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package org.broadinstitute.gatk.utils.pairhmm;

import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import static org.broadinstitute.gatk.utils.pairhmm.PairHMMModel.*;


/**
 * Created with IntelliJ IDEA.
 * User: rpoplin, carneiro
 * Date: 10/16/12
 */
public class DebugJNILoglessPairHMM extends LoglessPairHMM {

    private static final boolean dumpSandboxOnly = false;        //simulates ifdef
    private static final boolean debug = false;  //simulates ifdef
    private static final boolean verify = !dumpSandboxOnly && (debug || true);        //simulates ifdef
    private static final boolean debug0_1 = false;       //simulates ifdef
    private static final boolean debug1 = false; //simulates ifdef
    private static final boolean debug2 = false;
    private static final boolean debug3 = false;
   
    //Debugging stats 
    private int numCalls = 0;
    private int numComputeLikelihoodCalls = 0;
    protected HashMap<String, BufferedWriter> filenameToWriter = new HashMap<String, BufferedWriter>();

    private JNILoglessPairHMM jniPairHMM = null;
    public DebugJNILoglessPairHMM(final PairHMM.HMM_IMPLEMENTATION hmmType, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub, final boolean alwaysLoadVectorLoglessPairHMMLib) {
        super();
        switch(hmmType) {
            case VECTOR_LOGLESS_CACHING:
                jniPairHMM = new VectorLoglessPairHMM(pairHMMSub, alwaysLoadVectorLoglessPairHMMLib);
                break;
            default:
                throw new UserException.BadArgumentValue("pairHMM","Specified JNIPairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are VECTOR_LOGLESS_CACHING");
        }
    }

    @Override
    public void close()
    {
        jniPairHMM.close();
        debugClose();
    }

    //Used only when testing parts of the compute kernel
    /**
     * {@inheritDoc}
     */
    @Override
    public void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
        if(verify)
            super.initialize(readMaxLength, haplotypeMaxLength);
        if(debug3)
        {
            System.out.println("Java: alloc initialized readMaxLength : "+readMaxLength+" haplotypeMaxLength : "+haplotypeMaxLength);
            debugDump("lengths_java.txt", String.format("%d %d\n",readMaxLength, haplotypeMaxLength),
                    true);
        }
        if(debug2)
            jniInitialize(readMaxLength, haplotypeMaxLength);
    }

    private HashMap<Haplotype,Integer> haplotypeToHaplotypeListIdxMap = null;
    //Used to transfer data to JNI
    //Since the haplotypes are the same for all calls to computeLikelihoods within a region, transfer the haplotypes only once to the JNI per region
    /**
     * {@inheritDoc}
     */
    @Override
    public void initialize( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList,
            final int readMaxLength, final int haplotypeMaxLength ) {
        if(verify)
        {
            super.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
            jniPairHMM.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
            haplotypeToHaplotypeListIdxMap = jniPairHMM.getHaplotypeToHaplotypeListIdxMap();
        }
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void finalizeRegion()
    {
        if(!dumpSandboxOnly)
            jniPairHMM.finalizeRegion();
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void computeLikelihoods( final ReadLikelihoods.Matrix<Haplotype> likelihoods, final List<GATKSAMRecord> processedReads, final Map<GATKSAMRecord, byte[]> GCPArrayMap ) {
        // (re)initialize the pairHMM only if necessary
        final int readMaxLength = verify ? findMaxReadLength(processedReads) : 0;
        final int haplotypeMaxLength = verify ? findMaxHaplotypeLength(likelihoods.alleles()) : 0;
        if(verify)
        {
            if (!initialized || readMaxLength > maxReadLength || haplotypeMaxLength > maxHaplotypeLength)
            { initialize(readMaxLength, haplotypeMaxLength); }
            if ( ! initialized )
                throw new IllegalStateException("Must call initialize before calling jniComputeLikelihoods in debug/verify mode");
        }
        int readListSize = processedReads.size();
        int numHaplotypes = likelihoods.alleleCount();
        int numTestcases = readListSize*numHaplotypes;
        if(debug0_1)
            System.out.println("Java numReads "+readListSize+" numHaplotypes "+numHaplotypes);
        int idx = 0;
        for(final GATKSAMRecord read : processedReads)
        {
            final byte [] overallGCP = GCPArrayMap.get(read);
            if(debug0_1)
                System.out.println("Java read length "+read.getReadBases().length);
            if(debug3)
            {
                for(int i=0;i<read.getReadBases().length;++i)
                {
                    debugDump("reads_java.txt",String.format("%d\n",(int)read.getReadBases()[i]),true);
                    debugDump("reads_java.txt",String.format("%d\n",(int)read.getBaseQualities()[i]),true);
                    debugDump("reads_java.txt",String.format("%d\n",(int)read.getBaseInsertionQualities()[i]),true);
                    debugDump("reads_java.txt",String.format("%d\n",(int)read.getBaseDeletionQualities()[i]),true);
                    debugDump("reads_java.txt",String.format("%d\n",(int)overallGCP[i]),true);
                }
            }
            ++idx;
        }

