Formatted source

[jalview.git] / src / jalview / datamodel / AlignmentOrder.java

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 3e6fd9f..c0da1fc 100755 (executable)
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -15,12 +15,12 @@
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
-package jalview.datamodel;
-
-import java.util.*;
-
+*/\r
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+\r
+\r
 /**
  * <p>Title: </p>
  *
@@ -32,105 +32,94 @@ import java.util.*;
  *
  * @author not attributable
  * @version 1.0
- */
-public class AlignmentOrder
-{
-  public AlignmentOrder()
-  {
-  }
-
-  public void setType(int Type)
-  {
-    this.Type = Type;
-  }
-
-  public int getType()
-  {
-    return Type;
-  }
-
-  public void setName(String Name)
-  {
-    this.Name = Name;
-  }
-
-  public String getName()
-  {
-    return Name;
-  }
-
-  public void setOrder(Vector Order)
-  {
-    this.Order = Order;
-  }
-
-  public Vector getOrder()
-  {
-
-    return Order;
-  }
-// JBPNote : this method would return a vector containing all sequences in seqset
-// with those also contained in order at the beginning of the vector in the order
-// given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
-// should be here for completeness.
-
-/*  public Vector getOrder(AlignmentI seqset)
+ */\r
+public class AlignmentOrder {\r
+    // JBPNote : this method would return a vector containing all sequences in seqset\r
+    // with those also contained in order at the beginning of the vector in the order\r
+    // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
+    // should be here for completeness.\r
+\r
+    /*  public Vector getOrder(AlignmentI seqset)
   {
     Vector perm = new Vector(seqset.getHeight());
     for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
       perm.setElement(i,...).
     return Order;
   }
- */
-  public static final int FILE = 0;
-  public static final int MSA = 1;
-  public static final int USER = 2;
-
-  private int Type = 0;
-  private String Name;
-  private Vector Order = null;
-
-  /**
-   * AlignmentOrder
-   *
-   * @param anOrder Vector
-   */
-  public AlignmentOrder(Vector anOrder)
-  {
-    Order = anOrder;
-  }
-
-  /**
-   * AlignmentOrder
-   *
-   * @param orderFrom AlignmentI
-   */
-  public AlignmentOrder(AlignmentI orderFrom)
-  {
-    Order = new Vector();
-
-    for (int i=0,ns=orderFrom.getHeight(); i<ns; i++)
-      Order.addElement(orderFrom.getSequenceAt(i));
-  }
-  public AlignmentOrder(SequenceI[] orderFrom) {
-    Order = new Vector();
-    for (int i=0,ns=orderFrom.length; i<ns; i++)
-      Order.addElement(orderFrom[i]);
-  }
-
-
-
-  /**
-   * AlignmentOrder
-   *
-   * @param orderThis AlignmentI
-   * @param byThat AlignmentI
-   */
-  /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
-  {
-    // Vector is an ordering of this alignment using the order of sequence objects in byThat,
-    // where ids and unaligned sequences must match
-
-  } */
+ */\r
+    public static final int FILE = 0;\r
+    public static final int MSA = 1;\r
+    public static final int USER = 2;\r
+    private int Type = 0;\r
+    private String Name;\r
+    private Vector Order = null;\r
+\r
+    public AlignmentOrder() {\r
+    }\r
+\r
+    /**
+ * AlignmentOrder
+ *
+ * @param anOrder Vector
+ */\r
+    public AlignmentOrder(Vector anOrder) {\r
+        Order = anOrder;\r
+    }\r
+\r
+    /**
+ * AlignmentOrder
+ *
+ * @param orderFrom AlignmentI
+ */\r
+    public AlignmentOrder(AlignmentI orderFrom) {\r
+        Order = new Vector();\r
+\r
+        for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)\r
+            Order.addElement(orderFrom.getSequenceAt(i));\r
+    }\r
+\r
+    public AlignmentOrder(SequenceI[] orderFrom) {\r
+        Order = new Vector();\r
+\r
+        for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
+            Order.addElement(orderFrom[i]);\r
+    }\r
+\r
+    public void setType(int Type) {\r
+        this.Type = Type;\r
+    }\r
+\r
+    public int getType() {\r
+        return Type;\r
+    }\r
+\r
+    public void setName(String Name) {\r
+        this.Name = Name;\r
+    }\r
+\r
+    public String getName() {\r
+        return Name;\r
+    }\r
+\r
+    public void setOrder(Vector Order) {\r
+        this.Order = Order;\r
+    }\r
+\r
+    public Vector getOrder() {\r
+        return Order;\r
+    }\r
+\r
+    /**
+ * AlignmentOrder
+ *
+ * @param orderThis AlignmentI
+ * @param byThat AlignmentI
+ */\r
+\r
+    /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
+{
+  // Vector is an ordering of this alignment using the order of sequence objects in byThat,
+  // where ids and unaligned sequences must match
 
-}
+} */\r
+}\r