package bin;

import java.io.PrintStream;
import java.util.Arrays;
import java.util.Collection;

import dna.AminoAcid;
import ml.CellNet;
import shared.Tools;
import structures.IntHashMap;
import tax.TaxTree;

/**
 * Superclass for binner classes
 * @author Brian Bushnell
 * @date Feb 4, 2025
 *
 */
public class BinObject {
	
	public static void setQuant(int x) {
		quant=x;
		assert(quant>0);
		initialize();
	}
	
//	public static void setK(int x) {
//		assert(k>0 && k<16);
//		k=x;
//	}
	
	private static void initialize() {
		remapMatrix=makeRemapMatrix(2, 5);
		canonicalKmers=makeCanonicalKmers();
		invCanonicalKmers=makeInvCanonicalKmers();
		gcmapMatrix=makeGCMapMatrix();
	}
	
	private static synchronized int[][] makeRemapMatrix(int mink, int maxk){
		int[][] matrix=new int[maxk+1][];
		for(int i=mink; i<=maxk; i++) {
			matrix[i]=makeRemap(i);
		}
		return matrix;
	}
	
	private static synchronized int[][] makeGCMapMatrix(){
		int[][] matrix=new int[remapMatrix.length][];
		for(int i=0; i<matrix.length; i++) {
			int[] remap=remapMatrix[i];
			if(remap!=null) {
				matrix[i]=gcmap(i, remap);
			}
		}
		return matrix;
	}
	
	private static synchronized int[] makeCanonicalKmers() {
		int[] array=new int[remapMatrix.length];
		for(int i=0; i<array.length; i++) {
			int[] remap=remapMatrix[i];
			int max=(remap==null ? 1 : Tools.max(remap)+1);
			array[i]=max;
		}
		return array;
	}
	
	private static synchronized float[] makeInvCanonicalKmers() {
		float[] array=new float[canonicalKmers.length];
		for(int i=0; i<array.length; i++) {
			array[i]=1f/canonicalKmers[i];
		}
		return array;
	}
	
	public static int[] makeRemap(int k){
		final int bits=2*k;
		final int max=(int)((1L<<bits)-1);
		int count=0;
		IntHashMap canonMap=new IntHashMap();
		IntHashMap kmerMap=new IntHashMap();
		for(int kmer=0; kmer<=max; kmer++){
//			int ungapped=ungap(kmer, k, gap);
			int canon=Tools.min(kmer, AminoAcid.reverseComplementBinaryFast(kmer, k));
			if(canon%quant==0 && !canonMap.containsKey(canon)) {
				canonMap.put(canon, count);
				count++;
			}
			int idx=canonMap.get(canon);
			kmerMap.put(kmer, idx);
		}
		int[] remap=new int[max+1];
		Arrays.fill(remap, -1);
		for(int kmer=0; kmer<=max; kmer++){
			remap[kmer]=kmerMap.get(kmer);
//			System.err.println(AminoAcid.kmerToString(kmer, k2)+" -> "+AminoAcid.kmerToString(remap[kmer], k));
		}
		return remap;
	}
	
	public static int ungap(int kmer, int k, int gap) {
		if(gap<1) {return kmer;}
		int half=k/2;
		int halfbits=half*2;
		int gapbits=2*gap;
		int mask=~((-1)<<halfbits);
		int ungapped=(kmer&mask)|((kmer>>gapbits)&~mask);
		return ungapped;
	}
	
	public static int[] gcmap(int k, int[] remap){
		int[] gcContent=new int[] {0, 1, 1, 0};
		final int bits=2*k;
		final int max=(int)((1L<<bits)-1);
		int[] gcmap=new int[canonicalKmers[k]];
		for(int kmer=0; kmer<=max; kmer++){
			int gc=0;
			for(int i=0, kmer2=kmer; i<k; i++) {
				gc+=gcContent[kmer2&3];
				kmer2>>=2;
			}
			int idx=remap[kmer];
			gcmap[idx]=gc;
		}
		return gcmap;
	}
	
	public static int countKmers(final byte[] bases, final int[] counts, int k){
		if(quant>1) {return countKmers_quantized(bases, counts, k);}
		if(bases==null || bases.length<k){return 0;}
		
		final int shift=2*k;
		final int mask=~((-1)<<shift);
		
		int kmer=0;
//		int rkmer=0;
		int len=0;
		int valid=0;
		int[] remap=remapMatrix[k];
		
		for(int i=0; i<bases.length; i++){
			byte b=bases[i];
			int x=AminoAcid.baseToNumber[b];
//			int x2=AminoAcid.baseToComplementNumber[b];
			kmer=((kmer<<2)|x)&mask;
//			rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
			if(x>=0){
				len++;
				if(len>=k) {
					valid++;
					counts[remap[kmer]]++;
				}
			}else{len=kmer=0;}
		}
		return valid;
	}
	
	public static int countKmers_quantized(final byte[] bases, final int[] counts, int k){
		if(bases==null || bases.length<k){return 0;}
//		counts=(counts!=null ? counts : new int[canonicalKmers]);
		
		final int shift=2*k;
		final int mask=~((-1)<<shift);
		int[] remap=remapMatrix[k];
		
		int kmer=0;
		int len=0;
		int valid=0;
		for(int i=0; i<bases.length; i++){
			byte b=bases[i];
			int x=AminoAcid.baseToNumber[b];
			kmer=((kmer<<2)|x)&mask;
			if(x>=0){
				len++;
				if(len>=k) {
					valid++;
					int pos=remap[kmer];
					if(pos>=0) {counts[pos]++;}
				}
			}else{len=kmer=0;}
		}
		return valid;
	}
	
