src2/fr/orsay/lri/varna/models/treealign/RNANodeValue.java

   1 package fr.orsay.lri.varna.models.treealign;
   2
   3 /**
   4  * We use the following convention: If the node is marked by a couple (n,m)
   5  * these integers are stored in leftBasePosition and rightBasePosition
   6  * (ie. we have a pair of bases), if only
   7  * one value is present, it is stored in leftBasePosition and rightBasePosition
   8  * contains -1 (ie. we have a non-paired base).
   9  * The right and left nucleotides follow the same rule, but are optional,
  10  * and '_' is used as undefined instead of -1.
  11  * Note that it is part of the contract of this class that default
  12  * values are -1 and _.
  13  *
  14  * @author Raphael Champeimont
  15  */
  16 public class RNANodeValue implements GraphvizDrawableNodeValue {
  17         private int leftBasePosition = -1;
  18         private int rightBasePosition = -1;
  19
  20         private String leftNucleotide = "_";
  21         private String rightNucleotide = "_";
  22
  23         public enum Origin {
  24                 BASE_PAIR_FROM_HELIX,
  25                 BASE_FROM_HELIX_STRAND5,
  26                 BASE_FROM_HELIX_STRAND3,
  27                 BASE_FROM_UNPAIRED_REGION;
  28         }
  29
  30         /**
  31          * Used to store the origin of this base / base pair.
  32          */
  33         private Origin origin = null;
  34
  35         public Origin getOrigin() {
  36                 return origin;
  37         }
  38         public void setOrigin(Origin comesFromAnHelix) {
  39                 this.origin = comesFromAnHelix;
  40         }
  41
  42
  43
  44         public String getLeftNucleotide() {
  45                 return leftNucleotide;
  46         }
  47         public void setLeftNucleotide(String leftNucleotide) {
  48                 this.leftNucleotide = leftNucleotide;
  49         }
  50         public String getRightNucleotide() {
  51                 return rightNucleotide;
  52         }
  53         public void setRightNucleotide(String rightNucleotide) {
  54                 this.rightNucleotide = rightNucleotide;
  55         }
  56         public int getLeftBasePosition() {
  57                 return leftBasePosition;
  58         }
  59         public void setLeftBasePosition(int leftBasePosition) {
  60                 this.leftBasePosition = leftBasePosition;
  61         }
  62         public int getRightBasePosition() {
  63                 return rightBasePosition;
  64         }
  65         public void setRightBasePosition(int rightBasePosition) {
  66                 this.rightBasePosition = rightBasePosition;
  67         }
  68
  69         public String toGraphvizNodeName() {
  70                 if (rightNucleotide.equals("_")) {
  71                         if (leftNucleotide.equals("_")) {
  72                                 if (rightBasePosition == -1) {
  73                                         if (leftBasePosition == -1) {
  74                                                 return super.toString();
  75                                         } else {
  76                                                 return Integer.toString(leftBasePosition);
  77                                         }
  78                                 } else {
  79                                         return "(" + leftBasePosition + "," + rightBasePosition + ")";
  80                                 }
  81                         } else {
  82                                 return leftNucleotide;
  83                         }
  84                 } else {
  85                         return "(" + leftNucleotide + "," + rightNucleotide + ")";
  86                 }
  87         }
  88
  89         public String toString() {
  90                 if (rightBasePosition == -1) {
  91                         if (leftBasePosition == -1) {
  92                                 return super.toString();
  93                         } else {
  94                                 return Integer.toString(leftBasePosition);
  95                         }
  96                 } else {
  97                         return "(" + leftBasePosition + "," + rightBasePosition + ")";
  98                 }
  99         }
 100
 101
 102 }