X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;fp=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=bd9adfa152155a280f2c9693cfea703c77235305;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=0055bafdfdee69408212c7c660f239695d3b6b30;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 0055baf..bd9adfa 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -6,163 +6,184 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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.
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * @return gapchar
- */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-    /**
- * Sets the gapchar value for this Alignment.
+ * 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.
  *
- * @param gapchar
- */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-    /**
- * Gets the method value for this Alignment.
+ * 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.
  *
- * @return method
+ * 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
  */
-    public java.lang.String[] getMethod() {
-        return method;
-    }
+package vamsas.objects.simple;
 
-    /**
- * Sets the method value for this Alignment.
- *
- * @param method
- */
-    public void setMethod(java.lang.String[] method) {
-        this.method = method;
+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;
     }
 
-    /**
- * Gets the seqs value for this Alignment.
- *
- * @return seqs
- */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
-    }
+    Alignment other = (Alignment) obj;
 
-    /**
- * Sets the seqs value for this Alignment.
- *
- * @param seqs
- */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
+    if (obj == null)
+    {
+      return false;
     }
 
-    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;
+    if (this == obj)
+    {
+      return true;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
 
-        __hashCodeCalc = true;
+    __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;
+    }
 
-        int _hashCode = super.hashCode();
+    __hashCodeCalc = true;
 
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
+    int _hashCode = super.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 (getGapchar() != null)
+    {
+      _hashCode += getGapchar().hashCode();
+    }
 
-                if ((obj != null) && !obj.getClass().isArray()) {
-                    _hashCode += obj.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 (getSeqs() != null)
+    {
+      _hashCode += getSeqs().hashCode();
+    }
 
-        __hashCodeCalc = false;
+    __hashCodeCalc = false;
 
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }