1 /* Generating, shuffling, and randomizing sequences. 2 */ 3 #ifndef eslRANDOMSEQ_INCLUDED 4 #define eslRANDOMSEQ_INCLUDED 5 #include "esl_config.h" 6 7 #include "esl_alphabet.h" 8 #include "esl_random.h" 9 10 /* Control flag passed to esl_rsq_Sample(): */ 11 #define eslRSQ_SAMPLE_ALNUM 1 /* isalpha | isdigit */ 12 #define eslRSQ_SAMPLE_ALPHA 2 /* islower | isupper */ 13 #define eslRSQ_SAMPLE_LOWER 3 /* ASCII: a-z */ 14 #define eslRSQ_SAMPLE_UPPER 4 /* ASCII: A-Z */ 15 #define eslRSQ_SAMPLE_DIGIT 5 /* 0-9 */ 16 #define eslRSQ_SAMPLE_XDIGIT 6 /* 0-9, a-f, A-F */ 17 #define eslRSQ_SAMPLE_CNTRL 7 /* ASCII: 0..0x1F, plus 0x7F (DEL) */ 18 #define eslRSQ_SAMPLE_GRAPH 8 /* isprint && ! ' ' (space) */ 19 #define eslRSQ_SAMPLE_SPACE 9 /* ' ', '\f', '\n', '\r', '\t', '\v' */ 20 #define eslRSQ_SAMPLE_BLANK 10 /* ' ', '\t' */ 21 #define eslRSQ_SAMPLE_PRINT 11 /* ASCII: 0x20 ' ' through 0x7E '~' */ 22 #define eslRSQ_SAMPLE_PUNCT 12 /* isprint && !(isspace || isalnum) */ 23 24 25 /* 1. Generating simple random character strings. */ 26 extern int esl_rsq_Sample(ESL_RANDOMNESS *rng, int allowed_chars_flag, int L, char **ret_s); 27 28 /* 2. Generating iid sequences. */ 29 extern int esl_rsq_IID (ESL_RANDOMNESS *r, const char *alphabet, const double *p, int K, int L, char *s); 30 extern int esl_rsq_fIID (ESL_RANDOMNESS *r, const char *alphabet, const float *p, int K, int L, char *s); 31 32 /* 3. Shuffling sequences. */ 33 extern int esl_rsq_CShuffle (ESL_RANDOMNESS *r, const char *s, char *shuffled); 34 extern int esl_rsq_CShuffleDP (ESL_RANDOMNESS *r, const char *s, char *shuffled); 35 extern int esl_rsq_CShuffleKmers (ESL_RANDOMNESS *r, const char *s, int K, char *shuffled); 36 extern int esl_rsq_CReverse (const char *s, char *rev); 37 extern int esl_rsq_CShuffleWindows(ESL_RANDOMNESS *r, const char *s, int w, char *shuffled); 38 39 /* 4. Randomizing sequences */ 40 extern int esl_rsq_CMarkov0 (ESL_RANDOMNESS *r, const char *s, char *markoved); 41 extern int esl_rsq_CMarkov1 (ESL_RANDOMNESS *r, const char *s, char *markoved); 42 43 /* 5. Generating iid sequences (digital mode). */ 44 extern int esl_rsq_xIID (ESL_RANDOMNESS *r, const double *p, int K, int L, ESL_DSQ *dsq); 45 extern int esl_rsq_xfIID (ESL_RANDOMNESS *r, const float *p, int K, int L, ESL_DSQ *dsq); 46 extern int esl_rsq_SampleDirty(ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, double **byp_p, int L, ESL_DSQ *dsq); 47 48 /* 6. Shuffling sequences (digital mode). */ 49 extern int esl_rsq_XShuffle (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, ESL_DSQ *shuffled); 50 extern int esl_rsq_XShuffleDP (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled); 51 extern int esl_rsq_XShuffleKmers (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled); 52 extern int esl_rsq_XReverse(const ESL_DSQ *dsq, int L, ESL_DSQ *rev); 53 extern int esl_rsq_XShuffleWindows(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int w, ESL_DSQ *shuffled); 54 55 /* 7. Randomizing sequences (digital mode) */ 56 extern int esl_rsq_XMarkov0 (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved); 57 extern int esl_rsq_XMarkov1 (ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved); 58 59 #endif /*eslRANDOMSEQ_INCLUDED*/ 60 61