X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FExampleDistance2.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftreealign%2FExampleDistance2.java;h=0000000000000000000000000000000000000000;hb=a1225b9392dc7657d5cef12907385b07527d6122;hp=f58bcbb6b22bf1aa2f872119238545e83b99ae98;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java b/src2/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java
deleted file mode 100644
index f58bcbb..0000000
--- a/src2/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package fr.orsay.lri.varna.models.treealign;
-
-
-/**
- * This distance is such that a substitution costs nothing.
- * 
- * @author Raphael Champeimont
- *
- */
-public class ExampleDistance2 implements TreeAlignLabelDistanceSymmetric<RNANodeValue2> {
-	public double f(RNANodeValue2 v1, RNANodeValue2 v2) {
-		if (v1 == null) {
-			if (v2 == null) {
-				return 0;
-			} else if (!v2.isSingleNode()) { // v2 is a list of bases
-				return v2.getNodes().size();
-			} else { // v2 is a single node
-				return 2;
-			}
-		} else if (!v1.isSingleNode()) { // v1 is a list of bases
-			if (v2 == null) {
-				return v1.getNodes().size();
-			} else if (!v2.isSingleNode()) { // v2 is a list of bases
-				return Math.abs(v2.getNodes().size() - v1.getNodes().size());
-			} else { // v2 is a single node
-				return 2 + v1.getNodes().size();
-			}
-		} else { // v1 is a single node
-			// all the same as when v1 == null
-			if (v2 == null) {
-				return 2;
-			} else if (!v2.isSingleNode()) { // v2 is a list of bases
-				return 2 + v2.getNodes().size();
-			} else { // v2 is a single node
-				return 0;
-			}
-		}
-	}
-}