From e467b8e1aeae88f9967001b8a8212c43db0ebf4c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 21 Nov 2011 09:34:57 -0500
Subject: [PATCH] More contracts on LazyGenotypesContext

---
 .../sting/utils/variantcontext/GenotypesContext.java         | 2 +-
 .../sting/utils/variantcontext/LazyGenotypesContext.java     | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
index ab5ab9465..25b277298 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
@@ -604,7 +604,7 @@ public class GenotypesContext implements List<Genotype> {
         }
     }
 
-    private final static boolean sameSamples(List<Genotype> genotypes, Collection<String> sampleNamesInOrder) {
+    protected final static boolean sameSamples(List<Genotype> genotypes, Collection<String> sampleNamesInOrder) {
         Set<String> names = new HashSet<String>(sampleNamesInOrder);
         if ( names.size() != sampleNamesInOrder.size() )
             return false;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
index 7facfacf6..b3a24aef5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
@@ -65,6 +65,8 @@ public class LazyGenotypesContext extends GenotypesContext {
      * to the LazyGenotypesContext holding encoded genotypes data
      */
     public interface LazyParser {
+        @Requires("data != null")
+        @Ensures("result != null")
         public LazyData parse(Object data);
     }
 
@@ -78,6 +80,9 @@ public class LazyGenotypesContext extends GenotypesContext {
         final Map<String, Integer> sampleNameToOffset;
         final List<String> sampleNamesInOrder;
 
+        @Requires({"genotypes != null", "sampleNamesInOrder != null", "sampleNameToOffset != null",
+            "sameSamples(genotypes, sampleNamesInOrder)",
+            "sameSamples(genotypes, sampleNameToOffset.keySet())"})
         public LazyData(final ArrayList<Genotype> genotypes,
                         final List<String> sampleNamesInOrder,
                         final Map<String, Integer> sampleNameToOffset) {