package jalview.io;

import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;

public class AnnotationUtil
{

  public static AlignmentAnnotation getConsensusAnnotationFromFile(
          String file)
  {
    AlignmentI alignment = readAlignmentFile(file);
    // AlignFrame af = new AlignFrame(alignment, 5, 5);
    // af.setVisible(false);
    // AlignmentAnnotation consensus = af.getViewport()
    // .getAlignmentConsensusAnnotation();
    // af.dispose();
    // System.out.println(consensus);

    SequenceI[] alignmentSeqs = alignment.getSequencesArray();
    int width = alignment.getWidth();
    long nseq = alignmentSeqs.length;
    boolean ignoreGapsConsensus = true;
    boolean showSequenceLogo = false;

    AlignmentAnnotation consensusAnnotation = new AlignmentAnnotation(
            "Consensus",
            "PID", new Annotation[1], 0f, 100f,
            AlignmentAnnotation.BAR_GRAPH);
    consensusAnnotation.hasText = true;
    consensusAnnotation.autoCalculated = true;

    alignment.addAnnotation(consensusAnnotation);
    ProfilesI hconsensus = AAFrequency.calculate(alignmentSeqs, width, 0,
            width,
            true);

    AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
            ignoreGapsConsensus, showSequenceLogo, nseq);

    System.out.println(">>>>> Consensus Annotation : "
            + consensusAnnotation);
    return consensusAnnotation;
  }

  public static AlignmentAnnotation getConservationAnnotationFromFile(
          String file, SequenceI seqRef)
  {
    AlignmentAnnotation conservationAnnotation = null;
    int foundAnnotCount = seqRef.getAnnotation().length;
    if (seqRef != null && foundAnnotCount < 3)
    {
      AlignmentI alignment = readAlignmentFile("/Users/tcnofoegbu/Desktop/query.jal");
      // AlignmentI alignment = readAlignmentFile(file);
      // ColumnSelection cs = new ColumnSelection();
      // SequenceI querySeq = alignment.getSequenceAt(0);
      // cs.hideInsertionsFor(querySeq);
      // AlignViewport av = new AlignViewport(alignment);
      // av.setColumnSelection(cs);
      //
      // alignment = av.getAlignment();
      int alWidth = alignment.getWidth();
      int ConsPercGaps = 25;

      AlignmentAnnotation quality = new AlignmentAnnotation("Quality",
              "Alignment Quality based on Blosum62 scores",
              new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
      quality.hasText = true;
      quality.autoCalculated = true;

      conservationAnnotation = new AlignmentAnnotation("Conservation",
              "PID", new Annotation[1], 0f, 100f,
              AlignmentAnnotation.BAR_GRAPH);
      conservationAnnotation.hasText = true;
      conservationAnnotation.autoCalculated = true;
      alignment.addAnnotation(conservationAnnotation);
      Conservation cons = Conservation.calculateConservation("All",
              alignment.getSequences(), 0, alWidth - 1, false,
              ConsPercGaps, quality != null);
      cons.completeAnnotations(conservationAnnotation, quality, 0, alWidth);
      System.out.println(">>>");

      conservationAnnotation.createSequenceMapping(seqRef, 1, true);
      seqRef.addAlignmentAnnotation(conservationAnnotation);

      // conservationAnnotation.createSequenceMapping(
      // seqRef.getDatasetSequence(), 1, true);
      // seqRef.getDatasetSequence().addAlignmentAnnotation(
      // conservationAnnotation);
    }

    return conservationAnnotation;
  }

  private static AlignmentI readAlignmentFile(String f)
  {
    System.out.println("Reading file: " + f);
    try
    {
      FormatAdapter rf = new FormatAdapter();
      DataSourceType protocol = AppletFormatAdapter.checkProtocol(f);
      AlignmentI al = rf.readFile(f, protocol,
              new IdentifyFile().identify(f, protocol));
      return al;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    return null;
  }

  public static void main(String[] args)
  {
    // getConservationAnnotationFromFile("http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/cd1b897af035cdf5/query.jal");
    getConsensusAnnotationFromFile("http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/cd1b897af035cdf5/query.jal");
  }

}