/*
 * 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 jalview.datamodel.xdb.uniprot;

import java.util.Vector;

/**
 * A data model class for binding from Uniprot XML via uniprot_mapping.xml
 */
public class UniprotFeature
{
  private String type;

  private String description = null;

  private String original = null;

  private Vector<String> variation = null;

  private String status;

  private int begin;

  private int end;

  public String getType()
  {
    return type;
  }

  public void setType(String t)
  {
    this.type = t;
  }

  public String getDescription()
  {
    if (description == null && variation == null && original == null)
    {
      return null;
    }
    StringBuilder sb = new StringBuilder();
    if (description != null)
    {
      sb.append(description);
    }
    if (variation != null && variation.size() > 0)
    {
      int i = 0;
      for (String var : variation)
      {
        if (i++ > 0)
        {
          sb.append(",");
        }
        if (sb.length() > 0)
        {
          sb.append(" ");
        }
        sb.append("Variation: '" + var + "'");
      }
    }
    if (original != null)
    {
      if (sb.length() > 0)
      {
        sb.append(" ");
      }
      sb.append("Original: '" + original + "'");
    }
    return sb.toString();
  }

  public void setDescription(String d)
  {
    this.description = d;
  }

  public String getStatus()
  {
    return status;
  }

  public void setStatus(String s)
  {
    this.status = s;
  }

  public int getBegin()
  {
    return begin;
  }

  public void setBegin(int b)
  {
    this.begin = b;
  }

  public int getEnd()
  {
    return end;
  }

  public void setEnd(int e)
  {
    this.end = e;
  }

  public int getPosition()
  {
    return begin;
  }

  public void setPosition(int p)
  {
    this.begin = p;
    this.end = p;
  }

  public String getOriginal()
  {
    return original;
  }

  public void setOriginal(String original)
  {
    this.original = original;
  }

  public Vector<String> getVariation()
  {
    return variation;
  }

  public void setVariation(Vector<String> variant)
  {
    this.variation = variant;
  }
}