public override string ToString()
{
var sb = new StringBuilder();
// list of protein accession numbers
sb.Append(ProteinGroupName);
sb.Append("\t");
// genes
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.GeneNames.Select(x => x.Item2).FirstOrDefault()))));
sb.Append("\t");
// organisms
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.Organism).Distinct())));
sb.Append("\t");
// list of protein names
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.FullName).Distinct())));
sb.Append("\t");
// list of masses
var sequences = ListOfProteinsOrderedByAccession.Select(p => p.BaseSequence).Distinct();
List <double> masses = new List <double>();
foreach (var sequence in sequences)
{
try
{
masses.Add(new Proteomics.AminoAcidPolymer.Peptide(sequence).MonoisotopicMass);
}
catch (System.Exception)
{
masses.Add(double.NaN);
}
}
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", masses)));
sb.Append("\t");
// number of proteins in group
sb.Append("" + Proteins.Count);
sb.Append("\t");
// list of unique peptides
if (UniquePeptidesOutput != null)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(UniquePeptidesOutput));
}
sb.Append("\t");
// list of shared peptides
if (SharedPeptidesOutput != null)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(SharedPeptidesOutput));
}
sb.Append("\t");
// number of peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + AllPeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + AllPeptides.Select(p => p.FullSequence).Distinct().Count());
}
sb.Append("\t");
// number of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + UniquePeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + UniquePeptides.Select(p => p.FullSequence).Distinct().Count());
}
sb.Append("\t");
// sequence coverage percent
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageFraction.Select(p => string.Format("{0:0.#####}", p)))));
sb.Append("\t");
// sequence coverage
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayList)));
sb.Append("\t");
// sequence coverage with mods
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayListWithMods)));
sb.Append("\t");
//Detailed mods information list
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ModsInfo)));
sb.Append("\t");
// MS1 intensity (retrieved from FlashLFQ in the SearchTask)
if (IntensitiesByFile != null && FilesForQuantification != null)
{
foreach (var sampleGroup in FilesForQuantification.GroupBy(p => p.Condition))
{
foreach (var sample in sampleGroup.GroupBy(p => p.BiologicalReplicate).OrderBy(p => p.Key))
{
// if the samples are fractionated, the protein will only have 1 intensity in the first fraction
// and the other fractions will be zero. we could find the first/only fraction with an intensity,
// but simply summing the fractions is easier than finding the single non-zero value
double summedIntensity = sample.Sum(file => IntensitiesByFile[file]);
if (summedIntensity > 0)
{
sb.Append(summedIntensity);
}
sb.Append("\t");
}
}
}
// number of PSMs for listed peptides
sb.Append("" + AllPsmsBelowOnePercentFDR.Count);
sb.Append("\t");
// isDecoy
if (IsDecoy)
{
sb.Append("D");
}
else if (IsContaminant)
{
sb.Append("C");
}
else
{
sb.Append("T");
}
sb.Append("\t");
// cumulative target
sb.Append(CumulativeTarget);
sb.Append("\t");
// cumulative decoy
sb.Append(CumulativeDecoy);
sb.Append("\t");
// q value
sb.Append(QValue);
sb.Append("\t");
// best peptide score
sb.Append(BestPeptideScore);
sb.Append("\t");
// best peptide q value
sb.Append(BestPeptideQValue);
sb.Append("\t");
return(sb.ToString());
}
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());
}
public override string ToString()
{
var sb = new StringBuilder();
// list of protein accession numbers
sb.Append(ProteinGroupName);
sb.Append("\t");
// genes
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.GeneNames.Select(x => x.Item2).FirstOrDefault()))));
sb.Append("\t");
// organisms
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.Organism).Distinct())));
sb.Append("\t");
// list of protein names
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.FullName).Distinct())));
sb.Append("\t");
// list of masses
var sequences = ListOfProteinsOrderedByAccession.Select(p => p.BaseSequence).Distinct();
List <double> masses = new List <double>();
foreach (var sequence in sequences)
{
try
{
masses.Add(new Proteomics.AminoAcidPolymer.Peptide(sequence).MonoisotopicMass);
}
catch (System.Exception)
{
masses.Add(double.NaN);
}
}
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", masses)));
sb.Append("\t");
// number of proteins in group
sb.Append("" + Proteins.Count);
sb.Append("\t");
// list of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.FullSequence).Distinct())));
}
sb.Append("\t");
// list of shared peptides
