Merge branch 'EntityEqualityAndProtectedParticipants' into 'develop'

Remove equals overriding of BioEntity and protects creation of BioParticipant

See merge request !6

met4j-chemUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_chemUtils/FormulaParser.java

@@ -15,12 +15,10 @@ public class FormulaParser {
     String formula;
     Pattern inorgaRegex;
     Pattern groupMatch;
-    Pattern genericFormula = Pattern.compile("^([\\*\\(\\)A-Z][a-z]*\\d*)+$");;
     List<String> atoms = Arrays.asList("H","B","C","N","O","F","Na","Mg","Al","Si","P","S","Cl","K","Ca","Cr","Mn","Fe","Co","Cu","Zn","Se","Mo","Cd","Sn","I");
 
-
     public FormulaParser(String formula){
-        if(StringUtils.isVoid(formula) || !genericFormula.matcher(formula).find()) throw new IllegalArgumentException("Unable to parse formula");
+        if(StringUtils.isVoid(formula) || ! StringUtils.checkMetaboliteFormula(formula)) throw new IllegalArgumentException("Unable to parse formula");
         this.formula=formula;
     }
 

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java

@@ -47,7 +47,7 @@ import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
  */
 public abstract class BioEntity {
 
-    private final String id;
+    final String id;
     private String name;
     private ArrayList<String> synonyms = new ArrayList<>();
     private String comment;
@@ -103,26 +103,6 @@ public abstract class BioEntity {
         this.setAttributes(new HashMap<>(e.getAttributes()));
     }
 
-
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
-        BioEntity bioEntity = (BioEntity) o;
-        return id.equals(bioEntity.id);
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public int hashCode() {
-        return Objects.hashCode(id);
-    }
-
     /**
      * Set the name of the entity
      *

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipant.java

@@ -54,8 +54,8 @@ public class BioEnzymeParticipant extends BioParticipant {
      * @param physicalEntity the physical entity that is contained in the enzyme
      * @param stoichiometry  the number of unities of the physical entity
      */
-    public BioEnzymeParticipant(BioPhysicalEntity physicalEntity, Double stoichiometry) {
-        super(physicalEntity, stoichiometry);
+    protected BioEnzymeParticipant(BioPhysicalEntity physicalEntity, Double stoichiometry) {
+        super(physicalEntity.getId() + "__" + stoichiometry, physicalEntity, stoichiometry);
     }
 
     /**
@@ -65,7 +65,7 @@ public class BioEnzymeParticipant extends BioParticipant {
      *                       The stoichiometry is put to 1.
      */
     public BioEnzymeParticipant(BioPhysicalEntity physicalEntity) {
-        super(physicalEntity, 1.0);
+        this(physicalEntity, 1.0);
     }
 
     /**
@@ -92,7 +92,7 @@ public class BioEnzymeParticipant extends BioParticipant {
 
         }
 
-        String buffer = quantityStr + " " + this.getId();
+        String buffer = quantityStr + " " + this.getPhysicalEntity().getId();
 
         return buffer;
 

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java

@@ -41,10 +41,7 @@ package fr.inrae.toulouse.metexplore.met4j_core.biodata;
 
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
 
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Objects;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 /**
@@ -72,6 +69,10 @@ public class BioNetwork extends BioEntity {
 
     private final BioCollection<BioEnzyme> enzymes = new BioCollection<>();
 
+    private final BioCollection<BioReactant> reactants = new BioCollection<>();
+
+    private final BioCollection<BioEnzymeParticipant> enzymeParticipants = new BioCollection<>();
+
     /**
      * <p>Constructor for BioNetwork.</p>
      *
@@ -533,7 +534,7 @@ public class BioNetwork extends BioEntity {
      * @param reaction  a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
      * @param reactants a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant}
      */
-    public void affectLeft(BioReaction reaction, BioCollection<BioReactant> reactants) {
+    protected void affectLeft(BioReaction reaction, BioCollection<BioReactant> reactants) {
         this.affectLeft(reaction, reactants.toArray(new BioReactant[0]));
     }
 