        if(verify)
        {
            idx = 0;
            for (final Haplotype h : likelihoods.alleles())       //order is important - access in same order always
            {
                byte[] haplotypeBases = h.getBases();
                if(debug0_1)
                    System.out.println("Java haplotype length "+haplotypeBases.length);
                if(debug3)
                {
                    for(int i=0;i<haplotypeBases.length;++i)
                        debugDump("haplotype_bases_java.txt",String.format("%d\n",(int)haplotypeBases[i]),true);
                }
                ++idx;
            }
        }
        double[] likelihoodArray = null;
        PerReadAlleleLikelihoodMap likelihoodMap  = null;
        if(verify)
        {
            jniPairHMM.computeLikelihoods(likelihoods, processedReads, GCPArrayMap);
            likelihoodArray = jniPairHMM.getLikelihoodArray();
            //to compare values
            super.computeLikelihoods(likelihoods, processedReads, GCPArrayMap);
        }
        else
        {
            likelihoodMap = new PerReadAlleleLikelihoodMap();
            likelihoodArray = new double[numTestcases];
            for(int i=0;i<numTestcases;++i)
                likelihoodArray[i] = -0.5;
        }
        if(verify || dumpSandboxOnly)
        {
            boolean toDump = dumpSandboxOnly ? true : false;
            if(verify)
            {
                //re-order values in likelihoodArray
                double[] tmpArray = new double[numHaplotypes];
                idx = 0;
                int idxInsideHaplotypeList = 0;
                int readIdx = 0;
                for(final GATKSAMRecord read : processedReads)
                {
                    for(int j=0;j<numHaplotypes;++j)
                        tmpArray[j] = likelihoodArray[readIdx+j];
                    for (final Haplotype haplotype : likelihoods.alleles())//order is important - access in same order always
                    {
                        idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(haplotype);
                        likelihoodArray[idx] = tmpArray[idxInsideHaplotypeList];
                        ++idx;
                    }
                    readIdx += numHaplotypes;
                }
                //for floating point values, no exact equality
                //check whether numbers are close in terms of abs_error or relative_error
                //For very large values, relative_error is relevant
                //For very small values, abs_error is relevant
                for(int i=0;i<likelihoodArray.length;++i)
                {
                    double abs_error = Math.abs(likelihoodArray[i] - mLikelihoodArray[i]);
                    double relative_error = 0;
                    if(mLikelihoodArray[i] == 0)
                        relative_error = 0;
                    else
                        relative_error = Math.abs(abs_error/mLikelihoodArray[i]);
                    if(abs_error > 1e-5 && relative_error > 1e-5)
                    {
                        toDump = true;
                        break;
                    }
                }
            }
            //if numbers are not close, then dump out the data that produced the inconsistency
            if(toDump)
            {
                idx = 0;
                System.out.println("Dump : Java numReads "+readListSize+" numHaplotypes "+numHaplotypes);
                boolean firstLine = true;
                for(final GATKSAMRecord read : processedReads)
                {
                    byte [] overallGCP = GCPArrayMap.get(read);
                    byte[] tmpByteArray = new byte[read.getReadBases().length];
                    for (final Haplotype haplotype : likelihoods.alleles())       //order is important - access in same order always
                    {
                        byte[] haplotypeBases = haplotype.getBases();
                        debugDump("debug_dump.txt",new String(haplotypeBases)+" ",true);
                        debugDump("debug_dump.txt",new String(read.getReadBases())+" ",true);
                        for(int k=0;k<read.getReadBases().length;++k)
                            tmpByteArray[k] = (byte)((int)((read.getBaseQualities())[k]) + 33);
                        debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
                        for(int k=0;k<read.getReadBases().length;++k)
                            tmpByteArray[k] = (byte)((int)((read.getBaseInsertionQualities())[k]) + 33);
                        debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
                        for(int k=0;k<read.getReadBases().length;++k)
                            tmpByteArray[k] = (byte)((int)((read.getBaseDeletionQualities())[k]) + 33);
                        debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
                        for(int k=0;k<read.getReadBases().length;++k)
                            tmpByteArray[k] = (byte)((int)(overallGCP[k]) + 33);
                        debugDump("debug_dump.txt",new String(tmpByteArray),true);
                        if(firstLine)
                        {
                            debugDump("debug_dump.txt",String.format(" %d %d\n",readListSize, numHaplotypes), true);
                            firstLine = false;
                        }
                        else
                            debugDump("debug_dump.txt","\n",true);
                        if(verify)
                            debugDump("debug_results.txt",String.format("%e %e\n",mLikelihoodArray[idx],likelihoodArray[idx]),true);
                        else
                            if(dumpSandboxOnly)
                                likelihoods.set(likelihoods.alleleIndex(haplotype),likelihoods.readIndex(read), likelihoodArray[idx]);
                        ++idx;
                    }
                }
            }   
            debugClose();
        }
        ++numComputeLikelihoodCalls;
        //if(numComputeLikelihoodCalls == 5)
        //jniPairHMM.close();
        //System.exit(0);
    }

