/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class align2_MultiStateAligner11tsJNI */

#ifndef _Included_align2_MultiStateAligner11tsJNI
#define _Included_align2_MultiStateAligner11tsJNI
#ifdef __cplusplus
extern "C" {
#endif
#undef align2_MultiStateAligner11tsJNI_GAPBUFFER
#define align2_MultiStateAligner11tsJNI_GAPBUFFER 64L
#undef align2_MultiStateAligner11tsJNI_GAPBUFFER2
#define align2_MultiStateAligner11tsJNI_GAPBUFFER2 128L
#undef align2_MultiStateAligner11tsJNI_GAPLEN
#define align2_MultiStateAligner11tsJNI_GAPLEN 128L
#undef align2_MultiStateAligner11tsJNI_MINGAP
#define align2_MultiStateAligner11tsJNI_MINGAP 256L
#undef align2_MultiStateAligner11tsJNI_GAPC
#define align2_MultiStateAligner11tsJNI_GAPC 45L
#undef align2_MultiStateAligner11tsJNI_GREFLIMIT2_CUSHION
#define align2_MultiStateAligner11tsJNI_GREFLIMIT2_CUSHION 128L
#undef align2_MultiStateAligner11tsJNI_MODE_MS
#define align2_MultiStateAligner11tsJNI_MODE_MS 0L
#undef align2_MultiStateAligner11tsJNI_MODE_DEL
#define align2_MultiStateAligner11tsJNI_MODE_DEL 1L
#undef align2_MultiStateAligner11tsJNI_MODE_INS
#define align2_MultiStateAligner11tsJNI_MODE_INS 2L
#undef align2_MultiStateAligner11tsJNI_MODE_SUB
#define align2_MultiStateAligner11tsJNI_MODE_SUB 3L
#undef align2_MultiStateAligner11tsJNI_MIN_SCORE_ADJUST
#define align2_MultiStateAligner11tsJNI_MIN_SCORE_ADJUST 120L
#undef align2_MultiStateAligner11tsJNI_TIMEBITS
#define align2_MultiStateAligner11tsJNI_TIMEBITS 11L
#undef align2_MultiStateAligner11tsJNI_SCOREBITS
#define align2_MultiStateAligner11tsJNI_SCOREBITS 21L
#undef align2_MultiStateAligner11tsJNI_MAX_TIME
#define align2_MultiStateAligner11tsJNI_MAX_TIME 2047L
#undef align2_MultiStateAligner11tsJNI_MAX_SCORE
#define align2_MultiStateAligner11tsJNI_MAX_SCORE 1046575L
#undef align2_MultiStateAligner11tsJNI_MIN_SCORE
#define align2_MultiStateAligner11tsJNI_MIN_SCORE -1046575L
#undef align2_MultiStateAligner11tsJNI_SCOREOFFSET
#define align2_MultiStateAligner11tsJNI_SCOREOFFSET 11L
#undef align2_MultiStateAligner11tsJNI_TIMEMASK
#define align2_MultiStateAligner11tsJNI_TIMEMASK 2047L
#undef align2_MultiStateAligner11tsJNI_SCOREMASK
#define align2_MultiStateAligner11tsJNI_SCOREMASK -2048L
#undef align2_MultiStateAligner11tsJNI_MODE_MS
#define align2_MultiStateAligner11tsJNI_MODE_MS 0L
#undef align2_MultiStateAligner11tsJNI_MODE_DEL
#define align2_MultiStateAligner11tsJNI_MODE_DEL 1L
#undef align2_MultiStateAligner11tsJNI_MODE_INS
#define align2_MultiStateAligner11tsJNI_MODE_INS 2L
#undef align2_MultiStateAligner11tsJNI_MODE_SUB
#define align2_MultiStateAligner11tsJNI_MODE_SUB 3L
#undef align2_MultiStateAligner11tsJNI_POINTS_NOREF
#define align2_MultiStateAligner11tsJNI_POINTS_NOREF 0L
#undef align2_MultiStateAligner11tsJNI_POINTS_NOCALL
#define align2_MultiStateAligner11tsJNI_POINTS_NOCALL 0L
#undef align2_MultiStateAligner11tsJNI_POINTS_MATCH
#define align2_MultiStateAligner11tsJNI_POINTS_MATCH 70L
#undef align2_MultiStateAligner11tsJNI_POINTS_MATCH2
#define align2_MultiStateAligner11tsJNI_POINTS_MATCH2 100L
#undef align2_MultiStateAligner11tsJNI_POINTS_COMPATIBLE
#define align2_MultiStateAligner11tsJNI_POINTS_COMPATIBLE 50L
#undef align2_MultiStateAligner11tsJNI_POINTS_SUB
#define align2_MultiStateAligner11tsJNI_POINTS_SUB -127L
#undef align2_MultiStateAligner11tsJNI_POINTS_SUBR
#define align2_MultiStateAligner11tsJNI_POINTS_SUBR -147L
#undef align2_MultiStateAligner11tsJNI_POINTS_SUB2
#define align2_MultiStateAligner11tsJNI_POINTS_SUB2 -51L
#undef align2_MultiStateAligner11tsJNI_POINTS_SUB3
#define align2_MultiStateAligner11tsJNI_POINTS_SUB3 -25L
#undef align2_MultiStateAligner11tsJNI_POINTS_MATCHSUB
#define align2_MultiStateAligner11tsJNI_POINTS_MATCHSUB -10L
#undef align2_MultiStateAligner11tsJNI_POINTS_INS
#define align2_MultiStateAligner11tsJNI_POINTS_INS -395L
#undef align2_MultiStateAligner11tsJNI_POINTS_INS2
#define align2_MultiStateAligner11tsJNI_POINTS_INS2 -39L
#undef align2_MultiStateAligner11tsJNI_POINTS_INS3
#define align2_MultiStateAligner11tsJNI_POINTS_INS3 -23L
#undef align2_MultiStateAligner11tsJNI_POINTS_INS4
#define align2_MultiStateAligner11tsJNI_POINTS_INS4 -8L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL
#define align2_MultiStateAligner11tsJNI_POINTS_DEL -472L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL2
#define align2_MultiStateAligner11tsJNI_POINTS_DEL2 -33L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL3
#define align2_MultiStateAligner11tsJNI_POINTS_DEL3 -9L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL4
#define align2_MultiStateAligner11tsJNI_POINTS_DEL4 -1L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL5
