public void TestMs1Filter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// QC_Shew
const string specFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string ms1FtFileName = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft";
const string idFilePath = @"D:\MassSpecFiles\training\IcTda\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(idFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, idFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
var massTolerance = new Tolerance(10);
var ms1ftFilter = new Ms1FtFilter(run, massTolerance, ms1FtFileName);
var n = 0;
var ms2ScanNums = run.GetScanNumbers(2);
foreach (var ms2ScanNum in ms2ScanNums)
{
var matchingMass = ms1ftFilter.GetMatchingMass(ms2ScanNum);
n += matchingMass.Count();
}
Console.WriteLine("{0} / {1}", n, ms2ScanNums.Count);
/*
* var tsvReader = new TsvFileParser(idFilePath);
*
* for (var i = 0; i < tsvReader.NumData; i++)
* {
* var qv = double.Parse(tsvReader.GetData("QValue")[i]);
* if (qv > 0.01) break;
*
* var scan = int.Parse(tsvReader.GetData("Scan")[i]);
* var charge = int.Parse(tsvReader.GetData("Charge")[i]);
* var mass = double.Parse(tsvReader.GetData("Mass")[i]);
*
* if (mass > 15000) continue;
*
* var seq = tsvReader.GetData("Sequence")[i];
* var mod = tsvReader.GetData("Modifications")[i];
* var nMatched = int.Parse(tsvReader.GetData("#MatchedFragments")[i]);
*
* var hit = false;
* foreach (var ms2Scan in ms1ftFilter.GetMatchingMs2ScanNums(mass))
* {
* if (ms2Scan == scan)
* {
* hit = true;
* break;
* }
* }
*
* if (!hit)
* {
* Console.WriteLine("{0}\t{1}\t{2}", scan, mass, nMatched);
* }
* }*/
}
