/*
 * 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.io.gff;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.StringUtils;

import java.io.IOException;
import java.util.List;
import java.util.Map;

/**
 * A handler to parse GFF in the format generated by InterProScan
 */
public class InterProScanHelper extends Gff3Helper
{
  private static final String INTER_PRO_SCAN = "InterProScan";

  private static final String SIGNATURE_DESC = "signature_desc";

  /**
   * Process one GFF feature line (as modelled by SequenceFeature)
   * 
   * @param seq
   *          the sequence with which this feature is associated
   * @param gff
   *          the gff column data
   * @param align
   *          the alignment we are adding GFF to
   * @param newseqs
   *          any new sequences referenced by the GFF
   * @param relaxedIdMatching
   *          if true, match word tokens in sequence names
   * @return a sequence feature if one should be added to the sequence, else
   *         null (i.e. it has been processed in another way e.g. to generate a
   *         mapping)
   * @throws IOException
   */
  @Override
  public SequenceFeature processGff(SequenceI seq, String[] gff,
          AlignmentI align, List<SequenceI> newseqs,
          boolean relaxedIdMatching) throws IOException
  {
    /*
     * ignore the 'polypeptide' match of the whole sequence
     */
    if (".".equals(gff[SOURCE_COL]))
    {
      return null;
    }

    return super.processGff(seq, gff, align, newseqs, relaxedIdMatching);
  }

  /**
  * 
  */
  @Override
  protected SequenceFeature buildSequenceFeature(String[] gff,
          Map<String, List<String>> attributes)
  {
    SequenceFeature sf = super.buildSequenceFeature(gff, attributes);

    /*
     * signature_desc is a more informative source of description
     */
    List<String> desc = attributes.get(SIGNATURE_DESC);
    String description = StringUtils.listToDelimitedString(desc, ", ");
    if (description.length() > 0)
    {
      sf.setDescription(description);
    }

    /*
     * Set sequence feature group as 'InterProScan', and type as the source
     * database for this match (e.g. 'Pfam')
     */
    sf.setType(gff[SOURCE_COL]);
    sf.setFeatureGroup(INTER_PRO_SCAN);

    return sf;
  }

  /**
   * Tests whether the GFF data looks like it was generated by InterProScan
   * 
   * @param columns
   * @return
   */
  public static boolean recognises(String[] columns)
  {
    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
    String type = columns[TYPE_COL];
    if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
            || (".".equals(columns[SOURCE_COL])
                    && so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
    {
      return true;
    }
    return false;
  }

  /**
   * Overriden method, because InterProScan GFF has the target sequence id in
   * GFF field 'ID' rather than the usual 'Target' :-O
   */
  @Override
  protected String findTargetId(String target,
          Map<String, List<String>> set)
  {
    List<String> ids = set.get(ID);
    if (ids == null || ids.size() != 1)
    {
      return null;
    }
    return ids.get(0);
  }

}