Merge branch 'main' of github.com:lifs-tools/jgoslin

lifs-tools · Oct 20, 2023 · 0510164 · 0510164
2 parents 974bfc9 + 7890743
commit 0510164
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Showing 6 changed files with 42 additions and 22 deletions.
diff --git a/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java b/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java
@@ -39,6 +39,7 @@ public class FattyAcid extends FunctionalGroup {
     public static final Set<LipidFaBondType> LCB_STATES = new HashSet<>(Arrays.asList(LipidFaBondType.LCB_REGULAR, LipidFaBondType.LCB_EXCEPTION));
     protected int numCarbon;
     protected LipidFaBondType lipidFaBondType;
+    public boolean unresolvedHiddenFa = false;
 
     public FattyAcid(String _name, KnownFunctionalGroups knownFunctionalGroups) {
         this(_name, 0, null, null, LipidFaBondType.ESTER, 0, knownFunctionalGroups);
@@ -275,6 +276,12 @@ public ElementTable getFunctionalGroupElements() {
     @Override
     public void computeElements() {
         elements = new ElementTable();
+
+        if (unresolvedHiddenFa){
+            elements.put(Element.O, 1);
+            elements.put(Element.H, -1);
+            return;
+        }
 
         int num_double_bonds = doubleBonds.getNumDoubleBonds();
         if (lipidFaBondType == LipidFaBondType.ETHER_PLASMENYL) {

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/domain/LipidMolecularSpecies.java b/parsers/src/main/java/org/lifstools/jgoslin/domain/LipidMolecularSpecies.java
@@ -46,11 +46,12 @@ public LipidMolecularSpecies(Headgroup _headgroup, Collection<FattyAcid> _fa, Kn
 
         // add 0:0 dummys
         for (int i = _fa.size(); i < info.totalFa; ++i) {
-            FattyAcid fatty_acid = new FattyAcid("FA" + Integer.toString(i + 1), knownFunctionalGroups);
-            fatty_acid.position = -1;
-            info.add(fatty_acid);
-            fa.put(fatty_acid.getName(), fatty_acid);
-            faList.add(fatty_acid);
+            FattyAcid fattyAcid = new FattyAcid("FA" + Integer.toString(i + 1), knownFunctionalGroups);
+            fattyAcid.position = -1;
+            fattyAcid.unresolvedHiddenFa = (1 < _fa.size() && _fa.size() < info.possFa);
+            info.add(fattyAcid);
+            fa.put(fattyAcid.getName(), fattyAcid);
+            faList.add(fattyAcid);
         }
     }
 

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/domain/LipidSpeciesInfo.java b/parsers/src/main/java/org/lifstools/jgoslin/domain/LipidSpeciesInfo.java
@@ -34,6 +34,7 @@ public final class LipidSpeciesInfo extends FattyAcid {
     private LipidLevel level;
     public int numEthers;
     public int numSpecifiedFa;
+    public int possFa;
     public int totalFa;
     public LipidFaBondType extendedClass;
     public static final String[] ETHER_PREFIX = {"", "O-", "dO-", "tO-", "eO-"};
@@ -47,6 +48,7 @@ public LipidSpeciesInfo(int _lipid_class, KnownFunctionalGroups knownFunctionalG
         numSpecifiedFa = 0;
         extendedClass = LipidFaBondType.ESTER;
         totalFa = (LipidClasses.getInstance().size() > lipidClass) ? LipidClasses.getInstance().get(lipidClass).maxNumFa : 0;
+        possFa = (LipidClasses.getInstance().size() > lipidClass) ? LipidClasses.getInstance().get(lipidClass).possibleNumFa : 0;
     }
 
     @Override

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/parser/LipidBaseParserEventHandler.java b/parsers/src/main/java/org/lifstools/jgoslin/parser/LipidBaseParserEventHandler.java
@@ -103,8 +103,13 @@ protected boolean check_full_structure(FunctionalGroup obj){
         }
         return full;
     }
-
+
+
     protected Headgroup prepareHeadgroupAndChecks() {
+        return prepareHeadgroupAndChecks(true);
+    }
+
+    protected Headgroup prepareHeadgroupAndChecks(boolean allowClassShift) {
         Headgroup headgroup = new Headgroup(headGroup, headgroupDecorators, useHeadGroup);
         if (useHeadGroup) {
             return headgroup;
@@ -118,21 +123,23 @@ protected Headgroup prepareHeadgroupAndChecks() {
         }
         int poss_fa = (LipidClasses.getInstance().size() > headgroup.getLipidClass()) ? LipidClasses.getInstance().get(headgroup.getLipidClass()).possibleNumFa : 0;
 
