package tax;

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

import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parse;
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 structures.ListNum;

/**
 * Filters sequences according to their taxonomy,
 * as determined by the sequence name.  Sequences should
 * be labeled with a gi number or NCBI taxID.
 * 
 * @author Brian Bushnell
 * @date November 23, 2015
 *
 */
public class SplitByTaxa {
	
	/*--------------------------------------------------------------*/
	/*----------------        Initialization        ----------------*/
	/*--------------------------------------------------------------*/
	
	/**
	 * Code entrance from the command line.
	 * @param args Command line arguments
	 */
	public static void main(String[] args){
		Timer t=new Timer();
		SplitByTaxa x=new SplitByTaxa(args);
		x.process(t);
		
		//Close the print stream if it was redirected
		Shared.closeStream(x.outstream);
	}
	
	/**
	 * Constructor.
	 * @param args Command line arguments
	 */
	public SplitByTaxa(String[] args){
		
		{//Preparse block for help, config files, and outstream
			PreParser pp=new PreParser(args, getClass(), false);
			args=pp.args;
			outstream=pp.outstream;
		}
		
		//Set some shared static variables
		Shared.capBuffers(4);
		ReadWrite.USE_UNPIGZ=true;
		ReadWrite.USE_PIGZ=false;
		ReadWrite.USE_GZIP=false;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();

		boolean setInterleaved=false; //Whether interleaved was explicitly set.
		String giTableFile=null;
		String taxTreeFile=null;
		
		//Create a parser object
		Parser parser=new Parser();
		
		//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(parser.parse(arg, a, b)){//Parse standard flags in the parser
				//do nothing
			}else if(a.equals("verbose")){
				verbose=Parse.parseBoolean(b);
			}else if(a.equals("taxlevel") || a.equals("tl") || a.equals("level") || a.equals("lv")){
				taxLevelE=TaxTree.parseLevelExtended(b);
			}else if(a.equals("table") || a.equals("gi") || a.equals("gitable")){
				giTableFile=b;
			}else if(a.equals("tree") || a.equals("taxtree")){
				taxTreeFile=b;
			}else{
				outstream.println("Unknown parameter "+args[i]);
				assert(false) : "Unknown parameter "+args[i];
				//				throw new RuntimeException("Unknown parameter "+args[i]);
			}
		}
		
		if("auto".equalsIgnoreCase(taxTreeFile)){taxTreeFile=TaxTree.defaultTreeFile();}
		if("auto".equalsIgnoreCase(giTableFile)){giTableFile=TaxTree.defaultTableFile();}
		
		{//Process parser fields
			Parser.processQuality();
			
			maxReads=parser.maxReads;
			
			overwrite=ReadStats.overwrite=parser.overwrite;
			append=ReadStats.append=parser.append;
			setInterleaved=parser.setInterleaved;
			
			in1=parser.in1;
			in2=parser.in2;

			out1=parser.out1;
			out2=parser.out2;
			
			extin=parser.extin;
			extout=parser.extout;
		}
		
		//Do input file # replacement
		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
			in2=in1.replace("#", "2");
			in1=in1.replace("#", "1");
		}
		
		//Do output file # replacement
		if(out1!=null && out2==null && out1.indexOf('#')>-1){
			out2=out1.replace("#", "2");
			out1=out1.replace("#", "1");
		}
		
		assert(out1==null || out1.contains("%")) : "Output filename must contain % symbol.";
		assert(out2==null || out2.contains("%")) : "Output filename must contain % symbol.";
		assert(taxTreeFile!=null) : "This requires a taxtree file.  On NERSC systems, set tree=auto.";
		
		//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;
		}
		
		assert(FastaReadInputStream.settingsOK());
		
		//Ensure there is an input file
		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
		
		//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;
		}
		
		//Ensure out2 is not set without out1
		if(out1==null && out2!=null){throw new RuntimeException("Error - cannot define out2 without defining out1.");}
		
		//Adjust interleaved settings based on number of output files
		if(!setInterleaved){
			assert(in1!=null && (out1!=null || out2==null)) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\nout2="+out2+"\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);
			}else{ //There is one input stream.
				if(out2!=null){
					FASTQ.FORCE_INTERLEAVED=true;
					FASTQ.TEST_INTERLEAVED=false;
					outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
				}
			}
		}
		
		//Ensure output files can be written
		if(!Tools.testOutputFiles(overwrite, append, false, out1, out2)){
			outstream.println((out1==null)+", "+(out2==null)+", "+out1+", "+out2);
			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+", "+out2+"\n");
		}
		
		//Ensure input files can be read
		if(!Tools.testInputFiles(false, true, in1, in2)){
			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, out2)){
			throw new RuntimeException("\nSome file names were specified multiple times.\n");
		}

		//Create input FileFormat objects
		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
		
