diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/VertexContraction.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/VertexContraction.java
index 4413ca4978d4cbabb25a37218d6cb2e61c952b23..481a4d8124e8f20ba27f293e07044396d04df0f0 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/VertexContraction.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/VertexContraction.java
@@ -40,6 +40,8 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaNode;
import java.util.*;
import java.util.function.Function;
@@ -103,7 +105,7 @@ public class VertexContraction<V extends BioEntity,E extends Edge<V>, G extends
*/
public static <V extends BioEntity, E extends Edge<V>, G extends BioGraph<V,E>> G contractBy(G g, Function<V,String> groupingFunction, Function<List<V>,V> pickFunction){
G g2 = (G) g.clone();
- Map<String, List<V>> groupedNodes = g.vertexSet().stream().collect(Collectors.groupingBy(groupingFunction));
+ Map<String, List<V>> groupedNodes = g.vertexSet().stream().filter(x->(groupingFunction.apply(x)!=null)).collect(Collectors.groupingBy(groupingFunction));
for(List<V> toContract : groupedNodes.values()){
V v = pickFunction.apply(toContract);
toContract.remove(v);
@@ -112,6 +114,33 @@ public class VertexContraction<V extends BioEntity,E extends Edge<V>, G extends
return g2;
}
+ /**
+ * Contract all nodes in graph from an aggregation function, which provide a common group id (key) for each member of a set to contract
+ * creates a MetaGraph, where each node contains the set of contracted nodes sharing the same group id
+ * @param g the graph
+ * @param groupingFunction the aggregation function
+ * @param <V> the node class
+ * @param <E> the edge class
+ * @param <G> the graph class
+ * @return a meta-graph with super-vertices referencing the contracted nodes
+ */
+ public static <V extends BioEntity, E extends Edge<V>, G extends BioGraph<V,E>> MetaGraph<V,E> contractByAsMeta(G g, Function<V,String> groupingFunction){
+ MetaGraph<V,E> g2 = new MetaGraph<V,E>();
+ Map<String, List<V>> groupedNodes = g.vertexSet().stream().filter(x->(groupingFunction.apply(x)!=null)).collect(Collectors.groupingBy(groupingFunction));
+ for(Map.Entry<String, List<V>> toContract : groupedNodes.entrySet()) {
+ g2.addVertex(new MetaNode<>(toContract.getKey(), toContract.getValue()));
+ }
+ for(E edge : g.edgeSet()){
+ try{
+ g2.addEdgesFromSubVertices(edge);
+ }catch (IllegalArgumentException e){
+ System.err.println("Edge "+edge.getV1().getId()+"->"+edge.getV2().getId()+" contains node ignored during vertex contraction " +
+ " (this may happen if some node as undefined arguments)");
+ }
+ }
+ return g2;
+ }
+
/**
* Remove compartment in a compound graph by contracting all nodes sharing a given attribute provided by the mapper
* @param g the graph to decompartmentalize
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioGraph.java
index 5068f5eff25fc43e698bcaef4fc5e51133f878ac..eb18662c47162bc25a2ae4fdce8de13b4e47d9c2 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioGraph.java
@@ -417,7 +417,7 @@ public abstract class BioGraph<V extends BioEntity, E extends Edge<V>> extends D
*/
/** {@inheritDoc} */
@Override
- public final boolean removeEdge(E e) {
+ public boolean removeEdge(E e) {
return super.removeEdge(e);
}
@@ -426,7 +426,7 @@ public abstract class BioGraph<V extends BioEntity, E extends Edge<V>> extends D
*/
/** {@inheritDoc} */
@Override
- public final boolean removeVertex(V arg0) {
