diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..64ddbcfe48cca94fc70075fa967165cd528c562b
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
@@ -0,0 +1,209 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import lombok.SneakyThrows;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.*;
+import java.util.function.Function;
+import java.util.function.Supplier;
+import java.util.stream.Collectors;
+
+public abstract class AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ BioCollection<BioNetwork> networks;
+ Map<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> metaCompComposition;
+ MetaEntityFactory entityFactory;
+
+ Boolean keepGPR = false;
+ Boolean flush;
+
+ public AbstractMetaNetworkBuilder(){
+ this.entityFactory= new DefaultMetaEntityFactory();
+ }
+
+ public AbstractMetaNetworkBuilder(MetaEntityFactory entityFactory){
+ this.entityFactory=entityFactory;
+ }
+
+ protected void addSharedCompartment(BioCompartment sc) {
+ metaCompComposition.put(sc,new HashMap<>());
+ }
+ protected void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
+ HashMap<BioNetwork, BioCollection<BioMetabolite>> map = Arrays.stream(bn).collect(Collectors.toMap(
+ x -> x,
+ x -> new BioCollection<BioMetabolite>(),
+ (prev, next) -> {prev.addAll(next);return prev;},
+ HashMap::new
+ ));
+ if(metaCompComposition.containsKey(sc)){
+ metaCompComposition.get(sc).putAll(map);
+ }else{
+ metaCompComposition.put(sc,map);
+ }
+ }
+
+ protected void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ //TODO
+ }
+
+ protected void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ Map<BioNetwork, BioCollection<BioMetabolite>> compartmentContent = metaCompComposition.get(sc);
+ if(compartmentContent==null) throw new IllegalArgumentException("Shared Compartment not found");
+ BioCollection<BioMetabolite> sharedContent = compartmentContent.get(n);
+ if(compartmentContent==null) throw new IllegalArgumentException("SubNetwork not in shared compartment");
+ BioCollection<BioMetabolite> toShare = n.getMetabolitesView().stream()
+ .filter(x -> n.getCompartmentsOf(x).contains(c))
+ .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
+ sharedContent.addAll(toShare);
+ }
+
+ protected void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
+ //todo
+ }
+
+ protected void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
+ //todo
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ networks.add(bn);
+ }
+
+ @Override
+ public abstract void merge();
+
+ @Override
+ public abstract BioNetwork build();
+
+
+ void populateMetaNetwork(BioNetwork meta){
+
+ for(BioNetwork sub : networks){
+
+ Map<BioMetabolite,BioMetabolite> metaboliteConversion = new HashMap<>();
+ Map<BioCompartment,BioCompartment> compartmentConversion = new HashMap<>();
+ Map<BioReaction,BioReaction> reactionConversion = new HashMap<>();
+ Map<BioProtein,BioProtein> proteinConversion = new HashMap<>();
+ Map<BioEnzyme,BioEnzyme> enzymeConversion = new HashMap<>();
+ Map<BioGene,BioGene> geneConversion = new HashMap<>();
+
+ for(BioMetabolite e : sub.getMetabolitesView()){
+ BioMetabolite e2 = entityFactory.copy(e,sub);
+ meta.add(e2);
+ metaboliteConversion.put(e,e2);
+ }
+ for(BioCompartment c : sub.getCompartmentsView()){
+ BioCompartment c2 = entityFactory.copy(c,sub);
+ meta.add(c2);
+ compartmentConversion.put(c,c2);
+ c.getComponentsView().stream().
+ filter((e) -> e.getClass().equals(BioMetabolite.class)).
