Refactored quantification util classes

Author: pcruzparri

mzLib/MzLibUtil/PositionFrequencyAnalysis.cs

@@ -0,0 +1,68 @@
+using Easy.Common.Extensions;
+using System.Collections.Generic;
+
+namespace MzLibUtil.PositionFrequencyAnalysis
+{
+    public class PositionFrequencyAnalysis
+    {
+        public Dictionary<string, QuantifiedProteinGroup> ProteinGroups { get; private set; }
+
+        //public Dictionary<string, (QuantifiedPeptide QuantifiedPeptide, string ProteinGroups)> Peptides { get; private set; }
+
+        /// <summary>
+        /// Calculates the occupancy of post-translational modifications at the peptide level. 
+        /// </summary>
+        /// <param name="peptides"> A List of Tuples whose entries are ordered as (string FullSequence, string BaseSequence, List<string> ProteinGroups, Intensity) for each peptide.</param>
+        /// <returns> A nested dictionary whose key mappings are as follows: string ProteinGroup-> string Protein-> string BaseSequence-> int ModifiedAminoAcidIndex-> string ModificationName-> double Intensity
+        /// Note: Each BaseSequence dictionary contains a ModifiedAminoAcidIndex key of -1 that then contains a ModificationName key called "Total" that is used to track the total intensity observed for 
+        /// all of the amino acids in that peptide.</returns>
+        ///
+        public void SetUpQuantificationObjectsFromFullSequences(List<(string fullSeq, List<string> proteinGroups, double intensity)> peptides, Dictionary<string, string> proteinSequences=null)
+        {
+            ProteinGroups = new Dictionary<string, QuantifiedProteinGroup>();
+
+            // Go through the peptides given
+            foreach (var pep in peptides)
+            {
+                string baseSeq = pep.fullSeq.GetBaseSequenceFromFullSequence();
+
+                // Go through the peptide's protein groups
+                foreach (var pg in pep.proteinGroups)
+                {
+                    // If have not seen that protein group, store it
+                    if (!ProteinGroups.ContainsKey(pg))
+                    {
+                        ProteinGroups[pg] = new QuantifiedProteinGroup(pg);
+                    }
+                    var proteinGroup = ProteinGroups[pg];
+
+                    // Go through the proteins in each protein group
+                    foreach (var proteinName in pg.Split('|'))
+                    {
+                        // Add the protein to the protein group's dictionary if it has not been added
+                        if (!proteinGroup.Proteins.ContainsKey(proteinName))
+                        {
+                            proteinGroup.Proteins[proteinName] = new QuantifiedProtein(proteinName);
+                            if (proteinSequences.IsNotNullOrEmpty() && proteinSequences.ContainsKey(proteinName))
+                            {
+                                proteinGroup.Proteins[proteinName].Sequence = proteinSequences[proteinName];
+                            }
+                        }
+                        var protein = proteinGroup.Proteins[proteinName];
+
+                        // If the peptide's base sequence has not been seen, add it to the protein's dictionary
+                        if (!protein.Peptides.ContainsKey(baseSeq))
+                        {
+                            protein.Peptides[baseSeq] = new QuantifiedPeptide(pep.fullSeq, intensity: pep.intensity);
+                        }
+                        else
+                        {
+                            // If the peptide's base sequence has been seen, add the new full sequence to the existing peptide
+                            protein.Peptides[baseSeq].AddFullSequence(pep.fullSeq, intensity: pep.intensity);
+                        }
+                    }
+                }
+            }
+        }
+    }
+}