Moved phasing-specific utilities to phasing sub-directory

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4987 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/phasing/DoublyLinkedList.java

@@ -1,7 +1,3 @@
-package org.broadinstitute.sting.utils;
-
-import java.util.NoSuchElementException;
-
 /*
  * Copyright (c) 2010, The Broad Institute
  *
@@ -25,6 +21,9 @@ import java.util.NoSuchElementException;
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import java.util.NoSuchElementException;
 
 public class DoublyLinkedList<E> {
     private DoublyLinkedNode<E> first;

java/src/org/broadinstitute/sting/gatk/walkers/phasing/Graph.java

@@ -1,10 +1,3 @@
-package org.broadinstitute.sting.utils;
-
-import org.broadinstitute.sting.utils.DisjointSet;
-import org.broadinstitute.sting.utils.GraphEdge;
-
-import java.util.*;
-
 /*
  * Copyright (c) 2010, The Broad Institute
  *
@@ -28,6 +21,11 @@ import java.util.*;
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.broadinstitute.sting.utils.DisjointSet;
+
+import java.util.*;
 
 // Represents an undirected graph with no self-edges:
 public class Graph implements Iterable<GraphEdge> {

java/src/org/broadinstitute/sting/gatk/walkers/phasing/GraphEdge.java

@@ -1,5 +1,3 @@
-package org.broadinstitute.sting.utils;
-
 /*
  * Copyright (c) 2010, The Broad Institute
  *
@@ -23,6 +21,7 @@ package org.broadinstitute.sting.utils;
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 public class GraphEdge implements Comparable<GraphEdge> {
     protected int v1;

java/src/org/broadinstitute/sting/utils/CardinalityCounter.java

@@ -1,17 +1,32 @@
+/*
+ * Copyright (c) 2010, 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.
+ */
 package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 
-/**
- * Created by IntelliJ IDEA.
- * User: fromer
- * Date: Aug 19, 2010
- * Time: 9:33:54 AM
- * To change this template use File | Settings | File Templates.
- */
-
 /*
 * CardinalityCounter object allows user to iterate over all assignment of arbitrary-cardinality variables.
  */

java/src/org/broadinstitute/sting/utils/DisjointSet.java

@@ -1,7 +1,3 @@
-package org.broadinstitute.sting.utils;
-
-import java.util.*;
-
 /*
  * Copyright (c) 2010, The Broad Institute
  *
@@ -25,6 +21,9 @@ import java.util.*;
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
+package org.broadinstitute.sting.utils;
+
+import java.util.*;
 
 public class DisjointSet {
     private ItemNode[] nodes;

java/src/org/broadinstitute/sting/utils/PreciseNonNegativeDouble.java

@@ -1,12 +1,27 @@
-package org.broadinstitute.sting.utils;
+/*
-
+ * Copyright (c) 2010, The Broad Institute
-/**
+ *
- * Created by IntelliJ IDEA.
+ * Permission is hereby granted, free of charge, to any person
- * User: fromer
+ * obtaining a copy of this software and associated documentation
- * Date: Aug 18, 2010
+ * files (the "Software"), to deal in the Software without
- * Time: 4:55:23 PM
+ * restriction, including without limitation the rights to use,
- * To change this template use File | Settings | File Templates.
+ * 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.
  */
+package org.broadinstitute.sting.utils;
 
 /* PreciseNonNegativeDouble permits arithmetic operations on NON-NEGATIVE double values
    with precision (prevents underflow by representing in log10 space).