/*
 * 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.xdb.embl;

import jalview.bin.Cache;
import jalview.util.ArrayUtils;

import java.util.Arrays;
import java.util.Vector;

/**
 * Data model for a &lt;location&gt; child element of a &lt;feature&gt; read
 * from an EMBL query reply
 * 
 * @see embl_mapping.xml
 * @see http://www.insdc.org/files/feature_table.html#3.4.2
 */
public class EmblFeatureLocations
{
  Vector<EmblFeatureLocElement> 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<EmblFeatureLocElement> getLocElements()
  {
    return locElements;
  }

  /**
   * @param locElements
   *          the locElements to set
   */
  public void setLocElements(Vector<EmblFeatureLocElement> 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.
   * If the CDS feature is on the forward strand, then start <= end, if on the
   * reverse strand then start > end.
   * 
   * @param accession
   *          the accession string for which locations are requested, or null
   *          for all locations
   * @return int[] { start1, end1, ... }
   */
  int[] getElementRanges(String accession)
  {
    int sepos = 0;
    int[] se = new int[locElements.size() * 2];
    if ("single".equalsIgnoreCase(locationType)
            || "join".equalsIgnoreCase(locationType))
    {
      for (EmblFeatureLocElement loce : locElements)
      {
        if (accession == null || loce.accession != null
                && accession.equals(loce.accession))
        {
          BasePosition bp[] = loce.getBasePositions();
          if (bp.length == 2)
          {
            try
            {
              int start = Integer.parseInt(bp[0].getPos());
              int end = Integer.parseInt(bp[1].getPos());
              se[sepos++] = start;
              se[sepos++] = end;
            } catch (NumberFormatException e)
            {
              System.err
                      .println("format error in EMBL CDS location basePosition: "
                              + e.getMessage());
            }
          }
          else
          {
            System.err
                    .println("format error in EMBL CDS location, basePosition count = "
                            + bp.length);
          }
        }
      }
    }
    else if (locationType != null)
    {
      if (Cache.log != null)
      {
        Cache.log
                .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
                        + locationType + "'");
      }
      else
      {
        System.err
                .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
                        + locationType + "'");
      }
    }

    if (sepos != se.length)
    {
      /*
       * we failed to parse something - trim off null values
       */
      se = Arrays.copyOf(se, sepos);
    }

    /*
     * If on the complement, reverse the ranges to [end, start, ...end1, start1].
     * For an example of a joined complement, see (tRNA feature) CAGL0B00165r on
     * http://www.ebi.ac.uk/ena/data/view/CR380948&display=xml
     * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CR380948/emblxml
     */
    if (locationComplement)
    {
      ArrayUtils.reverseIntArray(se);
    }
    return se;
  }
}