You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
296 lines
9.8 KiB
296 lines
9.8 KiB
/*!
|
|
\file gk_struct.h
|
|
\brief This file contains various datastructures used/provided by GKlib
|
|
|
|
\date Started 3/27/2007
|
|
\author George
|
|
\version\verbatim $Id: gk_struct.h 21988 2018-04-16 00:11:19Z karypis $ \endverbatim
|
|
*/
|
|
|
|
#ifndef _GK_STRUCT_H_
|
|
#define _GK_STRUCT_H_
|
|
|
|
|
|
/********************************************************************/
|
|
/*! Generator for gk_??KeyVal_t data structure */
|
|
/********************************************************************/
|
|
#define GK_MKKEYVALUE_T(NAME, KEYTYPE, VALTYPE) \
|
|
typedef struct {\
|
|
KEYTYPE key;\
|
|
VALTYPE val;\
|
|
} NAME;\
|
|
|
|
/* The actual KeyVal data structures */
|
|
GK_MKKEYVALUE_T(gk_ckv_t, char, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_ikv_t, int, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_i8kv_t, int8_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_i16kv_t, int16_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_i32kv_t, int32_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_i64kv_t, int64_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_zkv_t, ssize_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_zukv_t, size_t, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_fkv_t, float, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_dkv_t, double, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_skv_t, char *, ssize_t)
|
|
GK_MKKEYVALUE_T(gk_idxkv_t, gk_idx_t, gk_idx_t)
|
|
|
|
|
|
|
|
/********************************************************************/
|
|
/*! Generator for gk_?pq_t data structure */
|
|
/********************************************************************/
|
|
#define GK_MKPQUEUE_T(NAME, KVTYPE)\
|
|
typedef struct {\
|
|
size_t nnodes;\
|
|
size_t maxnodes;\
|
|
\
|
|
/* Heap version of the data structure */ \
|
|
KVTYPE *heap;\
|
|
ssize_t *locator;\
|
|
} NAME;\
|
|
|
|
GK_MKPQUEUE_T(gk_ipq_t, gk_ikv_t)
|
|
GK_MKPQUEUE_T(gk_i32pq_t, gk_i32kv_t)
|
|
GK_MKPQUEUE_T(gk_i64pq_t, gk_i64kv_t)
|
|
GK_MKPQUEUE_T(gk_fpq_t, gk_fkv_t)
|
|
GK_MKPQUEUE_T(gk_dpq_t, gk_dkv_t)
|
|
GK_MKPQUEUE_T(gk_idxpq_t, gk_idxkv_t)
|
|
|
|
|
|
#define GK_MKPQUEUE2_T(NAME, KTYPE, VTYPE)\
|
|
typedef struct {\
|
|
ssize_t nnodes;\
|
|
ssize_t maxnodes;\
|
|
\
|
|
/* Heap version of the data structure */ \
|
|
KTYPE *keys;\
|
|
VTYPE *vals;\
|
|
} NAME;\
|
|
|
|
|
|
|
|
/*-------------------------------------------------------------
|
|
* The following data structure stores a sparse CSR format
|
|
*-------------------------------------------------------------*/
|
|
typedef struct gk_csr_t {
|
|
int32_t nrows, ncols;
|
|
ssize_t *rowptr, *colptr;
|
|
int32_t *rowind, *colind;
|
|
int32_t *rowids, *colids;
|
|
int32_t *rlabels, *clabels;
|
|
int32_t *rmap, *cmap;
|
|
float *rowval, *colval;
|
|
float *rnorms, *cnorms;
|
|
float *rsums, *csums;
|
|
float *rsizes, *csizes;
|
|
float *rvols, *cvols;
|
|
float *rwgts, *cwgts;
|
|
} gk_csr_t;
|
|
|
|
|
|
/*-------------------------------------------------------------
|
|
* The following data structure stores a sparse graph
|
|
*-------------------------------------------------------------*/
|
|
typedef struct gk_graph_t {
|
|
int32_t nvtxs; /*!< The number of vertices in the graph */
|
|
ssize_t *xadj; /*!< The ptr-structure of the adjncy list */
|
|
int32_t *adjncy; /*!< The adjacency list of the graph */
|
|
int32_t *iadjwgt; /*!< The integer edge weights */
|
|
float *fadjwgt; /*!< The floating point edge weights */
|
|
int32_t *ivwgts; /*!< The integer vertex weights */
|
|
float *fvwgts; /*!< The floating point vertex weights */
|
|
int32_t *ivsizes; /*!< The integer vertex sizes */
|
|
float *fvsizes; /*!< The floating point vertex sizes */
|
|
int32_t *vlabels; /*!< The labels of the vertices */
|
|
} gk_graph_t;
|
|
|
|
|
|
/*-------------------------------------------------------------
|
|
* The following data structure stores stores a string as a
|
|
* pair of its allocated buffer and the buffer itself.
