package driver;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Arrays;

import dna.Gene;
import dna.Timer;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;

public class ConcatenateFiles {
	
	public static void main(String[] args){
		
		Timer t=new Timer();
		final String in=args[0];
		final String out=(args.length>1 ? args[1] : null);
		if(new File(in).isDirectory()){
			try {
				concatenateDirectory(in, out);
			} catch (IOException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			}
		}else{
			concatenatePattern(in, out);
		}
		t.stop();
		System.err.println(t);
		
	}
	
	public static void concatenatePattern(final String basename, final String out){
		assert(false) : "This is human-specific.";
		String outname=(out==null ? basename.replace("#", "ALL") : out);
		
		TextStreamWriter tsw=new TextStreamWriter(outname, true, false, true);
		tsw.start();
		
		for(int chrom=1; chrom<26; chrom++){
			String fname=basename.replace("#", ""+chrom);
			TextFile tf=new TextFile(fname, false, true);
			
			tsw.print(">chr"+chrom+"\n");
			for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
				char c=s.charAt(0);
				if(c!='>' && c!=';'){
					tsw.println(s);
				}
			}
			System.err.print(".");
		}
		tsw.poison();
		tsw.waitForFinish();
	}
	
	public static void concatenateDirectory(final String in, String out) throws IOException{
		if(out==null){out="stdout";}
		
		final byte[] buf=new byte[32768];
		
		final File dir=new File(in);
		final File[] files=dir.listFiles();
		Arrays.sort(files);
		
		final File outfile=new File(out);
		final OutputStream os=ReadWrite.getOutputStream(out, false, true, true);
		
		for(File f : files){
			if(f!=null && f.isFile() && !f.equals(outfile)){
				String fname=f.getAbsolutePath();
				System.err.println("Processing "+fname);
				
				InputStream is=ReadWrite.getInputStream(fname, false, false);
				
				for(int lim=is.read(buf); lim>0; lim=is.read(buf)){
					os.write(buf, 0, lim);
				}
				
				is.close();
				System.err.print(".");
			}
		}
		ReadWrite.close(os);
	}
	
	
}
