[jalview.git] / src / jalview / datamodel / SequenceFeature.java

/*
 * 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;

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 Vector<String> 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;
      if (cpy.type != null)
      {
        type = new String(cpy.type);
      }
      if (cpy.description != null)
      {
        description = new String(cpy.description);
      }
      if (cpy.featureGroup != null)
      {
        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<String>();
        for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
        {
          links.addElement(cpy.links.elementAt(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 Vector<String>();
    }

    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)
    {
      String stat = (String) otherDetails.get("status");
      if (stat != null)
      {
        return new String(stat);
      }
    }
    return null;
  }

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

  public int getPosition()
  {
    return begin;
  }

  public int getStrand()
  {
    String str;
    if (otherDetails == null
            || (str = otherDetails.get("STRAND").toString()) == null)
    {
      return 0;
    }
    if (str.equals("-"))
    {
      return -1;
    }
    if (str.equals("+"))
    {
      return 1;
    }
    return 0;
  }

}