X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=82df8bd506da3b1c0d910c0490acd98b3e45c3ba;hb=42e022a59de649375c8878c1d26361cb6bc89cb8;hp=9072c41c2e606eeaf3c8c182b2a01177b1015a81;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 9072c41..82df8bd 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,25 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package vamsas.objects.simple;
 
-public class Alignment extends vamsas.objects.simple.Object implements
-        java.io.Serializable
+public class Alignment extends vamsas.objects.simple.Object
+        implements java.io.Serializable
 {
   private java.lang.String gapchar;
 
@@ -101,15 +103,22 @@ public class Alignment extends vamsas.objects.simple.Object implements
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof Alignment))
+    {
       return false;
+    }
     Alignment other = (Alignment) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -117,18 +126,22 @@ public class Alignment extends vamsas.objects.simple.Object implements
     __equalsCalc = obj;
     boolean _equals;
     _equals = super.equals(obj)
-            && ((this.gapchar == null && other.getGapchar() == null) || (this.gapchar != null && this.gapchar
-                    .equals(other.getGapchar())))
-            && ((this.method == null && other.getMethod() == null) || (this.method != null && java.util.Arrays
-                    .equals(this.method, other.getMethod())))
-            && ((this.seqs == null && other.getSeqs() == null) || (this.seqs != null && this.seqs
-                    .equals(other.getSeqs())));
+            && ((this.gapchar == null && other.getGapchar() == null)
+                    || (this.gapchar != null
+                            && this.gapchar.equals(other.getGapchar())))
+            && ((this.method == null && other.getMethod() == null)
+                    || (this.method != null && java.util.Arrays
+                            .equals(this.method, other.getMethod())))
+            && ((this.seqs == null && other.getSeqs() == null)
+                    || (this.seqs != null
+                            && this.seqs.equals(other.getSeqs())));
     __equalsCalc = null;
     return _equals;
   }
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)
@@ -143,7 +156,8 @@ public class Alignment extends vamsas.objects.simple.Object implements
     }
     if (getMethod() != null)
     {
-      for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod()); i++)
+      for (int i = 0; i < java.lang.reflect.Array
+              .getLength(getMethod()); i++)
       {
         java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
         if (obj != null && !obj.getClass().isArray())