Matt make a good point that the Reference Iterator we were using wasn't bounded; The BoundedReferenceIterator takes a GenomeLoc to bound the iterations by

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@305 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 
+import org.broadinstitute.sting.gatk.iterators.BoundedReferenceIterator;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -44,17 +45,11 @@ public class ReferenceDataSource implements SimpleDataSource {
      * @param location the genome location to extract data for
      * @return an iterator of the appropriate type, that is limited by the region
      */
-    public ReferenceIterator seek(GenomeLoc location) {
-        ReferenceIterator refSite = refIter.seekForward(location);
-        return refSite;
+    public BoundedReferenceIterator seek(GenomeLoc location) {
+        BoundedReferenceIterator ret = new BoundedReferenceIterator(refIter.seekForward(location), location);
+        return ret;
     }
 
-    /**
-     * Constructor - ReferenceDataSource
-     *
-     * @param refFileName the reference file
-     * @throws SimpleDataSourceLoadException
-     */
     public ReferenceDataSource(String refFileName) throws SimpleDataSourceLoadException {
         if (refFileName == null) {
             throw new SimpleDataSourceLoadException("ReferenceDataSource: refFileName passed in is null");
@@ -63,6 +58,7 @@ public class ReferenceDataSource implements SimpleDataSource {
         if (!infile.canRead()) {
             throw new SimpleDataSourceLoadException("ReferenceDataSource: Unable to load file: " + refFileName);
         }
+        //this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName);
         refFile = new FastaSequenceFile2(new File(refFileName));
         refIter = new ReferenceIterator(this.refFile);
 

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

@@ -0,0 +1,114 @@
+package org.broadinstitute.sting.gatk.iterators;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.Iterator;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 2, 2009
+ * Time: 2:12:12 PM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date Apr 2, 2009
+ * <p/>
+ * Class EnclosedIterator
+ * <p/>
+ * This class is a decorator class from Reference Iterator (though it is constrained
+ * by the fact that referenceIterator.seekForwardOffset explicitly returns a referenceIterator
+ * for now
+ * <p/>
+ * TODO: Fix the underlying iterator and this class to model a real decorator pattern
+ */
+public class BoundedReferenceIterator implements Iterator<ReferenceIterator> {
+    // the location to screen over
+    private final GenomeLoc mLoc;
+    private final ReferenceIterator referenceIterator;
+
+    /**
+     * Default constructor
+     *
+     * @param referenceIterator
+     * @param loc
+     */
+    public BoundedReferenceIterator(ReferenceIterator referenceIterator, GenomeLoc loc) {
+        this.referenceIterator = referenceIterator;
+        this.mLoc = loc;
+    }
+
+
+    /**
+     * isSubRegion
+     * <p/>
+     * returns true if we include the whole passed in region
+     *
+     * @param loc the genome region to check
+     * @return true if we include THE WHOLE specified region
+     */
+    protected boolean isSubRegion(GenomeLoc loc) {
+        // if the location is null, we assume we're all inclusive (we represent the whole genome).
+        if (mLoc == null || loc.isBetween(mLoc, mLoc)) {
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * returns true if we include the whole passed in region
+     *
+     * @param contig
+     * @param start
+     * @param stop
+     * @return true if we enclose the passed region, false otherwise
+     */
+    protected boolean isSubRegion(final String contig, final int start, final int stop) {
+        final GenomeLoc lc = new GenomeLoc(contig, start, stop);
+        return isSubRegion(lc);
+    }
+
+    /**
+     * If we're less then the limiting genomeLoc
+     *
+     * @param loc
+     * @return
+     */
+    protected boolean isLessThan(GenomeLoc loc) {
+        return loc.isPast(mLoc);
+    }
+
+
+    // our adapted next function
+    public boolean hasNext() {
+        // first check that we are within the search place
+        GenomeLoc loc = referenceIterator.getLocation();
+        if (!isSubRegion(loc)) {
+            return false;
+        }
+
+        return referenceIterator.hasNext();
+    }
+
+    public ReferenceIterator next() {
+        return referenceIterator.next();
+    }
+
+    public void remove() {
+        referenceIterator.remove();
+    }
+
+
+}