    //Used to test parts of the compute kernel separately    
    private native void jniInitialize( final int readMaxLength, final int haplotypeMaxLength);
    private native static void jniInitializeProbabilities( final double[][] transition, final byte[] insertionGOP,
            final byte[] deletionGOP, final byte[] overallGCP);
    private native double jniInitializePriorsAndUpdateCells( boolean doInitialization, final int paddedReadLength,
            final int paddedHaplotypeLength, final byte[] readBases, final byte[] haplotypeBases, final byte[] readQuals,
            final int hapStartIndex);
    private native double jniSubComputeReadLikelihoodGivenHaplotypeLog10( final int readLength, final int haplotypeLength,
            final byte[] readBases, final byte[] haplotypeBases, final byte[] readQuals, final byte[] insertionGOP,
            final byte[] deletionGOP, final byte[] overallGCP, final int hapStartIndex);
    /**
     * {@inheritDoc}
     */
    @Override
    public double subComputeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,  final byte[] readBases,
            final byte[] readQuals, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP,
            final int hapStartIndex, final boolean recacheReadValues, final int nextHapStartIndex) {
        //System.out.println("#### START STACK TRACE ####");
        //for (StackTraceElement ste : Thread.currentThread().getStackTrace()) {
        //System.out.println(ste);
        //}
        //System.out.println("#### END STACK TRACE ####");
        //
        if(debug1)
            jniSubComputeReadLikelihoodGivenHaplotypeLog10(readBases.length, haplotypeBases.length,
                    readBases, haplotypeBases, readQuals,
                    insertionGOP, deletionGOP, overallGCP,
                    hapStartIndex);

        boolean doInitialization = (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length);
        if (doInitialization) {
            final double initialValue = INITIAL_CONDITION / haplotypeBases.length;
            // set the initial value (free deletions in the beginning) for the first row in the deletion matrix
            for( int j = 0; j < paddedHaplotypeLength; j++ ) {
                deletionMatrix[0][j] = initialValue;
            }
        }

        if ( ! constantsAreInitialized || recacheReadValues ) {
            initializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP); 
            if(debug3)
            {
                System.out.println("Java: initializeProbabilities lengths : "+insertionGOP.length+" padded "+paddedReadLength+" "+paddedHaplotypeLength);
                for(int i=0;i<insertionGOP.length;++i)
                    for(int j=0;j<6;++j)
                        debugDump("transitions_java.txt",String.format("%e\n",transition[i+1][j]),true);
            }
            if(debug2)
                jniInitializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP); 

            // note that we initialized the constants
            constantsAreInitialized = true;
        }

        if(debug3)
            System.out.println("Java: initializePriors : lengths "+readBases.length+" "+haplotypeBases.length+" padded "+paddedReadLength+" "+paddedHaplotypeLength + " doNotUseTristateCorrection "+doNotUseTristateCorrection);
        initializePriors(haplotypeBases, readBases, readQuals, hapStartIndex);

        for (int i = 1; i < paddedReadLength; i++) {
            // +1 here is because hapStartIndex is 0-based, but our matrices are 1 based
            for (int j = hapStartIndex+1; j < paddedHaplotypeLength; j++) {
                updateCell(i, j, prior[i][j], transition[i]);
            }
        }

        // final probability is the log10 sum of the last element in the Match and Insertion state arrays
        // this way we ignore all paths that ended in deletions! (huge)
        // but we have to sum all the paths ending in the M and I matrices, because they're no longer extended.
        final int endI = paddedReadLength - 1;
        double finalSumProbabilities = 0.0;
        for (int j = 1; j < paddedHaplotypeLength; j++) {
            finalSumProbabilities += matchMatrix[endI][j] + insertionMatrix[endI][j];
        }
        if(debug2)
            jniInitializePriorsAndUpdateCells(doInitialization, paddedReadLength, paddedHaplotypeLength,
                    readBases, haplotypeBases, readQuals,
                    hapStartIndex);
        if(debug)
            debugDump("return_values_java.txt",String.format("%e\n",Math.log10(finalSumProbabilities) - INITIAL_CONDITION_LOG10),true);
        ++numCalls;
        //if(numCalls == 100)
        //{
        //debugClose();
        //System.exit(0);
        //}
        return Math.log10(finalSumProbabilities) - INITIAL_CONDITION_LOG10;
    }