+ public boolean removeVertex(V arg0) {
return super.removeVertex(arg0);
}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaGraph.java
new file mode 100644
index 0000000000000000000000000000000000000000..143bfed1c57c7cc3e5e59b14e67a26ffb162142f
--- /dev/null
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaGraph.java
@@ -0,0 +1,115 @@
+package fr.inrae.toulouse.metexplore.met4j_graph.core.meta;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MergedGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MetaEdge;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
+public class MetaGraph<V extends BioEntity, E extends Edge<V>> extends MergedGraph<MetaNode<V>,E> {
+
+ public MetaNodeFactory getNodeFactory() {
+ return factory;
+ }
+ public void setNodeFactory(MetaNodeFactory<V> factory) {
+ this.factory = factory;
+ }
+ private HashMap<V,Collection<MetaNode<V>>> nodeMap = new HashMap<>();
+
+ private MetaNodeFactory<V> factory = new MetaNodeFactory<V>().useRandomId();
+
+ public boolean addMetaVertex(Collection<V> content) {
+ return this.addVertex(factory.createMetaNode(content));
+ }
+
+ public Collection<MetaNode<V>> getMetaVerticiesOf(V vertex){
+ return nodeMap.get(vertex);
+ }
+
+ @Override
+ public boolean addVertex(MetaNode<V> vertex){
+ boolean res = super.addVertex(vertex);
+ for(V node : vertex.content){
+ Collection<MetaNode<V>> matchingMeta = nodeMap.get(node);
+ if (matchingMeta==null){
+ matchingMeta = new HashSet<>();
+ nodeMap.put(node,matchingMeta);
+ }
+ matchingMeta.add(vertex);
+ }
+ return res;
+ }
+
+ public void addSubVertex(MetaNode<V> metaNode, V ... nodes){
+ if(!this.vertexSet().contains(metaNode)){
+ throw new IllegalArgumentException("meta-node not present in graph");
+ }else{
+ for (V node : nodes){
+ metaNode.content.add(node);
+ Collection<MetaNode<V>> matchingMeta = nodeMap.get(node);
+ if (matchingMeta==null){
+ matchingMeta = new HashSet<>();
+ nodeMap.put(node,matchingMeta);
+ }
+ matchingMeta.add(metaNode);
+ }
+ }
+ }
+
+ @Override
+ public boolean removeVertex(MetaNode<V> vertex){
+ boolean res = super.removeVertex(vertex);
+ if(res){
+ for(Collection<MetaNode<V>> list : nodeMap.values()){
+ list.remove(vertex);
+ }
+ }
+ return res;
+ }
+
+ public Collection<MetaEdge<MetaNode<V>,E>> addEdgesFromSubVertices(E edge){
+ return addEdgesFromSubVertices(edge.getV1(),edge.getV2(),edge);
+ }
+ private Collection<MetaEdge<MetaNode<V>,E>> addEdgesFromSubVertices(V arg0, V arg1) {
+ return addEdgesFromSubVertices(arg0,arg1,null);
+ }
+
+
+ private Collection<MetaEdge<MetaNode<V>,E>> addEdgesFromSubVertices(V arg0, V arg1, E edge) {
+ if(!nodeMap.containsKey(arg0)) throw new IllegalArgumentException("first vertex not present in any meta node");
+ if(!nodeMap.containsKey(arg1)) throw new IllegalArgumentException("first vertex not present in any meta node");
+
+ ArrayList<MetaEdge<MetaNode<V>,E>> newlyAddedEdges = new ArrayList<>();
+ for(MetaNode<V> v1 : nodeMap.get(arg0)){
+ for(MetaNode<V> v2 : nodeMap.get(arg1)){
+ if(v1!=v2){
+ MetaEdge<MetaNode<V>,E> e = this.getEdge(v1,v2);
+ if(e==null){
+ e = new MetaEdge<>(v1,v2);
+ if(edge!=null) e.addEdge(edge);
+ boolean res=this.addEdge(e);
+ if(res) newlyAddedEdges.add(e);
+ }else{
+ if(edge!=null) e.addEdge(edge);
+ }
+ }
+ }
+ }
+ return newlyAddedEdges;
+ }
+
+
+ @Override
+ public MetaNode<V> createVertex(String id) {
+ return new MetaNode<>(id);
+ }
+
+ @Override
+ public void setEdgeWeight(MetaNode<V> sourceVertex, MetaNode<V> targetVertex, double weight) {