@@ -613,7 +614,7 @@ public class BioNetwork extends BioEntity {
      * @param reaction  a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
      * @param reactants a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant} of {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant}
      */
-    public void affectRight(BioReaction reaction, BioCollection<BioReactant> reactants) {
+    protected void affectRight(BioReaction reaction, BioCollection<BioReactant> reactants) {
         this.affectRight(reaction, reactants.toArray(new BioReactant[0]));
     }
 
@@ -629,8 +630,27 @@ public class BioNetwork extends BioEntity {
         removeSideReaction(e, localisation, reaction, BioReaction.Side.RIGHT);
     }
 
+    /**
+     * get a reactant with the same metabolite, stoichiometry and compartment
+     *
+     * @param metabolite
+     * @param stoichiometry
+     * @param compartment
+     * @return
+     */
+    protected BioReactant getReactant(BioMetabolite metabolite, Double stoichiometry, BioCompartment compartment) {
+        Optional<BioReactant> any = this.reactants.stream()
+                .filter(r -> r.getMetabolite().equals(metabolite) &&
+                        r.getQuantity().equals(stoichiometry)
+                        && r.getLocation().equals(compartment)).findAny();
+        if (any.isPresent()) {
+            return any.get();
+        }
+        return null;
+    }
+
     private void affectSideReaction(BioReaction reaction, Double stoichiometry, BioCompartment localisation, BioReaction.Side side, BioMetabolite e) {
-        BioReactant reactant = new BioReactant(e, stoichiometry, localisation);
+
 
         // The network must contain the compartment
         if (!this.compartments.contains(localisation)) {
@@ -651,6 +671,13 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Reaction " + reaction.getId() + " not in the network");
         }
 
+        BioReactant reactant = this.getReactant(e, stoichiometry, localisation);
+
+        if (reactant == null) {
+            reactant = new BioReactant(e, stoichiometry, localisation);
+            this.reactants.add(reactant);
+        }
+
         if (side.equals(BioReaction.Side.LEFT)) {
             reaction.getLeftReactants().add(reactant);
         } else {
@@ -658,11 +685,29 @@ public class BioNetwork extends BioEntity {
         }
     }
 
+    private void addReactant(BioReactant reactant) {
+        this.reactants.add(reactant);
+    }
+
+    /**
+     * Add reactants in the list of reactants
+     * @param reactants
+     */
+    protected void addReactants(BioReactant ...reactants) {
+        for(BioReactant r : reactants) {
+            this.addReactant(r);
+        }
+    }
+
 
     private void affectSideReaction(BioReactant reactant, BioReaction reaction, BioReaction.Side side) {
 
         BioCompartment localisation = reactant.getLocation();
 
+        if (! this.reactants.contains(reactant)) {
+            throw new IllegalArgumentException("Reactant " + reactant.getId() + " not in the network");
+        }
+
         // The network must contain the compartment
         if (!this.compartments.contains(localisation)) {
             throw new IllegalArgumentException("Compartment " + localisation.getId() + " not in the network");
@@ -685,9 +730,13 @@ public class BioNetwork extends BioEntity {
         }
 
         if (side.equals(BioReaction.Side.LEFT)) {
-            reaction.getLeftReactants().add(reactant);
+            if (!reaction.getLeftReactants().containsId(reactant.getId())) {
+                reaction.getLeftReactants().add(reactant);
+            }
         } else {
-            reaction.getRightReactants().add(reactant);
+            if (!reaction.getRightReactants().containsId(reactant.getId())) {
+                reaction.getRightReactants().add(reactant);
+            }
         }
     }
 
@@ -786,6 +835,23 @@ public class BioNetwork extends BioEntity {
 
     }
 
+    /**
+     * Get enzyme participant with the same quantity and the same entity
+     *
+     * @param quantity
+     * @param unit
+     * @return
+     */
+    protected BioEnzymeParticipant getEnzymeParticipant(BioPhysicalEntity unit, Double quantity) {
+        Optional<BioEnzymeParticipant> any = this.enzymeParticipants.stream()
+                .filter(e -> e.getPhysicalEntity().equals(unit) && e.getQuantity().equals(quantity))
+                .findAny();
+
+        if (any.isPresent()) {
+            return any.get();
+        } else return null;
+    }
+
     /**
      * Add a subunit to an enzymes
      *
@@ -796,8 +862,6 @@ public class BioNetwork extends BioEntity {
      */
     private void affectSubUnit(BioEnzyme enzyme, Double quantity, BioPhysicalEntity unit) {
 
