private void ReadFromFile(string paramFile, Boolean verbose)
{
if (!File.Exists(paramFile))
return;
using (var reader = new BigEndianReader(File.Open(paramFile, FileMode.Open)))
{
// Version
var version = reader.ReadInt32();
if(verbose) Console.WriteLine("Version: {0}", version);
// Activation method
var actMethodChars = reader.ReadChars(reader.ReadByte());
var actMethod = new string(actMethodChars);
// Instrument type
var instType = new string(reader.ReadChars(reader.ReadByte()));
// Enzyme
var enzyme = new string(reader.ReadChars(reader.ReadByte()));
// Protocol
var protocol = new string(reader.ReadChars(reader.ReadByte()));
if (verbose) Console.WriteLine("Spectral type: {0}_{1}_{2}_{3}", actMethod, instType, enzyme, protocol);
// TODO: set up spectral type
//// Tolerance
//var isTolerancePpm = reader.ReadBoolean();
//var mmeVal = reader.ReadSingle();
//// Ignore mme
////_mme = new Tolerance(mmeVal, isTolerancePpm ? ToleranceUnit.Ppm : ToleranceUnit.Dalton);
//// Deconvolution information
//_applyDeconvolution = reader.ReadBoolean();
//_deconvolutionErrorToleranceDa = reader.ReadSingle();
//if (verbose) Console.WriteLine("Apply deconvolution: {0}, Tolerance: {1}", _applyDeconvolution, _deconvolutionErrorToleranceDa);
//// Charge histogram
//if (verbose) Console.WriteLine("Charge Histogram");
//var chargeHistSize = reader.ReadInt32();
//_chargeHistogram = new Dictionary<int, int>();
//for (var i = 0; i < chargeHistSize; i++)
//{
// var charge = reader.ReadInt32();
// var numSpecs = reader.ReadInt32();
// _chargeHistogram[charge] = numSpecs;
// if(verbose) Console.WriteLine(charge+"\t"+numSpecs);
//}
//// Partition information
//if (verbose) Console.WriteLine("Partition Information");
//var numPartitions = reader.ReadInt32();
//_numSegments = reader.ReadInt32();
//_partitionSet = new SortedSet<Partition>();
//for (var i = 0; i < numPartitions; i++)
//{
// var charge = reader.ReadInt32();
// var neutralPeptideMass = reader.ReadInt32();
// var segIndex = reader.ReadInt32();
// _partitionSet.Add(new Partition(charge, neutralPeptideMass, segIndex));
// if(verbose) Console.WriteLine("{0}\t{1}\t{2}", charge, neutralPeptideMass, segIndex);
//}
//// Precursor offset frequency function
//if (verbose) Console.WriteLine("Precursor Offset Frequency Function");
//_precursorOffMap = new Dictionary<int, IList<PrecursorOffsetFrequency>>();
//_numPrecursorOffsets = reader.ReadInt32();
//for (var i = 0; i < _numPrecursorOffsets; i++)
//{
// var charge = reader.ReadInt32();
// var reducedCharge = reader.ReadInt32();
// var offset = reader.ReadSingle();
// var isTolPpm = reader.ReadBoolean();
// var tolVal = reader.ReadSingle();
// var tolerance = new Tolerance(tolVal, isTolPpm ? ToleranceUnit.Ppm : ToleranceUnit.Dalton);
// var frequency = reader.ReadSingle();
// IList<PrecursorOffsetFrequency> offList;
// if (!_precursorOffMap.TryGetValue(charge, out offList))
// {
// offList = new List<PrecursorOffsetFrequency>();
// _precursorOffMap[charge] = offList;
// }
// offList.Add(new PrecursorOffsetFrequency(reducedCharge, offset, frequency, tolerance));
// if (verbose) Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}",
// charge, reducedCharge, offset, tolerance, frequency);
//}
//// Fragment ion offset frequency function
//if (verbose) Console.WriteLine("Fragment Offset Frequency Function");
//_fragmentOffMap = new Dictionary<Partition, IEnumerable<FragmentOffsetFrequency>>();
//foreach(var partition in _partitionSet)
//{
// if(verbose) Console.WriteLine("{0}\t{1}\t{2}", partition.Charge, partition.SegmentIndex, partition.NeutralPeptideMass);
// var numIons = reader.ReadInt32();
// var fragmentOff = new FragmentOffsetFrequency[numIons];
// for (var ionIndex = 0; ionIndex < numIons; ionIndex++)
// {
// var isPrefix = reader.ReadBoolean();
// var charge = reader.ReadInt32();
// var offset = reader.ReadSingle();
// var frequency = reader.ReadSingle();
// }
//}
//// TODO: determine fragment ions
//// Rank distributions
//var maxRank = reader.ReadInt32();
//for (var i = 0; i < numPartitions; i++)
//{
// // repeat this for #Ions
// for (var rank = 0; rank < maxRank + 1; rank++)
// {
// var frequency = reader.ReadSingle();
// }
//}
//// Error distributions
//var errorScalingFactor = reader.ReadInt32();
//if (errorScalingFactor > 0)
//{
// var numErrorBins = errorScalingFactor*2 + 1;
// // Ion error distribution
// for (var i = 0; i < numErrorBins; i++)
// {
// var ionErrorDist = reader.ReadSingle();
// }
// // Noise error distribution
// for (var i = 0; i < numErrorBins; i++)
// {
// var noiseErrorDist = reader.ReadSingle();
// }
// // Ion existence table
// for (var i = 0; i < 4; i++)
// {
// var ionExFreq = reader.ReadSingle();
// }
//}
//// Validation
//var validationCode = reader.ReadInt32();
//if (validationCode != Int32.MaxValue)
//{
// Console.WriteLine("Error while reading parameter file {0}", paramFile);
// System.Environment.Exit(-1); // Error
//}
}
}