+ super.setEdgeWeight(sourceVertex, targetVertex, weight);
+ }
+}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNode.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNode.java
new file mode 100644
index 0000000000000000000000000000000000000000..273fd65606cf7370e99aa227937761547f81b82e
--- /dev/null
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNode.java
@@ -0,0 +1,30 @@
+package fr.inrae.toulouse.metexplore.met4j_graph.core.meta;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.Collection;
+
+
+public class MetaNode<V extends BioEntity> extends BioEntity {
+
+ protected BioCollection<V> content=new BioCollection<>();
+ public MetaNode(String id, Collection<V> content){
+ super(id);
+ this.content.addAll(content);
+ }
+
+ public MetaNode(String id){
+ super(id);
+ }
+
+ public int getSize(){
+ return content.size();
+ }
+
+ public BioCollection<V> getContentView() {
+ return new BioCollection<>(content);
+ }
+
+
+}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNodeFactory.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNodeFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..5676c0a7605345b6e33e8a0ceb53473b46d3121a
--- /dev/null
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/meta/MetaNodeFactory.java
@@ -0,0 +1,32 @@
+package fr.inrae.toulouse.metexplore.met4j_graph.core.meta;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+
+import java.util.Collection;
+import java.util.UUID;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+public class MetaNodeFactory<V extends BioEntity> {
+
+ private Function<Collection<V>, String> idGenerator;
+ private final Function<Collection<V>, String> randomIdGenerator = (v -> UUID.randomUUID().toString());
+ private final Function<Collection<V>, String> concatIdGenerator = (v -> v.stream().map(BioEntity::getId).collect(Collectors.joining()));
+
+ public MetaNodeFactory<V> useRandomId(){
+ this.idGenerator=randomIdGenerator;
+ return this;
+ }
+ public MetaNodeFactory<V> useConcatenedId(){
+ this.idGenerator=concatIdGenerator;
+ return this;
+ }
+ public MetaNodeFactory<V> setIdGenerator(Function<Collection<V>, String> idGenerator){
+ this.idGenerator=idGenerator;
+ return this;
+ }
+
+ public MetaNode<V> createMetaNode(Collection<V> content){
+ return new MetaNode<>(idGenerator.apply(content),content);
+ }
+}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MergedGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MergedGraph.java
index d1d47534cf469dc8245e2e60b34586f053645ab9..48af45b09901f380475a16307fcd49424a816761 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MergedGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MergedGraph.java
@@ -38,7 +38,6 @@ package fr.inrae.toulouse.metexplore.met4j_graph.core.parallel;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.GraphFactory;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
@@ -54,7 +53,7 @@ import java.util.HashSet;
* @author lcottret
* @version $Id: $Id
*/
-public class MergedGraph<V extends BioEntity, E extends Edge<V>> extends BioGraph<V,MetaEdge<V,E>> {
+public class MergedGraph<V extends BioEntity, E extends Edge<?>> extends BioGraph<V,MetaEdge<V,E>> {
/** The Constant serialVersionUID. */
private static final long serialVersionUID = 1L;
@@ -66,30 +65,14 @@ public class MergedGraph<V extends BioEntity, E extends Edge<V>> extends BioGrap
public MergedGraph() {
super();
}
-
-
- /**
- * Gets the factory.
