X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FRNANodeValue2TemplateDistance.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FRNANodeValue2TemplateDistance.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=51e8b46683841d82d1237aab7db5644328fbd8c0;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

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
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;
-			}
-		}
-	}
-}