Finish 0.9.1

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.9.1
+
+### Fixed
+
+[met4j-io] Great speed improvements to read gene reaction associations
+
 ## 0.9.0
 
 ### Features

coverage/pom.xml

@@ -44,7 +44,7 @@
     <parent>
         <groupId>fr.inrae.toulouse.metexplore</groupId>
         <artifactId>met4j</artifactId>
-        <version>0.9.0-SNAPSHOT</version>
+        <version>0.9.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

met4j-chemUtils/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>fr.inrae.toulouse.metexplore</groupId>
     <artifactId>met4j</artifactId>
-    <version>0.9.0-SNAPSHOT</version>
+    <version>0.9.1-SNAPSHOT</version>
   </parent>
 
     <properties>
@@ -35,7 +35,7 @@
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-core</artifactId>
-            <version>0.9.0-SNAPSHOT</version>
+            <version>0.9.1-SNAPSHOT</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
         <dependency>

met4j-core/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>fr.inrae.toulouse.metexplore</groupId>
     <artifactId>met4j</artifactId>
-    <version>0.9.0-SNAPSHOT</version>
+    <version>0.9.1-SNAPSHOT</version>
   </parent>
 
     <scm>

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

@@ -90,6 +90,144 @@ public class BioNetwork extends BioEntity {
         super("NA");
     }
 
+
+    /**
+     * Get a reaction by its id
+     *
+     * @param id a String
+     * @return a {@link BioReaction}
+     */
+    public BioReaction getReaction(@NonNull String id) {
+        return this.reactions.get(id);
+    }
+
+    /**
+     * Check if a reaction with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioReaction} with this id exists in the BioNetwork
+     */
+    public boolean containsReaction(@NonNull String id) {
+        return this.reactions.containsId(id);
+    }
+
+
+    /**
+     * Get a metabolite by its id
+     * @param id a String
+     * @return a {@link BioMetabolite}
+     */
+    public BioMetabolite getMetabolite(@NonNull String id) {
+        return this.metabolites.get(id);
+    }
+
+    /**
+     * Check if a metabolite with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioMetabolite} with this id exists in the BioNetwork
+     */
+    public boolean containsMetabolite(@NonNull String id) {
+        return this.metabolites.containsId(id);
+    }
+
+    /**
+     * Get a pathway by its id
+     * @param id a String
+     * @return a {@link BioPathway}
+     */
+    public BioPathway getPathway(@NonNull String id) {
+        return this.pathways.get(id);
+    }
+
+    /**
+     * Check if a pathway with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioPathway} with this id exists in the BioNetwork
+     */
+    public boolean containsPathway(@NonNull String id) {
+        return this.pathways.containsId(id);
+    }
+
+    /**
+     * Get a protein by its id
+     * @param id a String
+     * @return a {@link BioProtein}
+     */
+    public BioProtein getProtein(@NonNull String id) {
+        return this.proteins.get(id);
+    }
+
+    /**
+     * Check if a pathway with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioPathway} with this id exists in the BioNetwork
+     */
+    public boolean containsProtein(@NonNull String id) {
+        return this.proteins.containsId(id);
+    }
+
+
+    /**
+     * Get a gene by its id
+     * @param id a String
+     * @return a {@link BioGene}
+     */
+    public BioGene getGene(String id) {
+        return this.genes.get(id);
+    }
+
+    /**
+     * Check if a gene with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioGene} with this id exists in the BioNetwork
+     */
+    public boolean containsGene(String id) {
+        return this.genes.containsId(id);
+    }
+
+    /**
+     * Get a compartment by its id
+     * @param id a String
+     * @return a {@link BioCompartment}
+     */
+    public BioCompartment getCompartment(String id) {
+        return this.compartments.get(id);
+    }
+
+    /**
+     * Check if a compartment with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioCompartment} with this id exists in the BioNetwork
+     */
+    public boolean containsCompartment(String id) {
+        return this.compartments.containsId(id);
+    }
+
+    /**
+     * Get an enzyme by its id
+     * @param id a String
+     * @return a {@link BioEnzyme}
+     */
+    public BioEnzyme getEnzyme(String id) {
+        return this.enzymes.get(id);
+    }
+
+    /**
+     * Check if an enzyme with a specific id already exists in the network
+     *
+     * @param id a String
+     * @return true if there is a {@link BioEnzyme} with this id exists in the BioNetwork
+     */
+    public boolean containsEnzyme(String id) {
+        return this.enzymes.containsId(id);
+    }
+
+
     /**
      * Add several entities
      *
@@ -134,8 +272,7 @@ public class BioNetwork extends BioEntity {
             this.addCompartment((BioCompartment) e);
         } else if (e instanceof BioEnzyme) {
             this.addEnzyme((BioEnzyme) e);
-        }
-        else {
+        } else {
             throw new IllegalArgumentException(
                     "BioEntity \"" + e.getClass().getSimpleName() + "\" not supported by BioNetwork");
         }
@@ -583,7 +720,7 @@ public class BioNetwork extends BioEntity {
      * @param localisation  a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
      * @param products      a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} of {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite} to add to the right side of the reaction
      */
-    public void affectRight(@NonNull  BioReaction reaction, @NonNull Double stoichiometry, @NonNull BioCompartment localisation, @NonNull BioCollection<BioMetabolite> products) {
+    public void affectRight(@NonNull BioReaction reaction, @NonNull Double stoichiometry, @NonNull BioCompartment localisation, @NonNull BioCollection<BioMetabolite> products) {
         for (BioMetabolite product : products)
             affectSideReaction(reaction, stoichiometry, localisation, BioReaction.Side.RIGHT, product);
     }
@@ -632,9 +769,9 @@ public class BioNetwork extends BioEntity {
     /**
      * get a reactant with the same metabolite, stoichiometry and compartment
      *
-     * @param metabolite a {@link BioMetabolite}
+     * @param metabolite    a {@link BioMetabolite}
      * @param stoichiometry a {@link Double}
-     * @param compartment a {@link BioCompartment}
+     * @param compartment   a {@link BioCompartment}
      * @return a {@link BioReactant}
      */
     protected BioReactant getReactant(@NonNull BioMetabolite metabolite, @NonNull Double stoichiometry, @NonNull BioCompartment compartment) {
@@ -646,12 +783,11 @@ public class BioNetwork extends BioEntity {
     }
 