- *
- * @return the factory
- */
- public GraphFactory<V,MetaEdge<V,E>,MergedGraph<V,E>> getFactory(){
- return new GraphFactory<>() {
- @Override
- public MergedGraph<V, E> createGraph() {
- return new MergedGraph<>();
- }
- };
- }
-
/* (non-Javadoc)
* @see parsebionet.computation.graphe.BioGraph#copyEdge(parsebionet.computation.graphe.Edge)
*/
/** {@inheritDoc} */
@Override
- public MetaEdge<V, E> copyEdge(MetaEdge<V, E> edge) {
- MetaEdge<V, E> newEdge = new MetaEdge<>(edge.getV1(), edge.getV2(), edge.getEdgeList());
+ public MetaEdge<V,E> copyEdge(MetaEdge<V,E> edge) {
+ MetaEdge<V,E> newEdge = new MetaEdge<>(edge.getV1(), edge.getV2(), edge.getEdgeList());
return newEdge;
}
@@ -107,20 +90,26 @@ public class MergedGraph<V extends BioEntity, E extends Edge<V>> extends BioGrap
}
@Override
- public MetaEdge<V, E> createEdge(V v1, V v2) {
+ public MetaEdge<V,E> createEdge(V v1, V v2) {
return new MetaEdge<>(v1, v2, new HashSet<>());
}
+ public void setNumberOfSubEdgesAsWeight(){
+ for(MetaEdge<V,E> edge : this.edgeSet()){
+ this.setEdgeWeight(edge,edge.getEdgeList().size());
+ }
+ }
+
/** {@inheritDoc} */
@Override
- public MetaEdge<V, E> reverseEdge(MetaEdge<V, E> edge) {
- MetaEdge<V, E> reversed = new MetaEdge<>(edge.getV2(), edge.getV1(), edge.getEdgeList());
+ public MetaEdge<V,E> reverseEdge(MetaEdge<V,E> edge) {
+ MetaEdge<V,E> reversed = new MetaEdge<>(edge.getV2(), edge.getV1(), edge.getEdgeList());
return reversed;
}
@Override
- public MetaEdge<V, E> createEdgeFromModel(V v1, V v2, MetaEdge<V, E> edge){
- return new MetaEdge<V, E>(v1, v2, edge.getEdgeList());
+ public MetaEdge<V,E> createEdgeFromModel(V v1, V v2, MetaEdge<V,E> edge){
+ return new MetaEdge<V,E>(v1, v2, edge.getEdgeList());
}
}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdge.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdge.java
index 73e88661b66850d309d501d8e415d02d22313c17..b0492cc1f621abcecf1cca59c3de6bd433c097d7 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdge.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdge.java
@@ -35,13 +35,13 @@
*/
package fr.inrae.toulouse.metexplore.met4j_graph.core.parallel;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
+
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
-
/**
* Edges that represent a set of sub-edges
* It can be used to store the merging of edges sharing same source and target
@@ -51,7 +51,7 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
* @param <E> the sub-edges Type
* @version $Id: $Id
*/
-public class MetaEdge<V extends BioEntity,E extends Edge<V>> extends Edge<V> {
+public class MetaEdge<V extends BioEntity,E extends Edge<?>> extends Edge<V> {
/** The Constant serialVersionUID. */
private static final long serialVersionUID = -4274083588408838186L;
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/ExportGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/ExportGraph.java
index 06b296ce4c8bfcd36d4d232cf27a3f104e218763..415ecd1269145c150e65b5e12819da38b97f76a2 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/ExportGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/ExportGraph.java
@@ -35,32 +35,25 @@
*/
package fr.inrae.toulouse.metexplore.met4j_graph.io;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.HashMap;
-import java.util.Map;
-
import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollections;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
-
import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.bipartite.BipartiteEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.bipartite.BipartiteGraph;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollections;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.pathway.PathwayGraph;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.pathway.PathwayGraphEdge;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.CompoundEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph;
import org.jgrapht.nio.Attribute;
import org.jgrapht.nio.DefaultAttribute;
import org.jgrapht.nio.gml.GmlExporter;
+import java.io.*;
+import java.util.HashMap;
+import java.util.Map;
+
/**
