package jalview.schemes;

import jalview.datamodel.*;
import jalview.jbgui.*;

import java.util.*;
import java.awt.*;

public class PIDColourScheme extends ResidueColourScheme {
    public Color[] pidColours;
    public float[] thresholds;

    SequenceGroup group;

    public PIDColourScheme() {
	this.pidColours = ResidueProperties.pidColours;
	this.thresholds = ResidueProperties.pidThresholds;
    }
  public Color getColour(SequenceI seq, int j,Vector aa) {
    Color c = Color.white;

    String       s = seq.getSequence(j,j+1);

    if (aa != null && j < aa.size()) {
	c = findColour(seq,s,j,aa);
    }

    return c;
  }

  public Color findColour(SequenceI seq,String s, int j,Vector aa) {
      Color     c    = Color.white;
      Hashtable hash = null;

      if (aa != null) {
	  hash = (Hashtable)aa.elementAt(j);
      }
      else
        return c;

      String    max  = (String)hash.get("maxResidue");

      double sc = 0;
      if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
	  sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));

	  // MC Should be isGap
	  if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
	      for (int i=0; i < thresholds.length; i++) {
		  if (sc > thresholds[i]) {
		      c = pidColours[i];
		      break;
		  }
	      }
	  } else {
	      c = Color.white;
	  }
      }
      return c;
  }
}