package jalview.datamodel.xdb.embl;

import java.util.Enumeration;
import java.util.Iterator;
import java.util.Vector;

public class EmblFeatureLocations {
    Vector locElements;
    String locationType;
    boolean locationComplement;
    /**
     * @return the locationComplement
     */
    public boolean isLocationComplement() {
        return locationComplement;
    }
    /**
     * @param locationComplement the locationComplement to set
     */
    public void setLocationComplement(boolean locationComplement) {
        this.locationComplement = locationComplement;
    }
    /**
     * @return the locationType
     */
    public String getLocationType() {
        return locationType;
    }
    /**
     * @param locationType the locationType to set
     */
    public void setLocationType(String locationType) {
        this.locationType = locationType;
    }
    /**
     * @return the locElements
     */
    public Vector getLocElements() {
        return locElements;
    }
    /**
     * @param locElements the locElements to set
     */
    public void setLocElements(Vector locElements) {
        this.locElements = locElements;
    }
    /**
     * Return all location elements as start-end pairs (without accessions)  
     * TODO: pass back complement and 'less than or more than' range information
     * Note: do not use this since it throws away any accessionIds associated with
     * each location!
     * @return int[] { start1, end1, ... }
     */
    public int[] getElementRanges() {
      return getElementRanges(null);
    }
    /**
     * Return all location elements concerning given accession as start-end pairs  
     * TODO: pass back complement and 'less than or more than' range information
     * TODO: deal with multiple accessions
     * @param accession the accession string for which locations are requested, or null for all locations
     * @return null or int[] { start1, end1, ... }
     */
    
    public int[] getElementRanges(String accession)
    {
      int sepos=0;
      int[] se = new int[locElements.size()*2];
      if (locationType.equalsIgnoreCase("single")) {
        for (Enumeration le=locElements.elements();le.hasMoreElements();) {
            EmblFeatureLocElement loce = (EmblFeatureLocElement) le.nextElement();
            if (accession==null || loce.accession!=null && accession.equals(loce.accession))
            {
              BasePosition bp[] = loce.getBasePositions();
              if (bp.length==2) {
                se[sepos++] = Integer.parseInt(bp[0].getPos());
                se[sepos++] = Integer.parseInt(bp[1].getPos());
              }
            }
        }
    } else 
    if (locationType.equalsIgnoreCase("join")) {
        for (Enumeration le=locElements.elements();le.hasMoreElements();) {
          EmblFeatureLocElement loce = (EmblFeatureLocElement) le.nextElement();
          if (accession==null || loce.accession!=null && accession.equals(loce.accession))
          {
            BasePosition bp[] = loce.getBasePositions();
            if (bp.length==2) {
                se[sepos++] = Integer.parseInt(bp[0].getPos());
                se[sepos++] = Integer.parseInt(bp[1].getPos());
            }
          }
        }
        return se;
    } else
    if (locationType!=null)
    {
      if (jalview.bin.Cache.log!=null)
        jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
      else
        System.err.println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
    }
    // trim range if necessary.
    if (se!=null && sepos!=se.length)
    {
      int[] trimmed = new int[sepos];
      System.arraycopy(se,0,trimmed, 0, sepos);
      se = trimmed;
    }
    return se;
    }
}