-        BioEnzymeParticipant p = new BioEnzymeParticipant(unit, quantity);
-
         if (!this.contains(enzyme)) {
             throw new IllegalArgumentException("Enzyme " + enzyme.getId() + " not present in the network");
         }
@@ -806,6 +870,12 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Physical entity " + unit.getId() + " not present in the network");
         }
 
+        BioEnzymeParticipant p = this.getEnzymeParticipant(unit, quantity);
+        if (p == null) {
+            p = new BioEnzymeParticipant(unit, quantity);
+            this.enzymeParticipants.add(p);
+        }
+
         enzyme.addParticipant(p);
 
     }
@@ -819,6 +889,9 @@ public class BioNetwork extends BioEntity {
      */
     private void affectSubUnit(BioEnzyme enzyme, BioEnzymeParticipant unit) {
 
+        if(! this.enzymeParticipants.contains(unit)) {
+            throw new IllegalArgumentException("Enzyme participant " + unit.getId() + " not present in the network");
+        }
 
         if (!this.contains(enzyme)) {
             throw new IllegalArgumentException("Enzyme " + enzyme.getId() + " not present in the network");
@@ -828,7 +901,9 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Physical entity " + unit.getPhysicalEntity().getId() + " not present in the network");
         }
 
-        enzyme.addParticipant(unit);
+        if(! enzyme.getParticipants().containsId(unit.getId())) {
+            enzyme.addParticipant(unit);
+        }
 
     }
 
@@ -882,7 +957,7 @@ public class BioNetwork extends BioEntity {
      * @param enzyme a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEnzyme}
      * @param units  a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} of {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEnzymeParticipant}
      */
-    public void affectSubUnit(BioEnzyme enzyme, BioCollection<BioEnzymeParticipant> units) {
+    protected void affectSubUnit(BioEnzyme enzyme, BioCollection<BioEnzymeParticipant> units) {
 
         for (BioEnzymeParticipant unit : units) {
             affectSubUnit(enzyme, unit);
@@ -1178,7 +1253,7 @@ public class BioNetwork extends BioEntity {
     }
 
     /**
-     * @param m a {@link BioMetabolite}
+     * @param m           a {@link BioMetabolite}
      * @param isSubstrate a {@link Boolean} indicating if the metabolite is a substrate or a product
      * @return a {@link BioCollection} of {@link BioReaction}
      */
@@ -1776,4 +1851,56 @@ public class BioNetwork extends BioEntity {
     public int hashCode() {
         return Objects.hash(super.hashCode(), pathways, metabolites, proteins, genes, reactions, compartments, enzymes);
     }
+
+
+    /**
+     * @param e
+     * @return
+     */
+    public Boolean containsEntityWithSameId(BioEntity e) {
+        if (e == null) {
+            throw new NullPointerException();
+        }
+
+        String id = e.getId();
+
+        Boolean flag;
+
+        if (e instanceof BioPathway) {
+            flag = this.pathways.containsId(id);
+        } else if (e instanceof BioMetabolite) {
+            flag = this.metabolites.containsId(id);
+        } else if (e instanceof BioProtein) {
+            flag = this.proteins.containsId(id);
+        } else if (e instanceof BioGene) {
+            flag = this.genes.containsId(id);
+        } else if (e instanceof BioReaction) {
+            flag = this.reactions.containsId(id);
+        } else if (e instanceof BioCompartment) {
+            flag = this.compartments.containsId(id);
+        } else if (e instanceof BioEnzyme) {
+            flag = this.enzymes.containsId(id);
+        } else {
+
+            throw new IllegalArgumentException(
+                    "BioEntity \"" + e.getClass().getSimpleName() + "\" not supported by BioNetwork");
+        }
+        return flag;
+
+    }
+
+    /**
+     * Adds enzymes participants in the network
+     * @param enzymeParticipants
+     */
+    protected void addEnzymeParticipants(BioEnzymeParticipant ...enzymeParticipants) {
+        for(BioEnzymeParticipant ep : enzymeParticipants) {
+            this.addEnzymeParticipant(ep);
+        }
+
+    }
+
+    private void addEnzymeParticipant(BioEnzymeParticipant ep) {
+        this.enzymeParticipants.add(ep);
+    }
 }

