static void Main_Peakpick_Test(string[] args)
{
Console.WriteLine("Peakpicking test!");
string spectrumfile = "//rc-data1/blaise/ms_data_share/Max/QE_API/peakpick_testing/segment.txt";
string outputfile = "//rc-data1/blaise/ms_data_share/Max/QE_API/peakpick_testing/seg_output.txt";
List <Peak> spectrum_agg = new List <Peak>();
int scan_number = -1;
StreamReader spectrum_data = File.OpenText(spectrumfile);
StreamWriter peak_output = new StreamWriter(outputfile);
string line = null;
while ((line = spectrum_data.ReadLine()) != null)
{
if (line.Contains('#'))
{
List <Peak> pickedpeaks = Spectral_Processing.deisotope_scan(spectrum_agg);
peak_output.WriteLine("SCAN {0}", scan_number.ToString());
foreach (Peak charge_peak in pickedpeaks)
{
peak_output.WriteLine("{0} {1} {2}",
charge_peak.Item1,
charge_peak.Item2,
charge_peak.Item3);
}
peak_output.WriteLine("#");
Console.WriteLine(scan_number.ToString() + " " + pickedpeaks.Count().ToString());
}
else if (line.Contains("SCAN"))
{
string scannumstr = line.Split(' ')[1];
Debug.Assert(Int32.TryParse(scannumstr, out scan_number));
spectrum_agg.Clear();
}
else
{
string[] words = line.Split(' ');
Debug.Assert(words.Length == 2);
double mz = -1;
double intensity = -1;
Debug.Assert(Double.TryParse(words[0], out mz));
Debug.Assert(Double.TryParse(words[1], out intensity));
spectrum_agg.Add(new Peak(mz, intensity, null));
}
}
peak_output.Close();
}
public override void receiveScan(IMsScan scanData)
{
//IInfoContainer info = scanData.CommonInformation;
//IInfoContainer more_info = scanData.SpecificInformation;
//MsScanInformationSource infosource = MsScanInformationSource.Unknown;
object obj_holder = null;
ScanType scan_id = ScanType.Unknown;
int scannum = -1;
//if (info.TryGetRawValue("Scan", out obj_holder, ref infosource))
//{
// scannum = (int)obj_holder;
// if (ScanID.ContainsKey(scannum)) // Auto-scans also have Scan numbers!
// {
// scan_id = ScanID[scannum];
// ScanID.Remove(scannum);
// }
//}
//object accessid = null;
if (scanData.SpecificInformation.TryGetRawValue("Access Id:", out obj_holder))
{
scannum = (int)obj_holder;
if (ScanID.ContainsKey(scannum))
{
scan_id = ScanID[scannum];
ScanID.Remove(scannum);
}
}
//Debug.Assert(false);
if (scannum >= ScanCount)
{
Console.WriteLine("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
log_write("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
ScanCount = scannum + 1;
}
//else if (scannum + 100 < ScanCount)
//{
// Console.WriteLine("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// log_write("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// ScanCount = scannum + 1;
//}
Console.WriteLine("Received a " + scan_id.ToString() + " " + scannum.ToString());
log_write("Received a " + scan_id.ToString() + " " + scannum.ToString());
switch (scan_id)
{
case ScanType.MS2:
case ScanType.Auto:
case ScanType.Unknown:
return;
case ScanType.MS1:
MS1_outstanding = false;
IEnumerable <Tuple <double, double> > scan = Spectral_Processing.ConvertCentroids(scanData.Centroids);
List <Tuple <int, Tuple <double, double> > > molecular_peaks = Spectral_Processing.deisotope_scan(scan);
IEnumerable <Tuple <int, Tuple <double, double> > > valid_precursors = molecular_peaks.Where(x => x.Item1 > 1);
IEnumerable <Tuple <int, Tuple <double, double> > > precursors_by_int = valid_precursors.OrderByDescending(OrderPeak);
GenerateMS2s(precursors_by_int);
Console.WriteLine("MS1 stats: " + scan.Count() + " " + valid_precursors.Count());
log_write("MS1 stats: " + scan.Count() + " " + valid_precursors.Count());
return;
default:
Debug.Assert(false);
return;
}
}
public override void receiveScan(IMsScan scanData)
{
//IInfoContainer info = scanData.CommonInformation;
//IInfoContainer more_info = scanData.SpecificInformation;
//MsScanInformationSource infosource = MsScanInformationSource.Unknown;
object obj_holder = null;
ScanType scan_id = ScanType.Unknown;
int scannum = -1;
//if (info.TryGetRawValue("Scan", out obj_holder, ref infosource))
//{
// scannum = (int)obj_holder;
// if (ScanID.ContainsKey(scannum)) // Auto-scans also have Scan numbers!
// {
// scan_id = ScanID[scannum];
// ScanID.Remove(scannum);
// }
//}
//object accessid = null;
if (scanData.SpecificInformation.TryGetRawValue("Access Id:", out obj_holder))
{
scannum = (int)obj_holder;
if (ScanID.ContainsKey(scannum))
{
scan_id = ScanID[scannum];
ScanID.Remove(scannum);
}
}
if (scannum > ScanCount)
{
Console.WriteLine("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
log_write("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
ScanCount = scannum + 1;
}
//else if (scannum + 100 < ScanCount)
//{
// Console.WriteLine("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// log_write("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// ScanCount = scannum + 1;
//}
Console.WriteLine("Received a " + scan_id.ToString() + " " + scannum.ToString());
log_write("Received a " + scan_id.ToString() + " " + scannum.ToString());
switch (scan_id)
{
case ScanType.MS1:
case ScanType.MS2:
case ScanType.Auto:
case ScanType.Unknown:
// Only Box-MS1 scans are being used for precursor assignment.
// Other scans are merely written to the file automatically.
return;
case ScanType.BoxMS1_1:
case ScanType.BoxMS1_2:
case ScanType.BoxMS1_3:
//MS1_outstanding -= 1;
Debug.Assert(!BoxAggregation.ContainsKey(scan_id));
BoxAggregation.Add(scan_id, Spectral_Processing.ConvertCentroids(scanData.Centroids).ToList());
Console.WriteLine("Received MS1 " + MS1_outstanding.ToString() + " " + BoxAggregation.Count().ToString());
if (BoxAggregation.Count() >= 3)
{
log_write("Processing boxes. " + BoxAggregation.Keys.ToString());
MS1_outstanding = false;
IEnumerable <Peak> scan = BoxesToMS1();
List <Peak> molecular_peaks = Spectral_Processing.deisotope_scan(scan);
IEnumerable <Peak> valid_precursors = molecular_peaks.Where(x => x.Item1 > 1);
IEnumerable <Peak> precursors_by_int = valid_precursors.OrderByDescending(OrderPeak);
GenerateMS2s(precursors_by_int);
}
return;
default:
Debug.Assert(false);
return;
}
}