JAL-3026 srcjar files for VARNA and log4j

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

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 (file)
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;
+                       }
+               }
+       }
+}