package prok;

import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.PriorityQueue;

import dna.AminoAcid;
import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parser;
import shared.PreParser;
import shared.ReadStats;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.FASTQ;
import stream.FastaReadInputStream;
import stream.Read;
import stream.ReadInputStream;
import structures.LongHashSet;
import structures.ListNum;
import template.Accumulator;
import template.ThreadWaiter;

/**
 * Makes a consensus ribosomal sequence using raw reads as input.
 * 
 * @author Brian Bushnell
 * @date October 10, 2019
 *
 */
public class RiboMaker implements Accumulator<RiboMaker.ProcessThread> {
	
	/*--------------------------------------------------------------*/
	/*----------------        Initialization        ----------------*/
	/*--------------------------------------------------------------*/
	
	/**
	 * Code entrance from the command line.
	 * @param args Command line arguments
	 */
	public static void main(String[] args){
		//Start a timer immediately upon code entrance.
		Timer t=new Timer();
		
		//Create an instance of this class
		RiboMaker x=new RiboMaker(args);
		
		//Run the object
		x.process(t);
		
		//Close the print stream if it was redirected
		Shared.closeStream(x.outstream);
	}
	
	/**
	 * Constructor.
	 * @param args Command line arguments
	 */
	public RiboMaker(String[] args){
		
		{//Preparse block for help, config files, and outstream
			PreParser pp=new PreParser(args, getClass(), false);
			args=pp.args;
			outstream=pp.outstream;
		}
		
		//Set shared static variables prior to parsing
		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
		
		{//Parse the arguments
			final Parser parser=parse(args);
			Parser.processQuality();
			
			maxReads=parser.maxReads;
			overwrite=ReadStats.overwrite=parser.overwrite;
			append=ReadStats.append=parser.append;
			setInterleaved=parser.setInterleaved;
			
			in1=parser.in1;
			in2=parser.in2;
			qfin1=parser.qfin1;
			qfin2=parser.qfin2;
			extin=parser.extin;

			out1=parser.out1;
			qfout1=parser.qfout1;
			extout=parser.extout;
		}

		validateParams();
		doPoundReplacement(); //Replace # with 1 and 2
		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
		fixExtensions(); //Add or remove .gz or .bz2 as needed
		checkFileExistence(); //Ensure files can be read and written
		checkStatics(); //Adjust file-related static fields as needed for this program 
		
		//Create output FileFormat objects
		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
		
		fffilter=FileFormat.testInput(filterFile, FileFormat.FASTA, null, true, true);
		ffref=FileFormat.testInput(refFile, FileFormat.FASTA, null, true, true);

		//Create input FileFormat objects
		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
		
		if(fffilter==null){
			filter=null;
		}else{
			filter=loadFilter(fffilter, k);
		}
		loadRef();
	}
	
	/*--------------------------------------------------------------*/
	/*----------------    Initialization Helpers    ----------------*/
	/*--------------------------------------------------------------*/
	
	/** Parse arguments from the command line */
	private Parser parse(String[] args){
		
		//Create a parser object
		Parser parser=new Parser();
		
		//Set any necessary Parser defaults here
		//parser.foo=bar;
		
		//Parse each argument
		for(int i=0; i<args.length; i++){
			String arg=args[i];
			
			//Break arguments into their constituent parts, in the form of "a=b"
			String[] split=arg.split("=");
			String a=split[0].toLowerCase();
			String b=split.length>1 ? split[1] : null;
			if(b!=null && b.equalsIgnoreCase("null")){b=null;}
			
			if(a.equals("verbose")){
				verbose=Tools.parseBoolean(b);
			}else if(a.equals("ordered")){
				ordered=Tools.parseBoolean(b);
			}else if(a.equals("filter")){
				filterFile=b;
			}else if(a.equals("ref")){
				refFile=b;
			}else if(a.equals("parse_flag_goes_here")){
				long fake_variable=Tools.parseKMG(b);
				//Set a variable here
			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
				//do nothing
			}else{
				outstream.println("Unknown parameter "+args[i]);
				assert(false) : "Unknown parameter "+args[i];
			}
		}
		
		return parser;
	}
	
	/** Replace # with 1 and 2 in headers */
	private void doPoundReplacement(){
		//Do input file # replacement
		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
			in2=in1.replace("#", "2");
			in1=in1.replace("#", "1");
		}
		
		//Ensure there is an input file
		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
	}
	
	/** Add or remove .gz or .bz2 as needed */
	private void fixExtensions(){
		in1=Tools.fixExtension(in1);
		in2=Tools.fixExtension(in2);
		qfin1=Tools.fixExtension(qfin1);
		qfin2=Tools.fixExtension(qfin2);
	}
	