|
|
*-------------------------------------------------------------*/
|
|
typedef struct gk_str_t {
|
|
size_t len;
|
|
char *buf;
|
|
} gk_str_t;
|
|
|
|
|
|
|
|
|
|
/*-------------------------------------------------------------
|
|
* The following data structure implements a string-2-int mapping
|
|
* table used for parsing command-line options
|
|
*-------------------------------------------------------------*/
|
|
typedef struct gk_StringMap_t {
|
|
char *name;
|
|
int id;
|
|
} gk_StringMap_t;
|
|
|
|
|
|
/*------------------------------------------------------------
|
|
* This structure implements a simple hash table
|
|
*------------------------------------------------------------*/
|
|
typedef struct gk_HTable_t {
|
|
int nelements; /* The overall size of the hash-table */
|
|
int htsize; /* The current size of the hash-table */
|
|
gk_ikv_t *harray; /* The actual hash-table */
|
|
} gk_HTable_t;
|
|
|
|
|
|
/*------------------------------------------------------------
|
|
* This structure implements a gk_Tokens_t list returned by the
|
|
* string tokenizer
|
|
*------------------------------------------------------------*/
|
|
typedef struct gk_Tokens_t {
|
|
int ntoks; /* The number of tokens in the input string */
|
|
char *strbuf; /* The memory that stores all the entries */
|
|
char **list; /* Pointers to the strbuf for each element */
|
|
} gk_Tokens_t;
|
|
|
|
|
|
/*------------------------------------------------------------
|
|
* This structure implements storage for an atom in a pdb file
|
|
*------------------------------------------------------------*/
|
|
typedef struct atom {
|
|
int serial;
|
|
char *name;
|
|
char altLoc;
|
|
char *resname;
|
|
char chainid;
|
|
int rserial;
|
|
char icode;
|
|
char element;
|
|
double x;
|
|
double y;
|
|
double z;
|
|
double opcy;
|
|
double tmpt;
|
|
} atom;
|
|
|
|
|
|
/*------------------------------------------------------------
|
|
* This structure implements storage for a center of mass for
|
|
* a single residue.
