public static void PlaceFullScan(IScans m_scans, Parameters parameters)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.FullScanSetting.MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.FullScanSetting.MzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = parameters.FullScanSetting.MzRangeLowBound.ToString();
scan.Values["IsolationRangeHigh"] = parameters.FullScanSetting.MzRangeHighBound.ToString();
scan.Values["MaxIT"] = parameters.FullScanSetting.MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.FullScanSetting.Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString();
scan.Values["Microscans"] = parameters.FullScanSetting.Microscans.ToString();
scan.Values["AGC_Target"] = parameters.FullScanSetting.AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectRanges"] = "[]";
scan.Values["MsxInjectTargets"] = "[]";
scan.Values["MsxInjectMaxITs"] = "[]";
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing Full MS1 scan", DateTime.Now);
m_scans.SetCustomScan(scan);
}
/// <summary>
/// Start a new custom scan.
/// </summary>
private void StartNewScan()
{
ICustomScan cs = m_scans.CreateCustomScan();
cs.RunningNumber = m_runningNumber++;
// Allow an extra delay of 500 ms, we will answer as fast as possible, so this is a maximum value.
cs.SingleProcessingDelay = 0.50D;
// Toggle the polarity:
m_polarity = (m_polarity == 0) ? 1 : 0;
cs.Values["Polarity"] = m_polarity.ToString(NumberFormatInfo.InvariantInfo);
try
{
DateTime now = Instrument.Now;
if (!m_scans.SetCustomScan(cs))
{
Console.WriteLine("NEW CUSTOM SCAN HAS NOT BEEN PLACED, CONNECTION TO SERVICE BROKEN.");
}
Console.WriteLine(now.ToString(Program.TimeFormat) + ": Placed a new custom scan(" + cs.RunningNumber + ")");
}
catch (Exception e)
{
Console.WriteLine("PLACING A NEW SCAN: " + e.Message);
}
}
private ICustomScan baseMS1()
{
ICustomScan newscan = ScanManager.CreateCustomScan();
newscan.SingleProcessingDelay = 10.0D;
newscan.Values["FirstMass"] = Parameters["MS1_FirstMass"];
newscan.Values["LastMass"] = Parameters["MS1_LastMass"];
newscan.Values["Polarity"] = Parameters["MS1_Polarity"];
newscan.Values["NCE"] = "0"; // Whether this is set seems to control whether its an MS1 or MS2.
newscan.Values["Resolution"] = Parameters["MS1_Resolution"];
newscan.Values["AGC_Target"] = Parameters["MS1_AGC_Target"];
newscan.Values["MaxIT"] = Parameters["MS1_MaxIT"];
newscan.Values["Microscans"] = Parameters["MS1_Microscans"];
newscan.RunningNumber = ScanCount++;
return(newscan);
}
private void GenerateMS1()
{
ICustomScan newscan = ScanManager.CreateCustomScan();
newscan.SingleProcessingDelay = 10.0D;
newscan.Values["FirstMass"] = Parameters["MS1_FirstMass"];
newscan.Values["LastMass"] = Parameters["MS1_LastMass"];
newscan.Values["Polarity"] = Parameters["MS1_Polarity"];
newscan.Values["NCE"] = "0"; // Whether this is set seems to control whether its an MS1 or MS2.
newscan.Values["Resolution"] = Parameters["MS1_Resolution"];
newscan.Values["AGC_Target"] = Parameters["MS1_AGC_Target"];
newscan.Values["MaxIT"] = Parameters["MS1_MaxIT"];
newscan.Values["Microscans"] = Parameters["MS1_Microscans"];
newscan.RunningNumber = ScanCount++;
ScanID.Add(newscan.RunningNumber, ScanType.MS1);
//Console.WriteLine("Submitting |" + scanlabel + "| starting from " + sweep_mz.ToString() + " scan number " + current_scan_number);
scan_queue.Enqueue(newscan);
//log_write("Submitting MS1.");
}
private void PlaceScan()
{
// If no information about possible settings are available yet or if we finished our job, we bail out.
