public override bool Equals(object anObject)
{
if (this == anObject)
{
return(true);
}
if (anObject is MsmsPeakAnnotation)
{
MsmsPeakAnnotation other = (MsmsPeakAnnotation)anObject;
if (other.type != type)
{
return(false);
}
if (other.index != index)
{
return(false);
}
if (other.charge != charge)
{
return(false);
}
if (other.neutralLoss != neutralLoss)
{
return(false);
}
return(true);
}
return(false);
}
public MsmsHit(BinaryReader reader)
{
rawFileIndex = reader.ReadInt32();
scanNumber = reader.ReadInt32();
silacIndex = reader.ReadInt32();
byte x = reader.ReadByte();
switch (x)
{
case 0:
type = MascotQueryType.Silac;
break;
case 1:
type = MascotQueryType.Isotope;
break;
case 2:
type = MascotQueryType.Peak;
break;
}
pep = reader.ReadDouble();
score = reader.ReadDouble();
altScore = reader.ReadDouble();
deltaScoreAll = reader.ReadDouble();
deltaScoreDifferentPep = reader.ReadDouble();
labelModifications = PeptideModificationState.Read(reader);
trueModifications = PeptideModificationState.Read(reader);
elutionTime = reader.ReadDouble();
id = reader.ReadInt32();
mz = reader.ReadDouble();
monoisotopicMz = reader.ReadDouble();
evidenceId = reader.ReadInt32();
ptmScore = reader.ReadDouble();
deltaPtmScore = reader.ReadDouble();
ptmScoreCounts = reader.ReadInt32();
ptmScoreFinished = reader.ReadBoolean();
massErrorPpm = reader.ReadDouble();
changed = reader.ReadBoolean();
int len = reader.ReadInt32();
description = new MsmsPeakAnnotation[len];
intensities = new float[len];
massDiffs = new float[len];
for (int i = 0; i < len; i++)
{
description[i] = new MsmsPeakAnnotation(reader);
intensities[i] = reader.ReadSingle();
massDiffs[i] = reader.ReadSingle();
}
charge = reader.ReadInt32();
modProbabilities = new Dictionary <ushort, double[]>();
len = reader.ReadInt32();
ushort[] keys = new ushort[len];
for (int i = 0; i < keys.Length; i++)
{
keys[i] = reader.ReadUInt16();
}
foreach (ushort key in keys)
{
len = reader.ReadInt32();
double[] value = new double[len];
for (int i = 0; i < value.Length; i++)
{
value[i] = reader.ReadDouble();
}
modProbabilities.Add(key, value);
}
modScoreDiffs = new Dictionary <ushort, double[]>();
len = reader.ReadInt32();
keys = new ushort[len];
for (int i = 0; i < keys.Length; i++)
{
keys[i] = reader.ReadUInt16();
}
foreach (ushort key in keys)
{
len = reader.ReadInt32();
double[] value = new double[len];
for (int i = 0; i < value.Length; i++)
{
value[i] = reader.ReadDouble();
}
modScoreDiffs.Add(key, value);
}
}
public static int CountMatches(double[] massesArray, MsmsPeakAnnotation[] descriptionsArray, double[] specMasses, float[] specIntensities,
double tol, string tolUnit, out MsmsPeakAnnotation[] description,
out float[] intensities, out float[] massDiffs, out int n)
{
if (specMasses == null)
{
n = 0;
description = new MsmsPeakAnnotation[0];
intensities = new float[0];
massDiffs = new float[0];
return(0);
}
int npeaks = specMasses.Length;
if (npeaks == 0)
{
n = 0;
description = new MsmsPeakAnnotation[0];
intensities = new float[0];
massDiffs = new float[0];
return(0);
}
int k = 0;
n = 0;
List <MsmsPeakAnnotation> desc = null;
List <float> intens = null;
List <float> dm = null;
if (descriptionsArray != null)
{
desc = new List <MsmsPeakAnnotation>();
intens = new List <float>();
dm = new List <float>();
}
for (int i = 0; i < massesArray.Length; i++)
{
double m = massesArray[i];
n++;
int ind = ArrayUtil.ClosestIndex(specMasses, m);
if (ind != -1 && Match(m, specMasses[ind], tol, tolUnit))
{
k++;
if (descriptionsArray != null)
{
desc.Add(descriptionsArray[i]);
intens.Add(specIntensities[ind]);
dm.Add((float)(m - specMasses[ind]));
}
}
}
description = null;
intensities = null;
massDiffs = null;
if (descriptionsArray != null)
{
description = desc.ToArray();
intensities = intens.ToArray();
massDiffs = dm.ToArray();
}
return(k);
}