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java

@@ -38,6 +38,7 @@ package fr.inrae.toulouse.metexplore.met4j_core.biodata;
 
 import fr.inrae.toulouse.metexplore.met4j_core.utils.ErrorUtils;
 
+import javax.annotation.Nonnull;
 import java.util.Objects;
 
 /**
@@ -48,9 +49,9 @@ import java.util.Objects;
  */
 public abstract class BioParticipant extends BioEntity {
 
-	private BioPhysicalEntity physicalEntity;
+	private final BioPhysicalEntity physicalEntity;
 	
-	private Double quantity;
+	private final Double quantity;
 
 	/**
 	 * Constructor
@@ -58,13 +59,20 @@ public abstract class BioParticipant extends BioEntity {
 	 * @param physicalEntity a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity}
 	 * @param quantity number of units of physicalEntity
 	 */
-	public BioParticipant(BioPhysicalEntity physicalEntity, Double quantity) {
-		super(physicalEntity.getId());
+
+	public BioParticipant(String id, @Nonnull BioPhysicalEntity physicalEntity, Double quantity) {
+		super(id);
 		this.physicalEntity=physicalEntity;
-		this.setQuantity(quantity);
+		if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
+		{
+			ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
+			throw new IllegalArgumentException();
+		}
+
+		this.quantity = quantity;
 	}
-	
-	
+
+
 	/**
 	 * <p>Getter for the field <code>physicalEntity</code>.</p>
 	 *
@@ -75,18 +83,6 @@ public abstract class BioParticipant extends BioEntity {
 	}
 	
 
-	/**
-	 * <p>Setter for the field <code>physicalEntity</code>.</p>
-	 *
-	 * @param physicalEntity the physicalEntity to set
-	 */
-	public void setPhysicalEntity(BioPhysicalEntity physicalEntity) {
-		this.physicalEntity = physicalEntity;
-	}
-	
-	
-
-
 	/**
 	 * <p>Getter for the field <code>quantity</code>.</p>
 	 *
@@ -97,28 +93,11 @@ public abstract class BioParticipant extends BioEntity {
 	}
 
 
-	/**
-	 * <p>Setter for the field <code>quantity</code>.</p>
-	 *
-	 * @param quantity the quantity to set
-	 */
-	public void setQuantity(Double quantity) {
-		
-		if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
-		{
-			ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
-			throw new IllegalArgumentException();
-		}
-		
-		this.quantity = quantity;
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object o) {
 		if (this == o) return true;
 		if (o == null || getClass() != o.getClass()) return false;
-		if (!super.equals(o)) return false;
 		BioParticipant that = (BioParticipant) o;
 		return Objects.equals(physicalEntity, that.physicalEntity) &&
 				Objects.equals(quantity, that.quantity);

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java

@@ -35,6 +35,7 @@
  */
 package fr.inrae.toulouse.metexplore.met4j_core.biodata;
 
+import javax.annotation.Nonnull;
 import java.text.DecimalFormat;
 import java.text.DecimalFormatSymbols;
 import java.text.NumberFormat;
@@ -49,7 +50,7 @@ import java.util.Objects;
  */
 public class BioReactant extends BioParticipant {
 
-	private BioCompartment location = null;
+	private final BioCompartment location;
 
