JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / srcjar / fr / orsay / lri / varna / models / treealign / RNANodeValue2.java

diff --git a/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java b/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java
deleted file mode 100644 (file)
index 6fff9a9..0000000
--- a/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java
+++ /dev/null
@@ -1,136 +0,0 @@
-package fr.orsay.lri.varna.models.treealign;
-import java.util.ArrayList;
-import java.util.List;
-
-
-
-/**
- * In this model, nodes are either:
- * 1. a couple of paired bases, and in that case they may have children,
- *    in this case singleNode is true 
- * 2. a single base that comes from a broken base pair
- *    (broken during planarization), without children,
- *    in this case singleNode is true
- * 3. a list of consecutive non-paired bases, without children.
- *    in this case singleNode is false
- * Note that case 2 happens only if original sequences contained
- * pseudoknots, otherwise this case can be ignored.
- * 
- * @author Raphael Champeimont
- *
- */
-public class RNANodeValue2 implements GraphvizDrawableNodeValue {
-       /**
-        * Says whether we have a single node or a list of nodes.
-        */
-       private boolean singleNode = true;
-       
-       /**
-        * Defined if singleNode is true. 
-        */
-       private RNANodeValue node;
-       
-       /**
-        * Defined if singleNode is false; 
-        */
-       private List<RNANodeValue> nodes;
-       
-       public RNANodeValue2(boolean singleNode) {
-               this.singleNode = singleNode;
-               if (singleNode) {
-                       node = new RNANodeValue();
-               } else {
-                       nodes = new ArrayList<RNANodeValue>();
-               }
-       }
-
-       /**
-        * In case of a single node, return it.
-        * Will throw RNANodeValue2WrongTypeException if singleNode = false.
-        */
-       public RNANodeValue getNode() {
-               if (singleNode) {
-                       return node;
-               } else {
-                       throw (new RNANodeValue2WrongTypeException());
-               }
-       }
-       
-       public void setNode(RNANodeValue node) {
-               if (singleNode) {
-                       this.node = node;
-               } else {
-                       throw (new RNANodeValue2WrongTypeException());
-               }
-       }
-
-       /**
-        * In case of multiple nodes, return them.
-        * Will throw RNANodeValue2WrongTypeException if singleNode = true.
-        */
-       public List<RNANodeValue> getNodes() {
-               if (!singleNode) {
-                       return nodes;
-               } else {
-                       throw (new RNANodeValue2WrongTypeException());
-               }
-       }
-       /**
-        * In case of multiple nodes, return the sequence of nucleotides.
-        */
-       public char[] computeSequence() {
-               if (!singleNode) {
-                       final int n = nodes.size();
-                       char[] sequence = new char[n];
-                       for (int i=0; i<n; i++) {
-                               sequence[i] = nodes.get(i).getLeftNucleotide().charAt(0);
-                       }
-                       return sequence;
-               } else {
-                       throw (new RNANodeValue2WrongTypeException());
-               }
-       }
-       
-       public void setNodes(List<RNANodeValue> nodes) {
-               if (!singleNode) {
-                       this.nodes = nodes;
-               } else {
-                       throw (new RNANodeValue2WrongTypeException());
-               }
-       }
-
-       public boolean isSingleNode() {
-               return singleNode;
-       }
-       
-       public String toString() {
-               if (singleNode) {
-                       return node.toString();
-               } else {
-                       String s = "";
-                       for (RNANodeValue node: nodes) {
-                               if (s != "") {
-                                       s += " ";
-                               }
-                               s += node.toString();
-                       }
-                       return s;
-               }
-       }
-       
-       public String toGraphvizNodeName() {
-               if (singleNode) {
-                       return node.toGraphvizNodeName();
-               } else {
-                       String s = "";
-                       for (RNANodeValue node: nodes) {
-                               if (s != "") {
-                                       s += " ";
-                               }
-                               s += node.toGraphvizNodeName();
-                       }
-                       return s;
-               }
-       }
-
-}