/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, 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;
  }

}
