JAL-3026 srcjar files for VARNA and log4j

[jalview.git] / srcjar / fr / orsay / lri / varna / models / treealign / ExampleDistance2.java

diff --git a/srcjar/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java b/srcjar/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java
new file mode 100644 (file)
index 0000000..f58bcbb
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java
@@ -0,0 +1,39 @@
+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;
+                       }
+               }
+       }
+}