-        // make lyso
-        boolean can_be_lyso = (LipidClasses.getInstance().size() > Headgroup.getClass("L" + headGroup)) ? LipidClasses.getInstance().get(Headgroup.getClass("L" + headGroup)).specialCases.contains("Lyso") : false;
-        LipidClassMeta l = LipidClasses.getInstance().get(Headgroup.getClass("LCL"));
-        if ((true_fa + 1 == poss_fa || true_fa + 2 == poss_fa) && level != LipidLevel.SPECIES && headgroup.getLipidCategory() == LipidCategory.GP && can_be_lyso) {
-            if (true_fa + 1 == poss_fa) headGroup = "L" + headGroup;
-            else headGroup = "DL" + headGroup;
-            headgroup = new Headgroup(headGroup, headgroupDecorators, useHeadGroup);
-            poss_fa = (LipidClasses.getInstance().size() > headgroup.getLipidClass()) ? LipidClasses.getInstance().get(headgroup.getLipidClass()).possibleNumFa : 0;
-        }
-
-        else if ((true_fa + 1 == poss_fa || true_fa + 2 == poss_fa) && level != LipidLevel.SPECIES && headgroup.getLipidCategory() == LipidCategory.GL && headGroup.equals("TG")) {
-            if (true_fa + 1 == poss_fa) headGroup = "DG";
-            else headGroup = "MG";
-            headgroup = new Headgroup(headGroup, headgroupDecorators, useHeadGroup);
-            poss_fa = (LipidClasses.getInstance().size() > headgroup.getLipidClass()) ? LipidClasses.getInstance().get(headgroup.getLipidClass()).possibleNumFa : 0;
+        if (allowClassShift){
+            // make lyso
+            boolean can_be_lyso = (LipidClasses.getInstance().size() > Headgroup.getClass("L" + headGroup)) ? LipidClasses.getInstance().get(Headgroup.getClass("L" + headGroup)).specialCases.contains("Lyso") : false;
+            LipidClassMeta l = LipidClasses.getInstance().get(Headgroup.getClass("LCL"));
+            if ((true_fa + 1 == poss_fa || true_fa + 2 == poss_fa) && level != LipidLevel.SPECIES && headgroup.getLipidCategory() == LipidCategory.GP && can_be_lyso) {
+                if (true_fa + 1 == poss_fa) headGroup = "L" + headGroup;
+                else headGroup = "DL" + headGroup;
+                headgroup = new Headgroup(headGroup, headgroupDecorators, useHeadGroup);
+                poss_fa = (LipidClasses.getInstance().size() > headgroup.getLipidClass()) ? LipidClasses.getInstance().get(headgroup.getLipidClass()).possibleNumFa : 0;
+            }
+
+            else if ((true_fa + 1 == poss_fa || true_fa + 2 == poss_fa) && level != LipidLevel.SPECIES && headgroup.getLipidCategory() == LipidCategory.GL && headGroup.equals("TG")) {
+                if (true_fa + 1 == poss_fa) headGroup = "DG";
+                else headGroup = "MG";
+                headgroup = new Headgroup(headGroup, headgroupDecorators, useHeadGroup);
+                poss_fa = (LipidClasses.getInstance().size() > headgroup.getLipidClass()) ? LipidClasses.getInstance().get(headgroup.getLipidClass()).possibleNumFa : 0;
+            }
         }
 
         // check if all functional groups have a position to be full structure

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/parser/ShorthandParserEventHandler.java b/parsers/src/main/java/org/lifstools/jgoslin/parser/ShorthandParserEventHandler.java
@@ -221,7 +221,7 @@ private void buildLipid(TreeNode node) {
         if (acerSpecies) {
             faList.get(0).setNumCarbon(faList.get(0).getNumCarbon() - 2);
         }
-        Headgroup headgroup = prepareHeadgroupAndChecks();
+        Headgroup headgroup = prepareHeadgroupAndChecks(false);
 
         // add count numbers for fatty acyl chains
         int fa_it = (faList.size() > 0 && (faList.get(0).getLipidFaBondType() == LipidFaBondType.LCB_EXCEPTION || faList.get(0).getLipidFaBondType() == LipidFaBondType.LCB_REGULAR)) ? 1 : 0;

diff --git a/parsers/src/test/java/org/lifstools/jgoslin/parser/ShorthandParserTest.java b/parsers/src/test/java/org/lifstools/jgoslin/parser/ShorthandParserTest.java
@@ -199,6 +199,9 @@ public void testShorthandParserTest() {
 
         l = parser.parse("LHexCer(1) 18:1(5E);3OH/0:0", handler);
         assertEquals("LHexCer(1) 18:1(5E);3OH", l.getLipidString());
+
+        l = parser.parse("TG 18:0_42:2", handler);
+        assertEquals("TG 18:0_42:2", l.getLipidString());
 
 
         l = parser.parse("Gal-Glc-Cer(1) 17:1(5E);15Me[R];3OH[R],4OH[S]/22:0;2OH[R]", handler);