* Export informations from graphs generated from {@link Bionetwork2BioGraph} into Cytoscape-readable files
* @author clement
@@ -592,5 +585,18 @@ public class ExportGraph {
e1.printStackTrace();
}
}
-
+
+ public static <V extends BioEntity, E extends Edge<V>, G extends BioGraph<V,E>> void toAdjacencyList(G graph, String outputPath){
+ try {
+ BufferedWriter bw = new BufferedWriter(new FileWriter(outputPath, true));
+ bw.newLine();
+ for(E e:graph.edgeSet()){
+ bw.write(e.getV1()+"\t"+e.getV2());
+ bw.newLine();
+ }
+ bw.close();
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
}
diff --git a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestEdgeMerger.java b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestEdgeMerger.java
index 3fd51575573e5a1be69ba085c04813eb1c0020f0..05a28e916c10a44201a7eafc69cd03fe0c9394a4 100644
--- a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestEdgeMerger.java
+++ b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestEdgeMerger.java
@@ -39,11 +39,8 @@
*/
package fr.inrae.toulouse.metexplore.met4j_graph;
-import static org.junit.Assert.*;
-
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.EdgeMerger;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.GraphFactory;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MergedGraph;
@@ -52,15 +49,10 @@ import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEnzyme;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioProtein;
-
import java.util.Comparator;
+import static org.junit.Assert.assertTrue;
+
public class TestEdgeMerger {
public static CompoundGraph g;
diff --git a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestMergedGraph.java b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestMergedGraph.java
index 950485b0bd0f30501002f419343e24e00434f13a..338118a712f4f68adf6d6600628a89d4b0b5bb0a 100644
--- a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestMergedGraph.java
+++ b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestMergedGraph.java
@@ -36,10 +36,10 @@
package fr.inrae.toulouse.metexplore.met4j_graph;
-import static org.junit.Assert.*;
-
-import java.util.HashSet;
-
+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.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MergedGraph;
@@ -47,10 +47,10 @@ import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MetaEdge;
import org.junit.BeforeClass;
import org.junit.Test;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import java.util.HashSet;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
public class TestMergedGraph {
@@ -125,7 +125,7 @@ public class TestMergedGraph {
@Test
public void testAddEdge(){
- MergedGraph<BioMetabolite, ReactionEdge> cg3
+ MergedGraph<BioMetabolite, ReactionEdge> cg3
= (MergedGraph<BioMetabolite, ReactionEdge>) cg2.clone();
cg3.addEdge(v2, v1);
assertEquals(2, cg3.edgeSet().size());
diff --git a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestVertexContraction.java b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestVertexContraction.java
index 6e72798d0277ff4ba8a3b550af4ba2648d2e973f..6fae48afb931ee6998a3b6329aa1c4e020258888 100644
--- a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestVertexContraction.java
+++ b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestVertexContraction.java
@@ -39,10 +39,15 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.VertexContraction;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaNode;
import org.junit.BeforeClass;
import org.junit.Test;
-import static org.junit.Assert.*;
+import java.util.Iterator;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
public class TestVertexContraction {
public static CompoundGraph g;
@@ -66,21 +71,25 @@ public class TestVertexContraction {
bn.affectToCompartment(comp1, a1);
a1.setName("A");
a1.setInchi("InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)");
+ a1.setChemicalFormula("C4H6O4");
g.addVertex(a1);
b1 = new BioMetabolite("M_b_1"); bn.add(b1);
bn.affectToCompartment(comp1, b1);
b1.setName("B");
b1.setInchi("InChI=1S/C4H10NO6P/c5-3(4(6)7)1-2-11-12(8,9)10/h3H,1-2,5H2,(H,6,7)(H2,8,9,10)/t3-/m0/s1");
