public override bool Equals(object obj)
{
if (this == obj)
{
return(true);
}
if (obj is PeptideModificationCounts)
{
PeptideModificationCounts other = (PeptideModificationCounts)obj;
if (other.modificationTypes.Length != modificationTypes.Length)
{
return(false);
}
for (int i = 0; i < modificationTypes.Length; i++)
{
if (modificationTypes[i] != other.modificationTypes[i])
{
return(false);
}
}
for (int i = 0; i < modificationTypes.Length; i++)
{
if (modificationCounts[i] != other.modificationCounts[i])
{
return(false);
}
}
return(true);
}
return(false);
}
public bool ValidModifications()
{
PeptideModificationCounts counts = modifications.ProjectToCounts();
ushort[] c = counts.ModificationCounts;
foreach (ushort cc in c)
{
if (cc > 7)
{
return(false);
}
}
return(true);
}
public void CalcPtmScore(double ms2Tol, string ms2TolUnit, int topx, string[] fixedModifications, string sequence, double[] specMasses, float[] specIntensities)
{
List <string> fixedMods = new List <string>();
for (int i = 0; i < fixedModifications.Length; i++)
{
fixedMods.Add(fixedModifications[i]);
}
ushort[] ltypes = labelModifications.ProjectToCounts().ModificationTypes;
foreach (ushort ltype in ltypes)
{
fixedMods.Add(Tables.modificationList[ltype].Title);
}
PeptideModificationCounts c = trueModifications.ProjectToCounts();
ushort[] ttypes = c.ModificationTypes;
string[] varMods = new string[ttypes.Length];
int[] tcounts = new int[ttypes.Length];
for (int i = 0; i < ttypes.Length; i++)
{
varMods[i] = Tables.modificationList[ttypes[i]].Title;
tcounts[i] = c.GetModificationCount(ttypes[i]);
}
PeptideModificationState modstr;
ptmScore = Pscore.CalcPtmScore(ms2Tol, ms2TolUnit, topx, sequence, Tables.ToModifications(fixedMods.ToArray()),
Tables.ToModifications(varMods), tcounts, specMasses, specIntensities,
mz, charge, out ptmScoreFinished, out modstr, out ptmScoreCounts,
out deltaPtmScore, out description, out intensities, out massDiffs,
out modProbabilities,
out modScoreDiffs, false);
ptmScoreFinished = !ptmScoreFinished;
changed = false;
if (!modstr.Equals(trueModifications))
{
changed = true;
trueModifications = modstr;
}
}