	/**
	 * @param a Contig kmer frequencies
	 * @param b Cluster kmer frequencies
	 * @return Score
	 */
	static final float absDif(float[] a, float[] b){
		assert(a.length==b.length);
		double sum=0;
		for(int i=0; i<a.length; i++){
			sum+=Math.abs(a[i]-b[i]);
		}

		return (float)sum;
	}
	
	static final float absDif(int[] a, int[] b){
		return absDif(a, b, 1f/Tools.sum(a), 1f/Tools.sum(b));
	}
	
	/**
	 * @param a Contig kmer counts
	 * @param b Cluster kmer counts
	 * @return Score
	 */
	static final float absDif(int[] a, int[] b, float inva, float invb){
		assert(a.length==b.length);
		float sum=0;
		for(int i=0; i<a.length; i++){
			float ai=a[i]*inva, bi=b[i]*invb;
			sum+=Math.abs(ai-bi);
		}
		return sum;
	}
	
	/**
	 * @param a Contig kmer frequencies
	 * @param b Cluster kmer frequencies
	 * @return Score
	 */
	static final float rmsDif(float[] a, float[] b){
		assert(a.length==b.length);
		double sum=0;
		for(int i=0; i<a.length; i++){
//			double d=Tools.absdif((double)a[i], (double)b[i]);
			double d=(a[i])-(b[i]);
			sum+=d*d;
		}

		return (float)Math.sqrt(sum/a.length);
	}
	
	static final float rmsDif(int[] a, int[] b){
		return rmsDif(a, b, 1f/Tools.sum(a), 1f/Tools.sum(b));
	}
	
	/**
	 * @param a Contig kmer counts
	 * @param b Cluster kmer counts
	 * @return Score
	 */
	static final float rmsDif(int[] a, int[] b, float inva, float invb){
		assert(a.length==b.length);
		long sum=0;
		for(int i=0; i<a.length; i++){
			float ai=a[i]*inva, bi=b[i]*invb;
			float d=(ai-bi);
			sum+=d*d;
		}
		return (float)Math.sqrt(sum/a.length);
	}
	
	/**
	 * @param a Contig kmer frequencies
	 * @param b Cluster kmer frequencies
	 * @return Score
	 */
	static final float ksFunction(float[] a, float[] b){
		assert(a.length==b.length);
		double sum=0;
		for(int i=0; i<a.length; i++){
			double ai=a[i]+0.0005;
			double bi=b[i]+0.0005;
			double d=(double)ai*Math.log(ai/bi);
			sum+=d;
		}
		
		return (float)sum;
	}
	
	static boolean isValid(Collection<? extends Bin> list, boolean allowLeafContigs) {
		for(Bin b : list) {
			if(b.isCluster()) {
				Cluster c=(Cluster)b;
				assert(c.isValid());
				for(Contig x : c.contigs) {assert(x.isValid());}
			}else {
				Contig c=(Contig)b;
				assert(c.isValid());
				assert(allowLeafContigs || c.cluster()==null);
//				assert(c.cluster()==null || c.cluster().isValid()); //This is too slow
			}
		}
		return true;
	}

//	public static int k() {return k;}
////	public static int gap() {return gap;}
//
//	/** Kmer length for frequencies */
//	private static int k=4;
//	/** Kmer gap length */
////	private static int gap=0;
	

	private static int quant=1;//Determines how many tetramers to use for comparisons
	/** Maps a kmer to index in frequency array */
	public static int[][] remapMatrix=makeRemapMatrix(2, 5);
	/** Number of canonical kmers; frequency array length */
	public static int[] canonicalKmers=makeCanonicalKmers();
	public static float[] invCanonicalKmers=makeInvCanonicalKmers();
	/** Maps a kmer to index in gc content array */
	public static int[][] gcmapMatrix=makeGCMapMatrix();
	
	/** Print status messages to this output stream */
	static PrintStream outstream=System.err;
	static TaxTree tree=null;
	
	static int minClusterSize=50000;
	static int minContigsPerCluster=1;
	static float depthBoost=0.25f;
	
	public static boolean countPentamers=true;
	public static int minPentamerSizeCount=2000;
	public static int minPentamerSizeCompare=40000;
	
	static boolean loud=false;
	static boolean verbose;
	static float sketchDensity=1/100f;
	static boolean sketchContigs=false;
	static boolean sketchClusters=false;
	static boolean sketchOutput=false;
	static boolean sketchInBulk=true;
	static int sketchSize=20000;
	
	static boolean validation=false;
	static boolean grading=false;
	static boolean parseTaxid=true;
	static boolean depthZeroProxy=true;
	static int globalTime=0;

	static CellNet net0small=null;
	static CellNet net0mid=null;
	static CellNet net0large=null;
	
//	static {setK(4, 0);}
//	static {
//		for(int i=0; i<6; i++) {
//			System.err.println("K="+i);
//			System.err.println("canonicalKmers="+canonicalKmers[i]);
//			System.err.println("invCanonicalKmers="+invCanonicalKmers[i]);
//			System.err.println("remapMatrix="+Arrays.toString(remapMatrix[i]));
//			System.err.println("gcmapMatrix="+Arrays.toString(gcmapMatrix[i]));
//		}
//		assert(false);
//	}
	
}