var spectrumList = new List<ProductSpectrum>();
var mass = feature.Item2;
var minElution = feature.Item3;
var maxElution = feature.Item4;
var featureId = feature.Item1 - 1;
var det = new Tuple<int, double, int>(-1, -1.0, -1);
for (var i = 0; i < ms2List.Count; i++)
{
var scanElutionTime = run.GetElutionTime(ms2List[i]);
if (scanElutionTime < minElution || scanElutionTime > maxElution) continue;
var spectrum = run.GetSpectrum(ms2List[i]) as ProductSpectrum;
var window = spectrum.IsolationWindow;
var minMz = window.MinMz - .5;
var maxMz = window.MaxMz + .5;
var mzTable = GetFeatureMassTable(mass);
for (var j = 0; j < mzTable.Length; j++)
{
var mz = mzTable[j];
if (mz < minMz || mz > maxMz) continue;
spectrumList.Add(spectrum);
if(!(det.Item1 > -1)) det = new Tuple<int, double, int>(ms2List[i],mz,j+2);
break;
}
_identifiedFeatures[featureId][fileIndex] = det;
}
return spectrumList;
}
private Tuple<int, int> GetMinMaxMs1ScanNum(LcMsRun run, double minTime, double maxTime)
{
var ms1ScanNums = run.GetMs1ScanVector();
var minScanNum = -1;
var maxScanNum = -1;
for(var i = 1; i < ms1ScanNums.Length; i++)
{
var time = run.GetElutionTime(ms1ScanNums[i]);
if (minScanNum < 0 && time > minTime)
{
minScanNum = ms1ScanNums[i - 1];
}
if (maxScanNum < 0 && time > maxTime)
{
maxScanNum = ms1ScanNums[i];
break;
}
}
return new Tuple<int, int>(minScanNum, maxScanNum);
}