		TaxFilter.loadGiTable(giTableFile);
		tree=TaxFilter.loadTree(taxTreeFile);
	}
	
	/*--------------------------------------------------------------*/
	/*----------------         Outer Methods        ----------------*/
	/*--------------------------------------------------------------*/

	/** Create read streams and process all data */
	public void process(Timer t){
		
		//Create a read input stream
		final ConcurrentReadInputStream cris;
		{
			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null);
			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"));}
		
		//Reset counters
		readsProcessed=0;
		basesProcessed=0;
		
		final HashMap<String, ConcurrentReadOutputStream> map=new HashMap<String, ConcurrentReadOutputStream>();
		
		//Process the read stream
		processInner(cris, map);
		
		if(verbose){outstream.println("Finished; closing streams.");}
		
		//Write anything that was accumulated by ReadStats
		errorState|=ReadStats.writeAll();
		//Close the read streams
		errorState|=ReadWrite.closeStream(cris);
		
		for(ConcurrentReadOutputStream ros : map.values()){
			ReadWrite.closeStream(ros);
		}
		
		//Report timing and results
		t.stop();
		outstream.println("Reads In:               \t"+readsProcessed+" reads       \t"+basesProcessed+" bases");
		outstream.println();
		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
		
		//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.");
		}
	}
	
	/** Iterate through the reads */
	void processInner(final ConcurrentReadInputStream cris, HashMap<String, ConcurrentReadOutputStream> map){
		
		{
			//Grab the first ListNum of reads
			ListNum<Read> ln=cris.nextList();
			//Grab the actual read list from the ListNum
			ArrayList<Read> reads=(ln!=null ? ln.list : null);
			
			//Check to ensure pairing is as expected
			if(reads!=null && !reads.isEmpty()){
				Read r=reads.get(0);
				assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
			}
			
			//As long as there is a nonempty read list...
			while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");}
				
				//Loop through each read in the list
				for(int idx=0; idx<reads.size(); idx++){
					final Read r1=reads.get(idx);
					
					//Track the initial length for statistics
					final int initialLength1=r1.length();
					final int initialLength2=(r1.mateLength());
					
					//Increment counters
					readsProcessed+=r1.pairCount();
					basesProcessed+=initialLength1+initialLength2;
					
					TaxNode tn=tree.parseNodeFromHeader(r1.id, true);
					if(tn==null){tn=tree.getNodeByName(r1.id);}
					if(tn==null){tn=unknown;}
					while(tn.levelExtended<taxLevelE && tn.id!=tn.pid){tn=tree.getNode(tn.pid);}
					
					if(out1!=null){
						ConcurrentReadOutputStream ros=map.get(tn.name);
						if(ros==null){
							final int buff=4;
							FileFormat ffout1=null, ffout2=null;
							ffout1=FileFormat.testOutput(out1.replaceFirst("%", tn.name.replaceAll("\\s+", "_").replaceAll("[/\\\\]", "")), FileFormat.FASTQ, extout, false, overwrite, append, false);
							if(out2!=null){ffout2=FileFormat.testOutput(out2.replaceFirst("%", tn.name.replaceAll("\\s+", "_").replaceAll("[/\\\\]", "")), FileFormat.FASTQ, extout, false, overwrite, append, false);}
							ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, null, null, buff, null, false);
							ros.start(); //Start the stream
							map.put(tn.name, ros);
						}
						ArrayList<Read> temp=new ArrayList<Read>(1); //Kind of inefficient
						temp.add(r1);
						ros.add(temp, 0);
					}
				}
				
				//Notify the input stream that the list was used
				cris.returnList(ln);
				if(verbose){outstream.println("Returned a list.");}
				
				//Fetch a new list
				ln=cris.nextList();
				reads=(ln!=null ? ln.list : null);
			}
			
			//Notify the input stream that the final list was used
			if(ln!=null){
				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
			}
		}
		
		//Do anything necessary after processing
		
	}
	
	/*--------------------------------------------------------------*/
	/*----------------         Inner Methods        ----------------*/
	/*--------------------------------------------------------------*/
	
	/*--------------------------------------------------------------*/
	/*----------------            Fields            ----------------*/
	/*--------------------------------------------------------------*/

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

	/** Primary output file path */
	private String out1=null;
	/** Secondary output file path */
	private String out2=null;
	
	/** Override input file extension */
	private String extin=null;
	/** Override output file extension */
	private String extout=null;
	
	/** The actual filter */
	private int taxLevelE=TaxTree.stringToLevelExtended("phylum");
	
	/*--------------------------------------------------------------*/

	/** Number of reads processed */
	protected long readsProcessed=0;
	/** Number of bases processed */
	protected long basesProcessed=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;
	
	private final TaxTree tree;
	
	private final TaxNode unknown=new TaxNode(-99, -99, TaxTree.LIFE, TaxTree.LIFE_E, "UNKNOWN");
	
	/*--------------------------------------------------------------*/
	/*----------------        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;
	/** This flag has no effect on singlethreaded programs */
	private final boolean ordered=false;
	
}