if ((m_scanId > 10) || (m_scans.PossibleParameters.Length == 0))
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.RunningNumber = m_scanId++;
scan.Values["Polarity"] = "1";
Console.WriteLine("{0:HH:mm:ss,fff} placing scan {1}", DateTime.Now, scan.RunningNumber);
m_scans.SetCustomScan(scan);
}
private void SubmitScan()
{
if (radioButton5.Checked)
{
IRepeatingScan rs = _scans.CreateRepeatingScan();
UpdateScan(rs);
_scans.SetRepetitionScan(rs);
}
else if (radioButton6.Checked)
{
ICustomScan cs = _scans.CreateCustomScan();
cs.SingleProcessingDelay = (double)numericUpDown4.Value;
UpdateScan(cs);
_scans.SetCustomScan(cs);
}
}
public static void PlaceMS2Scan(IScans m_scans, Parameters parameters, List <double> dynamicBox)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
double Range = parameters.MS1IonSelecting.IsolationWindow;
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.MS2ScanSetting.MS2MzRangeHighBound.ToString(); //TO THINK: Dynamic range as MqLive?
scan.Values["IsolationRangeLow"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["IsolationRangeHigh"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["MaxIT"] = parameters.MS2ScanSetting.MS2MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = parameters.MS2ScanSetting.NCE.ToString();
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
if (parameters.MS2ScanSetting.NCE_factors != "null")
{
scan.Values["NCE_Factors"] = parameters.MS2ScanSetting.NCE_factors;
}
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.MS2ScanSetting.MS2MicroScans.ToString();
scan.Values["AGC_Target"] = parameters.MS2ScanSetting.MS2AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
string dynamicTargets;
string dynamicMaxIts;
var dynamicBoxString = BuildDynamicBoxInclusionString(parameters, dynamicBox, out dynamicTargets, out dynamicMaxIts);
scan.Values["MsxInjectRanges"] = dynamicBoxString;
scan.Values["MsxInjectTargets"] = dynamicTargets;
scan.Values["MsxInjectMaxITs"] = dynamicMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing data dependent ms2 scan {1}", DateTime.Now, dynamicBoxString);
m_scans.SetCustomScan(scan);
}
private void PlaceScan()
{
if (m_scanId > 10)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.RunningNumber = m_scanId++;
scan.Values["Polarity"] = "1";
if (m_scanId == 5)
{
// Let the instrument wait for a maximum of 500 seconds, which will not happen under normal circumstances.
// Within that time, the instrument waits for placing a new scan
scan.SingleProcessingDelay = 500;
}
Console.WriteLine("{0:HH:mm:ss,fff} placing scan {1}", DateTime.Now, scan.RunningNumber);
m_scans.SetCustomScan(scan);
}
//parameter Tuple<double, double, double> for each box start m/z, end m/z, m/z length
public static void PlaceDynamicBoxCarScan(IScans m_scans, Parameters parameters, Tuple <double, double, double>[] dynamicBox)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = (parameters.BoxCarScanSetting.BoxCarMzRangeLowBound - 200).ToString();
scan.Values["IsolationRangeHigh"] = (parameters.BoxCarScanSetting.BoxCarMzRangeHighBound + 200).ToString();
scan.Values["MaxIT"] = parameters.BoxCarScanSetting.BoxCarMaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.BoxCarScanSetting.BoxCarResolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.BoxCarScanSetting.BoxCarNormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.BoxCarScanSetting.BoxCarMicroScans.ToString();
scan.Values["AGC_Target"] = parameters.BoxCarScanSetting.BoxCarAgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
string dynamicTargets;
string dynamicMaxIts;
var dynamicBoxString = BuildDynamicBoxString(parameters, dynamicBox, out dynamicTargets, out dynamicMaxIts);
scan.Values["MsxInjectRanges"] = dynamicBoxString;
scan.Values["MsxInjectTargets"] = dynamicTargets;
scan.Values["MsxInjectMaxITs"] = dynamicMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing Dynamic BoxCar MS1 scan {1}", DateTime.Now, dynamicBoxString);
m_scans.SetCustomScan(scan);
}
void send_inaugural_scan()
{
ICustomScan scan = scanner.CreateCustomScan();
scan.SingleProcessingDelay = 5.0D;
scan.Values["FirstMass"] = "345";
scan.Values["LastMass"] = "789";
scan.Values["Polarity"] = "0";
scan.Values["NCE"] = "0"; // Whether this is set seems to control whether its an MS1 or MS2.
