X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=82df8bd506da3b1c0d910c0490acd98b3e45c3ba;hb=42e022a59de649375c8878c1d26361cb6bc89cb8;hp=1ed69a4e29c38632d62ee10ae67022798ec7e40b;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 1ed69a4..82df8bd 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,8 @@
  */
 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;
 
@@ -126,12 +126,15 @@ 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;
   }
@@ -153,7 +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())