/* Generating, shuffling, and randomizing sequences.
 * 
 * SRE, Thu Apr 24 09:38:13 2008 [Janelia]
 * SVN $Id$
 */
#ifndef ESL_RANDOMSEQ_INCLUDED
#define ESL_RANDOMSEQ_INCLUDED

#include "esl_random.h"

/* 1. Generating iid sequences. */
extern int esl_rsq_IID  (ESL_RANDOMNESS *r, const char *alphabet, const double *p, int K, int L, char *s);
extern int esl_rsq_fIID (ESL_RANDOMNESS *r, const char *alphabet, const float  *p, int K, int L, char *s);

/* 2. Shuffling sequences. */
extern int esl_rsq_CShuffle       (ESL_RANDOMNESS *r, const char *s,        char *shuffled);
extern int esl_rsq_CShuffleDP     (ESL_RANDOMNESS *r, const char *s,        char *shuffled);
extern int esl_rsq_CShuffleKmers  (ESL_RANDOMNESS *r, const char *s, int K, char *shuffled);
extern int esl_rsq_CReverse       (const char *s, char *rev);
extern int esl_rsq_CShuffleWindows(ESL_RANDOMNESS *r, const char *s, int w, char *shuffled);

/* 3. Randomizing sequences */
extern int esl_rsq_CMarkov0  (ESL_RANDOMNESS *r, const char *s, char *markoved);
extern int esl_rsq_CMarkov1  (ESL_RANDOMNESS *r, const char *s, char *markoved);

/* 4. Generating iid sequences (digital mode). */
extern int esl_rsq_xIID (ESL_RANDOMNESS *r, const double *p, int K, int L, ESL_DSQ *dsq);
extern int esl_rsq_xfIID(ESL_RANDOMNESS *r, const float  *p, int K, int L, ESL_DSQ *dsq);

/* 5. Shuffling sequences (digital mode). */
extern int esl_rsq_XShuffle       (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L,        ESL_DSQ *shuffled);
extern int esl_rsq_XShuffleDP     (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled);
extern int esl_rsq_XShuffleKmers  (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled);
extern int esl_rsq_XReverse(const ESL_DSQ *dsq, int L, ESL_DSQ *rev);
extern int esl_rsq_XShuffleWindows(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int w, ESL_DSQ *shuffled);

/* 6. Randomizing sequences (digital mode) */
extern int esl_rsq_XMarkov0  (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved);
extern int esl_rsq_XMarkov1  (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved);

#endif /*ESL_RANDOMSEQ_INCLUDED*/

/*****************************************************************
 * Easel - a library of C functions for biological sequence analysis
 * Version h3.0; March 2010
 * Copyright (C) 2010 Howard Hughes Medical Institute.
 * Other copyrights also apply. See the COPYRIGHT file for a full list.
 * 
 * Easel is distributed under the Janelia Farm Software License, a BSD
 * license. See the LICENSE file for more details.
 *****************************************************************/