/*
 * 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 jalview.datamodel;

import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class SequenceFeature
{
    public int begin;
    public int end;
    public float score;
    public String type;
    public String description;
    public Hashtable otherDetails;
    public java.util.Vector links;

    // Feature group can be set from a features file
    // as a group of features between STARTGROUP and ENDGROUP markers
    public String featureGroup;

    public SequenceFeature()
    {}
    /**
     * Constructs a duplicate feature. 
     * Note: Uses clone on the otherDetails so only shallow copies are made 
     * of additional properties and method will silently fail if unclonable 
     * objects are found in the hash.
     * @param cpy
     */
    public SequenceFeature(SequenceFeature cpy) {
        if (cpy!=null) {
            begin = cpy.begin;
            end = cpy.end;
            score = cpy.score;
            type = new String(cpy.type);
            description = new String(cpy.description);
            featureGroup = new String(cpy.featureGroup);
            if (cpy.otherDetails!=null) {
                try {
                    otherDetails = (Hashtable) cpy.otherDetails.clone();
                } catch (Exception e) {
                    // Uncloneable objects in the otherDetails - don't complain
                }
            }
            if (cpy.links!=null && cpy.links.size()>0) {
                links=new Vector();
                for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {
                    links.setElementAt(cpy.links.elementAt(i), i);
                }
            }
        }
    }
    public SequenceFeature(String type,
                           String desc,
                           String status,
                           int begin, int end,
                           String featureGroup)
    {
      this.type = type;
      this.description = desc;
      setValue("status", status);
      this.begin = begin;
      this.end = end;
      this.featureGroup = featureGroup;
    }

    public SequenceFeature(String type,
                           String desc,
                           int begin, int end,
                           float score,
                           String featureGroup)
    {
      this.type = type;
      this.description = desc;
      this.begin = begin;
      this.end = end;
      this.score = score;
      this.featureGroup = featureGroup;
    }

    public boolean equals(SequenceFeature sf)
    {
      if (begin != sf.begin
          || end != sf.end
          || score != sf.score)
        return false;

      if(!(type+description+featureGroup).equals
         (sf.type+sf.description+sf.featureGroup))
        return false;

      return true;
    }


    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getBegin()
    {
        return begin;
    }

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

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getEnd()
    {
        return end;
    }

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

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getType()
    {
        return type;
    }

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

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getDescription()
    {
        return description;
    }

    public void setDescription(String desc)
    {
      description = desc;
    }

    public String getFeatureGroup()
    {
      return featureGroup;
    }

    public void setFeatureGroup(String featureGroup)
    {
      this.featureGroup = featureGroup;
    }

    public void addLink(String labelLink)
    {
      if(links==null)
        links = new java.util.Vector();

      links.insertElementAt(labelLink,0);
    }

    public float getScore()
    {
      return score;
    }

    public void setScore(float value)
    {
      score = value;
    }

    /**
     * Used for getting values which are not in the
     * basic set. eg STRAND, FRAME for GFF file
     * @param key String
     */
    public Object getValue(String key)
    {
      if(otherDetails==null)
        return null;
      else
        return otherDetails.get(key);
    }

    /**
     * Used for setting values which are not in the
     * basic set. eg STRAND, FRAME for GFF file
     * @param key   eg STRAND
     * @param value eg +
     */
    public void setValue(String key, Object value)
    {
      if(value!=null)
      {
        if (otherDetails == null)
          otherDetails = new Hashtable();

        otherDetails.put(key, value);
      }
    }


    /*
     * The following methods are added to maintain
     * the castor Uniprot mapping file for the moment.
     */
    public void setStatus(String status)
    {
      setValue("status", status);
    }

    public String getStatus()
    {
      if (otherDetails != null)
        return otherDetails.get("status").toString();
      else
        return null;
    }

    public void setPosition(int pos)
    {
      begin = pos;
      end = pos;
    }

    public int getPosition()
    {
      return begin;
    }

}