/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/package jalview.io;

import jalview.datamodel.*;
import java.net.URL;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.FileReader;


public class JnetAnnotationMaker
{
  /**
   * adds the annotation parsed by prediction to al.
   * @param prediction JPredFile
   * @param al AlignmentI
   * @param FirstSeq int -
   * @param noMsa boolean
   */
  public static void add_annotation(JPredFile prediction, AlignmentI al,
                                    int FirstSeq, boolean noMsa)
      throws Exception
  {
    int i = 0;
    SequenceI[] preds = prediction.getSeqsAsArray();
    // in the future we could search for the query
    // sequence in the alignment before calling this function.
    SequenceI seqRef = al.getSequenceAt(FirstSeq);
    int width = preds[0].getSequence().length();
    int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
    if (gapmap.length != width)
    {
      throw (new Exception(
          "Number of residues in supposed query sequence ('" +
          al.getSequenceAt(FirstSeq).getName() + "'\n" +
          al.getSequenceAt(FirstSeq).getSequence() +
          ")\ndiffer from number of prediction sites in prediction (" + width +
          ")"));
    }

    AlignmentAnnotation annot;
    Annotation[] annotations = null;

    while (i < preds.length)
    {
      String id = preds[i].getName().toUpperCase();

      if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
          id.startsWith("JPRED"))
      {
        annotations = new Annotation[al.getWidth()];

        if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
            id.equals("JNETFREQ") || id.equals("JNETHMM") ||
            id.equals("JNETALIGN") || id.equals("JPRED"))
        {
          for (int j = 0; j < width; j++)
          {
            annotations[gapmap[j]] = new Annotation("", "",
                preds[i].getCharAt(j), 0);
          }
        }
        else if (id.equals("JNETCONF"))
        {
          for (int j = 0; j < width; j++)
          {
            float value = new Float(preds[i].getCharAt(
                j) + "").floatValue();
            annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
                j) + "", "", preds[i].getCharAt(j),
                value);
          }
        }
        else
        {
          for (int j = 0; j < width; j++)
          {
            annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
                j) + "", "", ' ', 0);
          }
        }

        if (id.equals("JNETCONF"))
        {
          annot = new AlignmentAnnotation(preds[i].getName(),
                                          "JNet Output", annotations, 0f,
                                          10f,
                                          AlignmentAnnotation.BAR_GRAPH);
        }
        else
        {
          annot = new AlignmentAnnotation(preds[i].getName(),
                                          "JNet Output", annotations);
        }

        if (seqRef != null)
        {
          annot.createSequenceMapping(seqRef, 0);
          seqRef.addAlignmentAnnotation(annot);
        }

        al.addAnnotation(annot);

        if (noMsa)
        {
          al.deleteSequence(preds[i]);
        }
      }

      i++;
    }

    //Hashtable scores = prediction.getScores();

    /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
                          "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);

      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
     "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);

      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
                          "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
     */

  }
}