--- /dev/null
+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();
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / blobdiff