X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNANodeValue2.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNANodeValue2.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=6fff9a9b030618ad6e009d33f555d9cfda76405d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

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
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;
-		}
-	}
-
-}