/// <summary>
/// Generates a hash code.
/// </summary>
/// <returns>Hash code based on stored data.</returns>
public override int GetHashCode()
{
var hashCode =
PrecursorMz.GetHashCode() ^
PrecursorChargeState.GetHashCode() ^
Scan.GetHashCode() ^
Id.GetHashCode() ^
GroupId.GetHashCode() ^
TotalIonCurrent.GetHashCode() ^
RetentionTime.GetHashCode();
return(hashCode);
}
public override int GetHashCode()
{
unchecked
{
int hashCode = (Name != null ? Name.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Label != null ? Label.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Cohort != null ? Cohort.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Sample != null ? Sample.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (PrecursorPool != null ? PrecursorPool.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ TimePoint.GetHashCode();
hashCode = (hashCode * 397) ^ (Times != null ? Times.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (TotalIonCurrent != null ? TotalIonCurrent.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Compares two objects' values.
/// </summary>
/// <param name="obj">Other to compare with.</param>
/// <returns>True if values are the same, false if not.</returns>
public override bool Equals(object obj)
{
if (obj == null)
{
return(false);
}
var other = obj as MSSpectra;
if (other == null)
{
return(false);
}
if (!GroupId.Equals(other.GroupId))
{
return(false);
}
if (!MsLevel.Equals(other.MsLevel))
{
return(false);
}
if (!PrecursorChargeState.Equals(other.PrecursorChargeState))
{
return(false);
}
if (!PrecursorMz.Equals(other.PrecursorMz))
{
return(false);
}
if (!Net.Equals(other.Net))
{
return(false);
}
if (!Scan.Equals(other.Scan))
{
return(false);
}
if (!TotalIonCurrent.Equals(other.TotalIonCurrent))
{
return(false);
}
if (!CollisionType.Equals(other.CollisionType))
{
return(false);
}
return(true);
}
public string ToString(IReadOnlyDictionary <string, int> ModstoWritePruned)
{
var sb = new StringBuilder();
sb.Append(Path.GetFileNameWithoutExtension(FullFilePath));
sb.Append('\t' + ScanNumber.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + ScanRetentionTime.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanExperimentalPeaks.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + TotalIonCurrent.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + (PrecursorScanNumber.HasValue ? PrecursorScanNumber.Value.ToString(CultureInfo.InvariantCulture) : "unknown"));
sb.Append('\t' + ScanPrecursorCharge.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanPrecursorMonoisotopicPeakMz.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + ScanPrecursorMass.ToString("F5", CultureInfo.InvariantCulture));
sb.Append('\t' + Score.ToString("F3", CultureInfo.InvariantCulture));
sb.Append("\t" + Resolve(compactPeptides.Select(b => b.Value.Item1)).Item1); // Notch
sb.Append('\t' + NumDifferentCompactPeptides.ToString("F5", CultureInfo.InvariantCulture));
if (compactPeptides.First().Value.Item2 != null)
{
sb.Append("\t" + GlobalVariables.CheckLengthOfOutput(string.Join("|", compactPeptides.Select(b => b.Value.Item2.Count.ToString(CultureInfo.InvariantCulture)))));
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.BaseSequence)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Sequence)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.EssentialSequence(ModstoWritePruned))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.allModsOneIsNterminus)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => string.Join("|", b.allModsOneIsNterminus.OrderBy(c => c.Key).Where(c => c.Value is ModificationWithMassAndCf).Select(c => (c.Value as ModificationWithMassAndCf).chemicalFormula.Formula)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.allModsOneIsNterminus.Select(c => (c.Value as ModificationWithMassAndCf)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.NumVariableMods)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.MissedCleavages.HasValue ? b.MissedCleavages.Value.ToString(CultureInfo.InvariantCulture) : "unknown")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.MonoisotopicMass)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ScanPrecursorMass - b.MonoisotopicMass)).Item1);
sb.Append('\t' + ResolveF2(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ((ScanPrecursorMass - b.MonoisotopicMass) / b.MonoisotopicMass * 1e6))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.Accession)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.FullName)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => string.Join(", ", b.Protein.GeneNames.Select(d => d.Item1 + ":" + d.Item2)))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.Organism)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.IsContaminant ? "Y" : "N")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.IsDecoy ? "Y" : "N")).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.PeptideDescription)).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => ("[" + b.OneBasedStartResidueInProtein.ToString(CultureInfo.InvariantCulture) + " to " + b.OneBasedEndResidueInProtein.ToString(CultureInfo.InvariantCulture) + "]"))).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.PreviousAminoAcid.ToString())).Item1);
sb.Append('\t' + Resolve(compactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.NextAminoAcid.ToString())).Item1);
if (FdrInfo != null && FdrInfo.CalculateEValue)
{
int theoreticalsSearched = AllScores[0];
sb.Append('\t' + AllScores[0].ToString());
for (int i = 1; i < AllScores.Count; i++)
{
sb.Append("_" + AllScores[i]);
theoreticalsSearched += AllScores[i];
}
sb.Append('\t' + theoreticalsSearched.ToString());
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
// Unambiguous
if (IsDecoy)
{
sb.Append("\t" + "D");
}
else if (compactPeptides.Any(b => b.Value.Item2.Any(c => c.Protein.IsContaminant)))
{
sb.Append("\t" + "C");
}
else
{
sb.Append("\t" + "T");
}
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
if (MatchedIonDictOnlyMatches.Any())
{
//Count
sb.Append('\t' + string.Join(";", MatchedIonDictOnlyMatches.Select(b => b.Value.Count(c => c > 0))));
//Masses
sb.Append('\t' + "[");
StringBuilder sbTemp = new StringBuilder();
foreach (var kvp in MatchedIonDictOnlyMatches)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F5", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
//Mass error Da
sb.Append('\t' + "[");
sbTemp.Clear();
foreach (var kvp in ProductMassErrorDa)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F5", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
//Mass error ppm
sb.Append('\t' + "[");
sbTemp.Clear();
foreach (var kvp in ProductMassErrorPpm)
{
sbTemp.Append("[" + string.Join(",", kvp.Value.Select(b => b.ToString("F2", CultureInfo.InvariantCulture))) + "];");
}
sb.Append(GlobalVariables.CheckLengthOfOutput(sbTemp.ToString()));
sb.Append("]");
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
if (LocalizedScores != null)
{
sb.Append('\t' + GlobalVariables.CheckLengthOfOutput(("[" + string.Join(",", LocalizedScores.Select(b => b.ToString("F3", CultureInfo.InvariantCulture))) + "]")));
sb.Append('\t' + (LocalizedScores.Max() - Score).ToString("F3", CultureInfo.InvariantCulture));
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
if (FdrInfo != null)
{
sb.Append('\t' + FdrInfo.CumulativeTarget.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeDecoy.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.QValue.ToString("F6", CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeTargetNotch.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.CumulativeDecoyNotch.ToString(CultureInfo.InvariantCulture));
sb.Append('\t' + FdrInfo.QValueNotch.ToString("F6", CultureInfo.InvariantCulture));
if (FdrInfo.CalculateEValue)
{
sb.Append("\t" + FdrInfo.EValue.ToString("F6", CultureInfo.InvariantCulture));
sb.Append("\t" + FdrInfo.EScore.ToString("F6", CultureInfo.InvariantCulture));
}
else
{
sb.Append('\t' + " " + '\t' + " ");
}
}
else
{
sb.Append('\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " " + '\t' + " ");
}
return(sb.ToString());
}