Minor tweak to improve ease-of-use of iterator system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/Aligner.java

@@ -38,7 +38,7 @@ public interface Aligner {
      * @param bases List of bases.
      * @return Iterator to alignments.
      */
-    public Iterator<Alignment[]> getAllAlignments(final byte[] bases);
+    public Iterable<Alignment[]> getAllAlignments(final byte[] bases);
 
     /**
      * Get a iterator of aligned reads, batched by mapping quality.
@@ -46,7 +46,7 @@ public interface Aligner {
      * @param newHeader Optional new header to use when aligning the read.  If present, it must be null.
      * @return Iterator to alignments.
      */
-    public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader);
+    public Iterable<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader);
 }
 
 

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -66,13 +66,14 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
         if(read.getReadNegativeStrandFlag()) bases = BaseUtils.simpleReverseComplement(bases);
 
         boolean matches = true;
-        Iterator<Alignment[]> alignments = aligner.getAllAlignments(bases);
+        Iterable<Alignment[]> alignments = aligner.getAllAlignments(bases);
+        Iterator<Alignment[]> alignmentIterator = alignments.iterator();
 
-        if(!alignments.hasNext()) {
+        if(!alignmentIterator.hasNext()) {
             matches = read.getReadUnmappedFlag();
         }
         else {
-            Alignment[] alignmentsOfBestQuality = alignments.next();
+            Alignment[] alignmentsOfBestQuality = alignmentIterator.next();
             for(Alignment alignment: alignmentsOfBestQuality) {
                 matches = (alignment.getContigIndex() == read.getReferenceIndex());
                 matches &= (alignment.getAlignmentStart() == read.getAlignmentStart());
@@ -91,9 +92,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
             logger.error(String.format("    Negative strand: %b", read.getReadNegativeStrandFlag()));
             logger.error(String.format("    Cigar: %s%n", read.getCigarString()));
             logger.error(String.format("    Mapping quality: %s%n", read.getMappingQuality()));
-            Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(bases);
+            for(Alignment[] alignmentsByScore: alignments) {
-            while(alignmentIterator.hasNext()) {
-                Alignment[] alignmentsByScore = alignmentIterator.next();
                 for(int i = 0; i < alignmentsByScore.length; i++) {
                     logger.error(String.format("Alignment %d:",i));
                     logger.error(String.format("    Contig index: %d",alignmentsByScore[i].getContigIndex()));

java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java

@@ -94,37 +94,41 @@ public class BWACAligner extends BWAAligner {
      * @return Iterator to alignments.
      */
     @Override
-    public Iterator<Alignment[]> getAllAlignments(final byte[] bases) {
+    public Iterable<Alignment[]> getAllAlignments(final byte[] bases) {
         final BWAPath[] paths = getPaths(bases);
-        return new Iterator<Alignment[]>() {
+        return new Iterable<Alignment[]>() {
-            /**
+            public Iterator<Alignment[]> iterator() {
-             * The last position accessed.
+                return new Iterator<Alignment[]>() {
-             */
+                    /**
-            private int position = 0;
+                     * The last position accessed.
+                     */
+                    private int position = 0;
 
-            /**
+                    /**
-             * Whether all alignments have been seen based on the current position.
+                     * Whether all alignments have been seen based on the current position.
-             * @return True if any more alignments are pending.  False otherwise.
+                     * @return True if any more alignments are pending.  False otherwise.
-             */
+                     */
-            public boolean hasNext() { return position < paths.length; }
+                    public boolean hasNext() { return position < paths.length; }
 
-            /**
+                    /**
-             * Return the next cross-section of alignments, based on mapping quality.
+                     * Return the next cross-section of alignments, based on mapping quality.
-             * @return Array of the next set of alignments of a given mapping quality.
+                     * @return Array of the next set of alignments of a given mapping quality.
-             */
+                     */
-            public Alignment[] next() {
+                    public Alignment[] next() {
-                if(position >= paths.length)
+                        if(position >= paths.length)
-                    throw new UnsupportedOperationException("Out of alignments to return.");
+                            throw new UnsupportedOperationException("Out of alignments to return.");
-                int score = paths[position].score;
+                        int score = paths[position].score;
-                int startingPosition = position;
+                        int startingPosition = position;
-                while(position < paths.length && paths[position].score == score) position++;
+                        while(position < paths.length && paths[position].score == score) position++;
-                return convertPathsToAlignments(bases,Arrays.copyOfRange(paths,startingPosition,position));
+                        return convertPathsToAlignments(bases,Arrays.copyOfRange(paths,startingPosition,position));
+                    }
+
+                    /**
+                     * Unsupported.
+                     */
+                    public void remove() { throw new UnsupportedOperationException("Cannot remove from an alignment iterator"); }
+                };
             }
-
-            /**
-             * Unsupported.
-             */
-            public void remove() { throw new UnsupportedOperationException("Cannot remove from an alignment iterator"); }
         };
     }
 
