private void Read(string msDeconvFileName)
{
var curScan = 0;
var isMs1 = false;
var minMass = double.MaxValue;
var maxMass = 0.0;
var featureCountUnfiltered = 0;
var featureCountFiltered = 0;
foreach (var line in File.ReadLines(msDeconvFileName))
{
if (line.StartsWith("SCANS="))
{
curScan = Convert.ToInt32(line.Substring(line.LastIndexOf('=') + 1));
isMs1 = _run.GetMsLevel(curScan) == 1;
}
else if (isMs1 && line.Length > 0)
{
var token = line.Split();
if (token.Length != 3)
{
continue;
}
featureCountUnfiltered++;
var charge = Convert.ToInt32(token[2]);
if (charge == 1)
{
continue;
}
var monoMass = Convert.ToDouble(token[0]);
if (minMass > monoMass)
{
minMass = monoMass;
}
if (maxMass < monoMass)
{
maxMass = monoMass;
}
featureCountFiltered++;
var minScan = _run.GetPrevScanNum(curScan, 1);
var maxScan = _run.GetNextScanNum(curScan, 1);
_lcMsMatchMap.SetMatches(monoMass, minScan, maxScan);
}
}
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, featureCountUnfiltered);
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _massTolerance, minMass, maxMass);
}
public Ms1IsotopeMostAbundantPlusOneFilter(
InMemoryLcMsRun run,
int minCharge = 3, int maxCharge = 30,
double ppmTolerance = 10,
double minMass = 3000.0,
double maxMass = 50000.0,
int maxNumPeaksToConsider = 40)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
MaxNumPeaksToConsider = maxNumPeaksToConsider;
_tolerance = new Tolerance(ppmTolerance);
_comparer = new MzComparerWithTolerance(ppmTolerance);
_lcMsMatchMap = new LcMsMatchMap();
PrecomputePossibleSequenceMasses();
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _tolerance, minMass, maxMass);
}
private void Read(string isosFileName)
{
var icrToolsparser = new TsvFileParser(isosFileName, ',');
var monoMassArr = icrToolsparser.GetData("monoisotopic_mw").Select(Convert.ToDouble).ToArray();
var scanArray = icrToolsparser.GetData("scan_num").Select(s => Convert.ToInt32(s)).ToArray();
var chargeArray = icrToolsparser.GetData("charge").Select(s => Convert.ToInt32(s)).ToArray();
var fitStringArr = icrToolsparser.GetData("fit");
var fitArray = fitStringArr == null ? null : icrToolsparser.GetData("fit").Select(Convert.ToDouble).ToArray();
var featureCountFiltered = 0;
var minMass = double.MaxValue;
var maxMass = 0.0;
for (var i = 0; i < monoMassArr.Length; i++)
{
if (fitArray != null && fitArray[i] > _fitScoreThreshold || chargeArray[i] <= 1)
{
continue;
}
featureCountFiltered++;
var scan = scanArray[i];
var monoMass = monoMassArr[i];
if (minMass > monoMass)
{
minMass = monoMass;
}
if (maxMass < monoMass)
{
maxMass = monoMass;
}
var minScan = _run.GetPrevScanNum(scan, 1);
var maxScan = _run.GetNextScanNum(scan, 1);
_lcMsMatchMap.SetMatches(monoMass, minScan, maxScan);
}
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, monoMassArr.Length);
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _massTolerance, minMass, maxMass);
}
public Ms1IsotopeAndChargeCorrFilter(
LcMsRun run,
Tolerance tolerance,
int minCharge = 3, int maxCharge = 30,
double minMass = 3000.0,
double maxMass = 50000.0,
double isotopeCorrThreshold = 0.7,
double chargeCorrThreshold = 0.7,
double mostAbundantPlusOneIsotopeCorrThreshold = 0.7,
int maxNumPeaksToConsider = 40)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
_isotopeCorrThresholdThreshold = isotopeCorrThreshold;
_chargeCorrThresholdThreshold = chargeCorrThreshold;
_mostAbundantPlusOneIsotopeCorrThreshold = mostAbundantPlusOneIsotopeCorrThreshold;
MaxNumPeaksToConsider = maxNumPeaksToConsider;
_tolerance = tolerance;
_comparer = new MzComparerWithTolerance(tolerance);
_lcMsMatchMap = new LcMsMatchMap();
PrecomputePossibleSequenceMasses();
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _tolerance, minMass, maxMass);
}