#define align2_MultiStateAligner11tsJNI_POINTS_DEL5 -1L
#undef align2_MultiStateAligner11tsJNI_POINTS_DEL_REF_N
#define align2_MultiStateAligner11tsJNI_POINTS_DEL_REF_N -10L
#undef align2_MultiStateAligner11tsJNI_TIMESLIP
#define align2_MultiStateAligner11tsJNI_TIMESLIP 4L
#undef align2_MultiStateAligner11tsJNI_MASK5
#define align2_MultiStateAligner11tsJNI_MASK5 3L
#undef align2_MultiStateAligner11tsJNI_BARRIER_I1
#define align2_MultiStateAligner11tsJNI_BARRIER_I1 2L
#undef align2_MultiStateAligner11tsJNI_BARRIER_D1
#define align2_MultiStateAligner11tsJNI_BARRIER_D1 3L
#undef align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_3
#define align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_3 5L
#undef align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_4
#define align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_4 20L
#undef align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_5
#define align2_MultiStateAligner11tsJNI_LIMIT_FOR_COST_5 80L
#undef align2_MultiStateAligner11tsJNI_BAD
#define align2_MultiStateAligner11tsJNI_BAD -1046576L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_NOREF
#define align2_MultiStateAligner11tsJNI_POINTSoff_NOREF 0L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_NOCALL
#define align2_MultiStateAligner11tsJNI_POINTSoff_NOCALL 0L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_MATCH
#define align2_MultiStateAligner11tsJNI_POINTSoff_MATCH 143360L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_MATCH2
#define align2_MultiStateAligner11tsJNI_POINTSoff_MATCH2 204800L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_COMPATIBLE
#define align2_MultiStateAligner11tsJNI_POINTSoff_COMPATIBLE 102400L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_SUB
#define align2_MultiStateAligner11tsJNI_POINTSoff_SUB -260096L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_SUBR
#define align2_MultiStateAligner11tsJNI_POINTSoff_SUBR -301056L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_SUB2
#define align2_MultiStateAligner11tsJNI_POINTSoff_SUB2 -104448L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_SUB3
#define align2_MultiStateAligner11tsJNI_POINTSoff_SUB3 -51200L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_MATCHSUB
#define align2_MultiStateAligner11tsJNI_POINTSoff_MATCHSUB -20480L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_INS
#define align2_MultiStateAligner11tsJNI_POINTSoff_INS -808960L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_INS2
#define align2_MultiStateAligner11tsJNI_POINTSoff_INS2 -79872L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_INS3
#define align2_MultiStateAligner11tsJNI_POINTSoff_INS3 -47104L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_INS4
#define align2_MultiStateAligner11tsJNI_POINTSoff_INS4 -16384L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL -966656L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL2
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL2 -67584L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL3
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL3 -18432L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL4
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL4 -2048L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL5
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL5 -2048L
#undef align2_MultiStateAligner11tsJNI_POINTSoff_DEL_REF_N
#define align2_MultiStateAligner11tsJNI_POINTSoff_DEL_REF_N -20480L
#undef align2_MultiStateAligner11tsJNI_BADoff
#define align2_MultiStateAligner11tsJNI_BADoff -2143387648L
#undef align2_MultiStateAligner11tsJNI_MAXoff_SCORE
#define align2_MultiStateAligner11tsJNI_MAXoff_SCORE 2143385600L
#undef align2_MultiStateAligner11tsJNI_MINoff_SCORE
#define align2_MultiStateAligner11tsJNI_MINoff_SCORE -2143385600L
#undef align2_MultiStateAligner11tsJNI_AFFINE_ARRAYS
#define align2_MultiStateAligner11tsJNI_AFFINE_ARRAYS 1L
/*
 * Class:     align2_MultiStateAligner11tsJNI
 * Method:    fillUnlimitedJNI
 * Signature: ([B[BII[I[J[I[I[III)V
 */
JNIEXPORT void JNICALL Java_align2_MultiStateAligner11tsJNI_fillUnlimitedJNI
  (JNIEnv *, jobject, jbyteArray, jbyteArray, jint, jint, jintArray, jlongArray, jintArray, jintArray, jintArray, jint, jint);

/*
 * Class:     align2_MultiStateAligner11tsJNI
 * Method:    fillLimitedXJNI
 * Signature: ([B[BIII[I[J[I[I[IIIIF[I[I[B[I)V
 */
JNIEXPORT void JNICALL Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI
  (JNIEnv *, jobject, jbyteArray, jbyteArray, jint, jint, jint, jintArray, jlongArray, jintArray, jintArray, jintArray, jint, jint, jint, jfloat, jintArray, jintArray, jbyteArray, jintArray);

#ifdef __cplusplus
}
#endif
#endif
