public void Display()
{
Console.WriteLine("MaxThreads: " + MaxNumThreads);
foreach (var specFilePath in SpecFilePaths)
{
Console.WriteLine("SpectrumFilePath: " + specFilePath);
}
Console.WriteLine("DatabaseFilePath: " + DatabaseFilePath);
Console.WriteLine("FeatureFilePath: {0}", FeatureFilePath ?? "N/A");
Console.WriteLine("OutputDir: " + OutputDir);
Console.WriteLine("InternalCleavageMode: " + InternalCleavageMode);
Console.WriteLine("Tag-based search: " + TagBasedSearch);
Console.WriteLine("Tda: " + (TargetDecoySearchMode == DatabaseSearchMode.Both ? "Target+Decoy" : TargetDecoySearchMode.ToString()));
Console.WriteLine("PrecursorIonTolerancePpm: " + PrecursorIonTolerancePpm);
Console.WriteLine("ProductIonTolerancePpm: " + ProductIonTolerancePpm);
Console.WriteLine("MinSequenceLength: " + MinSequenceLength);
Console.WriteLine("MaxSequenceLength: " + MaxSequenceLength);
Console.WriteLine("MinPrecursorIonCharge: " + MinPrecursorIonCharge);
Console.WriteLine("MaxPrecursorIonCharge: " + MaxPrecursorIonCharge);
Console.WriteLine("MinProductIonCharge: " + MinProductIonCharge);
Console.WriteLine("MaxProductIonCharge: " + MaxProductIonCharge);
Console.WriteLine("MinSequenceMass: " + MinSequenceMass);
Console.WriteLine("MaxSequenceMass: " + MaxSequenceMass);
Console.WriteLine("MaxDynamicModificationsPerSequence: " + MaxDynamicModificationsPerSequence);
Console.WriteLine("Modifications: ");
foreach (var searchMod in Modifications)
{
Console.WriteLine(searchMod);
}
if (!string.IsNullOrWhiteSpace(FeatureFilePath))
{
Console.WriteLine("Getting MS1 features from " + FeatureFilePath);
}
if (ScanNumbers != null && ScanNumbers.Any())
{
Console.WriteLine("Processing specific MS2 scans:");
Console.WriteLine(string.Join(", ", ScanNumbers));
}
}
/// <summary>
/// Method responsible for parsing RAW File.
/// </summary>
/// <param name="fileName"></param>
/// <returns></returns>
public List <MSUltraLight> ParseFile(String rawFile, short fileIndex = -1, int MsnLevel = 2, List <int> ScanNumbers = null, bool toPrint_console = true)
{
if (!File.Exists(rawFile))
{
throw new Exception("ParserUltraLightRAW error:: Unable to find the file " + rawFile);
}
MSFileReaderLib.IXRawfile2 raw = (MSFileReaderLib.IXRawfile2) new MSFileReader_XRawfile();
raw.Open(rawFile);
raw.SetCurrentController(0, 1);
Dictionary <int, double[, ]> ms1s = null;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, double[, ]>();
}
int first_scan_number = -1;
raw.GetFirstSpectrumNumber(ref first_scan_number);
int last_scan_number = -1;
raw.GetLastSpectrumNumber(ref last_scan_number);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
MSUltraLight[] myTMSArray = new MSUltraLight[last_scan_number + 2];
//We will only retrieve certain scan numbers
if (ScanNumbers == null)
{
ScanNumbers = new List <int>();
for (int scan_number = first_scan_number; scan_number <= last_scan_number + 1; scan_number++)
{
ScanNumbers.Add(scan_number);
}
}
ScanNumbers.Sort();
foreach (int scan_number in ScanNumbers)
{
spectra_processed++;
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
if (String.IsNullOrEmpty(scan_filter))
{
Console.WriteLine("Scan " + scan_number + " is null");
continue;
}
if (MsnLevel == 1)
{
if (!isMS1.IsMatch(scan_filter))
{
if (!isMS1_1.IsMatch(scan_filter))
{
continue;
}
}
}
else if (MsnLevel == 2)
{
if (!isMS2.IsMatch(scan_filter))
{
continue;
}
}
else if (MsnLevel == 3)
{
if (!isMS3.IsMatch(scan_filter))
{
continue;
}
}
string spectrum_id = "controllerType=0 controllerNumber=1 scan=" + scan_number.ToString();
double retention_time = double.NaN;
raw.RTFromScanNum(scan_number, ref retention_time);
double precursor_mz;
double precursor_intensity;
int precursor_scanNumber;
double ionInjectionTime;
int charge;
if (MsnLevel > 1)
{
GetPrecursor(ms1s, raw, scan_number, scan_filter, first_scan_number, out precursor_mz, out precursor_intensity, out precursor_scanNumber);
DeterminePrecursorParams(raw, scan_number, out charge, out ionInjectionTime);
}
else
{
charge = -1;
precursor_mz = -1;
precursor_intensity = -1;
}
double[,] label_data = GetFragmentationData(raw, scan_number, scan_filter);
List <Tuple <float, float> > peaks = new List <Tuple <float, float> >(label_data.GetLength(1));
for (int peak_index = label_data.GetLowerBound(1); peak_index <= label_data.GetUpperBound(1); peak_index++)
{
// Calculate index in list of ions object
int index = peak_index - label_data.GetLowerBound(1);
// Get fragment ion m/z and intensity from RAW file
float mz = (float)label_data[(int)RawLabelDataColumn.MZ, peak_index];
float intensity = (float)label_data[(int)RawLabelDataColumn.Intensity, peak_index];
// Create new ion object
peaks.Add(new Tuple <float, float>(mz, intensity));
}
if (peaks.Count > 0)
{
MSUltraLight ms = new MSUltraLight((float)retention_time,
scan_number,
peaks,
new List <Tuple <float, short> >()
{
new Tuple <float, short>((float)precursor_mz, (short)charge)
},
(float)precursor_intensity,
1, //Instrument type
(short)MsnLevel,
fileIndex);
myTMSArray[scan_number] = ms;
}
lock (progress_lock)
{
int new_progress = (int)((double)spectra_processed / (last_scan_number - first_scan_number + 1) * 100);
if (new_progress > old_progress)
{
old_progress = new_progress;
if (toPrint_console)
{
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
Console.Write(" Reading RAW File: " + old_progress + "%");
Console.SetCursorPosition(0, currentLineCursor);
}
else
{
Console.Write(" Reading RAW File: " + old_progress + "%");
}
}
}
}
Console.Write(" Reading RAW File: 100%");
return(myTMSArray.Where(a => a != null).ToList());
}