returning src2 -> srcjar

[jalview.git] / src2 / fr / orsay / lri / varna / models / templates / RNANodeValue2TemplateDistance.java

diff --git a/src2/fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java b/src2/fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java
deleted file mode 100644 (file)
index 51e8b46..0000000
--- a/src2/fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java
+++ /dev/null
@@ -1,93 +0,0 @@
-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;
-                       }
-               }
-       }
-}