package jalview.io;

import jalview.io.xdb.genbank.GenBankFeature;
import jalview.io.xdb.genbank.GenBankSequence;

import java.util.ArrayList;
import java.util.List;
import java.util.Vector;

public class DnaUtils
{

  /**
   * @param gbf
   *          CDS feature data
   * @param sequences
   *          ORIGIN data
   * @return Nucleotid String (sequence) of CDS
   */
  public static String getSequence(GenBankFeature gbf,
          Vector<GenBankSequence> sequences)
  {
    if (!gbf.getType().equals(GenBankFeature.CDS))
    {
      // If the feature is not a CDS, no sequence is returned
      return null;
    }
    else
    {
      String range = gbf.getQualifier("range");
      if (range.startsWith("join"))
      {
        // TODO
        // It's a composed sequence
      }
      else
      {
        // It's a simple range
        String[] positions = range.split("..");
        int initRange = Integer.parseInt(positions[0]);
        int endRange = Integer.parseInt(positions[1]);
        String sourceSequence = getNucleotidesFromSequenceVector(sequences);
        return sourceSequence.substring(initRange, endRange);
      }
    }
    return null;

  }

  private static boolean isSequenceInRange(int initRange, int endRange,
          GenBankSequence gbs)
  {
    return ((initRange >= gbs.getId()) && (endRange >= gbs.getId()));
  }

  private static String getNucleotidesInRangeFromSequence(int initRange,
          int endRange, GenBankSequence gbs)
  {
    return "";
  }

  public static String getNucleotidesFromSequenceVector(
          Vector<GenBankSequence> v)
  {
    StringBuffer sb = new StringBuffer();
    for (GenBankSequence gbs : v)
    {
      Vector<String> seqs = gbs.getSequences();
      for (String s : seqs)
        sb.append(s);
    }
    return sb.toString();
  }

  /**
   * @param args
   */
  public static void main(String[] args)
  {
    // TODO Auto-generated method stub

  }

}