+ b1.setChemicalFormula("C4H10NO6P");
g.addVertex(b1);
a2 = new BioMetabolite("M_a_2"); bn.add(a2);
bn.affectToCompartment(comp2, a2);
a2.setName("A");
a2.setInchi("InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)");
+ a2.setChemicalFormula("C4H6O4");
g.addVertex(a2);
b2 = new BioMetabolite("M_b_2"); bn.add(b2);
bn.affectToCompartment(comp2, b2);
b2.setName("B");
b2.setInchi("InChI=1S/C4H10NO6P/c5-3(4(6)7)1-2-11-12(8,9)10/h3H,1-2,5H2,(H,6,7)(H2,8,9,10)/t3-/m0/s1");
+ b2.setChemicalFormula("C4H10NO6P");
g.addVertex(b2);
a3 = new BioMetabolite("M_a_3"); bn.add(a3);
bn.affectToCompartment(comp3, a3);
@@ -188,6 +197,25 @@ public class TestVertexContraction {
assertEquals("Wrong final number of edges", 6, g2.edgeSet().size());
}
+ @Test
+ public void testFormulaNetwork() {
+ MetaGraph<BioMetabolite,ReactionEdge> g2= VertexContraction.contractByAsMeta(g,BioMetabolite::getChemicalFormula);
+ g2.setNumberOfSubEdgesAsWeight();
+ assertEquals("Error in the initial graph", 5, g.vertexSet().size());
+ assertEquals("Error in the initial graph", 12, g.edgeSet().size());
+ assertEquals("Wrong final number of nodes", 2, g2.vertexSet().size());
+ assertEquals("Wrong final number of edges", 2, g2.edgeSet().size());
+// assertEquals("Wrong final number of edges", 6, g2.edgeSet().iterator().next().getEdgeList().size());
+ Iterator<MetaNode<BioMetabolite>> i = g2.vertexSet().iterator();
+ assertEquals("Wrong final number of edges", 2, i.next().getSize());
+ assertEquals("Wrong final number of edges", 2, i.next().getSize());
+ assertEquals(2,g2.getVertex("C4H6O4").getContentView().size());
+ assertTrue(g2.getVertex("C4H6O4").getContentView().contains(a1));
+ assertTrue(g2.getVertex("C4H6O4").getContentView().contains(a2));
+ assertTrue(g2.getVertex("C4H10NO6P").getContentView().contains(b1));
+ assertTrue(g2.getVertex("C4H10NO6P").getContentView().contains(b2));
+ }
+
/* @Test
public void testMergeCompartmentFromId() {
CompoundGraph g2 = Merger.mergeCompartmentFromId(g, "^(.+)_\\w$");
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/FormulaNet.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/FormulaNet.java
new file mode 100644
index 0000000000000000000000000000000000000000..b00fdd3cca482728589d13c75a12b5007f1a35b0
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/FormulaNet.java
@@ -0,0 +1,175 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
+
+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 fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.VertexContraction;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.meta.MetaNode;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.ExportGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.NodeMapping;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.FBCParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.GroupPathwayParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.NotesParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
+import org.kohsuke.args4j.Option;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.stream.Collectors;
+
+public class FormulaNet extends AbstractMet4jApplication {
+
+ @Format(name= EnumFormats.Sbml)
+ @ParameterType(name= EnumParameterTypes.InputFile)
+ @Option(name = "-s", usage = "input SBML file", required = true)
+ public String inputPath = null;
+
+ @ParameterType(name= EnumParameterTypes.InputFile)
+ @Format(name= EnumFormats.Txt)
+ @Option(name = "-sc", usage = "input Side compound file", required = false)
+ public String inputSide = null;
+
+ @ParameterType(name= EnumParameterTypes.OutputFile)
+ @Format(name= EnumFormats.Gml)
+ @Option(name = "-o", usage = "output Graph file", required = true)
+ public String outputPath = null;
+
+ @Option(name = "-ri", aliases = {"--removeIsolatedNodes"}, usage = "remove isolated nodes", required = false)
+ public boolean removeIsolated = false;
+
+// @ParameterType(name=EnumParameterTypes.InputFile)
+// @Format(name=EnumFormats.Tsv)
+// @Option(name = "-cw", aliases = {"--customWeights"}, usage = "an optional file containing weights for compound pairs", forbids = {"-dw"})