|
|
*------------------------------------------------------------*/
|
|
typedef struct center_of_mass {
|
|
char name;
|
|
double x;
|
|
double y;
|
|
double z;
|
|
} center_of_mass;
|
|
|
|
|
|
/*------------------------------------------------------------
|
|
* This structure implements storage for a pdb protein
|
|
*------------------------------------------------------------*/
|
|
typedef struct pdbf {
|
|
int natoms; /* Number of atoms */
|
|
int nresidues; /* Number of residues based on coordinates */
|
|
int ncas;
|
|
int nbbs;
|
|
int corruption;
|
|
char *resSeq; /* Residue sequence based on coordinates */
|
|
char **threeresSeq; /* three-letter residue sequence */
|
|
atom *atoms;
|
|
atom **bbs;
|
|
atom **cas;
|
|
center_of_mass *cm;
|
|
} pdbf;
|
|
|
|
|
|
|
|
/*************************************************************
|
|
* Localization Structures for converting characters to integers
|
|
**************************************************************/
|
|
typedef struct gk_i2cc2i_t {
|
|
int n;
|
|
char *i2c;
|
|
int *c2i;
|
|
} gk_i2cc2i_t;
|
|
|
|
|
|
/*******************************************************************
|
|
*This structure implements storage of a protein sequence
|
|
* *****************************************************************/
|
|
typedef struct gk_seq_t {
|
|
|
|
int len; /*Number of Residues */
|
|
int *sequence; /* Stores the sequence*/
|
|
|
|
|
|
int **pssm; /* Stores the pssm matrix */
|
|
int **psfm; /* Stores the psfm matrix */
|
|
char *name; /* Stores the name of the sequence */
|
|
|
|
int nsymbols;
|
|
|
|
|
|
} gk_seq_t;
|
|
|
|
|
|
|
|
|
|
/*************************************************************************/
|
|
/*! The following data structure stores information about a memory
|
|
allocation operation that can either be served from gk_mcore_t or by
|
|
a gk_malloc if not sufficient workspace memory is available. */
|
|
/*************************************************************************/
|
|
typedef struct gk_mop_t {
|
|
int type;
|
|
ssize_t nbytes;
|
|
void *ptr;
|
|
} gk_mop_t;
|
|
|
|
|
|
/*************************************************************************/
|
|
/*! The following structure defines the mcore for GKlib's customized
|
|
memory allocations. */
|
|
/*************************************************************************/
|
|
typedef struct gk_mcore_t {
|
|
/* Workspace information */
|
|
size_t coresize; /*!< The amount of core memory that has been allocated */
|
|
size_t corecpos; /*!< Index of the first free location in core */
|
|
void *core; /*!< Pointer to the core itself */
|
|
|
|
/* These are for implementing a stack-based allocation scheme using both
|
|
core and also dynamically allocated memory */
|
|
size_t nmops; /*!< The number of maop_t entries that have been allocated */
|
|
size_t cmop; /*!< Index of the first free location in maops */
|
|
gk_mop_t *mops; /*!< The array recording the maop_t operations */
|
|
|
|
/* These are for keeping various statistics for wspacemalloc */
|
|
size_t num_callocs; /*!< The number of core mallocs */
|
|
size_t num_hallocs; /*!< The number of heap mallocs */
|
|
size_t size_callocs; /*!< The total # of bytes in core mallocs */
|
|
size_t size_hallocs; /*!< The total # of bytes in heap mallocs */
|
|
size_t cur_callocs; /*!< The current # of bytes in core mallocs */
|
|
size_t cur_hallocs; /*!< The current # of bytes in heap mallocs */
|
|
size_t max_callocs; /*!< The maximum # of bytes in core mallocs at any given time */
|
|
size_t max_hallocs; /*!< The maximum # of bytes in heap mallocs at any given time */
|
|
|
|
} gk_mcore_t;
|
|
|
|
|
|
/*************************************************************************/
|
|
/*! The following structure is used for cache simulation for performance
|
|
modeling and analysis. */
|
|
/*************************************************************************/
|
|
typedef struct gk_cache_t {
|
|
/*! The total cache is nway*(2^(cnbits+lnbits)) bytes */
|
|
uint32_t nway; /*!< the associativity of the cache */
|
|
uint32_t lnbits; /*!< the number of address bits indexing the cache line */
|
|
uint32_t cnbits; /*!< the number of address bits indexing the cache */
|
|
size_t csize; /*!< 2^cnbits */
|
|
size_t cmask; /*!< csize-1 */
|
|
|
|
uint64_t clock; /*!< a clock in terms of accesses */
|
|
|
|
uint64_t *latimes; /*!< a cacheline-level last access time */
|
|
size_t *clines; /*!< the cache in terms of cachelines */
|
|
|
|
uint64_t nhits; /*!< counts the number of hits */
|
|
uint64_t nmisses; /*!< counts the number of misses */
|
|
} gk_cache_t;
|
|
|
|
|
|
#endif
|
|
|