var SharedPeptides = AllPeptides.Except(UniquePeptides);
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.FullSequence).Distinct())));
}
sb.Append("\t");
// number of peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + AllPeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + AllPeptides.Select(p => p.FullSequence).Distinct().Count());
}
sb.Append("\t");
// number of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + UniquePeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + UniquePeptides.Select(p => p.FullSequence).Distinct().Count());
}
sb.Append("\t");
// sequence coverage percent
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageFraction.Select(p => string.Format("{0:0.#####}", p)))));
sb.Append("\t");
// sequence coverage
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayList)));
sb.Append("\t");
// sequence coverage with mods
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayListWithMods)));
sb.Append("\t");
//Detailed mods information list
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ModsInfo)));
sb.Append("\t");
// MS1 intensity (retrieved from FlashLFQ in the SearchTask)
if (IntensitiesByFile != null && FilesForQuantification != null)
{
foreach (var file in FilesForQuantification)
{
if (IntensitiesByFile[file] > 0)
{
sb.Append(IntensitiesByFile[file]);
}
else
{
sb.Append("");
}
sb.Append("\t");
}
}
// number of PSMs for listed peptides
sb.Append("" + AllPsmsBelowOnePercentFDR.Count);
sb.Append("\t");
// isDecoy
if (IsDecoy)
{
sb.Append("D");
}
else if (IsContaminant)
{
sb.Append("C");
}
else
{
sb.Append("T");
}
sb.Append("\t");
// cumulative target
sb.Append(CumulativeTarget);
sb.Append("\t");
// cumulative decoy
sb.Append(CumulativeDecoy);
sb.Append("\t");
// q value
sb.Append(QValue);
sb.Append("\t");
// best peptide score
sb.Append(BestPeptideScore);
sb.Append("\t");
// best peptide q value
sb.Append(BestPeptideQValue);
sb.Append("\t");
return(sb.ToString());
}
public override string ToString()
{
var sb = new StringBuilder();
// list of protein accession numbers
sb.Append(ProteinGroupName);
sb.Append("\t");
// genes
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.GeneNames.Select(x => x.Item2).FirstOrDefault()))));
sb.Append("\t");
// organisms
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.Organism).Distinct())));
sb.Append("\t");
// list of protein names
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.FullName).Distinct())));
sb.Append("\t");
// list of masses
IDigestionParams digestionParams = new TDdigest();
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First().MonoisotopicMass).Distinct())));
sb.Append("\t");
// number of proteins in group
sb.Append("" + Proteins.Count);
sb.Append("\t");
// list of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.Sequence).Distinct())));
}
sb.Append("\t");
// list of shared peptides
var SharedPeptides = AllPeptides.Except(UniquePeptides);
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.Sequence).Distinct())));
}
sb.Append("\t");
// number of peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + AllPeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + AllPeptides.Select(p => p.Sequence).Distinct().Count());
}
sb.Append("\t");
// number of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + UniquePeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + UniquePeptides.Select(p => p.Sequence).Distinct().Count());
}
sb.Append("\t");
// sequence coverage percent
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoveragePercent.Select(p => string.Format("{0:0}" + "%", (p * 100))))));
sb.Append("\t");
// sequence coverage
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayList)));
sb.Append("\t");
// sequence coverage with mods
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayListWithMods)));
sb.Append("\t");
//Detailed mods information list
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ModsInfo)));
sb.Append("\t");
// MS1 intensity (retrieved from FlashLFQ in the SearchTask)
if (IntensitiesByFile != null && FilesForQuantification != null)
{
for (int i = 0; i < IntensitiesByFile.Length; i++)
{
if (IntensitiesByFile[i] > 0)
{
sb.Append(IntensitiesByFile[i]);
}
else
{
sb.Append("");
}
sb.Append("\t");
}
}
// number of PSMs for listed peptides
sb.Append("" + AllPsmsBelowOnePercentFDR.Count);
sb.Append("\t");
// isDecoy
if (isDecoy)
{
sb.Append("D");
}
else if (isContaminant)
{
sb.Append("C");
}
else
{
sb.Append("T");
}
sb.Append("\t");
// cumulative target
sb.Append(CumulativeTarget);
sb.Append("\t");
// cumulative decoy
sb.Append(CumulativeDecoy);
sb.Append("\t");
// q value
sb.Append(QValue);
sb.Append("\t");
// best peptide score
sb.Append(BestPeptideScore);
sb.Append("\t");
// best peptide q value
sb.Append(BestPeptideQValue);
sb.Append("\t");
return(sb.ToString());
}
