Revert "Encyclopedia formated peptide full sequence including mass shift in brackets"

mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs

@@ -929,11 +929,6 @@ public override string ToString()
             return FullSequence + string.Join("\t", AllModsOneIsNterminus.Select(m => m.ToString()));
         }
 
-        public string FullSequenceWithMassShift()
-        {
-            return DetermineFullSequenceWithMassShifts();
-        }
-
         public override bool Equals(object obj)
         {
             var q = obj as PeptideWithSetModifications;
@@ -1040,6 +1035,7 @@ private void GetProteinAfterDeserialization(Dictionary<string, Protein> idToProt
             {
                 throw new MzLibUtil.MzLibException("Could not find protein accession after deserialization! " + ProteinAccession);
             }
+
             Protein = protein;
         }
 
@@ -1094,55 +1090,6 @@ private void DetermineFullSequence()
 
             FullSequence = subsequence.ToString();
         }
-        /// <summary>
-        /// This method returns the full sequence with mass shifts INSTEAD OF PTMs in brackets []
-        /// Some external tools cannot parse PTMs, instead requiring a numerical input indicating the mass of a PTM in brackets
-        /// after the position of that modification
-        /// N-terminal mas shifts are in brackets prior to the first amino acid and apparently missing the + sign
-        /// </summary>
-        /// <returns></returns>
-        private string DetermineFullSequenceWithMassShifts()
-        {
-            var subsequence = new StringBuilder();
-
-            // modification on peptide N-terminus
-            if (AllModsOneIsNterminus.TryGetValue(1, out Modification mod))
-            {
-                subsequence.Append('[' + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
-            }
-
-            for (int r = 0; r < Length; r++)
-            {
-                subsequence.Append(this[r]);
-
-                // modification on this residue
-                if (AllModsOneIsNterminus.TryGetValue(r + 2, out mod))
-                {
-                    if (mod.MonoisotopicMass > 0)
-                    {
-                        subsequence.Append("[+" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
-                    }
-                    else
-                    {
-                        subsequence.Append("[" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
-                    }
-                }
-            }
-
-            // modification on peptide C-terminus
-            if (AllModsOneIsNterminus.TryGetValue(Length + 2, out mod))
-            {
-                if (mod.MonoisotopicMass > 0)
-                {
-                    subsequence.Append("[+" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
-                }
-                else
-                {
-                    subsequence.Append("[" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
-                }
-            }
-            return subsequence.ToString();
-        }
 
         private void UpdateCleavageSpecificity()
         {