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fixed a bunch of comments and license headers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-10 14:10:46 +00:00
parent 6bb7f7e9d8
commit ec2f015447
7 changed files with 116 additions and 73 deletions
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43
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java
View File

@ -1,23 +1,34 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
import org.broadinstitute.sting.utils.StingException;
/**
*
* User: aaron
* Date: Apr 1, 2009
* Time: 11:08:06 AM
*
* 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.
*
*/
/*
* Copyright (c) 2009 The Broad Institute
*
* 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 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
@ -26,7 +37,7 @@ import org.broadinstitute.sting.utils.StingException;
* <p/>
* Class SimpleDataSourceSplitFailure
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
* an exception that get's thrown if we can't split up a data source appropriately
*/
public class SimpleDataSourceSplitException extends StingException {
public SimpleDataSourceSplitException(String msg) {

20
java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
View File

@ -31,10 +31,11 @@ import net.sf.samtools.SAMRecord;
/**
* @author aaron
* <p/>
* Class ArtificialPatternedSAMIterator
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*
* Class ArtificialPatternedSAMIterator
*
* This class allows you to pattern the artificial sam iterator, asking for reads
* in order or out of order.
*/
public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
@ -85,10 +86,10 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
* up to this point there's no garauntee that the random() has made the reads out of order (though it's
* extremely extremely unlikely it's failed). Let's make sure there at least out of order:
*/
if (this.reads[0] < this.reads[reads.length -1]) {
if (this.reads[0] < this.reads[reads.length - 1]) {
int temp = reads[0];
reads[0] = reads[reads.length -1];
reads[reads.length -1] = temp;
reads[0] = reads[reads.length - 1];
reads[reads.length - 1] = temp;
}
}
@ -97,6 +98,7 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
/**
* override the default ArtificialSAMIterator createNextRead method, which creates the next read
*
* @return
*/
protected boolean createNextRead() {
@ -126,8 +128,10 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
/**
* get the next read, given it's index in the chromosome
*
* @param read the read index in the chromosome
* @return a SAMRecord
*
* @return a SAMRecord
*/
private SAMRecord getNextRecord( int read ) {
if (read > this.readCount) {

6
java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
View File

@ -43,10 +43,8 @@ import net.sf.samtools.SAMFileHeader;
/**
* @author aaron
* <p/>
* Class ArtificialReadsTraversal
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*
* this class acts as a fake reads traversal engine for testing out reads based traversals.
*/
public class ArtificialReadsTraversal extends TraversalEngine {

8
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
View File

@ -36,10 +36,10 @@ import org.broadinstitute.sting.utils.StingException;
/**
* @author aaron
* <p/>
* Class ArtificialSAMQueryIterator
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*
* allows query calls to the artificial sam iterator, which allows you
* to test out classes that use specific itervals. The reads returned will
* all lie in order in the specified interval.
*/
public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {

36
java/test/org/broadinstitute/sting/TrivialInstrumenter.java
View File

@ -8,23 +8,35 @@ import java.lang.instrument.ClassFileTransformer;
import java.lang.instrument.IllegalClassFormatException;
import java.lang.instrument.Instrumentation;
/**
/*
* Copyright (c) 2009 The Broad Institute
*
* User: aaron
* Date: May 5, 2009
* Time: 4:27:04 PM
* 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
@ -32,7 +44,7 @@ import java.lang.instrument.Instrumentation;
* <p/>
* Class TrivalInstrumenter
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
* A simple instrumentation class, that adds information to our test cases.
*/
/** A trivial example program that basically just says hello! */

34
java/test/org/broadinstitute/sting/gatk/GATKArgumentCollectionTest.java
View File

@ -13,23 +13,31 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
/*
* Copyright (c) 2009 The Broad Institute
*
* User: aaron
* Date: May 7, 2009
* Time: 1:12:58 PM
* 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
@ -37,7 +45,7 @@ import java.util.Map;
* <p/>
* Class GATKArgumentCollection
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
* Test out the argument collection class
*/
public class GATKArgumentCollectionTest extends BaseTest {

42
java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java
View File

@ -20,23 +20,33 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
/**
*
* User: aaron
* Date: Apr 14, 2009
* Time: 5:48:48 PM
*
* 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.
*
*/
/*
* Copyright (c) 2009 The Broad Institute
*
* 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 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
@ -44,7 +54,7 @@ import java.util.List;
* <p/>
* Class BoundedReadIteratorTest
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
* tests for the bounded read iterator.
*/
public class BoundedReadIteratorTest extends BaseTest {