X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=38c10795160deaadc556641e07be73a20e9572c1;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=bd9adfa152155a280f2c9693cfea703c77235305;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index bd9adfa..38c1079 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,189 +1,162 @@
-/**
- * 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
- * Copyright (C) 2007 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
-{
-  private java.lang.String gapchar;
-  private java.lang.String[] method;
-  private vamsas.objects.simple.SequenceSet seqs;
-  private java.lang.Object __equalsCalc = null;
-  private boolean __hashCodeCalc = false;
-
-  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;
-  }
-
-  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);
-    }
-
-    __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;
-  }
-
-  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();
-    }
-
-    __hashCodeCalc = false;
-
-    return _hashCode;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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;
+
+  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;
+
+  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);
+    }
+    __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;
+
+  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();
+    }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
+
+}