X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=82df8bd506da3b1c0d910c0490acd98b3e45c3ba;hb=72a9ef4b4e3763c857ef095eadc8c656ccb441ff;hp=27d233d620724e5c498213e4f9c874c94c1d9ab3;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 27d233d..82df8bd 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,24 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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;
@@ -100,15 +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);
@@ -116,18 +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)
@@ -142,7 +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())