scan.Values["Resolution"] = "15000";
scan.Values["AGC_Target"] = "10000";
scan.Values["MaxIT"] = "10";
scan.Values["Microscans"] = "1";
can_submit_scan.WaitOne();
while (!scanner.SetCustomScan(scan))
{
Thread.Sleep(5);
}
Console.WriteLine("Submitted starting scan.");
}
public static void PlaceStaticBoxCarScan(IScans m_scans, Parameters parameters)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = (parameters.BoxCarScanSetting.BoxCarMzRangeLowBound).ToString();
scan.Values["IsolationRangeHigh"] = (parameters.BoxCarScanSetting.BoxCarMzRangeHighBound).ToString();
scan.Values["MaxIT"] = parameters.BoxCarScanSetting.BoxCarMaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.BoxCarScanSetting.BoxCarResolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.BoxCarScanSetting.BoxCarNormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.BoxCarScanSetting.BoxCarMicroScans.ToString();
scan.Values["AGC_Target"] = parameters.BoxCarScanSetting.BoxCarAgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectTargets"] = StaticBoxCarScanTargets;
scan.Values["MsxInjectMaxITs"] = StaticBoxCarScanMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
for (int i = 0; i < parameters.BoxCarScanSetting.NumberOfBoxCarScans; i++)
{
scan.Values["MsxInjectRanges"] = StaticBoxCarScanRanges[i];
Console.WriteLine("{0:HH:mm:ss,fff} placing BoxCar MS1 scan", DateTime.Now);
m_scans.SetCustomScan(scan);
}
}
public static void PlaceMS2Scan(IScans m_scans, Parameters parameters, double mz)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
double Range = parameters.MS1IonSelecting.IsolationWindow;
string xl = (mz - Range).ToString("0.000");
string xh = (mz + Range).ToString("0.000");
if (mz - Range < 50.0)
{
Console.WriteLine("placing data dependent ms2 scan wrong, the Ms2MzRangeLowBound should larger than 50!!!");
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.MS2ScanSetting.MS2MzRangeHighBound.ToString(); //TO THINK: Dynamic range as MqLive?
scan.Values["IsolationRangeLow"] = xl;
scan.Values["IsolationRangeHigh"] = xh;
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["MaxIT"] = parameters.MS2ScanSetting.MS2MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = parameters.MS2ScanSetting.NCE.ToString();
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
if (parameters.MS2ScanSetting.NCE_factors != "null")
{
scan.Values["NCE_Factors"] = parameters.MS2ScanSetting.NCE_factors;
}
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.MS2ScanSetting.MS2MicroScans.ToString();
scan.Values["AGC_Target"] = parameters.MS2ScanSetting.MS2AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectRanges"] = "[]";
scan.Values["MsxInjectTargets"] = "[]";
scan.Values["MsxInjectMaxITs"] = "[]";
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
//Console.WriteLine("++++++++++++++++++");
//Console.WriteLine("Target Isolation Mass: {0}, {1}", xl, xh);
//foreach (var v in scan.Values)
//{
// Console.WriteLine(v);
//}
////This is the code where we find all the scan settings.
////foreach (var item in m_scans.PossibleParameters)
////{
//// Console.WriteLine(item.Name + "----" + item.DefaultValue + "----" + item.Help + "----" + item.Selection);
////}
Console.WriteLine("{0:HH:mm:ss,fff} placing data dependent ms2 scan {1}", DateTime.Now, mz);
m_scans.SetCustomScan(scan);
}