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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
This commit is contained in:
aaron 2009-04-07 16:50:56 +00:00
parent e95f427965
commit 6369d23b43
4 changed files with 13 additions and 13 deletions
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4
java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShard.java → java/src/org/broadinstitute/sting/gatk/dataSources/shards/AdaptiveShardStrategy.java
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@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
* <p/> * <p/>
* A descriptions should go here. Blame aaron if it's missing. * 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 // default the next size to 100,000
private long nextShardSize = 100000; private long nextShardSize = 100000;
@ -38,7 +38,7 @@ class AdaptiveShard extends Shard {
* *
* @param dic the seq dictionary * @param dic the seq dictionary
*/ */
AdaptiveShard(SAMSequenceDictionary dic, long startSize) { AdaptiveShardStrategy(SAMSequenceDictionary dic, long startSize) {
super(dic); super(dic);
this.nextShardSize = startSize; this.nextShardSize = startSize;
} }

4
java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShard.java → java/src/org/broadinstitute/sting/gatk/dataSources/shards/LinearShardStrategy.java
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@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
* <p/> * <p/>
* A descriptions should go here. Blame aaron if it's missing. * A descriptions should go here. Blame aaron if it's missing.
*/ */
public class LinearShard extends Shard { public class LinearShardStrategy extends ShardStrategy {
// fixed size // fixed size
private long nextShardSize = 100000; private long nextShardSize = 100000;
@ -38,7 +38,7 @@ public class LinearShard extends Shard {
* *
* @param dic the seq dictionary * @param dic the seq dictionary
*/ */
LinearShard(SAMSequenceDictionary dic, long startSize) { LinearShardStrategy(SAMSequenceDictionary dic, long startSize) {
super(dic); super(dic);
this.nextShardSize = startSize; this.nextShardSize = startSize;
} }

4
java/src/org/broadinstitute/sting/gatk/dataSources/shards/Shard.java → java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategy.java
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@ -29,7 +29,7 @@ import java.util.Iterator;
* <p/> * <p/>
* The shard interface, which controls how data is divided * 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 // this stores the seq dictionary, which is a reference for the
// lengths and names of contigs, which you need to generate an iterative stratagy // 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 * @param dic the seq dictionary
*/ */
Shard(SAMSequenceDictionary dic) { ShardStrategy(SAMSequenceDictionary dic) {
this.dic = dic; this.dic = dic;
mLoc = new GenomeLoc(dic.getSequence(0).getSequenceName(), 0, 0); mLoc = new GenomeLoc(dic.getSequence(0).getSequenceName(), 0, 0);
if (dic.getSequences().size() > 0) { if (dic.getSequences().size() > 0) {

14
java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardFactory.java → java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java
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@ -28,7 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
* <p/> * <p/>
* A descriptions should go here. Blame aaron if it's missing. * A descriptions should go here. Blame aaron if it's missing.
*/ */
public class ShardFactory { public class ShardStrategyFactory {
public enum SHATTER_STRATEGY { public enum SHATTER_STRATEGY {
ADAPTIVE, LINEAR ADAPTIVE, LINEAR
} }
@ -41,13 +41,13 @@ public class ShardFactory {
* @param startingSize the starting size * @param startingSize the starting size
* @return * @return
*/ */
static public Shard shatter(SHATTER_STRATEGY strat, SAMSequenceDictionary dic, long startingSize) { static public ShardStrategy shatter(SHATTER_STRATEGY strat, SAMSequenceDictionary dic, long startingSize) {
Shard d = null; ShardStrategy d = null;
switch (strat) { switch (strat) {
case ADAPTIVE: case ADAPTIVE:
d = new AdaptiveShard(dic, startingSize); d = new AdaptiveShardStrategy(dic, startingSize);
default: default:
d = new LinearShard(dic, startingSize); // default d = new LinearShardStrategy(dic, startingSize); // default
} }
return d; return d;
} }
@ -59,8 +59,8 @@ public class ShardFactory {
* @param startingSize the starting size * @param startingSize the starting size
* @return * @return
*/ */
static public AdaptiveShard getAdaptiveShard(SAMSequenceDictionary dic, long startingSize) { static public AdaptiveShardStrategy getAdaptiveShard(SAMSequenceDictionary dic, long startingSize) {
return new AdaptiveShard(dic, startingSize); return new AdaptiveShardStrategy(dic, startingSize);
} }
} }