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);
}
}
public FusionBridge(string debugMzML, string logDir, bool showConsoleLogs)
{
Logs = new List <string>();
LogDir = logDir;
ShowConsoleLogs = showConsoleLogs;
IFusionInstrumentAccessContainer fusionContainer = null;
if (!String.IsNullOrEmpty(debugMzML)) // create fake Fusion container that reads from mzML file
{
WriteLog("FusionBridge constructor called in debug mode");
WriteLog(string.Format("Reading scans from {0}", debugMzML));
fusionContainer = new MzMLFusionContainer(debugMzML);
}
else // needs license to connect to the real instrument
{
//// Use the Factory creation method to create a Fusion Access Container
WriteLog("FusionBridge constructor called");
fusionContainer = getIFusionInstrumentAccessContainer();
}
// Connect to the service by going 'online'
fusionContainer.StartOnlineAccess();
// Wait until the service is connected
// (better through the event, but this is nice and simple)
while (!fusionContainer.ServiceConnected)
{
;
}
// From the instrument container, get access to a particular instrument
InstrumentAccess = fusionContainer.Get(1);
ScanContainer = InstrumentAccess.GetMsScanContainer(0);
WriteLog("Detector class: " + ScanContainer.DetectorClass);
// Dump key-value pairs in cs.Values
WriteLog("Custom scan parameters: ");
InstrumentControl = InstrumentAccess.Control;
ScanControl = InstrumentControl.GetScans(false);
ICustomScan cs = ScanControl.CreateCustomScan();
foreach (KeyValuePair <string, string> kvp in cs.Values)
{
string kvpString = string.Format("- cs.Values\tKey = {0}, Value = {1}", kvp.Key, kvp.Value);
WriteLog(kvpString);
}
// Print instrument state
WriteLog("FusionBridge constructor initialised");
IState state = InstrumentControl.Acquisition.State;
string msg = string.Format("System mode = {0}, system state = {1}", state.SystemMode,
state.SystemState);
WriteLog(msg);
}
public bool SetCustomScan(ICustomScan cs)
{
// select whether to generate ms1 or msn spectra from the read mzML data
List <SimpleSpectrum> spectraList = null;
if (cs.Values["ScanType"] == "Full")
{
// if empty, copy ms1 spectra from the original list
if (this.myScanContainer.ms1Spectra.Count == 0)
{
this.myScanContainer.ms1Spectra = new List <SimpleSpectrum>(this.myScanContainer.originalMs1Spectra);
}
spectraList = this.myScanContainer.ms1Spectra;
}
else if (cs.Values["ScanType"] == "MSn")
{
// if empty, copy msn spectra from the original list
if (this.myScanContainer.msnSpectra.Count == 0)
{
this.myScanContainer.msnSpectra = new List <SimpleSpectrum>(this.myScanContainer.originalMsnSpectra);
}
spectraList = this.myScanContainer.msnSpectra;
}
// if we can actually generate a custom scan ...
if (spectraList.Count > 0)
{
// pop a spectrum from the list
SimpleSpectrum current = spectraList[0];
spectraList.RemoveAt(0);
// pretend to do a scan for some time
double scanDuration = this.myScanContainer.scanDurations.ContainsKey(current.ScanNumber) ?
this.myScanContainer.scanDurations[current.ScanNumber] : 0.25;
//Console.WriteLine("Scan number={0} duration={1}", current.ScanNumber, scanDuration);
// delay for scan duration + half of single processing delay
//double spdDelay = cs.SingleProcessingDelay / 2;
//double totalDelay = scanDuration + spdDelay;
// delay for scan duration only
double totalDelay = scanDuration;
// send the scan and trigger canAcceptNextCustomScan event some time later
int milliSecondDelay = ((int)totalDelay) * 1000;
IMsScan msScan = new MyMsScan(current, cs.RunningNumber, this.startTime);
Task.Delay(milliSecondDelay).ContinueWith(t => OnSingleProcessingDelay(msScan));
return(true);
}
return(false);
}
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);
