public void Add(PeptideSpectrumMatch psm)
{
insertRow(Table.PeptideSpectrumMatch, new object[]
{
psm.Id, psm.Peptide.Id, psm.Spectrum.Id, psm.Analysis.Id,
psm.ObservedNeutralMass,
psm.MonoisotopicMassError, psm.MolecularWeightError,
psm.Rank, psm.QValue, psm.Charge
});
if (psm.Scores != null)
{
foreach (var score in psm.Scores)
{
long scoreId;
if (!scoreIdByName.TryGetValue(score.Key, out scoreId))
{
if (scoreIdByName.Count > 0)
{
scoreIdByName[score.Key] = scoreId = scoreIdByName.Max(o => o.Value) + 1;
}
else
{
scoreIdByName[score.Key] = scoreId = 1;
}
insertRow(Table.PeptideSpectrumMatchScoreName, new object[] { scoreId, score.Key });
}
insertRow(Table.PeptideSpectrumMatchScore, new object[] { psm.Id, scoreId, score.Value });
}
}
}
public DistinctMatchKey(Peptide peptide, PeptideSpectrumMatch psm, DistinctMatchFormat format, string key, long?id)
{
Peptide = peptide;
Key = key;
Format = format;
Id = id;
if (format.IsChargeDistinct)
{
Charge = psm.Charge;
}
if (format.IsAnalysisDistinct)
{
Analysis = psm.Analysis;
}
}
public DistinctMatchKey(Peptide peptide, PeptideSpectrumMatch psm, DistinctMatchFormat format, string key, long?id)
{
Peptide = peptide;
Key = key.Replace(",", Properties.Settings.Default.GroupConcatSeparator);
Format = format;
Id = id;
if (format.IsChargeDistinct)
{
Charge = psm.Charge;
}
if (format.IsAnalysisDistinct)
{
Analysis = psm.Analysis;
}
}
public static string ToModifiedString(this PeptideSpectrumMatch psm, int precision)
{
string format = String.Format("[{{0:f{0}}}]", precision);
StringBuilder sb = new StringBuilder(psm.Peptide.Sequence);
foreach (var mod in (from m in psm.Modifications orderby m.Offset descending select m))
{
if (mod.Offset == int.MinValue)
{
sb.Insert(0, String.Format(format, mod.Modification.MonoMassDelta));
}
else if (mod.Offset == int.MaxValue)
{
sb.AppendFormat(format, mod.Modification.MonoMassDelta);
}
else
{
sb.Insert(mod.Offset + 1, String.Format(format, mod.Modification.MonoMassDelta));
}
}
return(sb.ToString());
}
public static string ToModifiedString(this PeptideSpectrumMatch psm)
{
return(ToModifiedString(psm, 0));
}
