JAL-1619 refactoring / tests to support 'align linked dna as protein'

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

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 69555e6..f2c16d0 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,37 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.Vector;
-
 import jalview.util.MapList;
 
+import java.util.Vector;
+
 public class Mapping
 {
   /**
    * Contains the start-end pairs mapping from the associated sequence to the
-   * sequence in the database coordinate system it also takes care of step
-   * difference between coordinate systems
+   * sequence in the database coordinate system. It also takes care of step
+   * difference between coordinate systems.
    */
   MapList map = null;
 
   /**
-   * The seuqence that map maps the associated seuqence to (if any).
+   * The sequence that map maps the associated sequence to (if any).
    */
   SequenceI to = null;
 
@@ -108,19 +111,31 @@ public class Mapping
    * @param other
    * @return
    */
-  public boolean equals(Mapping other)
+  @Override
+  public boolean equals(Object o)
   {
-    if (other == null)
+    if (o == null || !(o instanceof Mapping))
+    {
       return false;
+    }
+    Mapping other = (Mapping) o;
     if (other == this)
+    {
       return true;
+    }
     if (other.to != to)
+    {
       return false;
+    }
     if ((map != null && other.map == null)
             || (map == null && other.map != null))
+    {
       return false;
+    }
     if (map.equals(other.map))
+    {
       return true;
+    }
     return false;
   }
 
@@ -248,7 +263,9 @@ public class Mapping
           vf[v].setBegin(frange[i]);
           vf[v].setEnd(frange[i + 1]);
           if (frange.length > 2)
+          {
             vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
+          }
         }
         return vf;
       }
@@ -297,14 +314,18 @@ public class Mapping
         from = (map.getToLowest() < from) ? from : map.getToLowest();
         to = (map.getToHighest() > to) ? to : map.getToHighest();
         if (from > to)
+        {
           return null;
+        }
       }
       else
       {
         from = (map.getToHighest() > from) ? from : map.getToHighest();
         to = (map.getToLowest() < to) ? to : map.getToLowest();
         if (from < to)
+        {
           return null;
+        }
       }
       return map.locateInFrom(from, to);
     }
@@ -330,14 +351,18 @@ public class Mapping
         from = (map.getFromLowest() < from) ? from : map.getFromLowest();
         to = (map.getFromHighest() > to) ? to : map.getFromHighest();
         if (from > to)
+        {
           return null;
+        }
       }
       else
       {
         from = (map.getFromHighest() > from) ? from : map.getFromHighest();
         to = (map.getFromLowest() < to) ? to : map.getFromLowest();
         if (from < to)
+        {
           return null;
+        }
       }
       return map.locateInTo(from, to);
     }