}
}
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);
}
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);
}
private void GenerateMS1()
{
ICustomScan basic_ms1 = baseMS1();
ScanID.Add(basic_ms1.RunningNumber, ScanType.MS1);
ICustomScan box_1 = baseMS1();
box_1.Values["MsxInjectRanges"] = Parameters["Box_1_Ranges"];
box_1.Values["MsxInjectTarget"] = Parameters["Box_InjectTargets"];
box_1.Values["MsxInjectMaxITs"] = Parameters["Box_MaxITs"];
box_1.Values["MsxInjectNCEs"] = Parameters["Box_InjectNCEs"];
ScanID.Add(box_1.RunningNumber, ScanType.BoxMS1_1);
ICustomScan box_2 = baseMS1();
box_2.Values["MsxInjectRanges"] = Parameters["Box_2_Ranges"];
box_2.Values["MsxInjectTarget"] = Parameters["Box_InjectTargets"];
box_2.Values["MsxInjectMaxITs"] = Parameters["Box_MaxITs"];
box_2.Values["MsxInjectNCEs"] = Parameters["Box_InjectNCEs"];
ScanID.Add(box_2.RunningNumber, ScanType.BoxMS1_2);
ICustomScan box_3 = baseMS1();
box_3.Values["MsxInjectRanges"] = Parameters["Box_3_Ranges"];
box_3.Values["MsxInjectTarget"] = Parameters["Box_InjectTargets"];
box_3.Values["MsxInjectMaxITs"] = Parameters["Box_MaxITs"];
box_3.Values["MsxInjectNCEs"] = Parameters["Box_InjectNCEs"];
ScanID.Add(box_3.RunningNumber, ScanType.BoxMS1_3);
Console.WriteLine("BOXED." + " " + basic_ms1.RunningNumber.ToString()
+ " " + box_1.RunningNumber.ToString()
+ " " + box_2.RunningNumber.ToString()
+ " " + box_2.RunningNumber.ToString());
scan_queue.Enqueue(basic_ms1);
scan_queue.Enqueue(box_1);
scan_queue.Enqueue(box_2);
scan_queue.Enqueue(box_3);
MS1_outstanding = true;
}
public override bool assignScan(out ICustomScan newscan)
{
newscan = null;
//Console.WriteLine("Attempting assignment; " + MS1_outstanding.ToString());
if (scan_queue.IsEmpty && MS1_tardiness.Elapsed > MS1_expiration_span)
{
//Debug.Assert(false);
Console.WriteLine("ERRANT MS1, resubmitting MS1.");
log_write("MS1 TIMEOUT AT " + RunTimer.Elapsed.ToString());
MS1_outstanding = false;
}
//ICustomScan newscan;
if (!scan_queue.TryDequeue(out newscan) && !MS1_outstanding)
{
GenerateMS1();
MS1_outstanding = true;
MS1_tardiness.Restart();
Debug.Assert(scan_queue.Count == 1);
Debug.Assert(scan_queue.TryDequeue(out newscan));
Console.WriteLine("Generated MS1.");
log_write("Generated MS1.");
}
if (newscan == null)
{
Console.Write(".");
//log_write("Waiting for assignment. " + MS1_tardiness.Elapsed.ToString());
logfile.Flush();
return(false);
}
else
{
ScanType scantype = ScanType.Unknown;
ScanID.TryGetValue(newscan.RunningNumber, out scantype);
Console.WriteLine("Assigning " + scantype.ToString() + " " + newscan.RunningNumber.ToString());
log_write("Assigning " + scantype.ToString() + " " + newscan.RunningNumber.ToString());
logfile.Flush();
return(true);
}
}
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.");
}
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.");
}
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);
}
}
void submitScan() // Separate from readyForScan_Response so that it can be called directly to begin custom scans.
{
try
{
acquisition.WaitFor(TimeSpan.FromSeconds(0.5), SystemMode.On, SystemMode.DirectControl);
ICustomScan newscan = null;
while (accepting_scans && newscan == null)
{
//Console.WriteLine("Entering mutex2.");
planner_MUT.WaitOne();
//Console.WriteLine("Got mutex2.");
runProgram.assignScan(out newscan);
//Console.WriteLine("Leaving mutex2.");
planner_MUT.ReleaseMutex();
//Console.WriteLine("Out of mutex2.");
Thread.Sleep(5);
}
//bool result = scanner.SetCustomScan(newscan);
//Console.WriteLine("Waiting to submit.");
logfile.WriteLine("Waiting to submit.");
can_submit_scan.WaitOne(); // WaitOne also grabs a semaphore-unit, apparently.
