removed the dependence on removeRegion() in GenomeLocSortedSet

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -94,7 +94,7 @@ public class IntervalShardStrategy implements ShardStrategy {
         // get the first region in the list
         GenomeLoc loc = regions.iterator().next();
 
-        regions.removeRegion(loc);
+        regions.remove(loc);
         return new IntervalShard(loc,type);
 
     }

java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java

@@ -62,7 +62,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
      *
      * @param dic the seq dictionary
      */
-    LocusShardStrategy( SAMSequenceDictionary dic ) {
+    LocusShardStrategy(SAMSequenceDictionary dic) {
         this.dic = dic;
         limitingFactor = -1;
         mLoc = GenomeLocParser.createGenomeLoc(0, 0, 0);
@@ -76,7 +76,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
      *
      * @param old the old strategy
      */
-    LocusShardStrategy( LocusShardStrategy old ) {
+    LocusShardStrategy(LocusShardStrategy old) {
         this.dic = old.dic;
         this.mLoc = old.mLoc;
         this.seqLoc = old.seqLoc;
@@ -92,7 +92,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
      * @param dic       the seq dictionary
      * @param intervals file
      */
-    LocusShardStrategy( SAMSequenceDictionary dic, GenomeLocSortedSet intervals ) {
+    LocusShardStrategy(SAMSequenceDictionary dic, GenomeLocSortedSet intervals) {
         this.dic = dic;
         this.intervals = intervals.clone();
         // set the starting point to the beginning interval
@@ -152,7 +152,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
         if (this.intervals == null) {
             return nonIntervaledNext(length, proposedSize, nextStart);
         } else {
-            return intervaledNext(proposedSize);
+            return intervaledNext();
         }
 
     }
@@ -160,26 +160,20 @@ public abstract class LocusShardStrategy implements ShardStrategy {
     /**
      * Interval based next processing
      *
-     * @param proposedSize the proposed size
      *
      * @return the shard that represents this data
      */
-    private Shard intervaledNext( long proposedSize ) {
-        if (( this.intervals == null ) || ( intervals.isEmpty() )) {
+    private Shard intervaledNext() {
+        if ((this.intervals == null) || (intervals.isEmpty())) {
             throw new StingException("LocusShardStrategy: genomic regions list is empty in next() function.");
         }
 
         // get the first region in the list
         GenomeLoc loc = intervals.iterator().next();
 
-        if (loc.getStop() - loc.getStart() <= proposedSize) {
-            intervals.removeRegion(loc);
-            return new IntervalShard(loc,Shard.ShardType.LOCUS_INTERVAL);
-        } else {
-            GenomeLoc subLoc = GenomeLocParser.createGenomeLoc(loc.getContigIndex(), loc.getStart(), loc.getStart() + proposedSize - 1);
-            intervals.removeRegion(subLoc);
-            return new IntervalShard(subLoc,Shard.ShardType.LOCUS_INTERVAL);
-        }
+        intervals.remove(loc);
+        return new IntervalShard(loc, Shard.ShardType.LOCUS_INTERVAL);
+
     }
 
     /**
@@ -191,7 +185,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
      *
      * @return the shard to return to the user
      */
-    private Shard nonIntervaledNext( long length, long proposedSize, long nextStart ) {
+    private Shard nonIntervaledNext(long length, long proposedSize, long nextStart) {
         // can we fit it into the current seq size?
         if (nextStart + proposedSize - 1 < length) {
             lastGenomeLocSize = proposedSize;
@@ -223,7 +217,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
     private void jumpContig() {
         ++seqLoc;
 
-        if (!( seqLoc < dic.getSequences().size() )) {
+        if (!(seqLoc < dic.getSequences().size())) {
             nextContig = false;
             return;
         }
@@ -246,7 +240,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
         if (this.intervals == null) {
             return nextContig;
         } else {
-            return ( this.intervals.size() > 0 );
+            return (this.intervals.size() > 0);
         }
     }
 

java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java

@@ -223,6 +223,15 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         return returnValue;
     }
 
+    /**
+     * a simple removal of an interval contained in this list.  The interval must be identical to one in the list (no partial locations or overlapping)
+     * @param location the GenomeLoc to remove
+     */
+    public void remove(GenomeLoc location) {
+        if (!mArray.contains(location)) throw new IllegalArgumentException("Unable to remove location: " + location + ", not in the list");
+        mArray.remove(location);
+    }
+
     /**
      * create a list of genomic locations, given a reference sequence
      *

java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java

@@ -113,7 +113,7 @@ public class LinearLocusShardStrategyTest extends BaseTest {
             Shard d = strat.next();
             assertTrue(d instanceof LocusShard);
             assertEquals("Sharding strategy must emit single locus shards",1,d.getGenomeLocs().size());
-            assertTrue((d.getGenomeLocs().get(0).getStop() - d.getGenomeLocs().get(0).getStart()) == 199);
+            assertEquals(199,(d.getGenomeLocs().get(0).getStop() - d.getGenomeLocs().get(0).getStart()));
             ++counter;
         }
         assertTrue(counter == 1);