X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=177d373dc77e70daa02a77e1187b7284d2000236;hb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;hp=18fa20c85fb6f6deb4800300ec684fdf32e6a2eb;hpb=5711da5558bce5aa7c96837fd6cb9b49a914c231;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 18fa20c..177d373 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -5,6 +5,25 @@
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
  */
 
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* 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 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.
+*
+* 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 vamsas.objects.simple;
 
 public class Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
@@ -27,7 +46,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Gets the gapchar value for this Alignment.
-     * 
+     *
      * @return gapchar
      */
     public java.lang.String getGapchar() {
@@ -37,7 +56,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Sets the gapchar value for this Alignment.
-     * 
+     *
      * @param gapchar
      */
     public void setGapchar(java.lang.String gapchar) {
@@ -47,7 +66,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Gets the method value for this Alignment.
-     * 
+     *
      * @return method
      */
     public java.lang.String[] getMethod() {
@@ -57,7 +76,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Sets the method value for this Alignment.
-     * 
+     *
      * @param method
      */
     public void setMethod(java.lang.String[] method) {
@@ -67,7 +86,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Gets the seqs value for this Alignment.
-     * 
+     *
      * @return seqs
      */
     public vamsas.objects.simple.SequenceSet getSeqs() {
@@ -77,7 +96,7 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
 
     /**
      * Sets the seqs value for this Alignment.
-     * 
+     *
      * @param seqs
      */
     public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
@@ -95,14 +114,14 @@ public class Alignment  extends vamsas.objects.simple.Object  implements java.io
         }
         __equalsCalc = obj;
         boolean _equals;
-        _equals = super.equals(obj) && 
-            ((this.gapchar==null && other.getGapchar()==null) || 
+        _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 && other.getMethod()==null) ||
              (this.method!=null &&
               java.util.Arrays.equals(this.method, other.getMethod()))) &&
-            ((this.seqs==null && other.getSeqs()==null) || 
+            ((this.seqs==null && other.getSeqs()==null) ||
              (this.seqs!=null &&
               this.seqs.equals(other.getSeqs())));
         __equalsCalc = null;