+ forEach((m) -> {
+ BioMetabolite newMetabolite = metaboliteConversion.get(m);
+ meta.affectToCompartment(c, newMetabolite);
+ });
+ }
+
+ // Copy genes
+ if (keepGPR) {
+ //TODO case shared Genome
+ for (BioGene gene : sub.getGenesView()) {
+ BioGene newGene = entityFactory.copy(gene,sub);
+ meta.add(newGene);
+ geneConversion.put(gene,newGene);
+ }
+ for (BioProtein protein : sub.getProteinsView()) {
+ BioProtein newProtein = entityFactory.copy(protein,sub);
+ meta.add(newProtein);
+ proteinConversion.put(protein,newProtein);
+
+ if (protein.getGene() != null) {
+ BioGene newGene = geneConversion.get(protein.getGene());
+ meta.affectGeneProduct(newProtein, newGene);
+ }
+ }
+ for (BioEnzyme enzyme : sub.getEnzymesView()) {
+
+ BioEnzyme newEnzyme = entityFactory.copy(enzyme,sub);
+ meta.add(newEnzyme);
+ enzymeConversion.put(enzyme,newEnzyme);
+
+ BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
+
+ for (BioEnzymeParticipant participant : participants) {
+ Double quantity = participant.getQuantity();
+
+ if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
+ BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
+ BioMetabolite newMetabolite = metaboliteConversion.get(metabolite);
+ meta.affectSubUnit(newEnzyme, quantity, newMetabolite);
+ } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
+ BioProtein protein = (BioProtein) participant.getPhysicalEntity();
+ BioProtein newProtein = proteinConversion.get(protein);
+ meta.affectSubUnit(newEnzyme, quantity, newProtein);
+ }
+ }
+ }
+ }
+
+ for (BioReaction r : sub.getReactionsView()) {
+
+ BioReaction newReaction = entityFactory.copy(r,sub);;
+ newReaction.setSpontaneous(r.isSpontaneous());
+ newReaction.setReversible(r.isReversible());
+ newReaction.setEcNumber(r.getEcNumber());
+
+ meta.add(newReaction);
+
+ // Copy lefts
+ for (BioReactant reactant : r.getLeftReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
+ Double sto = reactant.getQuantity();
+ meta.affectLeft(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy rights
+ for (BioReactant reactant : r.getRightReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
+ Double sto = reactant.getQuantity();
+ meta.affectRight(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy enzymes
+ if (keepGPR) {
+ for (BioEnzyme enzyme : r.getEnzymesView()) {
+ BioEnzyme newEnzyme = enzymeConversion.get(enzyme);
+ meta.affectEnzyme(newReaction, newEnzyme);
+ }
+ }
+ }
+
+ for (BioPathway pathway : sub.getPathwaysView()) {
+ BioPathway newPathway = entityFactory.copy(pathway,sub);
+ meta.add(newPathway);
+ // Add reactions into pathway
+ BioCollection<BioReaction> reactions = sub.getReactionsFromPathways(pathway);
+
+ for (BioReaction reaction : reactions) {
+ BioReaction newReaction = reactionConversion.get(reaction);
+ meta.affectToPathway(newPathway, newReaction);
+ }
+ }
+ }
+ }
+
+
+ void initSharedComp(BioNetwork meta){
+ for(Map.Entry<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> compDescriptor : metaCompComposition.entrySet()){
+ meta.addCompartment(compDescriptor.getKey());
+ for(Map.Entry<BioNetwork, BioCollection<BioMetabolite>> content : compDescriptor.getValue().entrySet()){
+ meta.affectToCompartment(compDescriptor.getKey(),content.getValue());
+ }
+ }
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..ce5227046b7c7cb0f504219ff9cf21c4d5cd6c2a
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
@@ -0,0 +1,42 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import lombok.SneakyThrows;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+
+public class DefaultMetaEntityFactory implements MetaEntityFactory {
+
+ public BiFunction<BioEntity, BioNetwork, String> idSupplier = (e,bn) -> {
+ return e.getId()+"_"+bn.getId();
+ };
+
+ public BiFunction<BioEntity, BioNetwork, String> getIdSupplier() {
+ return idSupplier;
+ }
+
+ public void setIdSupplier(BiFunction<BioEntity, BioNetwork, String> idSupplier) {
+ this.idSupplier = idSupplier;
+ }
+
+ @SneakyThrows
+ @Override
+ public <E extends BioEntity> E copy(E entity, BioNetwork source) {
+ return newEntityInstance(entity, this.idSupplier.apply(entity,source));
+ }
+
+ public static <E extends BioEntity> E newEntityInstance(E entity, String newId) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
+ E newEntity = (E) entity.getClass().getDeclaredConstructor(String.class).newInstance(newId);
+ newEntity.setName(entity.getName());
+ newEntity.setSynonyms(new ArrayList<>(entity.getSynonyms()));
+ newEntity.setComment(entity.getComment());
+ newEntity.setRefs(new HashMap<>(entity.getRefs()));
+ newEntity.setAttributes(new HashMap<>(entity.getAttributes()));
+ return newEntity;
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..554d7b182f8656fa02db3580521a18b00d9cefe7
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
@@ -0,0 +1,10 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public interface MetaEntityFactory {
+
+ public <E extends BioEntity> E copy(E entity, BioNetwork source);
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..7af6a2b5f6ecb764142f90077aa56599df73fa41
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -0,0 +1,45 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.UUID;
+
+public class MetaNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+
+ private BioCompartment medium;
+
+ public MetaNetworkBuilder(BioNetwork superNetwork){
+ setMedium();
+ }
+
+ private void setMedium(){
+ this.medium = new BioCompartment(UUID.randomUUID().toString(),"medium");
+ this.addSharedCompartment(medium);
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ super.add(bn);
+ this.addSharedCompartment(medium,this.networks.stream().toArray(BioNetwork[]::new));
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ public void exchangeWithMedium(BioNetwork n, BioMetabolite m){
+ this.exchangeWithSharedCompartment(n, m, medium);
+ };
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..c17e2cadc575dabf2fff0ccf5794af2409d96ec0
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
@@ -0,0 +1,21 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public interface MultiNetworkBuilder {
+
+ /**
+ * add network into meta-network
+ * @param bn
+ */
+ public void add(BioNetwork bn);
+
+ public void merge();
+
+ /**
+ * create a new network which encompass all added networks
+ * @return
+ */
+ public BioNetwork build();
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..ae4c1b699d22a8592769a0d657d6aa0d1be36322
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
@@ -0,0 +1,57 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+public class MultiOrganNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ @Override
+ public void merge() {
+ //TODO
+ }
+
+
+ @Override
+ public void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
+ super.addSharedCompartment(sc,bn);
+ }
+
+ @Override
+ public void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ super.fuseCompartmentIntoSharedCompartment(n,c,sc);
+ }
+
+ @Override
+ public void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ super.bumpCompartmentIntoSharedCompartment(n,c,sc);
+ }
+
+ @Override
+ public void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
+ super.exchangeWithSharedCompartment(n,m,sc);
+ }
+
+ @Override
+ public void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
+ super.exchangeWithSharedCompartment(n,m,sc);
+ }
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ //create empty meta network
+ BioNetwork meta = new BioNetwork();
+ //add each subnetwork content in dedicated compartment
+ this.populateMetaNetwork(meta);
+ //create shared compartment and the exchanged content
+ this.initSharedComp(meta);
+ return null;
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..aeca0c100c4bfde965c364f4547f09d35205bb0f
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
@@ -0,0 +1,43 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public class NestedNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ private BioNetwork superNet;
+ private BioCompartment superNetComp;
+
+ public NestedNetworkBuilder(BioNetwork superNetwork){
+ setSuperNetwork(superNetwork);
+ }
+
+ private void setSuperNetwork(BioNetwork bn){
+ superNet=bn;
+ this.superNetComp = new BioCompartment(bn.getId());
+ this.addSharedCompartment(superNetComp,superNet);
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ super.add(bn);
+ this.addSharedCompartment(superNetComp,this.networks.stream().toArray(BioNetwork[]::new));
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ public void exchangeWithSuperNetwork(BioNetwork n, BioMetabolite m){
+ this.exchangeWithSharedCompartment(n, m, superNetComp);
+ };
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..346f71cbfe702788ff6420621375320c99e86b07
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
@@ -0,0 +1,23 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+public class PanNetworkBuilder implements MultiNetworkBuilder {
+ @Override
+ public void add(BioNetwork bn) {
+ //todo
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+}