public Query(DBOptions dbOptions, Sample entry, ProductSpectrum spectrum, Precursor precursor, int spectraIndex = -1)
{
this.options = dbOptions;
this.sample = entry;
this.psms = new PeptideSpectrumMatches();
this.spectrum = spectrum;
this.precursor = precursor;
this.spectrumIndex = spectraIndex;
if (spectrum != null && precursor != null)
{
this.TrapDistance = Math.Abs(spectrum.PrecursorMZ - precursor.Track.MZ);
}
}
public static int AscendingRetentionTimeComparison(ProductSpectrum left, ProductSpectrum right)
{
return(left.RetentionTimeInMin.CompareTo(right.RetentionTimeInMin));
}
/*
* public ProductSpectrum(ProductSpectrum spectrum)
* {
* this.Filename = spectrum.Filename;
* this.ScanNumber = spectrum.ScanNumber;
* this.RetentionTimeInMin = spectrum.RetentionTimeInMin;
* this.FragmentationMethod = spectrum.FragmentationMethod;
* this.PrecursorMZ = spectrum.PrecursorMZ;
* this.PrecursorIntensity = spectrum.PrecursorIntensity;
* this.PrecursorCharge = spectrum.PrecursorCharge;
* this.PrecursorMass = spectrum.PrecursorMass;
* this.TotalIntensity = spectrum.TotalIntensity;
* this.Masses = spectrum.Masses;
* this.Intensities = spectrum.Intensities;
* }*/
public static int AscendingPrecursorMassComparison(ProductSpectrum left, ProductSpectrum right)
{
return(left.PrecursorMass.CompareTo(right.PrecursorMass));
}
public AnnotatedSpectrum(Sample sample, ProductSpectrum spectrum, Peptide peptide)
{
sequence = peptide.BaseSequence;
peaks = new double[spectrum.Peaks.Count][];
for (int i = 0; i < peaks.Length; i++)
{
peaks[i] = new double[2];
peaks[i][0] = spectrum.Peaks[i].MZ;
peaks[i][1] = spectrum.Peaks[i].Intensity;
}
scanNum = spectrum.ScanNumber;
charge = spectrum.PrecursorCharge;
precursorMz = spectrum.PrecursorMZ;
fileName = sample.sSDF;
//Fixed modifications
List <AnnotatedSpectrumModification> fixedMods = new List <AnnotatedSpectrumModification>();
if (peptide.FixedModifications != null)
{
foreach (int position in peptide.FixedModifications.Keys)
{
if (position == 1)
{
foreach (Modification mod in peptide.FixedModifications[position])
{
ntermMod += mod.MonoisotopicMassShift;
}
}
else
if (position == sequence.Length + 2)
{
foreach (Modification mod in peptide.FixedModifications[position])
{
ctermMod += mod.MonoisotopicMassShift;
}
}
else
{
foreach (Modification mod in peptide.FixedModifications[position])
{
fixedMods.Add(new AnnotatedSpectrumModification(mod.AminoAcid, mod.MonoisotopicMassShift, position - 1));
}
}
}
}
staticMods = fixedMods.ToArray();
//Variable modifications
List <AnnotatedSpectrumModification> varMods = new List <AnnotatedSpectrumModification>();
if (peptide.VariableModifications != null)
{
foreach (int position in peptide.VariableModifications.Keys)
{
if (position == 1)
{
ntermMod += peptide.VariableModifications[position].MonoisotopicMassShift;
}
else
if (position == sequence.Length + 2)
{
ctermMod += peptide.VariableModifications[position].MonoisotopicMassShift;
}
else
{
varMods.Add(new AnnotatedSpectrumModification(peptide.VariableModifications[position].AminoAcid, peptide.VariableModifications[position].MonoisotopicMassShift, position - 1));
}
}
}
variableMods = varMods.ToArray();
/*
* var sequence = "FDSFGDLSSASAIMGNPK";
* var varMods = [];
* // modification index = 14; modification mass = 16.0; modified residue = 'M'
* varMods[0] = { index: 14, modMass: 16.0, aminoAcid: 'M' };
* // mass to be added to the N-terminus
* var ntermMod = 164.07;//*/
}
