diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShardStrategy.java similarity index 91% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShard.java rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShardStrategy.java index 90180f02a..efc9d5159 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShard.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShardStrategy.java @@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary; *

* 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; } diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShardStrategy.java similarity index 90% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShard.java rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShardStrategy.java index 8287ea51f..c550d1157 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShard.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShardStrategy.java @@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary; *

* 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; } diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java index 9eeb3241c..3246a56ad 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java @@ -29,7 +29,7 @@ import java.util.Iterator; *

* The shard interface, which controls how data is divided */ -public abstract class Shard implements Iterator { +public abstract class ShardStrategy implements Iterator { // 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 { * * @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) { diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardFactory.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java similarity index 73% rename from java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardFactory.java rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java index 04ff96b3a..407604a08 100644 --- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardFactory.java +++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java @@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary; *

* 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); } }