Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().

Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).  

Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java

@@ -27,12 +27,21 @@ public class PushbackIterator<T> implements Iterator<T>, Iterable<T> {
         return this;
     }
 
-    public T peek() {
+    /**
+     * Retrieves, but does not remove, the head of this iterator.
+     * @return T the next element in the iterator
+     * @throws NoSuchElementException - if the iterator doesn't have a next element
+     */
+    public T element() {
         T x = next();
         pushback(x);
         return x;
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iteration has no more elements.
+     */
     public T next() {
         if (pushedElement != null) {
             final T ret = pushedElement;

java/src/org/broadinstitute/sting/gatk/refdata/IntervalRodIterator.java

@@ -34,8 +34,13 @@ public class IntervalRodIterator implements Iterator<IntervalRod> {
 		return iter.hasNext();
 	}
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
 	@Override
 	public IntervalRod next() {
+        if (!this.hasNext()) throw new NoSuchElementException("IntervalRodIterator next called on iterator with no more elements");
         IntervalRod r = new IntervalRod(trackName, iter.next());
         //System.out.printf("IntervalRod next is %s%n", r);
         return r;

java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java

@@ -16,6 +16,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 
 /**
@@ -349,8 +350,13 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
         return (mReader.hasNext());
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
     @Override
     public RodGLF next() {
+        if (!this.hasNext()) throw new NoSuchElementException("RodGLF next called on iterator with no more elements");
         mRecord = mReader.next();
         mLoc = GenomeLocParser.createGenomeLoc(mReader.getReferenceName(), mReader.getCurrentLocation(), mReader.getCurrentLocation());
         return this;

java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java

@@ -12,6 +12,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 
 /**
@@ -282,7 +283,12 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mReader.hasNext();
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
     public RodVCF next() {
+        if (!this.hasNext()) throw new NoSuchElementException("RodVCF next called on iterator with no more elements");
         return new RodVCF(name, mReader.next(), mReader);
     }
 

java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java

@@ -584,8 +584,13 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 			return parser.hasNext();
 		}
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		@Override
 		public SAMPileupRecord next() {
+             if (!this.hasNext()) throw new NoSuchElementException("SAMPileupRecord next called on iterator with no more elements");
 //			 if ( z == 0 ) t = System.currentTimeMillis();
 	          lastProcessedLine = parser.next();
 	          SAMPileupRecord n = new SAMPileupRecord(rodName);

java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java

@@ -78,7 +78,8 @@ public class SeekableRODIterator<ROD extends ReferenceOrderedDatum> implements I
     public SeekableRODIterator(Iterator<ROD> it) {
         this.it = new PushbackIterator<ROD>(it);
         records = new LinkedList<ROD>();
-        ROD r = this.it.peek();
+        ROD r = null;
+        if (this.it.hasNext()) r = this.it.element();
         name = (r==null?null:r.getName());
     }
 
@@ -132,7 +133,7 @@ public class SeekableRODIterator<ROD extends ReferenceOrderedDatum> implements I
          // covered by new records, so we need to load them too:
 
          while ( it.hasNext() ) {
-             ROD r = it.peek();
+             ROD r = it.element();
              if ( r == null ) {
                  it.next();
                  continue;

java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java

@@ -78,8 +78,12 @@ public class rodGELI extends BasicReferenceOrderedDatum {
 		public boolean hasNext() {
 			return iterator.hasNext();
 		}
-
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		public rodGELI next() {
+            if (!this.hasNext()) throw new NoSuchElementException("RodGELI next called on iterator with no more elements");
             return new rodGELI(rodName, iterator.next());
 		}
 

java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java

@@ -31,10 +31,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.Iterator;
+import java.util.*;
-import java.util.List;
-import java.util.Collections;
-import java.util.Arrays;
 
 /**
  * @author alecw@broadinstitute.org
@@ -270,7 +267,12 @@ public class rodPicardDbSNP implements VariationRod {
             return reader.hasNext();
         }
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
         public rodPicardDbSNP next() {
+            if (!this.hasNext()) throw new NoSuchElementException("rodPicardDbSNP next called on iterator with no more elements");
             return new rodPicardDbSNP(reader.next());
         }
 

java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java

@@ -113,9 +113,13 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 			return parser.hasNext();
 		}
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		@Override
 		public rodSAMPileup next() {
-
+            if (!this.hasNext()) throw new NoSuchElementException("rodSAMPileup next called on iterator with no more elements");
 			rodSAMPileup result = new rodSAMPileup(rodName);
 			
 			SAMPileupRecord r = parser.next();