package stream;

import java.util.ArrayList;

import align2.Shared;

import dna.Data;
import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.FileFormat;

/**
 * @author Brian Bushnell
 * @date June 1, 2016
 *
 */
public class HeaderInputStream extends ReadInputStream {
	
	public static void main(String[] args){
		
		HeaderInputStream his=new HeaderInputStream(args[0], true);
		
		Read r=his.next();
		System.out.println(r.toText(false));
		his.close();
		
	}
	
	public HeaderInputStream(String fname, boolean allowSubprocess_){
		this(FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess_, false));
	}

	
	public HeaderInputStream(FileFormat ff){
		if(verbose){System.err.println("FastqReadInputStream("+ff+")");}
		
		stdin=ff.stdio();
		
		tf=new ByteFile1(ff, false);
	}

	@Override
	public void start() {}
	
	
	@Override
	public boolean hasMore() {
		if(buffer==null || next>=buffer.size()){
			if(tf.isOpen()){
				fillBuffer();
			}else{
				assert(generated>0) : "Was the file empty?";
			}
		}
		return (buffer!=null && next<buffer.size());
	}

	@Override
	public Read next() {
		if(!hasMore()){return null;}
		Read r=buffer.set(next, null);
		next++;
		consumed++;
		return r;
	}
	
	@Override
	public synchronized ArrayList<Read> nextList() {
		if(next!=0){throw new RuntimeException("'next' should not be used when doing blockwise access.");}
		if(buffer==null || next>=buffer.size()){fillBuffer();}
		ArrayList<Read> list=buffer;
		buffer=null;
		if(list!=null && list.size()==0){list=null;}
		consumed+=(list==null ? 0 : list.size());
		return list;
	}
	
	private synchronized void fillBuffer(){
		
		assert(buffer==null || next>=buffer.size());
		
		buffer=null;
		next=0;
		
		buffer=toReadList(tf, BUF_LEN, nextReadID);
		int bsize=(buffer==null ? 0 : buffer.size());
		nextReadID+=bsize;
		if(bsize<BUF_LEN){tf.close();}
		
		generated+=bsize;
		if(buffer==null){
			if(!errorState){
				errorState=true;
				System.err.println("Null buffer in FastqReadInputStream.");
			}
		}
	}
	
	public boolean close(){
		if(verbose){System.err.println("Closing "+this.getClass().getName()+" for "+tf.name()+"; errorState="+errorState);}
		errorState|=tf.close();
		if(verbose){System.err.println("Closed "+this.getClass().getName()+" for "+tf.name()+"; errorState="+errorState);}
		return errorState;
	}

	@Override
	public synchronized void restart() {
		generated=0;
		consumed=0;
		next=0;
		nextReadID=0;
		buffer=null;
		tf.reset();
	}
	
	public static ArrayList<Read> toReadList(ByteFile tf, int maxReadsToReturn, long numericID){
		byte[] line=null;
		ArrayList<Read> list=new ArrayList<Read>(Data.min(8192, maxReadsToReturn));
		int added=0;
		
//		Read prev=null;
		
		for(line=tf.nextLine(); line!=null && added<maxReadsToReturn; line=tf.nextLine()){
			
			Read r=new Read(null, 0, (byte)0, 0, 0, new String(line), null, numericID);

//			if(interleaved){
//				if(prev==null){prev=r;}
//				else{
//					prev.mate=r;
//					r.mate=prev;
//					r.setPairnum(1);
//					list.add(prev);
//					added++;
//					numericID++;
//					prev=null;
//				}
//			}else
			{
				list.add(r);
				added++;
				numericID++;
			}

			if(added>=maxReadsToReturn){break;}
		}
		assert(list.size()<=maxReadsToReturn);
		return list;
	}

	@Override
	public boolean paired() {return false;}
	
	/** Return true if this stream has detected an error */
	public boolean errorState(){return errorState;}

	private ArrayList<Read> buffer=null;
	private int next=0;
	
	private final ByteFile tf;
//	private final boolean interleaved;

	private final int BUF_LEN=Shared.READ_BUFFER_LENGTH;
	
	public long generated=0;
	public long consumed=0;
	private long nextReadID=0;
	
	public final boolean stdin;
	public static boolean verbose=false;

}
