// The test mzxml contains 4 ms2 scans with +/- 10 ms1 scans
// around each. This method reads one ms2 scan and its ms1 scans.
private void GetBlock(MzXmlReader reader, int block, ref Scan ms2Scan, ref Scan parentScan, ref List <Scan> ms1Scans)
{
int skipCount = (block - 1) * 21;
Scan lastMs1 = null;
foreach (Scan scan in reader)
{
if (skipCount > 0)
{
--skipCount;
continue;
}
if (scan.MsOrder == 1)
{
ms1Scans.Add(scan);
lastMs1 = scan;
}
else if (scan.MsOrder == 2)
{
ms2Scan = scan;
parentScan = lastMs1;
}
if (ms1Scans.Count >= 20)
{
break;
}
}
}
public void Mono3()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml");
var scans = new List <Scan>();
Scan ms2Scan = new Scan();
Scan parentScan = new Scan();
GetBlock(reader, 3, ref ms2Scan, ref parentScan, ref scans);
MonocleOptions options = new MonocleOptions();
Monocle.Run(scans, parentScan, ms2Scan.Precursors[0], options);
Assert.Equal(869.449817, ms2Scan.Precursors[0].Mz, 3);
}
public void Mono2()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
var scans = new List <Scan>();
Scan ms2Scan = new Scan();
Scan parentScan = new Scan();
GetBlock(reader, 2, ref ms2Scan, ref parentScan, ref scans);
MonocleOptions options = new MonocleOptions();
Monocle.Run(scans, parentScan, ms2Scan.Precursors[0], options);
Assert.Equal(1009.98842, ms2Scan.Precursors[0].Mz, 2);
}
public void testOutput()
{
var reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
string dir = Directory.GetCurrentDirectory();
var writer = new MzXmlWriter();
writer.Open("data/mzxml-writer-test.mzxml");
var header = new ScanFileHeader();
header.FileName = "mzxml-writer-test.mzxml";
header.FilePath = "data/mzxml-writer-test.mzxml";
writer.WriteHeader(header);
var scans = reader.GetEnumerator();
scans.MoveNext();
Scan scan1 = (Scan)scans.Current;
scans.MoveNext();
Scan scan2 = (Scan)scans.Current;
writer.WriteScan(scan1);
writer.WriteScan(scan2);
writer.Close();
reader = new MzXmlReader();
reader.Open("data/mzxml-writer-test.mzxml", new ScanReaderOptions());
scans = reader.GetEnumerator();
scans.MoveNext();
Scan scan3 = (Scan)scans.Current;
scans.MoveNext();
Scan scan4 = (Scan)scans.Current;
Assert.Equal(scan1.ScanNumber, scan3.ScanNumber);
Assert.Equal(scan1.RetentionTime, scan3.RetentionTime);
Assert.Equal(scan1.PeakCount, scan3.PeakCount);
Assert.Equal(scan1.Centroids[0].Mz, scan3.Centroids[0].Mz);
Assert.Equal(scan1.Centroids[11].Intensity, scan3.Centroids[11].Intensity);
}
public void TestReadMs2()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
var scans = new List <Scan>();
foreach (Scan scan in reader)
{
scans.Add(scan);
}
var ms2Scan = scans[10];
Assert.Equal(2, ms2Scan.MsOrder);
Assert.Equal(1d, ms2Scan.Precursors.Count, 3);
Assert.Equal(687.3921, ms2Scan.Precursors[0].Mz, 3);
}
public void TestReadScans()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
var scans = new List <Scan>();
foreach (Scan scan in reader)
{
scans.Add(scan);
}
Assert.Equal(84, scans.Count);
Assert.Equal(1, scans[0].ScanNumber);
Assert.Equal(1, scans[0].MsOrder);
Assert.Equal(1396, scans[0].PeakCount);
Assert.Equal(1396, scans[0].Centroids.Count);
Assert.Equal(356.43359375, scans[0].Centroids[0].Mz, 6);
}
public void WindowTest()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml");
var scans = new List <Scan>();
foreach (Scan scan in reader)
{
scans.Add(scan);
}
MonocleOptions options = new MonocleOptions();
options.AveragingVector = AveragingVector.Both;
options.Number_Of_Scans_To_Average = 6;
var nearby = Monocle.GetNearbyScans(ref scans, scans[scans[10].PrecursorMasterScanNumber - 1], options);
Assert.Equal(13, nearby.Count);
}
public void MonoAll()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml");
var scans = new List <Scan>();
foreach (Scan scan in reader)
{
scans.Add(scan);
}
MonocleOptions options = new MonocleOptions();
options.AveragingVector = AveragingVector.Both;
Monocle.Run(ref scans, options);
Assert.Equal(687.39195, scans[10].Precursors[0].Mz, 3);
Assert.Equal(1009.98842, scans[31].Precursors[0].Mz, 2);
Assert.Equal(869.449817, scans[52].Precursors[0].Mz, 3);
}
public void TestOpen()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
}
public void TestOpen()
{
MzXmlReader reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml");
}