package converters;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Scanner;
import middlewares.Misc;

/**
 * Converts the detailed coverage data to the wig format. Used for the
 * visualization of the coverage data in the ucsc-browser.
 *
 * @author Ali Abdallah
 * @version 20.07.2011
 * @since Java 1.6
 */
public class ReadOnTarget2Wig {
	
    private int 
    /**
     * The maximal number of hits on a base.
     */
    max, 
    /**
     * The minimal number of hits on a base.
     */
    min, 
    /**
     * The minimal position on chr1.
     */
    gMin, 
    /**
     * the maximal position on chr1.
     */
    gMax;
    
    private String 
    /**
     * The name of the file of detailed coverage data.
     */
    filename, 
    /**
     * The title of the track.
     */
    title;

    /**
     * Constructs an new ReadOnTarget2Wig object, initializes the parameters
     * and call the conversion method.
     * 
     * @param filename
     * @param prefix
     * @param outDir
     * @param title
     * @throws IOException
     */
    public ReadOnTarget2Wig(String filename, String prefix, String outDir, String title) throws IOException{
    	this.filename = filename;
    	max = Integer.MIN_VALUE; gMax = Integer.MIN_VALUE;
    	min = Integer.MAX_VALUE; gMin = Integer.MAX_VALUE;
    	this.title = title;
    	File f=new File(this.filename);
    	FileWriter fw=new FileWriter(outDir+Misc.slash(outDir)
    												+prefix+"_onTarget.wig");
    	Scanner scanForMinMax=new Scanner(f);
    	computeExtremas(scanForMinMax);
    	scanForMinMax.close();
		
    	Scanner s = new Scanner(f);
    	annotationHeader(fw);
    	toWiggleFormat(fw,s);
    	fw.close();
    }
 
    /**
     * Writes the annotation header to the wig file.
     * 
     * @param fw FileWriter
     * @throws IOException if write operation is not possible.
     */
    private void annotationHeader(FileWriter fw) throws IOException{
    	String browserLines = 	"browser position chr1:"+gMin+"-"+gMax+"\r\n"+
	    						"browser hide all"+"\r\n"+
	    						"browser pack refGene encodeRegions"+"\r\n"+
	    						"browser full altGraph";
    	String trackLine = 	"track type=wiggle_0 name=\""+title+"\" " +
	    					"description=\"Base read coverage\" visibility=full " 
    						+"color=0,0,0 altColor=255,0,0 priority=20 " +
    						"autoScale=off graphType=bar " +
    						"viewLimits="+min+":"+max;
    	fw.write(browserLines+"\r\n"+trackLine+"\r\n");
    }
    
    /**
     * Computes the hit and position minimas and maxima.
     * 
     * @param s the reader of the file of detailed coverage data.
     */
    private void computeExtremas(Scanner s){
    	String chrom = "Datei falsch formatiert.";
    	int start = -1;	int end = -1;
    	while(s.hasNextLine()){
    		String line = s.nextLine();
    		if(isHeader(line)){
    			chrom = chrom(line); start = start(line); end = end(line);
    			if(gMin > start && chrom.equals("chr1")){gMin = start;}
    			if(gMax < end && chrom.equals("chr1")){gMax = end;}
    		}
    		else{
    			if(min > Integer.parseInt(line.trim())){
    				min = Integer.parseInt(line.trim());
    			}
    			if(max < Integer.parseInt(line.trim())){
    				max = Integer.parseInt(line.trim());
    			}
    		}
    	}
    }
	
    /**
     * The main computation: conversion to wiggle format. 
     * 
     * @param fw FileWriter into the wig-file.
     * @param s the reader of the file of detailed coverage data.
     * @throws IOException if i/o fails.
     */
    private void toWiggleFormat(FileWriter fw, Scanner s) throws IOException {
    	String chrom = "Datei falsch formatiert.";
    	int start = -1;
    	while(s.hasNextLine()){
    		String line = s.nextLine();
    		if(isHeader(line)){
    			chrom = chrom(line); start = start(line);
    			fw.write(declarationLine(chrom, start));
    		}
    		else fw.write(line+"\r\n");
    	}
    }

    /**
     * @param chrom
     * @param start
     * @return a String representing the declaration line corresponding to the
     * specified parameters.
     */
    private String declarationLine(String chrom, int start) {
    	return "fixedStep chrom="+chrom+" start="+start+" step=1\r\n";
    }
	
    /**
     * Check if the specified line is a header line.
     * 
     * @param 	line the current observerd line in the file of detailed coverage 
     * 			data.
     * @return true if line is a header and false otherwise.
     */
    private boolean isHeader(String line){
    	return line.indexOf("chr")!=-1;
    }
	
    /**
     * @param line
     * @return the start position of the current frame (header).
     */
    private int start(String line){
    	Scanner s = new Scanner(line);
    	s.next(); return s.nextInt();
    }
	
    /**
     * @param line
     * @return the end position of the current frame.
     */
    private int end(String line){
    	Scanner s = new Scanner(line);
    	s.next(); s.next();
    	return s.nextInt();
    }
	
    /**
     * @param line
     * @return the chromosome corresponding to the current frame.
     */
	private String chrom(String line){
		Scanner s = new Scanner(line);
		return s.next();
	}
}