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package org.broadinstitute.gatk.utils.pairhmm;

import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;

import java.io.*;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

//For loading library from jar

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

    protected final static Logger logger = Logger.getLogger(VectorLoglessPairHMM.class);

    //Used to copy references to byteArrays to JNI from reads
    protected class JNIReadDataHolderClass {
        public byte[] readBases = null;
        public byte[] readQuals = null;
        public byte[] insertionGOP = null;
        public byte[] deletionGOP = null;
        public byte[] overallGCP = null;
    }

    //Used to copy references to byteArrays to JNI from haplotypes
    protected class JNIHaplotypeDataHolderClass {
        public byte[] haplotypeBases = null;
    }

    /**
     * Return 64-bit mask representing machine capabilities
     * Bit 0 is LSB, bit 63 MSB
     * Bit 0 represents sse4.1 availability
     * Bit 1 represents sse4.2 availability
     * Bit 2 represents AVX availability
     */
    public native long jniGetMachineType();

    /**
     * Function to initialize the fields of JNIReadDataHolderClass and JNIHaplotypeDataHolderClass from JVM.
     * C++ codegets FieldIDs for these classes once and re-uses these IDs for the remainder of the program. Field IDs do not
     * change per JVM session
     *
     * @param readDataHolderClass      class type of JNIReadDataHolderClass
     * @param haplotypeDataHolderClass class type of JNIHaplotypeDataHolderClass
     * @param mask                     a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing bits in the mask
     */
    private native void jniInitializeClassFieldsAndMachineMask(Class<?> readDataHolderClass, Class<?> haplotypeDataHolderClass, long mask);

    private static Boolean isVectorLoglessPairHMMLibraryLoaded = false;

    //The constructor is called only once inside PairHMMLikelihoodCalculationEngine
    public VectorLoglessPairHMM(final PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub, final boolean alwaysLoadVectorLoglessPairHMMLib) throws UserException.HardwareFeatureException {
        super();

        synchronized (isVectorLoglessPairHMMLibraryLoaded) {
            // Get the mask for the requested hardware sub-implementation
            // If a specifically requested hardware feature can not be supported, throw an exception
            long mask = pairHMMSub.getMask();
            throwIfHardwareFeatureNotSupported(mask, pairHMMSub);

            // Load the library and initialize the FieldIDs
            // Load if not loaded or if the the always load flag is true
            if (!isVectorLoglessPairHMMLibraryLoaded || alwaysLoadVectorLoglessPairHMMLib) {
                try
                {
                    //Try loading from Java's library path first
                    //Useful if someone builds his/her own library and wants to override the bundled
                    //implementation without modifying the Java code
                    System.loadLibrary("VectorLoglessPairHMM");
                    logger.info("libVectorLoglessPairHMM found in JVM library path");
                } catch (UnsatisfiedLinkError ule) {
                    //Could not load from Java's library path - try unpacking from jar
                    try
                    {
                        logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from GATK jar file");
                        loadLibraryFromJar("/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so");
                        logger.info("libVectorLoglessPairHMM unpacked successfully from GATK jar file");
                    } catch (IOException ioe) {
                        //Throw the UnsatisfiedLinkError to make it clear to the user what failed
                        throw ule;
                    }
                }
                logger.info("Using vectorized implementation of PairHMM");
                isVectorLoglessPairHMMLibraryLoaded = true;

                //need to do this only once
                jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, mask);
            }
        }
    }

    private native void jniInitializeHaplotypes(final int numHaplotypes, JNIHaplotypeDataHolderClass[] haplotypeDataArray);

    //Hold the mapping between haplotype and index in the list of Haplotypes passed to initialize
    //Use this mapping in computeLikelihoods to find the likelihood value corresponding to a given Haplotype
    private HashMap<Haplotype, Integer> haplotypeToHaplotypeListIdxMap = new HashMap<>();
    private JNIHaplotypeDataHolderClass[] mHaplotypeDataArray;

