removed old shard strategy code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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package org.broadinstitute.sting.gatk.dataSources.shards;
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import net.sf.samtools.SAMSequenceDictionary;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.List;
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/**
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*
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* User: aaron
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* Date: Apr 6, 2009
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* Time: 8:23:19 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date Apr 6, 2009
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* <p/>
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* Class LinearShard
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* <p/>
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* A exponential strategy
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*/
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public class ExpGrowthShardStrategy extends ShardStrategy {
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// fixed size
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private long baseSize = 100000;
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private long currentExp = 0;
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param dic the seq dictionary
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*/
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ExpGrowthShardStrategy(SAMSequenceDictionary dic, long startSize) {
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super(dic);
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this.baseSize = startSize;
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currentExp = 0;
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}
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param dic the seq dictionary
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*/
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ExpGrowthShardStrategy(SAMSequenceDictionary dic, long startSize, List<GenomeLoc> lst) {
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super(dic, lst);
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this.baseSize = startSize;
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currentExp = 0;
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}
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param strat the shatter to convert from
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*/
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ExpGrowthShardStrategy(ShardStrategy strat) {
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super(strat);
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this.baseSize = strat.nextShardSize();
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currentExp = 0;
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}
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/**
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* set the next shards size
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*
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* @param size adjust the next size to this
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*/
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public void adjustNextShardSize(long size) {
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baseSize = size;
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currentExp = 0;
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}
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/**
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* This is how the various shards strategies implements their approach
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*
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* @return the next shard size
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*/
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protected long nextShardSize() {
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// we grow the exponentially, we just have to make sure we start at zero
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++currentExp;
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return (long) Math.floor(Math.pow((double) baseSize, (double) currentExp));
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}
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}
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@ -1,87 +0,0 @@
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package org.broadinstitute.sting.gatk.dataSources.shards;
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import net.sf.samtools.SAMSequenceDictionary;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.List;
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/**
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*
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* User: aaron
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* Date: Apr 6, 2009
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* Time: 7:18:19 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date Apr 6, 2009
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* <p/>
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* Class AdaptiveShard
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* <p/>
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* allows you to change the sharding length as you traverse
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*/
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class LinearShardStrategy extends ShardStrategy {
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// default the next size to 100,000
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private long nextShardSize = 100000;
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param dic the seq dictionary
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*/
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LinearShardStrategy(SAMSequenceDictionary dic, long startSize) {
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super(dic);
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this.nextShardSize = startSize;
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}
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param strat the shatter to convert from
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*/
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LinearShardStrategy(ShardStrategy strat) {
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super(strat);
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this.nextShardSize = strat.nextShardSize();
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}
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/**
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* the constructor, taking a seq dictionary to parse out contigs
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*
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* @param dic the seq dictionary
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* @param lst the list of genome locations to iterate over
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*/
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LinearShardStrategy(SAMSequenceDictionary dic, long startSize, List<GenomeLoc> lst) {
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super(dic, lst);
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this.nextShardSize = startSize;
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}
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/**
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* set the next shards size
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*
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* @param size adjust the next size to this
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*/
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public void adjustNextShardSize(long size) {
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nextShardSize = size;
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}
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/**
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* This is how the various shards strategies implements their approach
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*
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* @return the next shard size
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*/
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protected long nextShardSize() {
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return nextShardSize;
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}
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}
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