package jalview.analysis.scoremodels;

import java.awt.Color;
import java.util.List;

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

public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
{
  jalview.api.FeatureRenderer fr;

  @Override
  public boolean configureFromAlignmentView(
          jalview.api.AlignmentViewPanel view)
  {
    fr = view.cloneFeatureRenderer();
    return true;
  }

  @Override
  public float[][] findDistances(AlignmentView seqData)
  {

    SequenceI[] sequenceString = seqData.getVisibleAlignment(
            Comparison.GapChars.charAt(0)).getSequencesArray();
    int noseqs = sequenceString.length;
    int cpwidth = seqData.getWidth();
    float[][] distance = new float[noseqs][noseqs];
    float max = 0;
    for (int cpos = 0; cpos < cpwidth; cpos++)
    {
      // get visible features at cpos under view's display settings and compare
      // them
      for (int i = 0; i < (noseqs - 1); i++)
      {
        List<SequenceFeature> sf = fr.findFeaturesAtRes(sequenceString[i],
                cpos);
        for (int j = i + 1; j < noseqs; j++)
        {
          List<SequenceFeature> jsf = fr.findFeaturesAtRes(
                  sequenceString[i], cpos);
          // compare the two lists of features...

          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";
  }
}