internal static (string ResolvedString, Dictionary <string, int> ResolvedValue) Resolve(IEnumerable <Dictionary <int, Modification> > enumerable)
{
var list = enumerable.ToList();
Dictionary <string, int> firstDict = list[0].Values.OrderBy(b => b.IdWithMotif).GroupBy(b => b.IdWithMotif).ToDictionary(b => b.Key, b => b.Count());
bool equals = true;
foreach (var dict in list)
{
Dictionary <string, int> okTest = dict.Values.OrderBy(b => b.IdWithMotif).GroupBy(b => b.IdWithMotif).ToDictionary(b => b.Key, b => b.Count());
if (!firstDict.SequenceEqual(okTest))
{
equals = false;
break;
}
}
if (!equals)
{
var returnString = string.Join("|", list.Select(b => string.Join(" ", b.Values.Select(c => c.IdWithMotif).OrderBy(c => c))));
returnString = GlobalVariables.CheckLengthOfOutput(returnString);
return(returnString, null);
}
else
{
return(string.Join(" ", list[0].Values.Select(c => c.IdWithMotif).OrderBy(c => c)), firstDict);
}
}
//Get unique and identified peptides for output
//Convert the output if it's a SILAC experiment
public void GetIdentifiedPeptidesOutput(List <SilacLabel> labels)
{
var SharedPeptides = AllPeptides.Except(UniquePeptides);
if (labels == null)
{
//TODO add unit test with displaymodsonpeptides
if (!DisplayModsOnPeptides)
{
UniquePeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.BaseSequence).Distinct()));
SharedPeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.BaseSequence).Distinct()));
}
else
{
UniquePeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.FullSequence).Distinct()));
SharedPeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.FullSequence).Distinct()));
}
}
else
{
if (!DisplayModsOnPeptides)
{
UniquePeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => SilacConversions.GetAmbiguousLightSequence(p.BaseSequence, labels, true)).Distinct()));
SharedPeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => SilacConversions.GetAmbiguousLightSequence(p.BaseSequence, labels, true)).Distinct()));
}
else
{
UniquePeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => SilacConversions.GetAmbiguousLightSequence(p.FullSequence, labels, false)).Distinct()));
SharedPeptidesOutput = GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => SilacConversions.GetAmbiguousLightSequence(p.FullSequence, labels, false)).Distinct()));
}
}
}
private static void AddPeptideSequenceData(Dictionary <string, string> s, PeptideSpectralMatch peptide, IReadOnlyDictionary <string, int> ModsToWritePruned)
{
bool pepWithModsIsNull = peptide == null || peptide.CompactPeptides.First().Value.Item2 == null;
var pepsWithMods = pepWithModsIsNull ? null : peptide.CompactPeptides.SelectMany(b => b.Value.Item2)
.OrderBy(p => p.Sequence)
.ThenBy(p => p.Protein.Accession)
.ThenBy(p => p.OneBasedStartResidueInProtein).ToList();
s["Peptides Sharing Same Peaks"] = pepWithModsIsNull ? " " :
GlobalVariables.CheckLengthOfOutput(string.Join("|", peptide.CompactPeptides.Select(b => b.Value.Item2.Count.ToString(CultureInfo.InvariantCulture))));
s["Base Sequence"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.BaseSequence)).Item1;
s["Full Sequence"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Sequence)).Item1;
s["Essential Sequence"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.EssentialSequence(ModsToWritePruned))).Item1;
s["Mods"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.AllModsOneIsNterminus)).Item1;
s["Mods Chemical Formulas"] = pepWithModsIsNull ? " " :
Resolve(pepsWithMods.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;
s["Mods Combined Chemical Formula"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.AllModsOneIsNterminus.Select(c => (c.Value as ModificationWithMassAndCf)))).Item1;
s["Num Variable Mods"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.NumVariableMods)).Item1;
