package jgi;

import java.io.PrintStream;

import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.ByteFile2;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ByteBuilder;
import stream.ConcurrentGenericReadInputStream;
import stream.FastaReadInputStream;

/**
 * @author Brian Bushnell
 * @date May 9, 2016
 *
 */
public class A_SampleByteFile {
	
	public static void main(String[] args){
		//Start a timer immediately upon code entrance.
		Timer t=new Timer();
		
		//Create an instance of this class
		A_SampleByteFile x=new A_SampleByteFile(args);
		
		//Run the object
		x.process(t);
		
		//Close the print stream if it was redirected
		Shared.closeStream(x.outstream);
	}
	
	public A_SampleByteFile(String[] args){
		
		{//Preparse block for help, config files, and outstream
			PreParser pp=new PreParser(args, getClass(), false);
			args=pp.args;
			outstream=pp.outstream;
		}
		
		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
		
		Parser parser=new Parser();
		for(int i=0; i<args.length; i++){
			String arg=args[i];
			String[] split=arg.split("=");
			String a=split[0].toLowerCase();
			String b=split.length>1 ? split[1] : null;

			if(a.equals("invalid")){
				outInvalid=b;
			}else if(a.equals("lines")){
				maxLines=Long.parseLong(b);
				if(maxLines<0){maxLines=Long.MAX_VALUE;}
			}else if(a.equals("verbose")){
				verbose=Tools.parseBoolean(b);
				ByteFile1.verbose=verbose;
				ByteFile2.verbose=verbose;
				stream.FastaReadInputStream.verbose=verbose;
				ConcurrentGenericReadInputStream.verbose=verbose;
				stream.FastqReadInputStream.verbose=verbose;
				ReadWrite.verbose=verbose;
			}else if(parser.parse(arg, a, b)){
				//do nothing
			}else{
				outstream.println("Unknown parameter "+args[i]);
				assert(false) : "Unknown parameter "+args[i];
				//				throw new RuntimeException("Unknown parameter "+args[i]);
			}
		}
		
		{//Process parser fields
			overwrite=parser.overwrite;
			append=parser.append;
			
			in1=parser.in1;

			out1=parser.out1;
		}
		
		assert(FastaReadInputStream.settingsOK());
		
		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
		
		if(!ByteFile.FORCE_MODE_BF2){
			ByteFile.FORCE_MODE_BF2=false;
			ByteFile.FORCE_MODE_BF1=true;
		}

		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
		
		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
			outstream.println((out1==null)+", "+out1);
			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
		}

		ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, overwrite, append, false);
		ffoutInvalid=FileFormat.testOutput(outInvalid, FileFormat.TXT, null, true, overwrite, append, false);
		ffin1=FileFormat.testInput(in1, FileFormat.TXT, null, true, true);
	}
	
	void process(Timer t){
		
		ByteFile bf=ByteFile.makeByteFile(ffin1);
		ByteStreamWriter bsw=new ByteStreamWriter(ffout1);
		bsw.start();
		
		assert(false) : "Header goes here.";
//		bsw.print("#Name\tAncestor\tMajority\tTaxonomy...\n".getBytes());
		
		ByteStreamWriter bswInvalid=null;
		if(ffoutInvalid!=null){
			bswInvalid=new ByteStreamWriter(ffoutInvalid);
			bswInvalid.start();
		}
		
		byte[] line=bf.nextLine();
		ByteBuilder bb=new ByteBuilder();
		
		while(line!=null){
			if(line.length>0){
				if(maxLines>0 && linesProcessed>=maxLines){break;}
				linesProcessed++;
				bytesProcessed+=(line.length+1);
				
				final boolean valid=(line[0]!='#');
				
				if(valid){
					linesOut++;
					bytesOut+=(line.length+1);
					for(int i=0; i<line.length && line[i]!='\t'; i++){
						bb.append(line[i]);
					}
					bb.append('\n');
					bsw.print(bb.toBytes());
					bb.clear();
				}else{
					if(bswInvalid!=null){
						bswInvalid.println(line);
					}
				}
			}
			line=bf.nextLine();
		}
		
		errorState|=bf.close();
		if(bsw!=null){errorState|=bsw.poisonAndWait();}
		if(bswInvalid!=null){errorState|=bswInvalid.poisonAndWait();}
		
		t.stop();
		
		outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
		
		outstream.println();
		outstream.println("Valid Lines:       \t"+linesOut);
		outstream.println("Invalid Lines:     \t"+(linesProcessed-linesOut));
		
		if(errorState){
			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
		}
	}
	
	/*--------------------------------------------------------------*/
	
	
	/*--------------------------------------------------------------*/
	
	private String in1=null;
	private String out1=null;
	private String outInvalid=null;
	
	/*--------------------------------------------------------------*/
	
	private long linesProcessed=0;
	private long linesOut=0;
	private long bytesProcessed=0;
	private long bytesOut=0;
	
	private long maxLines=Long.MAX_VALUE;
	
	/*--------------------------------------------------------------*/
	
	private final FileFormat ffin1;
	private final FileFormat ffout1;
	private final FileFormat ffoutInvalid;
	
	
	/*--------------------------------------------------------------*/
	
	private PrintStream outstream=System.err;
	public static boolean verbose=false;
	public boolean errorState=false;
	private boolean overwrite=false;
	private boolean append=false;
	
}
