A BioGraph with meta-nodes

The merged graph allows for a graph with edges that contains a collection of edges. The idea is to have the same thing for nodes. This will extends the features of the vertexContraction class, able to convert a group of nodes as a single node, except that the latter was of the same type as the groups members, and that the grouped nodes are not easily retrievable.

This will open a new range of metabolic graph variants (ex: network of formulas, EC class...)

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