     /**
-     *
-     * @param reaction a {@link BioReaction}
+     * @param reaction      a {@link BioReaction}
      * @param stoichiometry a {@link Double}
-     * @param localisation a {@link BioCompartment}
-     * @param side a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction.Side}
-     * @param metabolite a {@link BioMetabolite}
+     * @param localisation  a {@link BioCompartment}
+     * @param side          a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction.Side}
+     * @param metabolite    a {@link BioMetabolite}
      */
     private void affectSideReaction(@NonNull BioReaction reaction, @NonNull Double stoichiometry, @NonNull BioCompartment localisation, @NonNull BioReaction.Side side, @NonNull BioMetabolite metabolite) {
 
@@ -672,10 +808,11 @@ public class BioNetwork extends BioEntity {
 
     /**
      * Add reactants in the list of reactants
+     *
      * @param reactants a list of {@link BioReactant}
      */
-    protected void addReactants(@NonNull BioReactant ...reactants) {
-        for(BioReactant r : reactants) {
+    protected void addReactants(@NonNull BioReactant... reactants) {
+        for (BioReactant r : reactants) {
             this.addReactant(r);
         }
     }
@@ -685,7 +822,7 @@ public class BioNetwork extends BioEntity {
 
         BioCompartment localisation = reactant.getLocation();
 
-        if (! this.reactants.contains(reactant)) {
+        if (!this.reactants.contains(reactant)) {
             throw new IllegalArgumentException("Reactant " + reactant.getId() + " not in the network");
         }
 
@@ -820,7 +957,7 @@ public class BioNetwork extends BioEntity {
      * Get enzyme participant with the same quantity and the same entity
      *
      * @param quantity a {@link Double}
-     * @param unit a {@link BioPhysicalEntity}
+     * @param unit     a {@link BioPhysicalEntity}
      * @return a {@link BioEnzymeParticipant}
      */
     protected BioEnzymeParticipant getEnzymeParticipant(@NonNull BioPhysicalEntity unit, @NonNull Double quantity) {
@@ -841,7 +978,7 @@ public class BioNetwork extends BioEntity {
      */
     private void affectSubUnit(@NonNull BioEnzyme enzyme, @NonNull Double quantity, @NonNull BioPhysicalEntity unit) {
 
-        if(! (unit instanceof  BioMetabolite) && ! (unit instanceof BioProtein) ) {
+        if (!(unit instanceof BioMetabolite) && !(unit instanceof BioProtein)) {
             throw new IllegalArgumentException("A subunit of a BioEnzyme must be a BioProtein or a BioMetabolite");
         }
         BioEnzymeParticipant p = this.getEnzymeParticipant(unit, quantity);
@@ -864,7 +1001,7 @@ public class BioNetwork extends BioEntity {
      */
     private void affectSubUnit(@NonNull BioEnzyme enzyme, @NonNull BioEnzymeParticipant unit) {
 
