From bcc3f4a221281e1d3568cd8bef3904407045c065 Mon Sep 17 00:00:00 2001
From: Tim Fennell <tfenne@tfenne.com>
Date: Thu, 16 Jun 2016 21:15:05 -0400
Subject: [PATCH] Removed PollableTreeSet in SortingCollection as it was no
 longer necessary. (#642)

Replaced with direct usage of TreeSet.pollFirst(). One advantage (other than removing unneeded code) is that this now only has to search the tree once, instead of twice for poll() then remove().
---
 .../samtools/util/SortingCollection.java      | 26 +++----------------
 1 file changed, 4 insertions(+), 22 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/util/SortingCollection.java b/src/main/java/htsjdk/samtools/util/SortingCollection.java
index 681f458944..6babd4e35a 100644
--- a/src/main/java/htsjdk/samtools/util/SortingCollection.java
+++ b/src/main/java/htsjdk/samtools/util/SortingCollection.java
@@ -393,10 +393,10 @@ public void remove() {
      * location in the PriorityQueue
      */
     class MergingIterator implements CloseableIterator<T> {
-        private final PollableTreeSet<PeekFileRecordIterator> queue;
+        private final TreeSet<PeekFileRecordIterator> queue;
 
         MergingIterator() {
-            this.queue = new PollableTreeSet<PeekFileRecordIterator>(new PeekFileRecordIteratorComparator());
+            this.queue = new TreeSet<PeekFileRecordIterator>(new PeekFileRecordIteratorComparator());
             int n = 0;
             for (final File f : SortingCollection.this.files) {
                 final FileRecordIterator it = new FileRecordIterator(f);
@@ -418,7 +418,7 @@ public T next() {
                 throw new NoSuchElementException();
             }
 
-            final PeekFileRecordIterator fileIterator = queue.poll();
+            final PeekFileRecordIterator fileIterator = queue.pollFirst();
             final T ret = fileIterator.next();
             if (fileIterator.hasNext()) {
                 this.queue.add(fileIterator);
@@ -436,7 +436,7 @@ public void remove() {
 
         public void close() {
             while (!this.queue.isEmpty()) {
-                final PeekFileRecordIterator it = this.queue.poll();
+                final PeekFileRecordIterator it = this.queue.pollFirst();
                 ((CloseableIterator<T>)it.getUnderlyingIterator()).close();
             }
         }
@@ -511,22 +511,4 @@ public int compare(final PeekFileRecordIterator lhs, final PeekFileRecordIterato
             else return result;
         }
     }
-
-    /** Little class that provides the Java 1.5 TreeSet with a poll() method */
-    static class PollableTreeSet<T> extends TreeSet<T> {
-        PollableTreeSet(final Comparator<? super T> comparator) {
-            super(comparator);
-        }
-
-        public T poll() {
-            if (isEmpty()) {
-                return null;
-            }
-            else {
-                final T t = first();
-                remove(t);
-                return t;
-            }
-        }
-    }
 }