    /**
     * Initializes the matrix that holds all the constants related to the editing
     * distance between the read and the haplotype.
     *
     * @param haplotypeBases the bases of the haplotype
     * @param readBases      the bases of the read
     * @param readQuals      the base quality scores of the read
     * @param startIndex     where to start updating the distanceMatrix (in case this read is similar to the previous read)
     */
    protected void initializePriors(final byte[] haplotypeBases, final byte[] readBases, final byte[] readQuals, final int startIndex) {

        // initialize the pBaseReadLog10 matrix for all combinations of read x haplotype bases
        // Abusing the fact that java initializes arrays with 0.0, so no need to fill in rows and columns below 2.

        if(debug3)
            System.out.println("hapStartIndex "+startIndex);

        for (int i = 0; i < readBases.length; i++) {
            final byte x = readBases[i];
            final byte qual = readQuals[i];
            for (int j = startIndex; j < haplotypeBases.length; j++) {
                final byte y = haplotypeBases[j];
                prior[i+1][j+1] = ( x == y || x == (byte) 'N' || y == (byte) 'N' ?
                        QualityUtils.qualToProb(qual) : (QualityUtils.qualToErrorProb(qual) / (doNotUseTristateCorrection ? 1.0 : TRISTATE_CORRECTION)) );
                if(debug3)
                    debugDump("priors_java.txt",String.format("%e\n",prior[i+1][j+1]),true);
            }
        }
    }

    /**
     * Initializes the matrix that holds all the constants related to quality scores.
     *
     * @param insertionGOP   insertion quality scores of the read
     * @param deletionGOP    deletion quality scores of the read
     * @param overallGCP     overall gap continuation penalty
     */
    @Requires({
        "insertionGOP != null",
        "deletionGOP != null",
        "overallGCP != null"
    })
    @Ensures("constantsAreInitialized")
    protected static void initializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
        PairHMMModel.qualToTransProbs(transition,insertionGOP,deletionGOP,overallGCP);
    }

    /**
     * Updates a cell in the HMM matrix
     *
     * The read and haplotype indices are offset by one because the state arrays have an extra column to hold the
     * initial conditions

     * @param indI             row index in the matrices to update
     * @param indJ             column index in the matrices to update
     * @param prior            the likelihood editing distance matrix for the read x haplotype
     * @param transition        an array with the six transition relevant to this location
     */
    protected void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {

        matchMatrix[indI][indJ] = prior * ( matchMatrix[indI - 1][indJ - 1] * transition[matchToMatch] +
                insertionMatrix[indI - 1][indJ - 1] * transition[indelToMatch] +
                deletionMatrix[indI - 1][indJ - 1] * transition[indelToMatch] );
        insertionMatrix[indI][indJ] = matchMatrix[indI - 1][indJ] * transition[matchToInsertion] + insertionMatrix[indI - 1][indJ] * transition[insertionToInsertion];
        deletionMatrix[indI][indJ] = matchMatrix[indI][indJ - 1] * transition[matchToDeletion] + deletionMatrix[indI][indJ - 1] * transition[deletionToDeletion];
        if(debug3)
        {
            debugDump("matrices_java.txt",String.format("%e\n",matchMatrix[indI][indJ]),true);
            debugDump("matrices_java.txt",String.format("%e\n",insertionMatrix[indI][indJ]),true);
            debugDump("matrices_java.txt",String.format("%e\n",deletionMatrix[indI][indJ]),true);
        }
    }

    protected void debugDump( String filename, String s, boolean toAppend ) {
        try {
            File file = new File(filename);
            if (!file.exists())
                file.createNewFile();
            BufferedWriter currWriter = filenameToWriter.get(filename);
            if(currWriter == null)
            {
                FileWriter fw = new FileWriter(file, toAppend);
                currWriter = new BufferedWriter(fw);
                filenameToWriter.put(filename, currWriter);
            }
            currWriter.write(s);
        }
        catch(IOException e)
        {
            e.printStackTrace();
        }
    }

    protected void debugClose()  {
        for(Map.Entry<String, BufferedWriter> currEntry : filenameToWriter.entrySet()) {
            BufferedWriter currWriter = currEntry.getValue();
            try
            {
                currWriter.flush();
                currWriter.close();
            }
            catch(IOException e)
            {
                e.printStackTrace();

            }
        }
        filenameToWriter.clear();
    }
}
