/*
 *                  BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 * 
 * Created on Feb 9, 2005
 *
 */
package org.biojava.dasobert.feature;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

/**
 * An Abstract class representing a Feature as being diplayed in the
 * SeqFeaturePanel A feature corresponds to everything that is visible in a
 * "line" and can contain one or multiple Segments.
 * 
 * 
 * @author Andreas Prlic
 * 
 */
public abstract class AbstractFeatureTrack implements FeatureTrack,
        Cloneable
{

  String name;

  String method;

  String type;

  List segments;

  String note;

  String link;

  String source;

  String score;

  String orientation;

  String typeID;

  String typeCategory;

  public AbstractFeatureTrack()
  {
    source = "Unknown";
    method = "Unknown";
    type = "Unknown";
    note = "";
    link = "";
    score = "";
    orientation = null;
    segments = new ArrayList();

  }

  public abstract Object clone();

  public String toString()
  {
    String str = "Feature: method: " + method + " type: " + type;
    if (name != null)
      str += " name: " + name;

    if ((note != null) && (!note.equals("null")))
    {
      if (note.length() > 40)
        str += "note: " + note.substring(0, 39) + "...";
      else
        str += " note: " + note;
    }
    str += " # segments: " + segments.size();
    return str;
  }

  /**
   * returns true if the specified sequence position is within the range of this
   * Feature
   * 
   * @param seqPosition
   *                the position to check
   * @return true if the position is within the ranges of the segments of this
   *         feature
   */
  public boolean overlaps(int seqPosition)
  {
    List segments = getSegments();
    Iterator iter = segments.iterator();

    while (iter.hasNext())
    {

      Segment seg = (Segment) iter.next();
      if (seg.overlaps(seqPosition))
        return true;
    }

    return false;
  }

  public void setSource(String s)
  {
    source = s;
  }

  public String getSource()
  {
    return source;
  };

  public void setName(String nam)
  {
    name = nam;
  }

  public String getName()
  {
    return name;
  }

  public void setMethod(String methd)
  {
    method = methd;
  }

  public String getMethod()
  {
    return method;
  }

  public void setType(String typ)
  {
    type = typ;
  }

  public String getType()
  {
    return type;
  }

  public void setNote(String nte)
  {
    if (nte != null)
      note = nte;
  }

  public String getNote()
  {
    return note;
  }

  public void setLink(String lnk)
  {
    link = lnk;
  }

  public String getLink()
  {
    return link;
  }

  public void setScore(String s)
  {
    score = s;
  }

  public String getScore()
  {
    return score;
  }

  /** add a segment to this feature */
  public void addSegment(int start, int end, String name)
  {
    Segment s = new SegmentImpl();
    s.setStart(start);
    s.setEnd(end);
    s.setName(name);
    s.setParent(this);
    segments.add(s);
  }

  public void addSegment(Segment s)
  {
    s.setParent(this);
    segments.add(s);
  }

  public List getSegments()
  {
    return segments;
  }

  public String getOrientation()
  {
    return orientation;
  }

  public void setOrientation(String orientation)
  {
    this.orientation = orientation;
  }

  /**
   * test if two features are equivalent important: only comares type,method and
   * source. The individual segments are not compared!
   * 
   */
  public boolean equals(FeatureTrack feat)
  {
    // if ( note == null) {
    // if (( feat.getNote() == null ) ||
    // ( feat.getNote().equals(""))) {
    // } else if ( this.note.equals(feat.getNote())){
    // return true;
    // }
    if (this.type.equals(feat.getType()))
    {
      if (this.method.equals(feat.getMethod()))
      {
        if (this.source.equals(feat.getSource()))
        {
          if (this.note.equals(feat.getNote()))
          {
            return true;
          }
        }
      }
    }
    return false;

  }

  public String getTypeCategory()
  {
    // TODO Auto-generated method stub
    return typeCategory;
  }

  public String getTypeID()
  {
    // TODO Auto-generated method stub
    return typeID;
  }

  public void setTypeCategory(String typeCategory)
  {
    this.typeCategory = typeCategory;

  }

  public void setTypeID(String typeID)
  {
    this.typeID = typeID;

  }

}