package jalview.io.gff;

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

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

/**
 * An interface to described common functionality of different flavours of GFF
 * 
 * @author gmcarstairs
 *
 */
public interface GffHelperI
{

  final String RENAME_TOKEN = "$RENAME_TO$";

  /**
   * Process one GFF feature line
   * 
   * @param seq
   *          the sequence with which this feature is associated
   * @param gffColumns
   *          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 SequenceFeature if one should be created, else null
   * @throws IOException
   */
  SequenceFeature processGff(SequenceI seq, String[] gffColumns,
          AlignmentI align, List<SequenceI> newseqs,
          boolean relaxedIdMatching) throws IOException;

  // java 8 will allow static methods in interfaces:
  // static boolean recognises(String [] columns);
}