 	/**
 	 * Constructor
@@ -58,9 +59,9 @@ public class BioReactant extends BioParticipant {
 	 * @param stoichiometry stoichiometric coefficient
 	 * @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
 	 */
-	public BioReactant(BioMetabolite metabolite, Double stoichiometry, BioCompartment location) {
-		super(metabolite, stoichiometry);
-		this.setLocation(location);
+	protected BioReactant(@Nonnull BioMetabolite metabolite, Double stoichiometry, @Nonnull BioCompartment location) {
+		super(metabolite.getId()+"__"+stoichiometry+"__"+location.getId(), metabolite, stoichiometry);
+		this.location = location;
 	}
 
 	/**
@@ -72,15 +73,6 @@ public class BioReactant extends BioParticipant {
 		return location;
 	}
 
-	/**
-	 * Set location
-	 *
-	 * @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
-	 */
-	protected void setLocation(BioCompartment location) {
-		this.location = location;
-	}
-
 	/**
 	 * Get the associated metabolite
 	 *
@@ -114,7 +106,7 @@ public class BioReactant extends BioParticipant {
 
 		StringBuilder buffer = new StringBuilder(quantityStr);
 		buffer.append(" ");
-		buffer.append(this.getId());
+		buffer.append(this.getPhysicalEntity().getId());
 		if (this.getLocation() != null) {
 			buffer.append("[");
 			buffer.append(this.getLocation().getId());

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java

@@ -198,7 +198,15 @@ public class BioCollection<E extends BioEntity> implements Collection<E> {
 	/** {@inheritDoc} */
 	@Override
 	public boolean add(E e) {
-		entities.put(e.getId(), e);
+		if(entities.containsValue(e)) {
+			return false;
+		}
+		else {
+			if (entities.keySet().contains(e.getId())) {
+				throw new IllegalArgumentException("An entity with the same id (" + e.getId() + ") is already present in the BioCollection");
+			}
+			entities.put(e.getId(), e);
+		}
 		return true;
 	}
 

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java

@@ -136,12 +136,14 @@ public class BioNetworkUtils {
         }
 
         for (BioMetabolite metabolite : metabolitesToCopy) {
-            BioMetabolite newMetabolite = new BioMetabolite(metabolite);
-            networkOut.add(newMetabolite);
+            BioMetabolite newMetabolite;
+            if (!networkOut.containsEntityWithSameId(metabolite)) {
+                newMetabolite = new BioMetabolite(metabolite);
+                networkOut.add(newMetabolite);
+            }
         }
 
-        // Copy compartments (empty for the moment)
-        // Copy metabolites
+        // Copy compartments
         BioCollection<BioCompartment> compartmentsToCopy = networkIn.getCompartmentsView();
         if (keepPrevious) {
             compartmentsToCopy.removeAll(networkOut.getCompartmentsView());
@@ -151,7 +153,7 @@ public class BioNetworkUtils {
 
             BioCompartment newCpt;
 
-            if (compartmentsToCopy.contains(cpt)) {
+            if (compartmentsToCopy.contains(cpt) && (!networkOut.containsEntityWithSameId(cpt))) {
                 newCpt = new BioCompartment(cpt);
                 networkOut.add(newCpt);
             } else {
@@ -176,8 +178,10 @@ public class BioNetworkUtils {
             }
 
             for (BioGene gene : genesToCopy) {
-                BioGene newGene = new BioGene(gene);
-                networkOut.add(newGene);
+                if (!networkOut.containsEntityWithSameId(gene)) {
+                    BioGene newGene = new BioGene(gene);
+                    networkOut.add(newGene);
+                }
             }
         }
 
@@ -191,7 +195,7 @@ public class BioNetworkUtils {
 
                 BioProtein newProtein;
 
-                if (proteinsToCopy.contains(protein)) {
+                if (proteinsToCopy.contains(protein) && (!networkOut.containsEntityWithSameId(protein))) {
                     newProtein = new BioProtein(protein);
                     networkOut.add(newProtein);
                 } else {
@@ -218,7 +222,7 @@ public class BioNetworkUtils {
 
                 BioEnzyme newEnzyme;
 
-                if (enzymesToCopy.contains(enzyme)) {
+                if (enzymesToCopy.contains(enzyme) && !networkOut.containsEntityWithSameId(enzyme)) {
                     newEnzyme = new BioEnzyme(enzyme);