	/** Ensure files can be read and written */
	private void checkFileExistence(){
		//Ensure output files can be written
		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");
		}
		
		//Ensure input files can be read
		if(!Tools.testInputFiles(false, true, in1, in2, filterFile, refFile)){
			throw new RuntimeException("\nCan't read some input files.\n");  
		}
		
		//Ensure that no file was specified multiple times
		if(!Tools.testForDuplicateFiles(true, in1, in2, out1, filterFile, refFile)){
			throw new RuntimeException("\nSome file names were specified multiple times.\n");
		}
		
		assert(refFile!=null);
	}
	
	/** Make sure interleaving agrees with number of input and output files */
	private void adjustInterleaving(){
		//Adjust interleaved detection based on the number of input files
		if(in2!=null){
			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
		}

		//Adjust interleaved settings based on number of output files
		if(!setInterleaved){
			assert(in1!=null) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\n";
			if(in2!=null){ //If there are 2 input streams.
				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
			}
		}
	}
	
	/** Adjust file-related static fields as needed for this program */
	private static void checkStatics(){
		//Adjust the number of threads for input file reading
		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
			ByteFile.FORCE_MODE_BF2=true;
		}
		
		assert(FastaReadInputStream.settingsOK());
	}
	
	/** Ensure parameter ranges are within bounds and required parameters are set */
	private boolean validateParams(){
//		assert(minfoo>0 && minfoo<=maxfoo) : minfoo+", "+maxfoo;
		assert(false) : "TODO";
		return true;
	}
	
	/*--------------------------------------------------------------*/
	/*----------------         Outer Methods        ----------------*/
	/*--------------------------------------------------------------*/

	/** Create read streams and process all data */
	void process(Timer t){
		
		//Turn off read validation in the input threads to increase speed
		final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
		Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;
		
		//Create a read input stream
		final ConcurrentReadInputStream cris=makeCris();
		
		//Optionally create a read output stream
		final ConcurrentReadOutputStream ros=makeCros(cris.paired());
		
		//Reset counters
		readsProcessed=readsOut=0;
		basesProcessed=basesOut=0;
		
		//Process the reads in separate threads
		spawnThreads(cris, ros);
		
		if(verbose){outstream.println("Finished; closing streams.");}
		
		//Write anything that was accumulated by ReadStats
		errorState|=ReadStats.writeAll();
		//Close the read streams
		errorState|=ReadWrite.closeStreams(cris, ros);
		
		//Reset read validation
		Read.VALIDATE_IN_CONSTRUCTOR=vic;
		
		//Report timing and results
		t.stop();
		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
		outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
		
		//Throw an exception of there was an error in a thread
		if(errorState){
			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
		}
	}
	
	private void loadRef(){
		ArrayList<Read> reads=ReadInputStream.toReads(ffref, -1);
		ref0=reads.get(0).bases;
		ref=new byte[ref0.length+2*padding];
		for(int i=0, j=-padding; i<ref.length; i++, j++){
			byte b=(j>=0 && j<ref0.length ? ref0[j] : (byte)'N');
			ref[i]=b;
		}
		
		queues=new PriorityQueue[1+ref.length/queueWidth];
		for(int i=0; i<queues.length; i++){
			queues[i]=new PriorityQueue<Alignment>(queueLen);
		}
	}
	
	public static LongHashSet loadFilter(FileFormat ff, int k){
		if(ff==null){return null;}
		ArrayList<Read> reads=ReadInputStream.toReads(ff, -1);
		if(reads==null || reads.size()==0){return null;}
		LongHashSet set=new LongHashSet(4096);

		final int shift=2*k;
		final int shift2=shift-2;
		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
		int len=0;
		
		long kmer=0, rkmer=0;
		for(Read r : reads){
			final byte[] bases=r.bases;
			for(byte b : bases) {
				long x=AminoAcid.baseToNumber[b];
				long x2=AminoAcid.baseToComplementNumber[b];
				kmer=((kmer<<2)|x)&mask;
				rkmer=(rkmer>>>2)|(x2<<shift2);
				
				if(x>=0){
					len++;
					if(len>=k){
						set.add(Tools.max(kmer, rkmer));
					}
				}else{
					len=0;
					kmer=rkmer=0;
				}
			}
		}
		return set;
	}
	
	public static boolean passesFilter(Read r, int k, LongHashSet set){
		if(r==null) {return false;}
		if(set==null){return true;}

		final int shift=2*k;
		final int shift2=shift-2;
		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
		int len=0;
		long kmer=0, rkmer=0;

		final byte[] bases=r.bases;
		for(byte b : bases) {
			long x=AminoAcid.baseToNumber[b];
			long x2=AminoAcid.baseToComplementNumber[b];
			kmer=((kmer<<2)|x)&mask;
			rkmer=(rkmer>>>2)|(x2<<shift2);

			if(x>=0){
				len++;
				if(len>=k){
					long key=Tools.max(kmer, rkmer);
					if(set.contains(key)){return true;}
				}
			}else{
				len=0;
				kmer=rkmer=0;
			}
		}
		return false;
	}
	
	private ConcurrentReadInputStream makeCris(){
		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
		cris.start(); //Start the stream
		if(verbose){outstream.println("Started cris");}
		boolean paired=cris.paired();
		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
		return cris;
	}
	
	private ConcurrentReadOutputStream makeCros(boolean pairedInput){
		if(ffout1==null){return null;}

