JAL-3026 srcjar files for VARNA and log4j

[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
new file mode 100644 (file)
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+++ b/srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java
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+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;
+               }
+       }
+
+}