From 7c20be157cb183f014bf7aaa2126928cdb2a834d Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Jul 2009 21:00:19 +0000
Subject: [PATCH] Added ability to sample from a list *without* replacement.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1304 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/ListUtils.java | 44 +++++++++++++++----
 1 file changed, 36 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/ListUtils.java b/java/src/org/broadinstitute/sting/utils/ListUtils.java
index d8581c06d..b79b2ab0a 100644
--- a/java/src/org/broadinstitute/sting/utils/ListUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/ListUtils.java
@@ -1,9 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import java.util.List;
-import java.util.HashSet;
-import java.util.ArrayList;
-import java.util.Random;
+import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
@@ -16,8 +13,14 @@ public class ListUtils {
 
     static Random rand = new Random(12321); //System.currentTimeMillis());
 
+    /**
+     * Returns n random indices drawn with replacement from the range 0..(k-1)
+     *
+     * @param n  the number of random indices to draw (with replacement)
+     * @param k  the total number of indices allowed
+     * @return a list of random indices ranging from 0 to (k-1) with possible duplicates
+     */
     static public ArrayList<Integer> sampleIndicesWithReplacement(int n, int k) {
-        // Returns n random indices drawn with replacement from the range 1..k
 
         ArrayList<Integer> chosen_balls = new ArrayList <Integer>();
         for (int i=0; i<n; i++) {
@@ -29,10 +32,35 @@ public class ListUtils {
         return chosen_balls;
     }
 
-    static public <T> ArrayList<T> sliceListByIndices(List<Integer> indices, List<T> list) {
-        // Given a list of indices into a list, return those elements of the list with the possibility
-        // of drawing list elements multiple times
+    /**
+     * Returns n random indices drawn without replacement from the range 0..(k-1)
+     *
+     * @param n  the number of random indices to draw (without replacement)
+     * @param k  the total number of indices allowed
+     * @return a list of random indices ranging from 0 to (k-1) without duplicates
+     */
+    static public ArrayList<Integer> sampleIndicesWithoutReplacement(int n, int k) {
+        ArrayList<Integer> chosen_balls = new ArrayList<Integer>(k);
 
+        for (int i = 0; i < n; i++) {
+            chosen_balls.add(i);
+        }
+
+        Collections.shuffle(chosen_balls, rand);
+
+        //return (ArrayList<Integer>) chosen_balls.subList(0, k);
+        return new ArrayList<Integer>(chosen_balls.subList(0, k));
+    }
+
+    /**
+     * Given a list of indices into a list, return those elements of the list with the possibility of drawing list elements multiple times
+
+     * @param indices  the list of indices for elements to extract
+     * @param list     the list from which the elements should be extracted
+     * @param <T>      the template type of the ArrayList
+     * @return         a new ArrayList consisting of the elements at the specified indices
+     */
+    static public <T> ArrayList<T> sliceListByIndices(List<Integer> indices, List<T> list) {
         ArrayList<T> subset = new ArrayList<T>();
 
         for (int i : indices) {