s["Missed Cleavages"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.MissedCleavages.ToString(CultureInfo.InvariantCulture))).Item1;
s["Peptide Monoisotopic Mass"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.MonoisotopicMass)).Item1;
s["Mass Diff (Da)"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => peptide.ScanPrecursorMass - b.MonoisotopicMass)).Item1;
s["Mass Diff (ppm)"] = pepWithModsIsNull ? " " : ResolveF2(pepsWithMods.Select(b => ((peptide.ScanPrecursorMass - b.MonoisotopicMass) / b.MonoisotopicMass * 1e6))).Item1;
s["Protein Accession"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Protein.Accession)).Item1;
s["Protein Name"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Protein.FullName)).Item1;
s["Gene Name"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => string.Join(", ", b.Protein.GeneNames.Select(d => d.Item1 + ":" + d.Item2)))).Item1;
s["Sequence Variations"] = pepWithModsIsNull ? " " :
Resolve(pepsWithMods.Select(b => string.Join(", ", b.Protein.SequenceVariations
.Where(d => peptide.OneBasedStartResidueInProtein <= d.OneBasedBeginPosition && d.OneBasedBeginPosition <= peptide.OneBasedEndResidueInProtein)
.Select(d => d.OriginalSequence + d.OneBasedBeginPosition.ToString() + d.VariantSequence)))).Item1;
s["Organism Name"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Protein.Organism)).Item1;
s["Contaminant"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Protein.IsContaminant ? "Y" : "N")).Item1;
s["Decoy"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.Protein.IsDecoy ? "Y" : "N")).Item1;
s["Peptide Description"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.PeptideDescription)).Item1;
s["Start and End Residues In Protein"] =
pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => ("[" + b.OneBasedStartResidueInProtein.ToString(CultureInfo.InvariantCulture) + " to " +
b.OneBasedEndResidueInProtein.ToString(CultureInfo.InvariantCulture) + "]"))).Item1;
s["Previous Amino Acid"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.PreviousAminoAcid.ToString())).Item1;
s["Next Amino Acid"] = pepWithModsIsNull ? " " : Resolve(pepsWithMods.Select(b => b.NextAminoAcid.ToString())).Item1;
string allScores = " ";
string theoreticalsSearched = " ";
if (!pepWithModsIsNull && peptide.FdrInfo != null && peptide.FdrInfo.CalculateEValue)
{
allScores = string.Join(";", peptide.AllScores.Select(p => p.ToString("F2", CultureInfo.InvariantCulture)));
theoreticalsSearched = peptide.AllScores.Count.ToString();
}
s["All Scores"] = allScores;
s["Theoreticals Searched"] = theoreticalsSearched;
s["Decoy/Contaminant/Target"] = pepWithModsIsNull ? " " : peptide.IsDecoy ? "D" : pepsWithMods.Any(c => c.Protein.IsContaminant) ? "C" : "T";
}
private Tuple <string, double?> Resolve(IEnumerable <double> enumerable)
{
var list = enumerable.ToList();
if (list.Max() - list.Min() < tolForDoubleResolution)
{
return(new Tuple <string, double?>(list.Average().ToString("F5", CultureInfo.InvariantCulture), list.Average()));
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list.Select(b => b.ToString("F5", CultureInfo.InvariantCulture))));
return(new Tuple <string, double?>(returnString, null));
}
}
internal static (string ResolvedString, double?ResolvedValue) ResolveF2(IEnumerable <double> enumerable)
{
var list = enumerable.ToList();
if (list.Max() - list.Min() < ToleranceForDoubleResolutionF2)
{
return(list.Average().ToString("F2", CultureInfo.InvariantCulture), list.Average());
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list.Select(b => b.ToString("F2", CultureInfo.InvariantCulture))));
return(returnString, null);
}
}
internal static (string ResolvedString, int?ResolvedValue) Resolve(IEnumerable <int> enumerable)
{
var list = enumerable.ToList();