-        if(! this.enzymeParticipants.contains(unit)) {
+        if (!this.enzymeParticipants.contains(unit)) {
             throw new IllegalArgumentException("Enzyme participant " + unit.getId() + " not present in the network");
         }
 
@@ -876,7 +1013,7 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Physical entity " + unit.getPhysicalEntity().getId() + " not present in the network");
         }
 
-        if(! enzyme.getParticipants().containsId(unit.getId())) {
+        if (!enzyme.getParticipants().containsId(unit.getId())) {
             enzyme.addParticipant(unit);
         }
 
@@ -1202,7 +1339,7 @@ public class BioNetwork extends BioEntity {
             }
         }
 
-        HashSet<BioReaction> reactionSet = this.getReactionsView().stream().filter(r -> {
+        HashSet<BioReaction> reactionSet = this.reactions.stream().filter(r -> {
 
             if (!r.isReversible()) {
 
@@ -1230,7 +1367,7 @@ public class BioNetwork extends BioEntity {
 
         BioCollection<BioReaction> reactions = new BioCollection<>();
 
-        this.getReactionsView().forEach(r -> {
+        this.reactions.forEach(r -> {
             boolean flag;
 
             BioCollection<BioMetabolite> lefts = r.getLeftsView();
@@ -1314,7 +1451,7 @@ public class BioNetwork extends BioEntity {
             }
         }
 
-        HashSet<BioReaction> reactionSet = this.getReactionsView().stream().
+        HashSet<BioReaction> reactionSet = this.reactions.stream().
                 filter(o -> all ? o.getGenes().containsAll(genes) : !Collections.disjoint(o.getGenes(), genes))
                 .collect(Collectors.toCollection(HashSet::new));
 
@@ -1334,7 +1471,7 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Gene " + gene + " not present in the network");
         }
 
-        HashSet<BioReaction> reactionSet = this.getReactionsView().stream().
+        HashSet<BioReaction> reactionSet = this.reactions.stream().
                 filter(o -> o.getGenes().contains(gene))
                 .collect(Collectors.toCollection(HashSet::new));
 
@@ -1678,8 +1815,8 @@ public class BioNetwork extends BioEntity {
         BioCollection<BioMetabolite> allMetabolites = new BioCollection<>();
 
         for (BioReaction reaction : reactions) {
-            if(! this.contains(reaction)) {
-                throw new IllegalArgumentException("Reaction "+reaction+" not present in the network");
+            if (!this.contains(reaction)) {
+                throw new IllegalArgumentException("Reaction " + reaction + " not present in the network");
             }
             if (this.contains(reaction)) {
                 allMetabolites.addAll(this.getLefts(reaction));
@@ -1721,7 +1858,7 @@ public class BioNetwork extends BioEntity {
             throw new IllegalArgumentException("Entity " + e + " not present in the network");
         }
 
-        for (BioCompartment c : this.getCompartmentsView()) {
+        for (BioCompartment c : this.compartments) {
             if (c.getComponents().contains(e)) {
                 cpts.add(c);
             }
@@ -1829,17 +1966,17 @@ public class BioNetwork extends BioEntity {
 
     /**
      * Adds enzymes participants in the network
+     *
      * @param enzymeParticipants a list of {@link BioEnzymeParticipant}
      */
-    protected void addEnzymeParticipants(@NonNull BioEnzymeParticipant ...enzymeParticipants) {
-        for(BioEnzymeParticipant ep : enzymeParticipants) {
+    protected void addEnzymeParticipants(@NonNull BioEnzymeParticipant... enzymeParticipants) {
+        for (BioEnzymeParticipant ep : enzymeParticipants) {
             this.addEnzymeParticipant(ep);
         }
 
     }
 
     /**
-     *
      * @param ep a {@link BioEnzymeParticipant}
      */
     private void addEnzymeParticipant(@NonNull BioEnzymeParticipant ep) {

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

@@ -63,7 +63,9 @@ public class BioNetworkUtils {
 
         BioCollection<BioReaction> chokeReactions = new BioCollection<>();
 
-        for (BioReaction r : network.getReactionsView()) {
+        BioCollection<BioReaction> reactions = network.getReactionsView();
+
+        for (BioReaction r : reactions) {
 
