From cc059e62de0f2a00e27fe774885d542cae59b271 Mon Sep 17 00:00:00 2001
From: Remco Bouckaert <higgs.ml@gmail.com>
Date: Tue, 5 May 2015 08:46:45 +1200
Subject: [PATCH] checkpoint

---
 src/snap/Data.java | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/snap/Data.java b/src/snap/Data.java
index dd03071..f2e1d64 100644
--- a/src/snap/Data.java
+++ b/src/snap/Data.java
@@ -500,4 +500,20 @@ protected boolean isEqual(int iSite1, int iSite2) {
     public int[] getPatternLineagCounts(int id) {
         return m_nPatternLineageCounts[id];
     }
+    
+    public double getProportionZeros() {
+    	int zeroCount = 0;
+    	int oneCount  = 0;
+    	for (int i = 0; i < sitePatterns.length; i++) {
+    		int [] p = getPattern(i);
+    		int [] n = getPatternLineagCounts(i);
+    		int w = getPatternWeight(i);
+    		for (int j = 0; j < p.length; j++) {
+    			oneCount += w * p[j];
+    			zeroCount += w * (n[j] - p[j]);
+    		}
+    	}
+    	return (double) zeroCount / ((double) zeroCount + oneCount);
+    }
+
 }