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

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java

@@ -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) {

java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java

@@ -31,10 +31,11 @@ import net.sf.samtools.SAMRecord;
 
 /**
  * @author aaron
- *         <p/>
+ *
- *         Class ArtificialPatternedSAMIterator
+ *  Class ArtificialPatternedSAMIterator
- *         <p/>
+ *
- *         A descriptions should go here. Blame aaron if it's missing.
+ * 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[0] = reads[reads.length - 1];
-                reads[reads.length -1] = temp;    
+                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() {
@@ -126,7 +128,9 @@ 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
      */
     private SAMRecord getNextRecord( int read ) {

java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java

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

java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java

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

java/test/org/broadinstitute/sting/TrivialInstrumenter.java

@@ -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
+ * Permission is hereby granted, free of charge, to any person
- * Date: May 5, 2009
+ * obtaining a copy of this software and associated documentation
- * Time: 4:27:04 PM
+ * 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
+ * The above copyright notice and this permission notice shall be
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * included in all copies or substantial portions of the Software.
- * 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 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! */

java/test/org/broadinstitute/sting/gatk/GATKArgumentCollectionTest.java

@@ -13,23 +13,31 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-/**
+/*
+ * Copyright (c) 2009 The Broad Institute
  *
- * User: aaron
+ * Permission is hereby granted, free of charge, to any person
- * Date: May 7, 2009
+ * obtaining a copy of this software and associated documentation
- * Time: 1:12:58 PM
+ * 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
+ * The above copyright notice and this permission notice shall be
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * included in all copies or substantial portions of the Software.
- * 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 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 {
 

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java

@@ -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 {