             BioCollection<BioMetabolite> metabolites = network.getLefts(r);
             metabolites.addAll(network.getRights(r));
@@ -117,7 +119,8 @@ public class BioNetworkUtils {
      *                     - add metabolites to a compartment
      *                     - add components to an enzyme
      *                     - add reactions to a pathway
-     *                     - add enzymes or reactants to a reaction
+     *                     - add enzymes to a reaction
+     *                     But, it does not change the reactants of a reaction, ie the formula of the reaction.
      */
     public static void deepCopy(@NonNull BioNetwork networkIn, @NonNull BioNetwork networkOut, Boolean keepGPR, Boolean keepPrevious) {
 
@@ -155,7 +158,7 @@ public class BioNetworkUtils {
                 newCpt = new BioCompartment(cpt);
                 networkOut.add(newCpt);
             } else {
-                newCpt = networkOut.getCompartmentsView().get(cpt.getId());
+                newCpt = networkOut.getCompartment(cpt.getId());
             }
 
             // Copy metabolites in the compartments
@@ -163,7 +166,7 @@ public class BioNetworkUtils {
                     filter((c) -> c.getClass().equals(BioMetabolite.class)).
                     map(BioEntity::getId).
                     forEach((id) -> {
-                        BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(id);
+                        BioMetabolite newMetabolite = networkOut.getMetabolite(id);
                         networkOut.affectToCompartment(newCpt, newMetabolite);
                     });
         }
@@ -197,12 +200,12 @@ public class BioNetworkUtils {
                     newProtein = new BioProtein(protein);
                     networkOut.add(newProtein);
                 } else {
-                    newProtein = networkOut.getProteinsView().get(protein.getId());
+                    newProtein = networkOut.getProtein(protein.getId());
                 }
 
                 if (protein.getGene() != null) {
                     String geneId = protein.getGene().getId();
-                    BioGene newGene = networkOut.getGenesView().get(geneId);
+                    BioGene newGene = networkOut.getGene(geneId);
                     networkOut.affectGeneProduct(newProtein, newGene);
                 }
             }
@@ -224,7 +227,7 @@ public class BioNetworkUtils {
                     newEnzyme = new BioEnzyme(enzyme);
                     networkOut.add(newEnzyme);
                 } else {
-                    newEnzyme = networkOut.getEnzymesView().get(enzyme.getId());
+                    newEnzyme = networkOut.getEnzyme(enzyme.getId());
                 }
 
                 BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
@@ -234,11 +237,11 @@ public class BioNetworkUtils {
 
                     if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
                         BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
-                        BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(metabolite.getId());
+                        BioMetabolite newMetabolite = networkOut.getMetabolite(metabolite.getId());
                         networkOut.affectSubUnit(newEnzyme, quantity, newMetabolite);
                     } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
                         BioProtein protein = (BioProtein) participant.getPhysicalEntity();
-                        BioProtein newProtein = networkOut.getProteinsView().get(protein.getId());
+                        BioProtein newProtein = networkOut.getProtein(protein.getId());
                         networkOut.affectSubUnit(newEnzyme, quantity, newProtein);
                     }
                 }
@@ -246,16 +249,19 @@ public class BioNetworkUtils {
         }
 
         // Copy reactions
+        BioCollection<BioReaction> reactionsIn = networkIn.getReactionsView();
+        BioCollection<BioReaction> reactionsOut = networkOut.getReactionsView();
+
         BioCollection<BioReaction> reactionsToCopy = networkIn.getReactionsView();
         if (keepPrevious) {
-            reactionsToCopy.removeAll(networkOut.getReactionsView());
+            reactionsToCopy.removeAll(reactionsOut);
         }
 
-        for (BioReaction r : networkIn.getReactionsView()) {
+        for (BioReaction r : reactionsIn) {
 
             BioReaction newReaction;
 
-            if (reactionsToCopy.contains(r) && !networkOut.containsEntityWithSameId(r)) {
+            if (reactionsToCopy.contains(r) && !networkOut.containsReaction(r.getId())) {
 
                 newReaction = new BioReaction(r);
                 newReaction.setSpontaneous(r.isSpontaneous());
@@ -263,30 +269,30 @@ public class BioNetworkUtils {
                 newReaction.setEcNumber(r.getEcNumber());
 
                 networkOut.add(newReaction);
-            } else {
-                newReaction = networkOut.getReactionsView().get(r.getId());
-            }
 