//Console.WriteLine("Initiating submission.");
logfile.WriteLine("Initiating submission.");
while (accepting_scans && !scanner.SetCustomScan(newscan))
{
Thread.Sleep(5);
}
//Console.WriteLine("Submitted.");
logfile.WriteLine("Submitted.");
}
catch (Exception err)
{
Console.WriteLine("Caught exception in submitScan! Cancelling voltage.");
change_voltage(0);
Console.WriteLine(err.ToString());
throw;
}
}
private void GenerateMS2s(IEnumerable <Tuple <int, Tuple <double, double> > > mz_sites)
{
HashSet <double> unexclude_mzs = new HashSet <double>();
foreach (var mz in mz_exclusion_intervals.Keys)
{
if (mz_exclusion_intervals[mz] + exclusion_time_interval < RunTimer.Elapsed)
{
unexclude_mzs.Add(mz);
}
}
Console.WriteLine("Unexcluding " + unexclude_mzs.Count.ToString() + " of " + mz_exclusion_intervals.Count.ToString());
foreach (var mz in unexclude_mzs)
{
mz_exclusion_intervals.Remove(mz);
}
int assigned_scan_count = 0;
int MS1_after_number = scan_limit_per_cycle - 4;
bool MS1_submitted = false;
foreach (var precursor in mz_sites)
{
double mz_site = precursor.Item2.Item1;
int charge = precursor.Item1;
if (assigned_scan_count > scan_limit_per_cycle)
{
break;
}
if (mz_site == 0)
{
continue;
}
if (precursor.Item2.Item2 < PrecursorIntensityThreshold)
{
continue;
}
bool excluded = false;
foreach (var mz in mz_exclusion_intervals.Keys)
{
if (Math.Abs(mz - mz_site) < mz_tolerance)
{
excluded = true;
break;
}
}
if (excluded)
{
continue;
}
// Setting charge above 5 seems to cause an error; higher-charge
// peptides can still be found if the charge is set to 5.
if (charge > 5)
{
charge = 5;
}
mz_exclusion_intervals[mz_site] = RunTimer.Elapsed;
ICustomScan newscan = ScanManager.CreateCustomScan();
newscan.SingleProcessingDelay = 10.0D;
newscan.Values["IsolationRangeLow"] = (mz_site - (isolation_width / 2)).ToString();
newscan.Values["IsolationRangeHigh"] = (mz_site + (isolation_width / 2)).ToString();
newscan.Values["FirstMass"] = Parameters["MS2_FirstMass"];
newscan.Values["LastMass"] = Parameters["MS2_LastMass"];
newscan.Values["Polarity"] = Parameters["MS2_Polarity"];
newscan.Values["NCE"] = Parameters["MS2_NCE"]; // Whether this is set seems to control whether its an MS1 or MS2.
newscan.Values["NCE_NormCharge"] = charge.ToString();
newscan.Values["Resolution"] = Parameters["MS2_Resolution"];
newscan.Values["AGC_Target"] = Parameters["MS2_AGC_Target"];
newscan.Values["MaxIT"] = Parameters["MS2_MaxIT"]; // Is this in ms???????
newscan.Values["Microscans"] = Parameters["MS2_Microscans"];
newscan.RunningNumber = ScanCount++;
ScanID.Add(newscan.RunningNumber, ScanType.MS2);
//Console.WriteLine("Normcharge: " + charge.ToString());
assigned_scan_count += 1;
scan_queue.Enqueue(newscan);
scaninfo_file.WriteLine(newscan.RunningNumber.ToString() + " " + mz_site.ToString() + " " + charge.ToString() + " " + precursor.Item2.Item2 + "__");
if ((!MS1_submitted) && assigned_scan_count >= MS1_after_number)
{
GenerateMS1();
Console.WriteLine("MS1 submitted midcycle.");
log_write("MS1 submitted midcycle.");
MS1_submitted = true;
MS1_outstanding = true;
MS1_tardiness.Restart();
}
}
if (!MS1_submitted)
{
GenerateMS1();
Console.WriteLine("MS1 submitted postcycle.");
log_write("MS1 submitted postcycle.");
MS1_submitted = true;
MS1_outstanding = true;
MS1_tardiness.Restart();
}
Console.WriteLine("MS2s: Submitted " + assigned_scan_count.ToString() + " out of " + mz_sites.Count() + " " + scan_queue.Count());
log_write("MS2s: Submitted " + assigned_scan_count.ToString() + " out of " + mz_sites.Count() + " " + scan_queue.Count());
}
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);
}
public abstract bool assignScan(out ICustomScan newscan);
public bool CreateCustomScan(long runningNumber, double precursorMass, double isolationWidth, double collisionEnergy, int msLevel,
string polarity, double firstMass, double lastMass, double singleProcessingDelay)
{
WriteLog(String.Format("Placing a custom scan (runningNumber={0}, singleProcessingDelay={1})", runningNumber, singleProcessingDelay));
// TODO: validate input
if (ScanControl.PossibleParameters.Length > 0)
{
ICustomScan cs = ScanControl.CreateCustomScan();
cs.RunningNumber = runningNumber;
// Allow an extra delay of 500 ms, we will answer as fast as possible, so this is a maximum value.
