fixing protein sequence issue. Also added a condition to check if variants can be written.

Author: pcruzparri

MetaMorpheus/EngineLayer/ProteinParsimony/ProteinGroup.cs

@@ -417,17 +417,16 @@ public string ModInfoStringFromGroupedFiles(List<SpectraFileInfo> spectraFiles)
 
                 foreach (var protein in proteinGroupOccupanciesPerProtein.Keys)
                 {
-                    if (!proteinGroupOccupanciesPerProtein[protein].IsNotNullOrEmpty())
+                    if (proteinGroupOccupanciesPerProtein[protein].IsNullOrEmpty())
                     {
                         continue;
                     }
 
                     modInfoString.Append(protein.Accession + ":{");
-                    var protSeq = Proteins.Where(prot => prot.Accession == protein.Accession).First().BaseSequence;
 
                     foreach (var modpos in proteinGroupOccupanciesPerProtein[protein].Keys.Order())
                     {
-                        var loc = modpos == 0 ? "N-term" : modpos == protein.Sequence.Length + 1 ? "C-term" : $"{protSeq[modpos-1]}#" + modpos.ToString(); //something's worng with the positions sometimes being longer than the sequence
+                        var loc = modpos == 0 ? "N-terminal" : modpos == protein.Sequence.Length + 1 ? "C-terminal" : $"{protein.Sequence[modpos-1]}#" + modpos.ToString(); 
                         modInfoString.Append(loc);
 
                         var modStrings = new List<string>();

MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs

@@ -600,28 +600,7 @@ private void QuantificationAnalysis()
 
                             PositionFrequencyAnalysis pfa = new PositionFrequencyAnalysis();
                             var proteins = proteinGroup.Proteins.Select(p => new KeyValuePair<string, string>(p.Accession, p.BaseSequence)).ToDictionary();
-                            pfa.SetUpQuantificationObjectsFromFullSequences(peptides, proteins); // one-based indexes, ignores terminal mods on all peptides.
-
-                            // set the one-based start index in protein for each peptide
-                            foreach (var protein in pfa.ProteinGroups.First().Value.Proteins.Values)
-                            {
-                                if (protein.Sequence == null)
-                                {
-                                    protein.Sequence = proteinGroup.Proteins.Where(p => p.Accession == protein.Accession).Select(p => p.BaseSequence).First();
-                                }
-                                List<string> peptideBaseSequencesSeen = new List<string>();
-                                foreach (var peptide in proteinGroup.AllPeptides)
-                                {
-                                    if (protein.Peptides.ContainsKey(peptide.BaseSequence)
-                                        && !peptideBaseSequencesSeen.Contains(peptide.BaseSequence))
-                                    {
-                                        protein.Peptides[peptide.BaseSequence]
-                                            .OneBasedStartIndexInProtein = peptide.OneBasedStartResidue;
-
-                                        peptideBaseSequencesSeen.Add(peptide.BaseSequence);
-                                    }
-                                }
-                            }
+                            pfa.SetUpQuantificationObjectsFromFullSequences(peptides, proteins); // uses zero-based indexes for the mods.
 
                             proteinGroup.ModsInfo.Add(spectraFile, pfa.ProteinGroups.First().Value); // Getting stoich one protein group at a time, so only getting First() is ok here.
 
@@ -1686,7 +1665,7 @@ private void WriteVariantResults()
 
                 foreach (var variant in variants)
                 {
-                    if (variantPWSM.IntersectsAndIdentifiesVariation(variant).identifies == true)
+                    if (variantPWSM.IntersectsAndIdentifiesVariation(variant).identifies == true && variant.Description.Description.IsNotNullOrEmpty())
                     {
                         if (culture.CompareInfo.IndexOf(variant.Description.Description, "missense_variant", CompareOptions.IgnoreCase) >= 0)
                         {