+// public String weightFile = null;
+
+ @Option(name = "-un", aliases = {"--undirected"}, usage = "create as undirected", required = false)
+ public boolean undirected = false;
+
+ public static void main(String[] args) {
+
+ FormulaNet app = new FormulaNet();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+
+ public void run() {
+ System.out.print("Reading SBML...");
+ JsbmlReader reader = new JsbmlReader(this.inputPath);
+ ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(
+ new NotesParser(false), new FBCParser(), new GroupPathwayParser()));
+
+ BioNetwork network = null;
+
+ try {
+ network = reader.read(pkgs);
+ } catch (Met4jSbmlReaderException e) {
+ System.err.println("Error while reading the SBML file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ System.out.println(" Done.");
+
+
+ System.out.print("Buildinig Network...");
+ Bionetwork2BioGraph builder = new Bionetwork2BioGraph(network);
+ CompoundGraph graph = builder.getCompoundGraph();
+ System.out.println(" Done.");
+
+ //Graph processing: side compound removal [optional]
+ if (inputSide != null) {
+ System.err.println("removing side compounds...");
+ NodeMapping<BioMetabolite, ReactionEdge, CompoundGraph> mapper = new NodeMapping<>(graph).skipIfNotFound();
+ BioCollection<BioMetabolite> sideCpds = null;
+ try {
+ sideCpds = mapper.map(inputSide);
+ } catch (IOException e) {
+ System.err.println("Error while reading the side compound file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ boolean removed = graph.removeAllVertices(sideCpds);
+ if (removed) System.err.println(sideCpds.size() + " compounds removed.");
+ }
+
+ //Graph processing: set weights [optional]
+// WeightingPolicy<BioMetabolite, ReactionEdge, CompoundGraph> wp = new UnweightedPolicy<>();
+// if (weightFile != null) {
+// System.err.println("Setting edge weights...");
+// wp = new WeightsFromFile(weightFile);
+// } else if (degree && !undirected) {
+// System.err.println("Setting edge weights...");
+// int pow = 2;
+// wp = new DegreeWeightPolicy(pow);
+// }
+// wp.setWeight(graph);
+// System.out.println(" Done.");
+
+ //invert graph as undirected (copy edge weight to reversed edge)
+ if(undirected){
+ System.out.print("Create Undirected...");
+ graph.asUndirected();
+ System.out.println(" Done.");
+ }
+
+ //remove isolated nodes
+ if(removeIsolated){
+ System.out.println("Remove isolated nodes...");
+ HashSet<BioMetabolite> nodes = new HashSet<>(graph.vertexSet());
+ graph.removeIsolatedNodes();
+ nodes.removeAll(graph.vertexSet());
+ for(BioMetabolite n : nodes){
+ System.out.println("\tremoving " + n.getName());
+ }
+ System.out.println(" Done.");
+ }
+
+ //create formula net
+ MetaGraph<BioMetabolite,ReactionEdge> meta= VertexContraction.contractByAsMeta(graph,BioMetabolite::getChemicalFormula);
+ meta.setNumberOfSubEdgesAsWeight();
+
+ //export graph
+ System.out.print("Exporting...");
+ HashMap<MetaNode<BioMetabolite>,Integer> att = meta.vertexSet().stream()
+ .collect(Collectors.toMap(
+ v -> v,
+ v -> v.getContentView().size(),
+ (existing, replacement) -> existing,
+ HashMap::new
+ ));
+ ExportGraph.toGmlWithAttributes(meta, this.outputPath,att,"node_size",true);
+ System.out.println(" Done.");
+ return;
+ }
+
+ @Override
+ public String getLabel() {return this.getClass().getSimpleName();}
+
+ @Override
+ public String getLongDescription() {
+ return "This application redefines metabolic compound graphs at the chemical formula level. It connects chemical" +
+ " formulas based on the existence of reactions where a reactant with the first formula is converted into a" +
+ " product with the second formula. This approach is particularly useful for metabolomics data with low-level " +
+ "annotation, where the exact compounds are unknown but their chemical formulas are available.";
+ }
+
+ @Override
+ public String getShortDescription() {return "Redefines metabolic compound graphs at the chemical formula level, connecting formulas based on reactions. Useful for mapping metabolomics data with low level annotations.";}
+}
\ No newline at end of file