cs.SingleProcessingDelay = singleProcessingDelay;
// Set the custom scan parameters
cs.Values["CollisionEnergy"] = collisionEnergy.ToString();
cs.Values["FirstMass"] = firstMass.ToString();
cs.Values["LastMass"] = lastMass.ToString();
cs.Values["Analyzer"] = "Orbitrap";
cs.Values["Polarity"] = polarity;
cs.Values["IsolationWidth"] = isolationWidth.ToString();
cs.Values["PrecursorMass"] = precursorMass.ToString();
if (msLevel == 1)
{
cs.Values["ScanType"] = "Full";
cs.Values["OrbitrapResolution"] = "120000";
}
else
{
cs.Values["ScanType"] = "MSn";
cs.Values["OrbitrapResolution"] = "7500";
}
cs.Values["ActivationType"] = "HCD";
cs.Values["DataType"] = "Centroid";
cs.Values["AGCTarget"] = "30000";
cs.Values["MaxIT"] = "100";
cs.Values["Microscans"] = "3";
// Dump key-value pairs in cs.Values
foreach (KeyValuePair <string, string> kvp in cs.Values)
{
string msg = string.Format("- cs.Values\tKey = {0}, Value = {1}", kvp.Key, kvp.Value);
WriteLog(msg);
}
try
{
if (!ScanControl.SetCustomScan(cs))
{
WriteLog(String.Format("FAILED to place a custom scan (runningNumber={0}): connection to service broken!!", cs.RunningNumber));
return(false);
}
else
{
if (cs.Values["ScanType"] == "Full")
{
WriteLog(String.Format("Successfully placed a custom fullscan scan (runningNumber={0})", cs.RunningNumber));
}
else if (cs.Values["ScanType"] == "MSn")
{
WriteLog(String.Format("Successfully placed a custom MSn scan (runningNumber={0})", cs.RunningNumber));
}
return(true);
}
}
catch (Exception e)
{
WriteLog(String.Format("FAILED to place a custom scan (runningNumber={0}): {1}", cs.RunningNumber, e.Message));
WriteLog(String.Format("Stacktrace: {0}", e.StackTrace));
throw;
}
}
else
{
WriteLog(String.Format("FAILED to place a custom scan (runningNumber={0}): no parameters available!!", runningNumber));
return(false);
}
}
private void GenerateMS2s(IEnumerable <Peak> mz_sites)
{
exclusion_list.Unexclude(RunTimer.Elapsed);
int assigned_scan_count = 0;
int MS1_after_number = scan_limit_per_cycle - 4;
bool MS1_submitted = false;
foreach (var precursor in mz_sites)
{
double mz_site = precursor.Item1;
int charge;
if (precursor.Item3 != null)
{
charge = (int)precursor.Item3;
}
else
{
charge = 2;
}
if (assigned_scan_count > scan_limit_per_cycle)
{
break;
}
if (mz_site == 0)
{
continue;
}
if (precursor.Item2 < PrecursorIntensityThreshold)
{
continue;
}
if (exclusion_list.Is_Excluded(RunTimer.Elapsed, precursor))
{
continue;
}
// Setting charge above 5 seems to cause an error; higher-charge
// peptides can still be found if the charge is set to 5.
if (charge > 5)
{
charge = 5;
}
exclusion_list.Exclude(RunTimer.Elapsed, precursor);
//double injection_time = (65000000.0 / precursor.Item2.Item2) + 0.03;
double prec_int = precursor.Item2;
double injection_time = -1;
if (prec_int < PrecursorAGCThreshold)
{
injection_time = 50.0;
}
//else
//{
// injection_time = (Convert.ToDouble(Parameters["INJ_Constant"]) / precursor.Item2.Item2) + 0.03;
// if (injection_time > 50.0)
// {
// injection_time = 50.0;
// }
//}
ICustomScan newscan = ScanManager.CreateCustomScan();
newscan.SingleProcessingDelay = 10.0D;
newscan.Values["IsolationRangeLow"] = (mz_site - (isolation_width / 2)).ToString();
newscan.Values["IsolationRangeHigh"] = (mz_site + (isolation_width / 2)).ToString();
newscan.Values["FirstMass"] = Parameters["MS2_FirstMass"];
newscan.Values["LastMass"] = Parameters["MS2_LastMass"];
newscan.Values["Polarity"] = Parameters["MS2_Polarity"];
newscan.Values["NCE"] = Parameters["MS2_NCE"]; // Whether this is set seems to control whether its an MS1 or MS2.
