From: Michael Andreen <harv@ruin.nu>
Date: Thu, 16 Aug 2007 09:17:46 +0000 (+0000)
Subject: calculate the proper distance, with hurdles
X-Git-Tag: v0.1~17
X-Git-Url: https://ruin.nu/git/?p=germs.git;a=commitdiff_plain;h=1fb658ea3ad9dc286e95ec515d7c90f5ad2d4a1f

calculate the proper distance, with hurdles
---

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 174c6f7..3fb2aaa 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -94,9 +94,20 @@ size_t countCycles(const GeneOrder& go){
 }
 
 size_t inversionDistance(const GeneOrder& go){
-	size_t cycles = countCycles(go);
+	size_t distance = go.size() - 1;
+	distance -= countCycles(go);
+
+	ComponentTree t(findComponents(go));
+	t.makeUnoriented();
+	size_t leaves = t.countLeaves();
+	distance += leaves;
+	if (leaves % 2 != 0){
+		size_t sb = t.shortBranches();
+		if (sb == 0)
+			distance += 1;
+	}
 
-	return go.size() - 1 - cycles;
+	return distance;
 }
 
 int sign(Gene g){