/* * @file seed.h * * A definition of the interface for SEED objects. * * $Id$ * * $Log$ * Revision 1.1.2.12 2006/03/10 06:58:01 twhitington * print_heaps and "eval_best_seed" command line switches added. * * Revision 1.1.2.11 2006/03/02 04:55:15 twhitington * Removed old FIXME comment regarding string and integer rep storage. * * Revision 1.1.2.10 2006/03/02 04:31:12 twhitington * Changed get_w to get_width. * * Revision 1.1.2.9 2006/02/22 01:53:32 twhitington * Changed SEED objects so they don't store e_seed, and are instantiated with * ascii strings instead of encoded representations. * * Revision 1.1.2.8 2006/02/01 02:26:04 twhitington * Changed formal parameter names in seed.h. * * Revision 1.1.2.7 2006/02/01 01:38:46 twhitington * Modified subseq7 so that Tcm make test is passed; * Catered for rejection of seeds by align_top_subsequences. * * Revision 1.1.2.6 2006/01/31 08:21:19 tbailey * Changed way functions are passed to create_heap * * Revision 1.1.2.5 2006/01/30 06:06:46 twhitington * Introduced serial number variable to seed objects. * Introduced str_seed variable to seed objects. * * Revision 1.1.2.4 2006/01/27 07:32:47 twhitington * Debugging changes made to subseq7.c, and debugging problems with get_key * in seed.c. * * Revision 1.1.2.3 2006/01/19 04:59:08 twhitington * Introduced heap objects to S_POINT objects. Changed get_nsites0 and get_starts accordingly, in starts.c. Corresponding changes were required in the seed interface and the Makefile. * * Revision 1.1.2.2 2006/01/18 07:09:08 twhitington * Implemented SEED object. Also introduced seed-tests program for testing SEED objects. * * Revision 1.1.2.1 2006/01/16 06:04:36 tbailey * Add seed.c and seed.h for branching project. * */ #ifndef SEED_H #define SEED_H #include "macros.h" #include "stdint.h" #include "alphabet.h" #ifdef DMALLOC #include "dmalloc.h" #endif /** * A SEED type, for encapsulating an alphabet sequence that could could as a * starting point for meme. */ typedef struct seed SEED; struct seed{ char *str_seed; ///< An ascii representation of the seed. double score; ///< Score of e_seed as a starting point for local search int iseq; ///< The sequence number index int ipos; ///< The sequence position index }; /** * new_seed generates a new SEED object. * \return A pointer to the new object. */ SEED *new_seed( char *str_seed, ///< An ascii representation of the seed. double score, ///< Score of the seed as a starting point for local search. int iseq, ///< Index of sequence seed is from. int ipos ///< Position in sequence seed is from. ); /** * compare_seed * * This function compares two seeds. The rule is: * Returns 1 if score1 > score2, * Returns -1 if score1 < score2, * If score1 == score2 then * Returns 1 if iseq_1 < iseq_2 * Returns -1 if iseq_1 > iseq_2 * else if iseq_1 == iseq_2 then * Returns 1 if ipos_1 < ipos_2 * Returns -1 if ipos_1 > ipos_2 * else if ipos_1 == ipos_2 then * Returns -1 if serial_no_1 > serial_no_2 * Returns 1 if serial_no_1 < serial_no_2 * else * Returns 0 * * */ int compare_seed( SEED *p1, ///< pointer to a SEED object SEED *p2 ///< pointer to a SEED object ); /** * get_seed_score retrieves the score for a given seed. * \return The score for the input seed. */ double get_seed_score( SEED *seed ///< seed object ); /** * get_e_seed * * Converts the string representation of the specified seed into an integer * encoded representation, and returns a pointer to the start of the resulting * array. Memory is allocated for the array in this function. Deallocation must * be controlled by the caller of this function. Note that the length of the * array can get retrieved via "get_width()" for the same SEED object. * * \return The e_seed for the input seed. */ uint8_t *get_e_seed( ALPH_T *alph, SEED *seed ); /** * set_seed sets the fields for the input pointer to a seed object. */ void set_seed( SEED *seed, ///< The seed object whose fields are to be set char *str_seed, ///< An ascii representation of the seed. double score, ///< Score of the seed as a local search starting point. int iseq, ///< Index of sequence seed is from. int ipos ///< Position in sequence seed is from. ); /** * copy_seed copies the fields of the input seed object into the fields of * the a new seed object. * An EXACT copy of the seed is made, such that compare_seed between the * original and the copy yields zero. In particular, note that the * serial_number of the new seed is equal to that of the old seed. * \return A pointer to a new seed that is a copy of the original. */ SEED *copy_seed( SEED *orig_object ///< The existing seed object that will be copied ); /** * free_seed destroyes the input seed object. */ void free_seed( SEED *obj ///< The seed object to be destroyed ); /** * print_seed prints a representation of the seed to standard out, thus * providing a way to debug code related to seed objects. */ void print_seed( FILE *outfile, ///< The file to print to SEED *seed ///< Seed to be printed. ); /** * get_str_seed retrieves the ascii string representation of this e_seed. * /return ascii representation of the e_seed. */ char *get_str_seed( SEED *seed ///< The seed whose representation is being retrieved. ); /** * get_width * * Retrieves the length of the seed. Note that this is an 0(w) operation * because w is not explicitly stored in the SEED object and is instead * determined by analysing str_seed. * * /return length of str_seed. */ int get_width( SEED *seed ///< The seed whose length is being retrieved. ); /** * to_str_seed * * This function converts an integer encoded representation of a seed into an * ascii representation of it. Memory for the string is dynamically allocated * here, and it is the caller's responsibility to later free that memory. */ char *to_str_seed( ALPH_T *alph, uint8_t *e_seed, ///< Integer encoded representation. int w ///< The length of the string. ); uint8_t *to_e_seed ( ALPH_T *alph, char *str_seed, ///< ASCII representation int *seed_len ///< The length of the resulting e_seed ); #endif /* * Local Variables: * mode: c * c-basic-offset: 2 * End: */