newscan.Values["NCE_NormCharge"] = charge.ToString();
newscan.Values["Resolution"] = Parameters["MS2_Resolution"];
newscan.Values["Microscans"] = Parameters["MS2_Microscans"];
if (injection_time > 0)
{
newscan.Values["AGC_Mode"] = "0";
newscan.Values["MaxIT"] = injection_time.ToString();
}
else
{
newscan.Values["AGC_Target"] = Parameters["MS2_AGC_Target"];
newscan.Values["MaxIT"] = Parameters["MS2_MaxIT"];
}
newscan.RunningNumber = ScanCount++;
ScanID.Add(newscan.RunningNumber, ScanType.MS2);
//Console.WriteLine("Normcharge: " + charge.ToString());
assigned_scan_count += 1;
scan_queue.Enqueue(newscan);
scaninfo_file.WriteLine(newscan.RunningNumber.ToString() + " " + mz_site.ToString() + " " + charge.ToString() + " " + injection_time.ToString() + " " + prec_int.ToString() + "__");
if ((!MS1_submitted) && assigned_scan_count >= MS1_after_number)
{
GenerateMS1();
Console.WriteLine("MS1 submitted midcycle.");
log_write("MS1 submitted midcycle.");
MS1_submitted = true;
MS1_outstanding = true;
MS1_tardiness.Restart();
}
}
if (!MS1_submitted)
{
GenerateMS1();
Console.WriteLine("MS1 submitted postcycle.");
log_write("MS1 submitted postcycle.");
MS1_submitted = true;
MS1_outstanding = true;
MS1_tardiness.Restart();
}
Console.WriteLine("MS2s: Submitted " + assigned_scan_count.ToString() + " out of " + mz_sites.Count() + " " + scan_queue.Count());
log_write("MS2s: Submitted " + assigned_scan_count.ToString() + " out of " + mz_sites.Count() + " " + scan_queue.Count());
scaninfo_file.Flush();
}
private void GenerateMS2s(IEnumerable <Peak> mz_sites)
{
HashSet <double> unexclude_mzs = new HashSet <double>();
foreach (var mz in mz_exclusion_intervals.Keys)
{
if (mz_exclusion_intervals[mz] + exclusion_time_interval < RunTimer.Elapsed)
{
unexclude_mzs.Add(mz);
}
}
Console.WriteLine("Unexcluding " + unexclude_mzs.Count.ToString() + " of " + mz_exclusion_intervals.Count.ToString());
foreach (var mz in unexclude_mzs)
{
mz_exclusion_intervals.Remove(mz);
}
int assigned_scan_count = 0;
foreach (var precursor in mz_sites)
{
//Tuple<double, double> precursor = charge_precursor.Item2;
//double mz_site = precursor.Item1;
//int charge = charge_precursor.Item1;
double mz_site = precursor.Item1;
int charge;
if (precursor.Item3 != null)
{
charge = (int)precursor.Item3;
}
else
{
charge = 2;
}
if (assigned_scan_count > scan_limit_per_cycle)
{
break;
}
// Setting charge above 5 seems to cause an error; higher-charge
// peptides can still be found if the charge is set to 5.
if (mz_site == 0 || charge > 5)
{
continue;
}
bool excluded = false;
foreach (var mz in mz_exclusion_intervals.Keys)
{
if (Math.Abs(mz - mz_site) < mz_tolerance)
{
excluded = true;
break;
}
}
if (excluded)
{
continue;
}
mz_exclusion_intervals[mz_site] = RunTimer.Elapsed;
ICustomScan newscan = ScanManager.CreateCustomScan();
newscan.SingleProcessingDelay = 10.0D;
newscan.Values["IsolationRangeLow"] = (mz_site - (isolation_width / 2)).ToString();
newscan.Values["IsolationRangeHigh"] = (mz_site + (isolation_width / 2)).ToString();
newscan.Values["FirstMass"] = "100";
newscan.Values["LastMass"] = "2000";
newscan.Values["Polarity"] = "0";
newscan.Values["NCE"] = "27"; // Whether this is set seems to control whether its an MS1 or MS2.
newscan.Values["NCE_NormCharge"] = charge.ToString();
newscan.Values["Resolution"] = "15000";
newscan.Values["AGC_Target"] = "10000";
newscan.Values["MaxIT"] = "50"; // Is this in ms???????
newscan.Values["Microscans"] = "1";
newscan.RunningNumber = ScanCount++;
ScanID.Add(newscan.RunningNumber, ScanType.MS2);
Console.WriteLine("Normcharge: " + charge.ToString());
assigned_scan_count += 1;
scan_queue.Enqueue(newscan);
}
Console.WriteLine("MS2s: Submitted " + assigned_scan_count.ToString() + " out of " + mz_sites.Count() + " " + scan_queue.Count());
}
