private void ReadFromFile(string paramFile, Boolean verbose)
{
if (!File.Exists(paramFile))
{
return;
}
var allIonTypes = new IonTypeFactory();
using (var reader = new JavaBinaryReader(File.Open(paramFile, FileMode.Open)))
{
// Version
var version = reader.ReadInt32();
if (verbose)
{
Console.WriteLine("Version: {0}", version);
}
// Activation method
var actMethod = new string(reader.ReadChars(reader.ReadByte()));
// Instrument type
var instType = new string(reader.ReadChars(reader.ReadByte()));
// Enzyme
var enzyme = new string(reader.ReadChars(reader.ReadByte()));
// Protocol
var len = reader.ReadByte();
var protocol = new string(reader.ReadChars(len));
if (verbose)
{
Console.WriteLine("Spectral type: {0}_{1}_{2}{3}", actMethod, instType, enzyme, protocol.Length > 0 ? "_" + 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.Da);
// 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
var numPartitions = reader.ReadInt32();
if (verbose)
{
Console.WriteLine("Partition Information\t" + numPartitions);
}
_numSegments = reader.ReadInt32();
_partitionSet = new SortedSet <Partition>();
for (var i = 0; i < numPartitions; i++)
{
var charge = reader.ReadInt32();
var neutralPeptideMass = reader.ReadSingle();
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.Da);
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)
{
var numIons = reader.ReadInt32();
if (verbose)
{
Console.WriteLine("Partition {0}\t{1}\t{2}\t{3}", partition.Charge, partition.SegmentIndex, partition.NeutralPeptideMass, numIons);
}
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();
fragmentOff[ionIndex] = new FragmentOffsetFrequency(allIonTypes.GetIonType(isPrefix, charge, offset), frequency);
if (verbose)
{
Console.WriteLine("{0}_{1}_{2}\t{3}\t{4}", isPrefix ? "P" : "S", charge, Math.Round(offset), frequency, offset);
}
}
_fragmentOffMap.Add(partition, fragmentOff);
}
//// TODO: determine fragment ions to be used for scoring
//// Rank distributions
//var maxRank = reader.ReadInt32();
//_rankDistTable = new Dictionary<Partition, Dictionary<IonType, float[]>>();
//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
//}
}
}
private void ReadFromFile(string paramFile, Boolean verbose)
{
if (!File.Exists(paramFile))
return;
var allIonTypes = new IonTypeFactory();
using (var reader = new JavaBinaryReader(File.Open(paramFile, FileMode.Open)))
{
// Version
var version = reader.ReadInt32();
if(verbose) Console.WriteLine("Version: {0}", version);
// Activation method
var actMethod = new string(reader.ReadChars(reader.ReadByte()));
// Instrument type
var instType = new string(reader.ReadChars(reader.ReadByte()));
// Enzyme
var enzyme = new string(reader.ReadChars(reader.ReadByte()));
// Protocol
var len = reader.ReadByte();
var protocol = new string(reader.ReadChars(len));
if (verbose) Console.WriteLine("Spectral type: {0}_{1}_{2}{3}", actMethod, instType, enzyme, protocol.Length > 0 ? "_"+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.Da);
// 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
var numPartitions = reader.ReadInt32();
if (verbose) Console.WriteLine("Partition Information\t" + numPartitions);
_numSegments = reader.ReadInt32();
_partitionSet = new SortedSet<Partition>();
for (var i = 0; i < numPartitions; i++)
{
var charge = reader.ReadInt32();
var neutralPeptideMass = reader.ReadSingle();
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.Da);
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)
{
var numIons = reader.ReadInt32();
if (verbose) Console.WriteLine("Partition {0}\t{1}\t{2}\t{3}", partition.Charge, partition.SegmentIndex, partition.NeutralPeptideMass, numIons);
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();
fragmentOff[ionIndex] = new FragmentOffsetFrequency(allIonTypes.GetIonType(isPrefix, charge, offset), frequency);
if(verbose) Console.WriteLine("{0}_{1}_{2}\t{3}\t{4}", isPrefix ? "P" : "S", charge, Math.Round(offset), frequency, offset);
}
_fragmentOffMap.Add(partition, fragmentOff);
}
//// TODO: determine fragment ions to be used for scoring
//// Rank distributions
//var maxRank = reader.ReadInt32();
//_rankDistTable = new Dictionary<Partition, Dictionary<IonType, float[]>>();
//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
//}
}
}
