+package fr.orsay.lri.varna.models.templates;
+
+import fr.orsay.lri.varna.models.treealign.RNANodeValue;
+import fr.orsay.lri.varna.models.treealign.RNANodeValue2;
+import fr.orsay.lri.varna.models.treealign.TreeAlignLabelDistanceAsymmetric;
+
+/**
+ * Distance between an RNANodeValue2 and an RNANodeValueTemplate.
+ *
+ * @author Raphael Champeimont
+ *
+ */
+public class RNANodeValue2TemplateDistance implements TreeAlignLabelDistanceAsymmetric<RNANodeValue2,RNANodeValueTemplate> {
+ public double delete(RNANodeValue2 v) {
+ if (v == null) {
+ // deleting nothing costs nothing
+ return 0;
+ } else {
+ if (v.isSingleNode()) {
+ if (v.getNode().getRightBasePosition() < 0) {
+ // delete one base (that comes from a broken base pair)
+ return 1;
+ } else {
+ // delete a base pair
+ return 2;
+ }
+ } else {
+ // delete a sequence
+ return v.getNodes().size();
+ }
+ }
+ }
+
+ public double insert(RNANodeValueTemplate v) {
+ if (v == null) {
+ // inserting nothing costs nothing
+ return 0;
+ } else {
+ if (v instanceof RNANodeValueTemplateSequence) {
+ return ((RNANodeValueTemplateSequence) v).getSequence().getLength();
+ } else if (v instanceof RNANodeValueTemplateBrokenBasePair) {
+ // insert one base
+ return 1;
+ } else { // this is a base pair
+ // delete the base pair
+ return 2;
+ }
+ }
+ }
+
+ public double f(RNANodeValue2 v1, RNANodeValueTemplate v2) {
+ if (v1 == null) {
+ return insert(v2);
+ } else if (v2 == null) {
+ return delete(v1);
+ } else if (!v1.isSingleNode()) { // v1 is a sequence
+ if (v2 instanceof RNANodeValueTemplateSequence) {
+ // the cost is the difference between the sequence lengths
+ return Math.abs(v1.getNodes().size() - ((RNANodeValueTemplateSequence) v2).getSequence().getLength());
+ } else {
+ // a sequence cannot be changed in something else
+ return Double.POSITIVE_INFINITY;
+ }
+ } else if (v1.getNode().getRightBasePosition() >= 0) { // v1 is a base pair
+ if (v2 instanceof RNANodeValueTemplateBasePair) {
+ // ok, a base pair can be mapped to a base pair
+ return 0;
+ } else {
+ // a base pair cannot be changed in something else
+ return Double.POSITIVE_INFINITY;
+ }
+ } else { // v1 is a broken base pair
+ if (v2 instanceof RNANodeValueTemplateBrokenBasePair) {
+ RNANodeValueTemplateBrokenBasePair brokenBasePair = ((RNANodeValueTemplateBrokenBasePair) v2);
+ boolean strand5onTemplateSide = brokenBasePair.getPositionInHelix() < brokenBasePair.getHelix().getLength();
+ boolean strand3onTemplateSide = ! strand5onTemplateSide;
+ boolean strand5onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND5);
+ boolean strand3onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND3);
+ if ((strand5onTemplateSide && strand5onRNASide)
+ || (strand3onTemplateSide && strand3onRNASide)) {
+ // Ok they can be mapped together
+ return 0.0;
+ } else {
+ // A base on a 5' strand of an helix
+ // cannot be mapped to base on a 3' strand of an helix
+ return Double.POSITIVE_INFINITY;
+ }
+ } else {
+ return Double.POSITIVE_INFINITY;
+ }
+ }
+ }
+}