var first = list[0];
if (list.All(b => first.Equals(b)))
{
return(first.ToString(CultureInfo.InvariantCulture), first);
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list.Select(b => b.ToString(CultureInfo.InvariantCulture))));
return(returnString, null);
}
}
private Tuple <string, int?> Resolve(IEnumerable <int> enumerable)
{
var list = enumerable.ToList();
var first = list[0];
if (list.All(b => first.Equals(b)))
{
return(new Tuple <string, int?>(first.ToString(CultureInfo.InvariantCulture), first));
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list.Select(b => b.ToString(CultureInfo.InvariantCulture))));
return(new Tuple <string, int?>(returnString, null));
}
}
internal static (string ResolvedString, string ResolvedValue) Resolve(IEnumerable <string> enumerable)
{
var list = enumerable.ToList();
string first = list.FirstOrDefault(b => b != null);
// Only first if list is either all null or all equal to the first
if (list.All(b => b == null) || list.All(b => first.Equals(b)))
{
return(first, first);
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list));
return(returnString, null);
}
}
private Tuple <string, string> Resolve(IEnumerable <string> enumerable)
{
var list = enumerable.ToList();
var first = list.FirstOrDefault(b => b != null);
// Only first if list is either all null or all equal to the first
if (list.All(b => b == null) || list.All(b => first.Equals(b)))
{
return(new Tuple <string, string>(first, first));
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list));
return(new Tuple <string, string>(returnString, null));
}
}
internal static void AddMatchScoreData(Dictionary <string, string> s, PeptideSpectralMatch peptide)
{
string localizedScores = " ";
string improvementPossible = " ";
if (peptide != null && peptide.LocalizedScores != null)
{
localizedScores = GlobalVariables.CheckLengthOfOutput(("[" + string.Join(",", peptide.LocalizedScores.Select(b => b.ToString("F3", CultureInfo.InvariantCulture))) + "]"));
improvementPossible = (peptide.LocalizedScores.Max() - peptide.Score).ToString("F3", CultureInfo.InvariantCulture);
}
s[PsmTsvHeader.LocalizedScores] = localizedScores;
s[PsmTsvHeader.ImprovementPossible] = improvementPossible;
string cumulativeTarget = " ";
string cumulativeDecoy = " ";
string qValue = " ";
string cumulativeTargetNotch = " ";
string cumulativeDecoyNotch = " ";
string qValueNotch = " ";
string eValue = " ";
string eScore = " ";
if (peptide != null && peptide.FdrInfo != null)
{
cumulativeTarget = peptide.FdrInfo.CumulativeTarget.ToString(CultureInfo.InvariantCulture);
cumulativeDecoy = peptide.FdrInfo.CumulativeDecoy.ToString(CultureInfo.InvariantCulture);
qValue = peptide.FdrInfo.QValue.ToString("F6", CultureInfo.InvariantCulture);
cumulativeTargetNotch = peptide.FdrInfo.CumulativeTargetNotch.ToString(CultureInfo.InvariantCulture);
cumulativeDecoyNotch = peptide.FdrInfo.CumulativeDecoyNotch.ToString(CultureInfo.InvariantCulture);
qValueNotch = peptide.FdrInfo.QValueNotch.ToString("F6", CultureInfo.InvariantCulture);
if (peptide.FdrInfo.CalculateEValue)
{
eValue = peptide.FdrInfo.EValue.ToString("F6", CultureInfo.InvariantCulture);
eScore = peptide.FdrInfo.EScore.ToString("F6", CultureInfo.InvariantCulture);
}
}
s[PsmTsvHeader.CumulativeTarget] = cumulativeTarget;
s[PsmTsvHeader.CumulativeDecoy] = cumulativeDecoy;
s[PsmTsvHeader.QValue] = qValue;
s[PsmTsvHeader.CumulativeTargetNotch] = cumulativeTargetNotch;
s[PsmTsvHeader.CumulativeDecoyNotch] = cumulativeDecoyNotch;
s[PsmTsvHeader.QValueNotch] = qValueNotch;
s[PsmTsvHeader.EValue] = eValue;
s[PsmTsvHeader.EScore] = eScore;
}
/// <summary>
/// Resolve Methods()
/// if all 'values' are the same this returns the one value otherwise you get a separated list of all values in their original order.