-            // Copy lefts
-            for (BioReactant reactant : r.getLeftReactantsView()) {
-                BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(reactant.getMetabolite().getId());
-                BioCompartment newCpt = networkOut.getCompartmentsView().get(reactant.getLocation().getId());
-                Double sto = reactant.getQuantity();
-                networkOut.affectLeft(newReaction, sto, newCpt, newMetabolite);
-            }
+                // Copy lefts
+                for (BioReactant reactant : r.getLeftReactantsView()) {
+                    BioMetabolite newMetabolite = networkOut.getMetabolite(reactant.getMetabolite().getId());
+                    BioCompartment newCpt = networkOut.getCompartment(reactant.getLocation().getId());
+                    Double sto = reactant.getQuantity();
+                    networkOut.affectLeft(newReaction, sto, newCpt, newMetabolite);
+                }
 
-            // Copy rights
-            for (BioReactant reactant : r.getRightReactantsView()) {
-                BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(reactant.getMetabolite().getId());
-                BioCompartment newCpt = networkOut.getCompartmentsView().get(reactant.getLocation().getId());
-                Double sto = reactant.getQuantity();
-                networkOut.affectRight(newReaction, sto, newCpt, newMetabolite);
+                // Copy rights
+                for (BioReactant reactant : r.getRightReactantsView()) {
+                    BioMetabolite newMetabolite = networkOut.getMetabolite(reactant.getMetabolite().getId());
+                    BioCompartment newCpt = networkOut.getCompartment(reactant.getLocation().getId());
+                    Double sto = reactant.getQuantity();
+                    networkOut.affectRight(newReaction, sto, newCpt, newMetabolite);
+                }
+            } else {
+                newReaction = networkOut.getReaction(r.getId());
             }
 
             // Copy enzymes
             if (keepGPR) {
                 for (BioEnzyme enzyme : r.getEnzymesView()) {
-                    BioEnzyme newEnzyme = networkOut.getEnzymesView().get(enzyme.getId());
+                    BioEnzyme newEnzyme = networkOut.getEnzyme(enzyme.getId());
                     networkOut.affectEnzyme(newReaction, newEnzyme);
                 }
             }
@@ -305,12 +311,12 @@ public class BioNetworkUtils {
                 networkOut.add(newPathway);
             }
 
-            BioPathway newPathway = networkOut.getPathwaysView().get(pathway.getId());
+            BioPathway newPathway = networkOut.getPathway(pathway.getId());
             // Add reactions into pathway
             BioCollection<BioReaction> reactions = networkIn.getReactionsFromPathways(pathway);
 
             for (BioReaction reaction : reactions) {
-                BioReaction newReaction = networkOut.getReactionsView().get(reaction.getId());
+                BioReaction newReaction = networkOut.getReaction(reaction.getId());
                 networkOut.affectToPathway(newPathway, newReaction);
             }
         }

met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java

@@ -1893,7 +1893,7 @@ public class BioNetworkTest {
         assertEquals("Bad number of pathways with these genes", 1, pathways.size());
 
         assertTrue("Bad pathway with these genes",
-                pathways.contains(network.getPathwaysView().get("pathway1")));
+                pathways.contains(network.getPathway("pathway1")));
 
         pathways = network.getPathwaysFromGenes(genes, true);
 
@@ -1989,7 +1989,7 @@ public class BioNetworkTest {
         BioReaction r3 = new BioReaction("r3");
         network.add(r3);
 
-        BioPathway pathway1 = network.getPathwaysView().get("pathway1");
+        BioPathway pathway1 = network.getPathway("pathway1");
 
         network.affectToPathway(pathway1, r2);
 

met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java

@@ -184,38 +184,38 @@ public class BioNetworkUtilsTest {
         assertEquals(1, newNetwork.getGenesView().size());
 
         r1.setName("newName");
-        assertNotEquals(r1.getName(), newNetwork.getReactionsView().get("R1").getName());
+        assertNotEquals(r1.getName(), newNetwork.getReaction("R1").getName());
 
         m1.setName("newName");
-        assertNotEquals(m1.getName(), newNetwork.getMetabolitesView().get("M1").getName());
+        assertNotEquals(m1.getName(), newNetwork.getMetabolite("M1").getName());
 
         c1.setName("newName");
-        assertNotEquals(c1.getName(), newNetwork.getCompartmentsView().get("c1").getName());
+        assertNotEquals(c1.getName(), newNetwork.getCompartment("c1").getName());
 
         pathway1.setName("newName");
-        assertNotEquals(pathway1.getName(), newNetwork.getPathwaysView().get("pathway1").getName());
+        assertNotEquals(pathway1.getName(), newNetwork.getPathway("pathway1").getName());