Louison Fresnais · Clement Frainay · Louison Fresnais
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java
 	public HashMap<String, E> getMapView() {
 		return new HashMap<>(this.entities);
 	}
-
+    public Set<E> asSet() {
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
 	public List<BioPath<V,E>> getAllShortestPaths(){
 		return getShortestPathsUnionList(g.vertexSet());
 	}
-
+	/**
+	 * Return the distance matrix of all the paiwise distances in the graph
+	 *
+	 * @return the distance matrix
+	 */
+	public BioMatrix getDistances(){
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+				j++;
+			}
+			i++;
+		}
+		//get the label-index matching
+		HashMap<String,Integer> rowLabelMap = distMatrix.getRowLabelMap();
+		HashMap<String,Integer> columnLabelMap = distMatrix.getColumnLabelMap();
+		//compute all sps in the graph
+		List<BioPath<V,E>> allShortest = getShortestPathsUnionList(nodeSet);
+		//fill the biomatrix
+		try {
+			for(BioPath bp:allShortest) {
+				distMatrix.set(rowLabelMap.get(bp.getStartVertex().toString()), columnLabelMap.get(bp.getEndVertex().toString()), bp.getLength());
+				}
+		} catch (NullPointerException e ) {
+			System.err.println("Null pointer exception raised, no BioPath computed");
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+			distMatrix.setColumnLabel(i,r1.getId());
+			int j = 0;
+			for(V r2:nodeSet){
+				//init value in matrix to inf if r1!=r2
+				if(r1!=r2) {
+				distMatrix.set(i, j, Double.POSITIVE_INFINITY);
+				}
+				j++;
+			}
+			i++;
+		}
+		//get the label-index matching
+		HashMap<String,Integer> rowLabelMap = distMatrix.getRowLabelMap();
+		HashMap<String,Integer> columnLabelMap = distMatrix.getColumnLabelMap();
+		//compute all sps in the graph
+		List<BioPath<V,E>> allShortest = getShortestPathsUnionList(nodeSet);