		//Select output buffer size based on whether it needs to be ordered
		final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);

		final ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ffout1, null, qfout1, null, buff, null, false);
		ros.start(); //Start the stream
		return ros;
	}
	
	/*--------------------------------------------------------------*/
	/*----------------       Thread Management      ----------------*/
	/*--------------------------------------------------------------*/
	
	/** Spawn process threads */
	private void spawnThreads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){
		
		//Do anything necessary prior to processing
		
		//Determine how many threads may be used
		final int threads=Shared.threads();
		
		//Fill a list with ProcessThreads
		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
		for(int i=0; i<threads; i++){
			alpt.add(new ProcessThread(cris, i));
		}
		
		//Start the threads and wait for them to finish
		boolean success=ThreadWaiter.startAndWait(alpt, this);
		errorState&=!success;
		
		//Do anything necessary after processing
		assert(false) : "TODO: Make consensus and write it?";
	}
	
	@Override
	public final void accumulate(ProcessThread pt){
		readsProcessed+=pt.readsProcessedT;
		basesProcessed+=pt.basesProcessedT;
		readsOut+=pt.readsOutT;
		basesOut+=pt.basesOutT;
		errorState|=(!pt.success);

		for(int i=0; i<queues.length; i++){
			PriorityQueue<Alignment> q=queues[i];
			PriorityQueue<Alignment> qt=pt.queuesT[i];
			for(Alignment a : qt){
				addToQueue(a, q);
			}
		}
	}
	
	@Override
	public final boolean success(){return !errorState;}
	
	/*--------------------------------------------------------------*/
	/*----------------         Inner Methods        ----------------*/
	/*--------------------------------------------------------------*/
	
	boolean addToQueue(Alignment best, PriorityQueue<Alignment>[] queues){
		int start=best.start;
		int qnum=start/queueWidth;
		PriorityQueue<Alignment> queue=queues[qnum];
		return addToQueue(best, queue);
	}
	
	boolean addToQueue(Alignment best, PriorityQueue<Alignment> queue){
		if(queue.size()<queueLen){queue.add(best);}
		else{
			Alignment bottom=queue.peek();
			if(bottom.compareTo(best)>=0){return false;}
			queue.poll();
			queue.add(best);
		}
		return true;
	}
	
	/*--------------------------------------------------------------*/
	/*----------------         Inner Classes        ----------------*/
	/*--------------------------------------------------------------*/
	
	/** This class is static to prevent accidental writing to shared variables.
	 * It is safe to remove the static modifier. */
	class ProcessThread extends Thread {
		
		//Constructor
		ProcessThread(final ConcurrentReadInputStream cris_, final int tid_){
			cris=cris_;
			tid=tid_;
			
			queuesT=new PriorityQueue[1+ref.length/queueWidth];
			for(int i=0; i<queuesT.length; i++){
				queuesT[i]=new PriorityQueue<Alignment>(queueLen);
			}
		}
		
		//Called by start()
		@Override
		public void run(){
			//Do anything necessary prior to processing
			
			//Process the reads
			processInner();
			
			//Do anything necessary after processing
			
			//Indicate successful exit status
			success=true;
		}
		
		/** Iterate through the reads */
		void processInner(){
			
			//Grab the first ListNum of reads
			ListNum<Read> ln=cris.nextList();

			//Check to ensure pairing is as expected
			if(ln!=null && !ln.isEmpty()){
				Read r=ln.get(0);
//				assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); //Disabled due to non-static access
			}

			//As long as there is a nonempty read list...
			while(ln!=null && ln.size()>0){
//				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");} //Disabled due to non-static access
				
				processList(ln);
				
				//Notify the input stream that the list was used
				cris.returnList(ln);
//				if(verbose){outstream.println("Returned a list.");} //Disabled due to non-static access
				
				//Fetch a new list
				ln=cris.nextList();
			}

			//Notify the input stream that the final list was used
			if(ln!=null){
				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
			}
		}
		
		void processList(ListNum<Read> ln){

			//Grab the actual read list from the ListNum
			final ArrayList<Read> reads=ln.list;
			
