private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
string accessId;
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
// The access ID gives a feedback about placed scans or scans generated by the instrument.
scan.SpecificInformation.TryGetValue("Access Id:", out accessId);
Console.WriteLine("{0:HH:mm:ss,fff} scan {1} arrived", DateTime.Now, accessId);
////// The common part is shared by all Thermo Fisher instruments, these settings mainly form the so called filter string
////// which also appears on top of each spectrum in many visualizers.
//Console.WriteLine("----------------Common--------------");
//Dump("Common", scan.CommonInformation);
////// The specific part is individual for each instrument type. Many values are shared by different Exactive Series models.
//Console.WriteLine("----------------Specific--------------");
// Dump("Specific", scan.SpecificInformation);
//Dump(scan);
var ib = IsBoxCarScan(scan);
Console.WriteLine("IsBoxCar Scan: {0}", ib);
FullScan.PlaceFullScan(m_scans, Parameters);
//List<double> dynamicBoxCarRange = new List<double> { 600, 700, 800, 900, 1000 };
//BoxCarScan.PlaceBoxCarScan(m_scans, Parameters, dynamicBoxCarRange);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, 750);
BoxCarScan.PlaceStaticBoxCarScan(m_scans, Parameters);
}
}
//In bottom up, it is possible to change the BoxCar ranges based on the real full mass scan.
//The workflow works, but the improvement is hard to evaluate so far.
private void AddScanIntoQueue_BynamicBoxCar_BU(IMsScan scan)
{
try
{
//Is MS1 Scan
if (scan.HasCentroidInformation && IsMS1Scan(scan))
{
bool isBoxCarScan = IsBoxCarScan(scan);
//string scanNumber;
//scan.CommonInformation.TryGetValue("ScanNumber", out scanNumber);
Console.WriteLine("In DynamicBoxCar_BU method, MS1 Scan arrived. Is BoxCar Scan: {0}.", isBoxCarScan);
if (!isBoxCarScan)
{
List <IsoEnvelop> isoEnvelops = Deconvolute_BU(scan);
if (isoEnvelops.Count > 0)
{
if (Parameters.MS2ScanSetting.DoMS2)
{
PlaceBU_MS2Scan(scan, isoEnvelops);
}
BoxCarScan.GenerateDynamicBoxes_BU(isoEnvelops, Parameters, Boxes);
FullScan.PlaceFullScan(m_scans, Parameters);
//The nearby Full mass scans in the current DDA method are very similar, so it is possible to use the previous full scan to generate the current boxes.
if (Boxes.Count > 0)
{
BoxCarScan.PlaceDynamicBoxCarScan_BU(m_scans, Parameters, Boxes);
//To generate data for comparison
BoxCarScan.PlaceStaticBoxCarScan(m_scans, Parameters);
Boxes.Clear();
}
}
else
{
FullScan.PlaceFullScan(m_scans, Parameters);
}
}
}
}
catch (Exception e)
{
Console.WriteLine("AddScanIntoQueue_DynamicBoxCar_Bu MS2FromFullScan Exception!");
Console.WriteLine(e.ToString() + " " + e.Source);
}
}
//In StaticBox, the MS1 scan contains a lot of features. There is no need to extract features from BoxCar Scans for placing MS2 scans.
//The workflow is similar to the 'BoxCar' paper in Nature Method.
private void AddScanIntoQueue_StaticBox(IMsScan scan)
{
try
{
//Is MS1 Scan
if (scan.HasCentroidInformation && IsMS1Scan(scan))
{
bool isBoxCarScan = IsBoxCarScan(scan);
string scanNumber;
scan.CommonInformation.TryGetValue("ScanNumber", out scanNumber);
Console.WriteLine("In StaticBox method, MS1 Scan arrived. Is BoxCar Scan: {0}.", isBoxCarScan);
if (!isBoxCarScan && Parameters.MS2ScanSetting.DoMS2)
{
DeconvoluteMS1ScanAddMS2Scan_TopN(scan);
}
if (isBoxCarScan)
{
BoxCarScanNum--;
}
if (BoxCarScanNum == 0)
{
lock (lockerScan)
{
FullScan.PlaceFullScan(m_scans, Parameters);
BoxCarScan.PlaceStaticBoxCarScan(m_scans, Parameters);
}
BoxCarScanNum = Parameters.BoxCarScanSetting.NumberOfBoxCarScans;
}
}
}
catch (Exception e)
{
Console.WriteLine("AddScanIntoQueue_StaticBoxMS2FromFullScan Exception!");
Console.WriteLine(e.ToString() + " " + e.Source);
}
}
