/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 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 jalview.datamodel;

import java.awt.*;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class Annotation
{
  /** DOCUMENT ME!! */
  public String displayCharacter = "";

  /** DOCUMENT ME!! */
  public String description = ""; // currently used as mouse over

  /** DOCUMENT ME!! */
  public char secondaryStructure = ' '; // recognises H and E

  /** DOCUMENT ME!! */
  public float value;

  // add visual cues here

  /** DOCUMENT ME!! */
  public Color colour;

  /**
   * Creates a new Annotation object.
   * 
   * @param displayChar
   *                DOCUMENT ME!
   * @param desc
   *                DOCUMENT ME!
   * @param ss
   *                DOCUMENT ME!
   * @param val
   *                DOCUMENT ME!
   */
  public Annotation(String displayChar, String desc, char ss, float val)
  {
    displayCharacter = displayChar;
    description = desc;
    secondaryStructure = ss;
    value = val;
  }

  /**
   * Creates a new Annotation object.
   * 
   * @param displayChar
   *                DOCUMENT ME!
   * @param desc
   *                DOCUMENT ME!
   * @param ss
   *                DOCUMENT ME!
   * @param val
   *                DOCUMENT ME!
   * @param colour
   *                DOCUMENT ME!
   */
  public Annotation(String displayChar, String desc, char ss, float val,
          Color colour)
  {
    this(displayChar, desc, ss, val);
    this.colour = colour;
  }

  /**
   * Copy constructor New annotation takes on the same (or duplicated)
   * attributes as the given template
   * 
   * @param that
   *                template annotation
   */
  public Annotation(Annotation that)
  {
    if (that == null || this == that)
    {
      return;
    }
    if (that.displayCharacter != null)
      displayCharacter = new String(that.displayCharacter);
    if (that.description != null)
      description = new String(that.description);
    secondaryStructure = that.secondaryStructure;
    value = that.value;
    colour = that.colour;
  }

  /**
   * Value only annotation.
   * 
   * @param val
   *                value at this annotation position
   */
  public Annotation(float val)
  {
    this(null, null, ' ', val);
  }
}