srcjar/fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java

   1 package fr.orsay.lri.varna.models.templates;
   2
   3 import fr.orsay.lri.varna.models.treealign.RNANodeValue;
   4 import fr.orsay.lri.varna.models.treealign.RNANodeValue2;
   5 import fr.orsay.lri.varna.models.treealign.TreeAlignLabelDistanceAsymmetric;
   6
   7 /**
   8  * Distance between an RNANodeValue2 and an RNANodeValueTemplate.
   9  *
  10  * @author Raphael Champeimont
  11  *
  12  */
  13 public class RNANodeValue2TemplateDistance implements TreeAlignLabelDistanceAsymmetric<RNANodeValue2,RNANodeValueTemplate> {
  14         public double delete(RNANodeValue2 v) {
  15                 if (v == null) {
  16                         // deleting nothing costs nothing
  17                         return 0;
  18                 } else {
  19                         if (v.isSingleNode()) {
  20                                 if (v.getNode().getRightBasePosition() < 0) {
  21                                         // delete one base (that comes from a broken base pair)
  22                                         return 1;
  23                                 } else {
  24                                         // delete a base pair
  25                                         return 2;
  26                                 }
  27                         } else {
  28                                 // delete a sequence
  29                                 return v.getNodes().size();
  30                         }
  31                 }
  32         }
  33
  34         public double insert(RNANodeValueTemplate v) {
  35                 if (v == null) {
  36                         // inserting nothing costs nothing
  37                         return 0;
  38                 } else {
  39                         if (v instanceof RNANodeValueTemplateSequence) {
  40                                 return ((RNANodeValueTemplateSequence) v).getSequence().getLength();
  41                         } else if (v instanceof RNANodeValueTemplateBrokenBasePair) {
  42                                 // insert one base
  43                                 return 1;
  44                         } else { // this is a base pair
  45                                 // delete the base pair
  46                                 return 2;
  47                         }
  48                 }
  49         }
  50
  51         public double f(RNANodeValue2 v1, RNANodeValueTemplate v2) {
  52                 if (v1 == null) {
  53                         return insert(v2);
  54                 } else if (v2 == null) {
  55                         return delete(v1);
  56                 } else if (!v1.isSingleNode()) { // v1 is a sequence
  57                         if (v2 instanceof RNANodeValueTemplateSequence) {
  58                                 // the cost is the difference between the sequence lengths
  59                                 return Math.abs(v1.getNodes().size() - ((RNANodeValueTemplateSequence) v2).getSequence().getLength());
  60                         } else {
  61                                 // a sequence cannot be changed in something else
  62                                 return Double.POSITIVE_INFINITY;
  63                         }
  64                 } else if (v1.getNode().getRightBasePosition() >= 0) { // v1 is a base pair
  65                         if (v2 instanceof RNANodeValueTemplateBasePair) {
  66                                 // ok, a base pair can be mapped to a base pair
  67                                 return 0;
  68                         } else {
  69                                 // a base pair cannot be changed in something else
  70                                 return Double.POSITIVE_INFINITY;
  71                         }
  72                 } else { // v1 is a broken base pair
  73                         if (v2 instanceof RNANodeValueTemplateBrokenBasePair) {
  74                                 RNANodeValueTemplateBrokenBasePair brokenBasePair = ((RNANodeValueTemplateBrokenBasePair) v2);
  75                                 boolean strand5onTemplateSide = brokenBasePair.getPositionInHelix() < brokenBasePair.getHelix().getLength();
  76                                 boolean strand3onTemplateSide = ! strand5onTemplateSide;
  77                                 boolean strand5onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND5);
  78                                 boolean strand3onRNASide = (v1.getNode().getOrigin() == RNANodeValue.Origin.BASE_FROM_HELIX_STRAND3);
  79                                 if ((strand5onTemplateSide && strand5onRNASide)
  80                                                 || (strand3onTemplateSide && strand3onRNASide)) {
  81                                         // Ok they can be mapped together
  82                                         return 0.0;
  83                                 } else {
  84                                         // A base on a 5' strand of an helix
  85                                         // cannot be mapped to base on a 3' strand of an helix
  86                                         return Double.POSITIVE_INFINITY;
  87                                 }
  88                         } else {
  89                                 return Double.POSITIVE_INFINITY;
  90                         }
  91                 }
  92         }
  93 }