X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNANodeValue.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FRNANodeValue.java;h=3b26b4717e544850b5de990de4798ba08841a679;hb=4898f0ae429e0c61ddba72ca46be89b34bb4df8b;hp=0000000000000000000000000000000000000000;hpb=5a6ac5b535856903629234ad43a71319a91ebee5;p=jalview.git

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
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 + ")";
+		}
+	}
+	
+
+}