X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FRNANodeValue2TemplateDistance.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FRNANodeValue2TemplateDistance.java;h=51e8b46683841d82d1237aab7db5644328fbd8c0;hp=0000000000000000000000000000000000000000;hb=2d6292c0377bc6b773c6844a45d3f2c5fac352c7;hpb=954af328a2a6a0055572cd1a09ee035301222574

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