Merge branch 'Jalview-JS/develop' into develop

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

diff --git a/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue.java b/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue.java
new file mode 100644 (file)
index 0000000..3b26b47
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue.java
@@ -0,0 +1,102 @@
+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 + ")";
+               }
+       }
+       
+
+}