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diff --git a/src2/fr/orsay/lri/varna/models/templates/Benchmark.java b/src2/fr/orsay/lri/varna/models/templates/Benchmark.java
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+package fr.orsay.lri.varna.models.templates;
+
+import java.awt.geom.Line2D;
+import java.util.Arrays;
+
+import fr.orsay.lri.varna.models.geom.LinesIntersect;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+/**
+ * @author Raphael Champeimont
+ *
+ */
+public class Benchmark {
+	private RNA rna;
+	
+	// number of backbone crossings
+	public int backboneCrossings;
+	// average distance between unpaired consecutive bases
+	public double averageUnpairedDistance;
+	// median distance between consecutive bases
+	public double medianConsecutiveBaseDistance;
+	// Number of consecutive bases that are too near from each other
+	public int tooNearConsecutiveBases;
+	// Number of consecutive bases that are too far from each other
+	public int tooFarConsecutiveBases;
+	
+	
+	
+	// Parameters
+	public double targetConsecutiveBaseDistance = RNA.LOOP_DISTANCE;
+	// If consecutive bases are nearer that tooNearFactor * target distance, we call them too near.
+	public double tooNearFactor = 0.5;
+	// If consecutive bases are further that tooFarFactor * target distance, we call them too far.
+	public double tooFarFactor = 2;
+	
+	
+	
+	public Benchmark(RNA rna) {
+		this.rna = rna;
+		computeAll();
+	}
+	
+	private void computeAll() {
+		// Compute number of backbone crossings
+		{
+			int n = rna.getSize();
+			Line2D.Double[] lines = new Line2D.Double[n-1];
+			for (int i=0; i<n-1; i++) {
+				lines[i] = new Line2D.Double(rna.getCoords(i), rna.getCoords(i+1));
+			}
+			int intersectLines = 0;
+			for (int i=0; i<n-1; i++) {
+				for (int j=i+2; j<n-1; j++) {
+					if (LinesIntersect.linesIntersect(lines[i], lines[j])) {
+						intersectLines++;
+					}
+				}
+			}
+			backboneCrossings = intersectLines;
+		}
+		
+		// Stats about distances between consecutive bases not both part of an helix
+		{
+			int n = rna.getSize();
+			double sum = 0;
+			int count = 0;
+			for (int i=0; i<n-1; i++) {
+				int indexOfAssociatedBase1 = rna.getBaseAt(i).getElementStructure();
+				int indexOfAssociatedBase2 = rna.getBaseAt(i+1).getElementStructure();
+				if (indexOfAssociatedBase1 != -1 || indexOfAssociatedBase2 != -1) {
+					// If they are not both associated (ie. not part of an helix)
+					sum += rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
+					count++;
+				}
+			}
+			averageUnpairedDistance = sum / count;
+		}
+		
+		// Stats about base distances
+		{
+			int n = rna.getSize();
+			double distances[] = new double[n-1];
+			for (int i=0; i<n-1; i++) {
+				// If they are not both associated (ie. not part of an helix)
+				distances[i] = rna.getBaseAt(i).getCoords().distance(rna.getBaseAt(i+1).getCoords());
+			}
+			Arrays.sort(distances);
+			double median = distances[distances.length/2];
+			medianConsecutiveBaseDistance = median;
+			
+			// We take the median as target distance, and count
+			// the number of consecutive bases with a distance too different
+			tooNearConsecutiveBases = 0;
+			tooFarConsecutiveBases = 0;
+			for (int i=0; i<n-1; i++) {
+				if (distances[i] < tooNearFactor*targetConsecutiveBaseDistance) {
+					tooNearConsecutiveBases++;
+				}
+				if (distances[i] > tooFarFactor*targetConsecutiveBaseDistance) {
+					tooFarConsecutiveBases++;
+				}
+			}
+		}
+	}
+	
+	@SuppressWarnings("unused")
+	private int percent(int a, int b) {
+		return (int) Math.round((double) a / (double) b * 100.0);
+	}
+
+	public void printAll() {
+		System.out.println("Benchmark:");
+		System.out.println("\tBackbone crossings = " + backboneCrossings);
+		System.out.println("\tAverage unpaired distance = " + averageUnpairedDistance);
+		System.out.println("\tMedian of consecutive base distance = " + medianConsecutiveBaseDistance);
+		System.out.println("\tNumber of too near consecutive bases = " + tooNearConsecutiveBases); // + " ie. " + percent(tooNearConsecutiveBases, rna.getSize()-1) + " %");
+		System.out.println("\tNumber of too far consecutive bases = " + tooFarConsecutiveBases); // + " ie. " + percent(tooFarConsecutiveBases, rna.getSize()-1) + " %");
+	}
+}
+