/// for example:
/// Notches 1,1,1,1 returns as 1
/// Notches 1,0,1,0 returns as 1|0|1|0
/// </summary>
internal static (string ResolvedString, ChemicalFormula ResolvedValue) Resolve(IEnumerable <IEnumerable <Modification> > enumerable)
{
var list = enumerable.ToList();
ChemicalFormula firstChemFormula = new ChemicalFormula();
foreach (var firstMods in list[0])
{
if (firstMods == null || firstMods.ChemicalFormula == null)
{
return("unknown", null);
}
firstChemFormula.Add(firstMods.ChemicalFormula);
}
bool equals = true;
List <ChemicalFormula> formulas = new List <ChemicalFormula>();
foreach (var anEnum in list)
{
ChemicalFormula fhere = new ChemicalFormula();
foreach (var mod in anEnum)
{
if (mod == null || mod.ChemicalFormula == null)
{
return("unknown", null);
}
fhere.Add(mod.ChemicalFormula);
}
if (!firstChemFormula.Equals(fhere))
{
equals = false;
}
formulas.Add(fhere);
}
if (!equals)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", formulas.Select(b => b.Formula)));
return(returnString, null);
}
else
{
return(firstChemFormula.Formula, firstChemFormula);
}
}
private static (string, ChemicalFormula) Resolve(IEnumerable <IEnumerable <ModificationWithMassAndCf> > enumerable)
{
ChemicalFormula f = new ChemicalFormula();
{
var firstEnum = enumerable.First();
foreach (var mod in firstEnum)
{
if (mod == null)
{
return("unknown", null);
}
f.Add(mod.chemicalFormula);
}
}
bool equals = true;
List <ChemicalFormula> formulas = new List <ChemicalFormula>();
foreach (var anEnum in enumerable)
{
ChemicalFormula fhere = new ChemicalFormula();
foreach (var mod in anEnum)
{
if (mod == null)
{
return("unknown", null);
}
fhere.Add(mod.chemicalFormula);
}
if (!f.Equals(fhere))
{
equals = false;
}
formulas.Add(fhere);
}
if (!equals)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", formulas.Select(b => b.Formula)));
return(returnString, null);
}
else
{
return(f.Formula, f);
}
}
internal static (string ResolvedString, string ResolvedValue) Resolve(IEnumerable <string> enumerable, string ambiguousIfNull)
{
var list = enumerable.ToList();
string first = list.FirstOrDefault(b => b != null);
// Only first if list is either all null or all equal to the first
if (list.All(b => b == null) || list.All(b => first.Equals(b)))
{
return(first, first);
}
// use only distinct names if all of the base sequences are the same
else if (ambiguousIfNull != null)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list.Distinct()));
return(returnString, null);
}
else
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", list));
return(returnString, null);
}
}
private Tuple <string, Dictionary <string, int> > Resolve(IEnumerable <Dictionary <int, ModificationWithMass> > enumerable)
{
Dictionary <string, int> ok = enumerable.First().Values.OrderBy(b => b.id).GroupBy(b => b.id).ToDictionary(b => b.Key, b => b.Count());
bool notEqual = false;
foreach (var ha in enumerable)
{
Dictionary <string, int> okTest = ha.Values.OrderBy(b => b.id).GroupBy(b => b.id).ToDictionary(b => b.Key, b => b.Count());
if (!ok.SequenceEqual(okTest))
{
notEqual = true;
break;
}
}
if (notEqual)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", enumerable.Select(b => string.Join(" ", b.Values.Select(c => c.id).OrderBy(c => c)))));
return(new Tuple <string, Dictionary <string, int> >(returnString, null));
}
else
{
return(new Tuple <string, Dictionary <string, int> >(string.Join(" ", enumerable.First().Values.Select(c => c.id).OrderBy(c => c)), ok));
}
}
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.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)
{
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 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 (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());
}