JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / models / treealign / RNANodeValue.java

diff --git a/src2/fr/orsay/lri/varna/models/treealign/RNANodeValue.java b/src2/fr/orsay/lri/varna/models/treealign/RNANodeValue.java
deleted file mode 100644 (file)
index 3b26b47..0000000
--- a/src2/fr/orsay/lri/varna/models/treealign/RNANodeValue.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package fr.orsay.lri.varna.models.treealign;
-
-/**
- * We use the following convention: If the node is marked by a couple (n,m)
- * these integers are stored in leftBasePosition and rightBasePosition
- * (ie. we have a pair of bases), if only
- * one value is present, it is stored in leftBasePosition and rightBasePosition
- * contains -1 (ie. we have a non-paired base).
- * The right and left nucleotides follow the same rule, but are optional,
- * and '_' is used as undefined instead of -1.
- * Note that it is part of the contract of this class that default
- * values are -1 and _.
- * 
- * @author Raphael Champeimont
- */
-public class RNANodeValue implements GraphvizDrawableNodeValue {
-       private int leftBasePosition = -1;
-       private int rightBasePosition = -1;
-       
-       private String leftNucleotide = "_";
-       private String rightNucleotide = "_";
-       
-       public enum Origin {
-               BASE_PAIR_FROM_HELIX,
-               BASE_FROM_HELIX_STRAND5,
-               BASE_FROM_HELIX_STRAND3,
-               BASE_FROM_UNPAIRED_REGION;
-       }
-       
-       /**
-        * Used to store the origin of this base / base pair.
-        */
-       private Origin origin = null;
-       
-       public Origin getOrigin() {
-               return origin;
-       }
-       public void setOrigin(Origin comesFromAnHelix) {
-               this.origin = comesFromAnHelix;
-       }
-       
-       
-       
-       public String getLeftNucleotide() {
-               return leftNucleotide;
-       }
-       public void setLeftNucleotide(String leftNucleotide) {
-               this.leftNucleotide = leftNucleotide;
-       }
-       public String getRightNucleotide() {
-               return rightNucleotide;
-       }
-       public void setRightNucleotide(String rightNucleotide) {
-               this.rightNucleotide = rightNucleotide;
-       }
-       public int getLeftBasePosition() {
-               return leftBasePosition;
-       }
-       public void setLeftBasePosition(int leftBasePosition) {
-               this.leftBasePosition = leftBasePosition;
-       }
-       public int getRightBasePosition() {
-               return rightBasePosition;
-       }
-       public void setRightBasePosition(int rightBasePosition) {
-               this.rightBasePosition = rightBasePosition;
-       }
-       
-       public String toGraphvizNodeName() {
-               if (rightNucleotide.equals("_")) {
-                       if (leftNucleotide.equals("_")) {
-                               if (rightBasePosition == -1) {
-                                       if (leftBasePosition == -1) {
-                                               return super.toString();
-                                       } else {
-                                               return Integer.toString(leftBasePosition);
-                                       }
-                               } else {
-                                       return "(" + leftBasePosition + "," + rightBasePosition + ")";
-                               }
-                       } else {
-                               return leftNucleotide;
-                       }
-               } else {
-                       return "(" + leftNucleotide + "," + rightNucleotide + ")";
-               }
-       }
-       
-       public String toString() {
-               if (rightBasePosition == -1) {
-                       if (leftBasePosition == -1) {
-                               return super.toString();
-                       } else {
-                               return Integer.toString(leftBasePosition);
-                       }
-               } else {
-                       return "(" + leftBasePosition + "," + rightBasePosition + ")";
-               }
-       }
-       
-
-}