fixed omega-linoleoyloxy-Cer bug

lifs-tools · Mar 17, 2022 · a872e2c · a872e2c
1 parent 75ca6eb
commit a872e2c
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diff --git a/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java b/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java
@@ -43,6 +43,10 @@ public FattyAcid(String _name, KnownFunctionalGroups knownFunctionalGroups) {
         this(_name, 0, null, null, LipidFaBondType.ESTER, 0, knownFunctionalGroups);
     }
 
+    public FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds) {
+        this(_name, _num_carbon, _double_bonds, null, LipidFaBondType.ESTER, 0, null);
+    }
+
     public FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, KnownFunctionalGroups knownFunctionalGroups) {
         this(_name, _num_carbon, _double_bonds, null, LipidFaBondType.ESTER, 0, knownFunctionalGroups);
     }

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/parser/LipidMapsParserEventHandler.java b/parsers/src/main/java/org/lifstools/jgoslin/parser/LipidMapsParserEventHandler.java
@@ -32,6 +32,7 @@
 import java.util.Map;
 import static java.util.Map.entry;
 import java.util.Set;
+import org.lifstools.jgoslin.domain.DoubleBonds;
 
 /**
  * Event handler implementation for the {@link LipidMapsParser}.
@@ -396,6 +397,20 @@ private void buildLipid(TreeNode node) {
         if (lcb != null) {
             faList.add(0, lcb);
         }
+
+        if (addOmegaLinoleoyloxyCer){
+            if (faList.size() != 2){
+                throw new RuntimeException("omega-linoleoyloxy-Cer with a different combination to one long chain base and one fatty acyl chain unknown");
+            }
+            Map<String, ArrayList<FunctionalGroup>> fgroups = faList.get(faList.size() - 1).getFunctionalGroupsInternal();
+            if (!fgroups.containsKey("acyl")) fgroups.put("acyl", new ArrayList<>());
+
+            DoubleBonds db = new DoubleBonds(2);
+            db.getDoubleBondPositions().put(9, "Z");
+            db.getDoubleBondPositions().put(12, "Z");
+            faList.get(faList.size() - 1).getFunctionalGroupsInternal().get("acyl").add(new FattyAcid("FA", 18, db));
+            headGroup = "Cer";
+        }
 
         Headgroup headgroup = prepareHeadgroupAndChecks();
         content = new LipidAdduct(assembleLipid(headgroup), adduct);