@@ -135,32 +139,37 @@ public class BWACAligner extends BWAAligner {
      * @return Iterator to alignments.
      */
     @Override
-    public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) {
+    public Iterable<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) {
-        final Iterator<Alignment[]> alignments = getAllAlignments(read.getReadBases());
+        final Iterable<Alignment[]> alignments = getAllAlignments(read.getReadBases());
-        return new Iterator<SAMRecord[]>() {
+        return new Iterable<SAMRecord[]>() {
-            /**
+            public Iterator<SAMRecord[]> iterator() {
-             * Whether all alignments have been seen based on the current position.
+                final Iterator<Alignment[]> alignmentIterator = alignments.iterator();
-             * @return True if any more alignments are pending.  False otherwise.
+                return new Iterator<SAMRecord[]>() {
-             */
+                    /**
-            public boolean hasNext() { return alignments.hasNext(); }
+                     * Whether all alignments have been seen based on the current position.
+                     * @return True if any more alignments are pending.  False otherwise.
+                     */
+                    public boolean hasNext() { return alignmentIterator.hasNext(); }
 
-            /**
+                    /**
-             * Return the next cross-section of alignments, based on mapping quality.
+                     * Return the next cross-section of alignments, based on mapping quality.
-             * @return Array of the next set of alignments of a given mapping quality.
+                     * @return Array of the next set of alignments of a given mapping quality.
-             */
+                     */
-            public SAMRecord[] next() {
+                    public SAMRecord[] next() {
-                Alignment[] alignmentsOfQuality = alignments.next();
+                        Alignment[] alignmentsOfQuality = alignmentIterator.next();
-                SAMRecord[] reads = new SAMRecord[alignmentsOfQuality.length];
+                        SAMRecord[] reads = new SAMRecord[alignmentsOfQuality.length];
-                for(int i = 0; i < alignmentsOfQuality.length; i++) {
+                        for(int i = 0; i < alignmentsOfQuality.length; i++) {
-                    reads[i] = Alignment.convertToRead(alignmentsOfQuality[i],read,newHeader);
+                            reads[i] = Alignment.convertToRead(alignmentsOfQuality[i],read,newHeader);
-                }
+                        }
-                return reads;
+                        return reads;
+                    }
+
+                    /**
+                     * Unsupported.
+                     */
+                    public void remove() { throw new UnsupportedOperationException("Cannot remove from an alignment iterator"); }
+                };
             }
-
-            /**
-             * Unsupported.
-             */
-            public void remove() { throw new UnsupportedOperationException("Cannot remove from an alignment iterator"); }
         };
     }
 

java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java

@@ -2,16 +2,12 @@ package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
-import org.broadinstitute.sting.alignment.bwa.java.BWAAlignment;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.util.Iterator;
 
 import net.sf.samtools.*;
 
@@ -79,16 +75,15 @@ public class AlignerTestHarness {
             // Clear everything except flags pertaining to pairing and set 'unmapped' status to true.
             alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
 
-            Iterator<Alignment[]> alignments = aligner.getAllAlignments(alignmentCleaned.getReadBases());
+            Iterable<Alignment[]> alignments = aligner.getAllAlignments(alignmentCleaned.getReadBases());
-            if(!alignments.hasNext() ) {
+            if(!alignments.iterator().hasNext() ) {
                 //throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
                 System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
                 failures++;
             }
 
             Alignment foundAlignment = null;
-            while(alignments.hasNext()) {
+            for(Alignment[] alignmentsOfQuality: alignments) {
-                Alignment[] alignmentsOfQuality = alignments.next();
                 for(Alignment alignment: alignmentsOfQuality) {
                     if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
                         continue;
@@ -116,9 +111,7 @@ public class AlignerTestHarness {
                 String expectedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),read.getAlignmentStart(),read.getAlignmentStart()+read.getReadLength()+numDeletions-1).getBases());
                 System.out.printf("expected ref  = %s%n", formatBasesBasedOnCigar(expectedRef,read.getCigar(),CigarOperator.INSERTION));
 
-                Iterator<Alignment[]> alignmentsToOutput = aligner.getAllAlignments(alignmentCleaned.getReadBases());
+                for(Alignment[] alignmentsOfQuality: alignments) {
-                while(alignmentsToOutput.hasNext()) {
-                    Alignment[] alignmentsOfQuality = alignments.next();
                     for(Alignment alignment: alignmentsOfQuality) {
                         System.out.println();
 

java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java

@@ -108,7 +108,7 @@ public class BWAJavaAligner implements Aligner {
      * @param bases List of bases.
      * @return Iterator to alignments.
      */
-    public Iterator<Alignment[]> getAllAlignments(final byte[] bases) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
+    public Iterable<Alignment[]> getAllAlignments(final byte[] bases) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
 
     /**
      * Get a iterator of aligned reads, batched by mapping quality.
@@ -116,7 +116,7 @@ public class BWAJavaAligner implements Aligner {
      * @param newHeader Optional new header to use when aligning the read.  If present, it must be null.
      * @return Iterator to alignments.
      */
-    public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
+    public Iterable<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
 
 
     public List<Alignment> align( SAMRecord read ) {