renamed; these files are more strategy than actual shards

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@312 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-class AdaptiveShard extends Shard {
+class AdaptiveShardStrategy extends ShardStrategy {
 
     // default the next size to 100,000
     private long nextShardSize = 100000;
@@ -38,7 +38,7 @@ class AdaptiveShard extends Shard {
      *
      * @param dic the seq dictionary
      */
-    AdaptiveShard(SAMSequenceDictionary dic, long startSize) {
+    AdaptiveShardStrategy(SAMSequenceDictionary dic, long startSize) {
         super(dic);
         this.nextShardSize = startSize;
     }

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

@@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-public class LinearShard extends Shard {
+public class LinearShardStrategy extends ShardStrategy {
 
     // fixed size
     private long nextShardSize = 100000;
@@ -38,7 +38,7 @@ public class LinearShard extends Shard {
      *
      * @param dic the seq dictionary
      */
-    LinearShard(SAMSequenceDictionary dic, long startSize) {
+    LinearShardStrategy(SAMSequenceDictionary dic, long startSize) {
         super(dic);
         this.nextShardSize = startSize;
     }

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

@@ -29,7 +29,7 @@ import java.util.Iterator;
  * <p/>
  * The shard interface, which controls how data is divided
  */
-public abstract class Shard implements Iterator<GenomeLoc> {
+public abstract class ShardStrategy implements Iterator<GenomeLoc> {
 
     // this stores the seq dictionary, which is a reference for the
     // lengths and names of contigs, which you need to generate an iterative stratagy
@@ -53,7 +53,7 @@ public abstract class Shard implements Iterator<GenomeLoc> {
      *
      * @param dic the seq dictionary
      */
-    Shard(SAMSequenceDictionary dic) {
+    ShardStrategy(SAMSequenceDictionary dic) {
         this.dic = dic;
         mLoc = new GenomeLoc(dic.getSequence(0).getSequenceName(), 0, 0);
         if (dic.getSequences().size() > 0) {

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

@@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-public class ShardFactory {
+public class ShardStrategyFactory {
     public enum SHATTER_STRATEGY {
         ADAPTIVE, LINEAR
     }
@@ -41,13 +41,13 @@ public class ShardFactory {
      * @param startingSize the starting size
      * @return
      */
-    static public Shard shatter(SHATTER_STRATEGY strat, SAMSequenceDictionary dic, long startingSize) {
-        Shard d = null;
+    static public ShardStrategy shatter(SHATTER_STRATEGY strat, SAMSequenceDictionary dic, long startingSize) {
+        ShardStrategy d = null;
         switch (strat) {
             case ADAPTIVE:
-                d = new AdaptiveShard(dic, startingSize);
+                d = new AdaptiveShardStrategy(dic, startingSize);
             default:
-                d = new LinearShard(dic, startingSize); // default
+                d = new LinearShardStrategy(dic, startingSize); // default
         }
         return d;
     }
@@ -59,8 +59,8 @@ public class ShardFactory {
      * @param startingSize the starting size
      * @return
      */
-    static public AdaptiveShard getAdaptiveShard(SAMSequenceDictionary dic, long startingSize) {
-        return new AdaptiveShard(dic, startingSize);
+    static public AdaptiveShardStrategy getAdaptiveShard(SAMSequenceDictionary dic, long startingSize) {
+        return new AdaptiveShardStrategy(dic, startingSize);
     }
 
 }