// This class represents a cluster of genes with similar expression data. It
// contains methods for creating an image of the cluster's expression data and
// for returning the centroid of the cluster.

import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.BufferedOutputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.*;
import javax.imageio.ImageIO;
import java.io.File;

public class Cluster 
{
  // Constants for creating Jpeg images. Do not change these.
  private static final double C_D_CUTOFF = 2;
  private static final int C_IX  = 8;
  private static final int C_IY  = 4;
  
  // Data members
  private HashSet<Gene> geneSet; // List of genes in cluster
  
  // Constructor; creates an empty cluster.
  public Cluster() 
  {
    // TODO
    // make a new HashSet of objects of type Gene
     
  }
  
  // Prints the names of all genes in the cluster
  public void printGeneNames() 
  {
    // TODO
    // This should print the name of each gene in the cluster
    // with one name printed per line
  }
  
  // Adds a gene to the cluster
  public void addGene(Gene gene) 
  {
    // Append a gene to the set
    geneSet.add(gene); 
  }

  // Getter method for geneSet
  public HashSet<Gene> getGeneSet()
  {
    return geneSet;
  }

  // Returns the centroid of the cluster as a Gene object with name "centroid".
  // The expression data of the returned gene is the centroid of the cluster.
  public Gene centroid() 
  {
    // TODO
    // Add code here to calculate and return the centroid
    // of the cluster of genes
    return null; 
  }
  
  // Creates an image of this cluster's expression data. The image will be
  // stored in file "<fileName><id>.jpg". Do not change this method.
  public void createJPG(String fileName, int id) 
  {
    String   strOut;
    int    i, j, iGenes, iConditions;
    double   dValue;
    BufferedImage bimg;
    Graphics2D  gr2d;
    Color   colr;
    
    strOut = fileName + id + ".jpg";
    
    // Initialize some values
    Vector<Gene> geneVector = new Vector<Gene>();
    Iterator<Gene> it = geneSet.iterator();
    while (it.hasNext())
        geneVector.add(it.next());

    Comparator<Gene> GENE_ORDER = new Comparator<Gene>() {
       public int compare(Gene g1, Gene g2) {
          return g1.getName().compareTo(g2.getName());
       }
    };

    Collections.sort(geneVector, GENE_ORDER);

    iGenes = geneVector.size();
    iConditions = (geneVector.get(0)).getValues().length;
    
    // Create the empty image and graphics2D
    bimg = new BufferedImage(C_IX * iConditions, C_IY * iGenes,
                             BufferedImage.TYPE_INT_RGB);
    gr2d = bimg.createGraphics();
    
    // Draw a rectangle for each gene/condition pair
    for (i = 0; i < iGenes; ++i) 
    {
      for (j = 0; j < iConditions; ++j) 
      {
        dValue = (geneVector.get(i)).getValues()[j];
        if (dValue < 0)
          colr = new Color(0.0f, (dValue < -C_D_CUTOFF) ? 1.0f
                               : (float) (dValue / -C_D_CUTOFF), 0.0f);
        else
          colr = new Color((dValue > C_D_CUTOFF) ? 1.0f
                               : (float) (dValue / C_D_CUTOFF), 0.0f, 0.0f);
        gr2d.setColor(colr);
        gr2d.fill(new Rectangle2D.Float(j * C_IX, i * C_IY, C_IX, C_IY)); 
      } 
    }
    gr2d.dispose();
    
    try 
    {
      // Output the image to file
      File outFile = new File(strOut);
      ImageIO.write(bimg, "jpg", outFile);
    }
    catch (IOException e) 
    {
      System.out.println("ERROR: Unable to write image in " + strOut + "."); 
    } 
  }
}