    @Override
    public HashMap<Haplotype, Integer> getHaplotypeToHaplotypeListIdxMap() {
        return haplotypeToHaplotypeListIdxMap;
    }

    //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) {
        int numHaplotypes = haplotypes.size();
        mHaplotypeDataArray = new JNIHaplotypeDataHolderClass[numHaplotypes];
        int idx = 0;
        haplotypeToHaplotypeListIdxMap.clear();
        for (final Haplotype currHaplotype : haplotypes) {
            mHaplotypeDataArray[idx] = new JNIHaplotypeDataHolderClass();
            mHaplotypeDataArray[idx].haplotypeBases = currHaplotype.getBases();
            haplotypeToHaplotypeListIdxMap.put(currHaplotype, idx);
            ++idx;
        }
        jniInitializeHaplotypes(numHaplotypes, mHaplotypeDataArray);
    }

    /**
     * Tell JNI to release arrays - really important if native code is directly accessing Java memory, if not
     * accessing Java memory directly, still important to release memory from C++
     */
    private native void jniFinalizeRegion();

    /**
     * {@inheritDoc}
     */
    @Override
    public void finalizeRegion()
    {
        jniFinalizeRegion();
    }

    /**
     * Real compute kernel
     */
    private native void jniComputeLikelihoods(int numReads, int numHaplotypes, JNIReadDataHolderClass[] readDataArray,
                                              JNIHaplotypeDataHolderClass[] haplotypeDataArray, double[] likelihoodArray, int maxNumThreadsToUse);

    /**
     * {@inheritDoc}
     */
    @Override
    public void computeLikelihoods(final ReadLikelihoods.Matrix<Haplotype> likelihoods, final List<GATKSAMRecord> processedReads, final Map<GATKSAMRecord, byte[]> gcp) {
        if (processedReads.isEmpty())
            return;
        if (doProfiling)
            startTime = System.nanoTime();
        int readListSize = processedReads.size();
        int numHaplotypes = likelihoods.alleleCount();
        JNIReadDataHolderClass[] readDataArray = new JNIReadDataHolderClass[readListSize];
        int idx = 0;
        for (GATKSAMRecord read : processedReads) {
            readDataArray[idx] = new JNIReadDataHolderClass();
            readDataArray[idx].readBases = read.getReadBases();
            readDataArray[idx].readQuals = read.getBaseQualities();
            readDataArray[idx].insertionGOP = read.getBaseInsertionQualities();
            readDataArray[idx].deletionGOP = read.getBaseDeletionQualities();
            readDataArray[idx].overallGCP = gcp.get(read);
            ++idx;
        }

        mLikelihoodArray = new double[readListSize * numHaplotypes];      //to store results
        if (doProfiling)
            threadLocalSetupTimeDiff = (System.nanoTime() - startTime);
        //for(reads)
        //   for(haplotypes)
        //       compute_full_prob()
        jniComputeLikelihoods(readListSize, numHaplotypes, readDataArray, mHaplotypeDataArray, mLikelihoodArray, 12);

        int readIdx = 0;
        for (int r = 0; r < readListSize; r++) {
            int hapIdx = 0;
            for (final Haplotype haplotype : likelihoods.alleles()) {

                //Since the order of haplotypes in the List<Haplotype> and alleleHaplotypeMap is different,
                //get idx of current haplotype in the list and use this idx to get the right likelihoodValue
                final int idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(haplotype);
                likelihoods.set(hapIdx, r, mLikelihoodArray[readIdx + idxInsideHaplotypeList]);
                ++hapIdx;
            }
            readIdx += numHaplotypes;
        }
        if (doProfiling) {
            threadLocalPairHMMComputeTimeDiff = (System.nanoTime() - startTime);
            //synchronized(doProfiling)
            {
                pairHMMComputeTime += threadLocalPairHMMComputeTimeDiff;
                pairHMMSetupTime += threadLocalSetupTimeDiff;
            }
        }
    }