			//Loop through each read in the list
			for(int idx=0; idx<reads.size(); idx++){
				final Read r1=reads.get(idx);
				final Read r2=r1.mate;
				
				//Validate reads in worker threads
				if(!r1.validated()){r1.validate(true);}
				if(r2!=null && !r2.validated()){r2.validate(true);}

				//Track the initial length for statistics
				final int initialLength1=r1.length();
				final int initialLength2=r1.mateLength();

				//Increment counters
				readsProcessedT+=r1.pairCount();
				basesProcessedT+=initialLength1+initialLength2;
				
				{
					//Reads are processed in this block.
					processReadPair(r1, r2);
					
//					if(!keep){reads.set(idx, null);}
//					else{
//						readsOutT+=r1.pairCount();
//						basesOutT+=r1.pairLength();
//					}
				}
			}

			//Output reads to the output stream
//			if(ros!=null){ros.add(reads, ln.id);}
		}
		
		/**
		 * Process a read or a read pair.
		 * @param r1 Read 1
		 * @param r2 Read 2 (may be null)
		 * @return True if the reads should be kept, false if they should be discarded.
		 */
		void processReadPair(final Read r1, final Read r2){
			boolean pass=passesFilter(r1, k, filter) || passesFilter(r2, k, filter);
			if(!pass){return;}
			processRead(r1);
			processRead(r2);
		}
		
		void processRead(final Read r){
			Alignment plus=new Alignment(r);
			plus.align(ref);
			
			r.reverseComplement();
			Alignment minus=new Alignment(r);
			minus.align(ref);
			
			Alignment best=null;
			if(plus.id>=minus.id){
				r.reverseComplement();
				best=plus;
			}else{
				best=minus;
			}
			if(best.id<minID) {return;}
			
			addToQueue(best, queuesT);
		}

		/** Number of reads processed by this thread */
		protected long readsProcessedT=0;
		/** Number of bases processed by this thread */
		protected long basesProcessedT=0;
		
		/** Number of reads retained by this thread */
		protected long readsOutT=0;
		/** Number of bases retained by this thread */
		protected long basesOutT=0;
		
		/** True only if this thread has completed successfully */
		boolean success=false;
		

		private PriorityQueue<Alignment>[] queuesT;
		
		/** Shared input stream */
		private final ConcurrentReadInputStream cris;
		/** Thread ID */
		final int tid;
	}
	
	/*--------------------------------------------------------------*/
	/*----------------            Fields            ----------------*/
	/*--------------------------------------------------------------*/

	/** Primary input file path */
	private String in1=null;
	/** Secondary input file path */
	private String in2=null;
	
	private String qfin1=null;
	private String qfin2=null;

	/** Primary output file path */
	private String out1=null;

	private String qfout1=null;
	
	private String filterFile;
	private String refFile;
	
	/** Override input file extension */
	private String extin=null;
	/** Override output file extension */
	private String extout=null;
	
	/** Whether interleaved was explicitly set. */
	private boolean setInterleaved=false;

	/** Original ref */
	private byte[] ref0;
	/** Padded ref */
	private byte[] ref;
	
	private int padding=100;
	private int queueLen=20;
	private int queueWidth=20;
	private float minID=0.4f;
	
	private PriorityQueue<Alignment>[] queues;
	
	/*--------------------------------------------------------------*/

	/** Number of reads processed */
	protected long readsProcessed=0;
	/** Number of bases processed */
	protected long basesProcessed=0;

	/** Number of reads retained */
	protected long readsOut=0;
	/** Number of bases retained */
	protected long basesOut=0;

	/** Quit after processing this many input reads; -1 means no limit */
	private long maxReads=-1;
	
	/*--------------------------------------------------------------*/
	/*----------------         Final Fields         ----------------*/
	/*--------------------------------------------------------------*/

	/** Primary input file */
	private final FileFormat ffin1;
	/** Secondary input file */
	private final FileFormat ffin2;
	/** Filter input file */
	private final FileFormat fffilter;
	/** Ref input file */
	private final FileFormat ffref;
	
	/** Primary output file */
	private final FileFormat ffout1;
	
	private final LongHashSet filter;
	private final int k=31;
	
	
	/*--------------------------------------------------------------*/
	/*----------------        Common Fields         ----------------*/
	/*--------------------------------------------------------------*/
	
	/** Print status messages to this output stream */
	private PrintStream outstream=System.err;
	/** Print verbose messages */
	public static boolean verbose=false;
	/** True if an error was encountered */
	public boolean errorState=false;
	/** Overwrite existing output files */
	private boolean overwrite=false;
	/** Append to existing output files */
	private boolean append=false;
	/** Reads are output in input order */
	private boolean ordered=false;
	
}
