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diff --git a/src2/fr/orsay/lri/varna/models/templates/RNATemplateMapping.java b/src2/fr/orsay/lri/varna/models/templates/RNATemplateMapping.java
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+package fr.orsay.lri.varna.models.templates;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import fr.orsay.lri.varna.applications.templateEditor.Couple;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
+
+/**
+ * A RNATemplateMapping is a mapping between bases in an RNA sequence
+ * and elements in a RNA template.
+ * A base is mapped to only one template element
+ * but a template element can be mapped to several bases.
+ * This class is designed to be similar to the Mapping class.
+ * 
+ * @author Raphael Champeimont
+ */
+public class RNATemplateMapping {
+	private Map<Integer, RNATemplateElement> map = new HashMap<Integer, RNATemplateElement>();
+	private Map<RNATemplateElement, ArrayList<Integer>> invmap = new HashMap<RNATemplateElement, ArrayList<Integer>>();
+	
+	/**
+	 * Alignment distance.
+	 */
+	private double distance;
+	
+	
+	public double getDistance() {
+		return distance;
+	}
+	
+	public void setDistance(double distance) {
+		this.distance = distance;
+	}
+	
+	/**
+	 * Tell this mapping object that this base index and this element are
+	 * mapped with each other. This will throw RNATemplateMappingException
+	 * and do nothing if the base index is already in the mapping.
+	 */
+	public void addCouple(int baseIndex, RNATemplateElement templateElement) throws RNATemplateMappingException {
+		if (map.containsKey(baseIndex)) {
+			throw (new RNATemplateMappingException("Base index already in mapping: " + baseIndex));
+		}
+		if (baseIndex < 0) {
+			throw (new RNATemplateMappingException("Invalid base index: " + baseIndex));
+		}
+		map.put(baseIndex, templateElement);
+		if (!invmap.containsKey(templateElement)) {
+			invmap.put(templateElement, new ArrayList<Integer>());
+		}
+		invmap.get(templateElement).add(baseIndex);
+	}
+
+
+	public String showCompact(RNA r)
+	{
+		HashMap<String,Couple<Integer,Integer> > ranges = new HashMap<String,Couple<Integer,Integer> >();
+		for(int i:map.keySet())
+		{
+			RNATemplateElement t = map.get(i);
+			String k = t.getName();
+			if (t instanceof RNATemplate.RNATemplateHelix)
+			{
+				k += " (" + ((RNATemplateHelix) t).getCaption() + ")";
+				ModeleBase mb = r.getBaseAt(i);
+				if (mb.getElementStructure()>i)
+				  k = k+":5'";
+				else
+				  k = k+":3'";
+			}
+			if (!ranges.containsKey(k))
+			{  ranges.put(k, new Couple<Integer,Integer>(Integer.MAX_VALUE,Integer.MIN_VALUE));  }
+			Couple<Integer,Integer> c = ranges.get(k);
+			c.first = Math.min(c.first, i);
+			c.second = Math.max(c.second, i);			
+		}
+		String result = "";
+		for(String k:ranges.keySet())
+		{
+			Couple<Integer,Integer> c = ranges.get(k);
+			RNATemplateElement t = map.get(c.first);
+			String type = ((t instanceof RNATemplate.RNATemplateHelix)?"strand":"loop");
+			if (t instanceof RNATemplate.RNATemplateHelix)
+			{
+				if (k.endsWith("5'"))
+				{
+					Couple<Integer,Integer> c3 = ranges.get(k.replace("5'", "3'"));
+					result += "dummyID\t1\t"+k.replace(":5'", "")+"\t"+type+"\t"+c.first+"-"+c.second+":"+c3.first+"-"+c3.second+"\n";
+				}
+			}
+			else if (t instanceof RNATemplate.RNATemplateUnpairedSequence)
+			{
+			  result += "dummyID\t1\t"+k+"\t"+type+"\t"+c.first+"-"+c.second+"\n";
+			}
+		}
+		result += "alignment distance = " + distance;
+		return result;
+	}
+	
+	
+	/**
+	 * If the given base index is in the mapping, return the
+	 * corresponding template element, otherwise return null.
+	 */
+	public RNATemplateElement getPartner(int baseIndex) {
+		if (map.containsKey(baseIndex)) {
+			return map.get(baseIndex);
+		} else {
+			return null;
+		}
+	}
+	
+	
+	
+	/**
+	 * If the given template element is in the mapping, return an ArrayList
+	 * containing the corresponding base indexes, otherwise return null.
+	 * Note that you should not modify the returned ArrayList because
+	 * no copy is made, so if you modify it this mapping object will
+	 * contain inconsistent data.
+	 */
+	public ArrayList<Integer> getAncestor(RNATemplateElement templateElement) {
+		if (invmap.containsKey(templateElement)) {
+			return invmap.get(templateElement);
+		} else {
+			return null;
+		}
+	}
+	
+	
+	
+	/**
+	 * Return a set containing all the base indexes in the mapping.
+	 * You should not modify the returned set.
+	 */
+	public Set<Integer> getSourceElemsAsSet() {
+		return map.keySet();
+	}
+	
+	
+	
+	/**
+	 * Return a set containing all the template elements in the mapping.
+	 * You should not modify the return set.
+	 */
+	public Set<RNATemplateElement> getTargetElemsAsSet() {
+		return invmap.keySet();
+	}
+	
+	
+	
+}