cleaned up code after unit test fixing

lifs-tools · Sep 29, 2023 · 6e811c0 · 6e811c0
1 parent 189f5b4
commit 6e811c0
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Showing 4 changed files with 3 additions and 12 deletions.
diff --git a/LipidCreator/FattyAcid.cs b/LipidCreator/FattyAcid.cs
@@ -95,7 +95,6 @@ public FattyAcid(int l, int db, int hydro, FattyAcidType fattyAcidType = FattyAc
                 atomsCount[(int)Molecule.O] = hydroxyl; // O
                 atomsCount[(int)Molecule.N] = 1; // N
             }
-            Console.WriteLine(ToString(false));
         }
 
         public FattyAcid(FattyAcid copy)

diff --git a/LipidCreator/Lipid.cs b/LipidCreator/Lipid.cs
@@ -436,8 +436,6 @@ public static void computeFragmentData(DataTable transitionList, PrecursorData p
                 if (insertedFragments.Contains(fragName)) continue;
                 insertedFragments.Add(fragName);
 
-                Console.WriteLine(fragName);
-
                 rowString[(int)LabelPosition.SPECIFIC_POS] = fragment.specific ? "1" : "0";
                 rowString[(int)LabelPosition.PRECURSOR_NAME_POS] = (((int)parameters[1] == 1 && fragment.specific) || (int)parameters[1] == 2) ? precursorData.precursorSpeciesName : precursorData.precursorName;
 

diff --git a/LipidCreator/LipidCreator.cs b/LipidCreator/LipidCreator.cs
@@ -815,7 +815,6 @@ public LipidCreator(string pipe, bool firstInit = false)
                 log.Error("Unable to read grammar file '" + Path.Combine(prefixPath, "data", "listing.grammar") + "': " + e);
                 throw new Exception();
             }
-
         }
 
 
@@ -1900,7 +1899,6 @@ public Lipid checkLipid(Lipid lipid, int charge = 0, string adduct = "")
             }
 
 
-            Console.WriteLine((lipid != null) + " " + !(lipid is UnsupportedLipid) + " " + lipid.headGroupNames[0]);
             if (lipid != null && !(lipid is UnsupportedLipid) && lipid.headGroupNames.Count > 0 && headgroups.ContainsKey(lipid.headGroupNames[0]))
             {
 
@@ -2020,13 +2018,9 @@ public Lipid translateLipid(csgoslin.LipidAdduct lipidAdduct)
                 default:
                     break;
             }
-
-
-            Dictionary<string, string> trans_table = new Dictionary<string, string>(){{"Hex3HexNAcCer", "GB4"}, {"Hex2NeuAc2Cer", "GD3"}, {"Hex3HexNAcNeuAcCer", "GM1"}, {"Hex2NeuAcCer", "GM3"}};
-
-            if (trans_table.ContainsKey(lipid.headGroupNames[0])) lipid.headGroupNames[0] = trans_table[lipid.headGroupNames[0]];
-
-
+
+            if (headgroups.ContainsKey(lipidAdduct.lipid.headgroup.unaltered_headgroup) && !headgroups.ContainsKey(lipid.headGroupNames[0])) lipid.headGroupNames[0] = lipidAdduct.lipid.headgroup.unaltered_headgroup;
+
 
             if (lipid != null && lipidAdduct.lipid.info.level == csgoslin.LipidLevel.SPECIES)
             {

diff --git a/LipidCreator/csgoslin.dll b/LipidCreator/csgoslin.dll