From a62bc6b05df021add322c13fb49b8e95d41c115f Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 9 Jun 2009 14:44:27 +0000 Subject: [PATCH] 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 --- .../sting/gatk/traversals/TraverseReads.java | 47 +++++++++++-------- 1 file changed, 28 insertions(+), 19 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 4646de4d9..f6046058a 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -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 the generic type - * @param 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 the map type of the walker + * @param the reduce type of the walker + * @return the reduce variable of the read walker */ public T traverse(Walker walker, Shard shard,