    /**
     * Print final profiling information from native code
     */
    public native void jniClose();

    @Override
    public void close() {
        if (doProfiling)
            logger.info("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9));
        super.close();
        jniClose();
    }

    //Copied from http://frommyplayground.com/how-to-load-native-jni-library-from-jar 

    /**
     * Loads library from current JAR archive
     * <p/>
     * The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting.
     * Method uses String as filename because the pathname is "abstract", not system-dependent.
     *
     * @param path The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext
     * @throws IOException  If temporary file creation or read/write operation fails
     * @throws IllegalArgumentException If source file (param path) does not exist
     * @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of {@see File#createTempFile(java.lang.String, java.lang.String)}).
     */
    public static void loadLibraryFromJar(String path) throws IOException {

        if (!path.startsWith("/")) {
            throw new IllegalArgumentException("The path to be absolute (start with '/').");
        }

        // Obtain filename from path
        String[] parts = path.split("/");
        String filename = (parts.length > 1) ? parts[parts.length - 1] : null;

        // Split filename to prexif and suffix (extension)
        String prefix = "";
        String suffix = null;
        if (filename != null) {
            parts = filename.split("\\.", 2);
            prefix = parts[0];
            suffix = (parts.length > 1) ? "." + parts[parts.length - 1] : null; // Thanks, davs! :-)
        }

        // Check if the filename is okay
        if (filename == null || prefix.length() < 3) {
            throw new IllegalArgumentException("The filename has to be at least 3 characters long.");
        }

        // Prepare temporary file
        File temp = File.createTempFile(prefix, suffix);
        //System.out.println("Temp lib file "+temp.getAbsolutePath());
        temp.deleteOnExit();

        if (!temp.exists()) {
            throw new FileNotFoundException("File " + temp.getAbsolutePath() + " does not exist.");
        }

        // Prepare buffer for data copying
        byte[] buffer = new byte[1024];
        int readBytes;

        // Open and check input stream
        InputStream is = VectorLoglessPairHMM.class.getResourceAsStream(path);
        if (is == null) {
            throw new FileNotFoundException("File " + path + " was not found inside JAR.");
        }

        // Open output stream and copy data between source file in JAR and the temporary file
        OutputStream os = new FileOutputStream(temp);
        try {
            while ((readBytes = is.read(buffer)) != -1) {
                os.write(buffer, 0, readBytes);
            }
        } finally {
            // If read/write fails, close streams safely before throwing an exception
            os.close();
            is.close();
        }

        // Finally, load the library
        System.load(temp.getAbsolutePath());
    }

    /**
     * If the machine does not support the requested hardware feature, throw an exception
     * <p/>
     * If requesting a specific hardware feature, check if the machine supports this feature.
     * If it does not, throw an exception.
     *
     * @param mask a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask.
     * @param pairHMMSub the PairHMM machine dependent sub-implementation to use for genotype likelihood calculations
     * @throws UserException.HardwareFeatureException if the hardware feature is not supported
     */
    private void throwIfHardwareFeatureNotSupported(long mask, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) throws UserException.HardwareFeatureException
    {
        if ( pairHMMSub.getIsSpecificHardwareRequest() ) {
            if ( !isHardwareFeatureSupported(mask) )
                throw new UserException.HardwareFeatureException("Machine does not support pairHMM hardware dependent sub-type = " + pairHMMSub);
        }
    }

    /**
     * Check if the machine supports the requested hardware feature
     * <p/>
     * Mask the bits for the hardware feature and check if they are set by the machine
     * If the bits are set, the machine supports this feature
     *
     * @param mask a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask.
     * @return true of machine supports the requested hardware feature, false otherwise
     */
    private boolean isHardwareFeatureSupported(long mask)
    {
        return (mask & jniGetMachineType()) != 0x0;
    }
}
