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fixed some documentation and attached a correct license 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@953 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-09 14:44:27 +00:00
parent bf6190b471
commit a62bc6b05d
1 changed files with 28 additions and 19 deletions
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47
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -20,23 +20,31 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
/*
* Copyright (c) 2009 The Broad Institute
*
* User: aaron
* Date: Apr 24, 2009
* Time: 10:35:22 AM
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* @author aaron
* @version 1.0
@ -67,13 +75,14 @@ public class TraverseReads extends TraversalEngine {
/**
* Traverse by reads, given the data and the walker
*
* @param walker the walker to execute over
* @param shard the shard of data to feed the walker
* @param sum of type T, the return from the walker
* @param <M> the generic type
* @param <T> the return type of the reduce function
* @return
*
* @param walker the walker to traverse with
* @param shard the shard, specifying the range of data to iterate over
* @param dataProvider the provider of the reads data
* @param sum the value of type T, specified by the walker, to feed to the walkers reduce function
* @param <M> the map type of the walker
* @param <T> the reduce type of the walker
* @return the reduce variable of the read walker
*/
public <M, T> T traverse(Walker<M, T> walker,
Shard shard,