X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=9d47b6ae179720a5f9a8128b62f807bf29230c09;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=7328cbd8a6c452538dd8c975b39bde8d26b8ce61;hpb=357598ffdf5c04f08a2a370218f0e22551ee9231;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 7328cbd..9d47b6a 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,177 +1,173 @@
-/**
- * Alignment.java
- *
- * This file was auto-generated from WSDL
- * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
+/*
+ * 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.
+ *  
+ * 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/>.
+ * 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 {
-    private java.lang.String gapchar;
-    private java.lang.String[] method;
-    private vamsas.objects.simple.SequenceSet seqs;
-    private vamsas.objects.simple.Sequence[] seqsAsArray;
-
-    public Alignment() {
-    }
-
-    public Alignment(
-           java.lang.String gapchar,
-           java.lang.String[] method,
-           vamsas.objects.simple.SequenceSet seqs,
-           vamsas.objects.simple.Sequence[] seqsAsArray) {
-           this.gapchar = gapchar;
-           this.method = method;
-           this.seqs = seqs;
-           this.seqsAsArray = seqsAsArray;
+public class Alignment extends vamsas.objects.simple.Object implements
+        java.io.Serializable
+{
+  private java.lang.String gapchar;
+
+  private java.lang.String[] method;
+
+  private vamsas.objects.simple.SequenceSet seqs;
+
+  public Alignment()
+  {
+  }
+
+  public Alignment(java.lang.String gapchar, java.lang.String[] method,
+          vamsas.objects.simple.SequenceSet seqs)
+  {
+    this.gapchar = gapchar;
+    this.method = method;
+    this.seqs = seqs;
+  }
+
+  /**
+   * Gets the gapchar value for this Alignment.
+   * 
+   * @return gapchar
+   */
+  public java.lang.String getGapchar()
+  {
+    return gapchar;
+  }
+
+  /**
+   * Sets the gapchar value for this Alignment.
+   * 
+   * @param gapchar
+   */
+  public void setGapchar(java.lang.String gapchar)
+  {
+    this.gapchar = gapchar;
+  }
+
+  /**
+   * Gets the method value for this Alignment.
+   * 
+   * @return method
+   */
+  public java.lang.String[] getMethod()
+  {
+    return method;
+  }
+
+  /**
+   * Sets the method value for this Alignment.
+   * 
+   * @param method
+   */
+  public void setMethod(java.lang.String[] method)
+  {
+    this.method = method;
+  }
+
+  /**
+   * Gets the seqs value for this Alignment.
+   * 
+   * @return seqs
+   */
+  public vamsas.objects.simple.SequenceSet getSeqs()
+  {
+    return seqs;
+  }
+
+  /**
+   * Sets the seqs value for this Alignment.
+   * 
+   * @param seqs
+   */
+  public void setSeqs(vamsas.objects.simple.SequenceSet seqs)
+  {
+    this.seqs = seqs;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+
+  @Override
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (obj == null)
+    {
+      return false;
     }
-
-
-    /**
-     * Gets the gapchar value for this Alignment.
-     * 
-     * @return gapchar
-     */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-
-    /**
-     * Sets the gapchar value for this Alignment.
-     * 
-     * @param gapchar
-     */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-
-    /**
-     * Gets the method value for this Alignment.
-     * 
-     * @return method
-     */
-    public java.lang.String[] getMethod() {
-        return method;
-    }
-
-
-    /**
-     * Sets the method value for this Alignment.
-     * 
-     * @param method
-     */
-    public void setMethod(java.lang.String[] method) {
-        this.method = method;
+    if (!(obj instanceof Alignment))
+    {
+      return false;
     }
-
-
-    /**
-     * Gets the seqs value for this Alignment.
-     * 
-     * @return seqs
-     */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
+    Alignment other = (Alignment) obj;
+    if (this == obj)
+    {
+      return true;
     }
-
-
-    /**
-     * Sets the seqs value for this Alignment.
-     * 
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-
-    /**
-     * Gets the seqsAsArray value for this Alignment.
-     * 
-     * @return seqsAsArray
-     */
-    public vamsas.objects.simple.Sequence[] getSeqsAsArray() {
-        return seqsAsArray;
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+
+  @Override
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
-
-
-    /**
-     * Sets the seqsAsArray value for this Alignment.
-     * 
-     * @param seqsAsArray
-     */
-    public void setSeqsAsArray(vamsas.objects.simple.Sequence[] seqsAsArray) {
-        this.seqsAsArray = seqsAsArray;
+    __hashCodeCalc = true;
+    int _hashCode = super.hashCode();
+    if (getGapchar() != null)
+    {
+      _hashCode += getGapchar().hashCode();
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        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);
+    if (getMethod() != null)
+    {
+      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())
+        {
+          _hashCode += obj.hashCode();
         }
-        __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.seqsAsArray==null && other.getSeqsAsArray()==null) || 
-             (this.seqsAsArray!=null &&
-              java.util.Arrays.equals(this.seqsAsArray, other.getSeqsAsArray())));
-        __equalsCalc = null;
-        return _equals;
+      }
     }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
-        if (getMethod() != null) {
-            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()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getSeqs() != null) {
-            _hashCode += getSeqs().hashCode();
-        }
-        if (getSeqsAsArray() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getSeqsAsArray());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getSeqsAsArray(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+    if (getSeqs() != null)
+    {
+      _hashCode += getSeqs().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }