private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
// If examining code takes longer, in particular for some scans, it is wise
// to use a processing queue in order to get the system as responsive as possible.
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("==================================================");
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
//TO THINK: If the coming scan is MS2 scan, start the timing of the scan precursor into exclusion list. Currently, start when add the scan precursor.
if (!IsTakeOverScan(scan))
{
if (IsMS1Scan(scan))
{
Console.WriteLine("MS1 Scan arrived.");
if (!TimeIsOver)
{
AddScanIntoQueueAction(scan);
}
}
else
{
Console.WriteLine("MS2 Scan arrived.");
}
}
else if (!firstFullScanPlaced)
{
FullScan.PlaceFullScan(m_scans, Parameters);
Console.WriteLine("Place First User defined Full Scan.");
firstFullScanPlaced = true;
}
}
}
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);
}
}
//Tranditional ShotGun DDA workflow.
private void AddScanIntoQueue_ShotGun(IMsScan scan)
{
try
{
//Is MS1 Scan
if (scan.HasCentroidInformation)
{
Console.WriteLine("MS1 Scan arrived. Is BoxCar Scan: {0}. Deconvolute.", IsBoxCarScan(scan));
DeconvoluteMS1ScanAddMS2Scan_TopN(scan);
lock (lockerScan)
{
FullScan.PlaceFullScan(m_scans, Parameters);
}
}
}
catch (Exception e)
{
Console.WriteLine("AddScanIntoQueue_BottomUp Exception!");
Console.WriteLine(e.ToString() + " " + e.Source);
}
}
private void PlaceUserDefined(IMsScan scan)
{
Console.WriteLine("\n{0:HH:mm:ss,fff} UserDefined Start", DateTime.Now);
var monomass = 16950.88339;
Dictionary <int, double> mz_z = new Dictionary <int, double>();
for (int i = 15; i <= 27; i++)
{
mz_z.Add(i, monomass.ToMz(i));
}
var mzs = mz_z.Values;
//foreach (var mz in mzs)
//{
// Parameters.MS2ScanSetting.NCE = 10;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 15;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 20;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 25;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 30;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 35;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 40;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 45;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 50;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
//}
//Parameters.MS2ScanSetting.NCE = 25;
//foreach (var mz in mzs)
//{
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "null";
//}
int j = 15;
while (j <= 27)
{
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "null";
j += 1;
}
List <double> comb = new List <double>();
comb.Add(mz_z[20]);
comb.Add(mz_z[21]);
comb.Add(mz_z[22]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[19]);
comb.Add(mz_z[21]);
comb.Add(mz_z[23]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[17]);
comb.Add(mz_z[21]);
comb.Add(mz_z[25]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[17]);
comb.Add(mz_z[19]);
comb.Add(mz_z[21]);
comb.Add(mz_z[23]);
comb.Add(mz_z[25]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
FullScan.PlaceFullScan(m_scans, Parameters);
}
private void AddScanIntoQueue_DynamicBoxCar_TD(IMsScan scan)
{
try
{
//Is MS1 Scan
if (scan.HasCentroidInformation)
{
List <ChargeEnvelop> chargeEnvelops;
var isoEnvelops = Deconvolute_TD(scan, out chargeEnvelops);
Console.WriteLine("chargeEnvelops.Count: {0}", isoEnvelops.Count);
if (Parameters.BoxCarScanSetting.DoDbcForMS1)
{
if (IsBoxCarScan(scan))
{
PlaceDynamicBoxCarMS2Scan(scan, chargeEnvelops, isoEnvelops);
FullScan.PlaceFullScan(m_scans, Parameters);
}
else
{
if (chargeEnvelops.Count >= 1 || isoEnvelops.Count >= 5)
{
lock (lockerExclude)
{
var thred = isoEnvelops.OrderByDescending(p => p.IntensityRatio).First().IntensityRatio / 20;
var isos = isoEnvelops.Where(p => p.IntensityRatio > thred);
foreach (var x in isos)
{
DynamicExclusionList.exclusionList.Enqueue(new Tuple <double, int, DateTime>(x.ExperimentIsoEnvelop.First().Mz, x.Charge, DateTime.Now));
}
}
var boxes = BoxCarScan.GenerateDynamicBoxes_TD(isoEnvelops);
BoxCarScan.PlaceDynamicBoxCarScan(m_scans, Parameters, boxes);
}
else
{
FullScan.PlaceFullScan(m_scans, Parameters);
}
}
}
else
{
if (Parameters.BoxCarScanSetting.PrecursorSkipScan)
{
FullScan.PlaceFullScan(m_scans, Parameters);
PlaceDynamicBoxCarMS2Scan(scan, chargeEnvelops, isoEnvelops);
}
else
{
PlaceDynamicBoxCarMS2Scan(scan, chargeEnvelops, isoEnvelops);
FullScan.PlaceFullScan(m_scans, Parameters);
}
}
}
}
catch (Exception e)
{
Console.WriteLine("AddScanIntoQueue_DynamicBox Exception!");
Console.WriteLine(e.ToString() + " " + e.Source);
}
}