package jalview.analysis.scoremodels;

import jalview.analysis.AlignSeq;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;

public class SWScoreModel implements ScoreModelI
{

  @Override
  public float[][] findDistances(AlignmentView seqData)
  {
    SequenceI[] sequenceString = seqData
            .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
    int noseqs = sequenceString.length;
    float[][] distance = new float[noseqs][noseqs];
    
     float max = -1;
      
      for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
      { AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j], seqData.isNa() ? "dna" : "pep");
      as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
      distance[i][j] = (float) as.maxscore;
      
      if (max < distance[i][j]) { max = distance[i][j]; } } }
     
      for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
      { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
      } } 
     
    return distance;
  }

  @Override
  public String getName()
  {
    return "Smith Waterman Score";
  }
  @Override
  public boolean isDNA()
  {
    return true;
  }
  @Override
  public boolean isProtein()
  {
    return true;
  }
  public String toString() {
    return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
  }
}