#include <cstdio>
#include <cstdlib>
#include <cstring>

#include "bntseq.h"
#include "bwt.h"
#include "bwtaln.h"
#include "bwa_gateway.h"
#include "org_broadinstitute_sting_alignment_bwa_BWACAligner.h"

static jclass java_alignment_array_class = NULL;
static jclass java_alignment_class = NULL;
static jmethodID java_alignment_constructor = NULL;

JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create(JNIEnv* env, 
										     jobject instance,
										     jstring java_ann,
										     jstring java_amb,
										     jstring java_pac,
										     jstring java_forward_bwt, 
										     jstring java_forward_sa,
										     jstring java_reverse_bwt,
										     jstring java_reverse_sa) 
{
  const char* ann_filename = env->GetStringUTFChars(java_ann, JNI_FALSE);
  const char* amb_filename = env->GetStringUTFChars(java_amb, JNI_FALSE);
  const char* pac_filename = env->GetStringUTFChars(java_pac, JNI_FALSE);
  const char* forward_bwt_filename = env->GetStringUTFChars(java_forward_bwt, JNI_FALSE);
  const char* forward_sa_filename = env->GetStringUTFChars(java_forward_sa, JNI_FALSE);
  const char* reverse_bwt_filename = env->GetStringUTFChars(java_reverse_bwt, JNI_FALSE);
  const char* reverse_sa_filename = env->GetStringUTFChars(java_reverse_sa, JNI_FALSE);

  BWA* bwa = new BWA(ann_filename,
		     amb_filename,
		     pac_filename,
		     forward_bwt_filename,
		     forward_sa_filename,
		     reverse_bwt_filename,
		     reverse_sa_filename);

  env->ReleaseStringUTFChars(java_ann,ann_filename);
  env->ReleaseStringUTFChars(java_amb,amb_filename);
  env->ReleaseStringUTFChars(java_pac,pac_filename);
  env->ReleaseStringUTFChars(java_forward_bwt,forward_bwt_filename);
  env->ReleaseStringUTFChars(java_forward_sa,forward_sa_filename);
  env->ReleaseStringUTFChars(java_reverse_bwt,reverse_bwt_filename);
  env->ReleaseStringUTFChars(java_reverse_sa,reverse_sa_filename);

  // Cache the class object for an array of alignments.
  java_alignment_array_class = env->FindClass("[Lorg/broadinstitute/sting/alignment/Alignment;");
  java_alignment_class = env->FindClass("org/broadinstitute/sting/alignment/Alignment");
  java_alignment_constructor = env->GetMethodID(java_alignment_class, "<init>", "(IIZI[C[I)V");

  return (jlong)bwa;
}

JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_destroy(JNIEnv* env, jobject instance, jlong java_bwa) 
{
  BWA* bwa = (BWA*)java_bwa;
  delete bwa;
}

JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_align(JNIEnv* env, jobject object, jlong java_bwa, jbyteArray java_bases) {
  BWA* bwa = (BWA*)java_bwa;

  const jsize read_length = env->GetArrayLength(java_bases);
  jbyte *read_bases = env->GetByteArrayElements(java_bases,JNI_FALSE); 

  Alignment* alignments = NULL;
  unsigned num_alignments = 1;
  bwa->align((const char*)read_bases,read_length,alignments,num_alignments);

  jobjectArray java_alignments = env->NewObjectArray(num_alignments, env->FindClass("org/broadinstitute/sting/alignment/Alignment"), NULL);  

  for(unsigned alignment_idx = 0; alignment_idx < (unsigned)num_alignments; alignment_idx++) {
    Alignment& alignment = *(alignments + alignment_idx);

    unsigned cigar_length;
    if(alignment.type == BWA_TYPE_NO_MATCH) cigar_length = 0;
    else if(!alignment.cigar) cigar_length = 1;
    else cigar_length = alignment.n_cigar;

    jcharArray java_cigar_operators = env->NewCharArray(cigar_length);
    jintArray java_cigar_lengths = env->NewIntArray(cigar_length);

    if(alignment.cigar) {
      for(unsigned cigar_idx = 0; cigar_idx < (unsigned)alignment.n_cigar; ++cigar_idx) {
	jchar cigar_operator = "MIDS"[alignment.cigar[cigar_idx]>>14];
	jint  cigar_length = alignment.cigar[cigar_idx]&0x3fff;
	env->SetCharArrayRegion(java_cigar_operators,cigar_idx,1,&cigar_operator);
	env->SetIntArrayRegion(java_cigar_lengths,cigar_idx,1,&cigar_length);
      }
    }
    else {
      if(alignment.type != BWA_TYPE_NO_MATCH) {
	jchar cigar_operator = 'M';
	env->SetCharArrayRegion(java_cigar_operators,0,1,&cigar_operator);
	env->SetIntArrayRegion(java_cigar_lengths,0,1,&read_length);
      }
    }

    jclass java_alignment_class = env->FindClass("org/broadinstitute/sting/alignment/Alignment");
    jmethodID java_alignment_constructor = env->GetMethodID(java_alignment_class, "<init>", "(IIZI[C[I)V");
    jobject java_alignment = env->NewObject(java_alignment_class,
					    java_alignment_constructor,
					    alignment.contig,
					    alignment.pos,
					    alignment.negative_strand,
					    alignment.mapQ,
					    java_cigar_operators,
					    java_cigar_lengths);
    env->SetObjectArrayElement(java_alignments,alignment_idx,java_alignment);
  }

  delete[] alignments;

  env->ReleaseByteArrayElements(java_bases,read_bases,0);

  return java_alignments;
}