missed a file in the add.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@841 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategy.java

@@ -0,0 +1,134 @@
+package org.broadinstitute.sting.gatk.dataSources.shards;
+
+import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.util.Iterator;
+
+/*
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class ReadByIntervalShardStrategy
+ *         <p/>
+ *         Impliments the sharding strategy for reads, given a list
+ *         of genomic locations.  Shards returned will be bounded by the interval,
+ *         but each provided interval may be split into a number of smaller regions.
+ */
+public class IntervalShardStrategy implements ShardStrategy {
+
+    /** our storage of the genomic locations they'd like to shard over */
+    private final GenomeLocSortedSet regions;
+
+    /** their prefered size of the shard, we can modify this based on what we see in the shards */
+    private long size;
+
+    /**
+     * change the recommended shard size for the next shard we generate.  The code will do it's
+     * best to respect this value, but there are no guarantees.
+     *
+     * @param size the next recommended shard size.
+     */
+    public void adjustNextShardSize(long size) {
+        this.size = size;
+    }
+
+    /**
+     * construct the shard strategy from a seq dictionary, a shard size, and and genomeLocs
+     * @param size
+     * @param locations
+     */
+    IntervalShardStrategy(long size, GenomeLocSortedSet locations) {
+        if (locations == null || locations.isEmpty()) {
+            throw new StingException("IntervalShardStrategy: genomic regions list is empty.");
+        }
+        this.regions = locations.clone();
+        this.size = size;
+    }
+
+     /**
+     * the default constructor
+     *
+     * @param dict  the sequence dictionary to use
+     */
+    IntervalShardStrategy(SAMSequenceDictionary dict, GenomeLocSortedSet locations) {
+        if (locations == null || locations.isEmpty()) {
+            throw new StingException("IntervalShardStrategy: genomic regions list is empty.");
+        }
+        this.regions = locations.clone();
+        this.size = size;
+    }
+
+    /**
+     * returns true if there are additional shards
+     * @return false if we're done processing shards
+     */
+    public boolean hasNext() {
+        return (!regions.isEmpty());
+    }
+
+    /**
+     * gets the next Shard
+     * @return the next shard
+     */
+    public Shard next() {
+        if ((this.regions == null) || (regions.isEmpty())) {
+            throw new StingException("IntervalShardStrategy: genomic regions list is empty in next() function.");
+        }
+
+        // get the first region in the list
+        GenomeLoc loc = regions.iterator().next();
+
+        if (loc.getStop() - loc.getStart() <= this.size) {
+            regions.removeRegion(loc);
+            return new IntervalShard(loc);
+        } else {
+            GenomeLoc subLoc = new GenomeLoc(loc.getContigIndex(),loc.getStart(),loc.getStart()+size-1);
+            regions.removeRegion(subLoc);
+            return new IntervalShard(subLoc);
+        }
+        
+    }
+
+    /**
+     * we don't support the remove command
+     */
+    public void remove() {
+        throw new UnsupportedOperationException("ShardStrategies don't support remove()");
+    }
+
+    /**
+     * makes the ReadIntervalShard iterable, i.e. usable in a for loop.
+     * @return
+     */
+    public Iterator<Shard> iterator() {
+        return this;
+    }
+}