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/* (C) Copyright 1993-7, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* blocks.h: declaration of blocks data type and basic block operations */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef BLOCKS_H_
#define BLOCKS_H_
#define MINAC 7 /* min & max possible AC lengths */
#define MAXAC 10
#include <output.h>
#include <sequences.h>
/*
* Exported variables and data structures
*/
/*
* Sequence, Cluster, and Block data types
*/
struct cluster_struct {
int num_sequences; /* number of sequences in the block */
Sequence *sequences; /* the array of Sequences of the cluster */
};
typedef struct cluster_struct Cluster;
struct block_struct {
char id[SMALL_BUFF_LENGTH]; /* Block ID string */
char ac[SMALL_BUFF_LENGTH]; /* Block AC string */
char de[SMALL_BUFF_LENGTH]; /* Block DE string */
char bl[SMALL_BUFF_LENGTH]; /* Block BL string */
char number[SMALL_BUFF_LENGTH]; /* AC: block number IPR123456A */
char family[SMALL_BUFF_LENGTH]; /* AC: block family IPR123456 */
char motif[20]; /* BL: motif */
int width; /* BL: block width */
int percentile; /* BL: 99.5% score */
int strength; /* BL: strength (median TP score) */
int max_sequences; /* max number of sequences in the block */
int num_sequences; /* number of sequences in the block */
int max_clusters; /* max number of clusters in the block */
int num_clusters; /* number of clusters in the block */
int min_prev; /* AC: min distance from previous block */
int max_prev; /* AC: max distance from previous block */
int undefined; /* for future use */
double undefined_dbl; /* for future use */
void *undefined_ptr; /* for future use */
Cluster *clusters; /* the array of Clusters of the block */
Sequence *sequences; /* the array of Sequences of the block */
Residue **residues; /* the 2-d array of residues [seq][pos] */
};
typedef struct block_struct Block;
/*
* Exported functions
*/
/*
* read_a_block
* reads a block from the data base and returns a pointer to the new
* block data structure
* Parameters:
* FILE *bfp: the file pointer the the blocks database/file
* Error codes: NULL if a block was not read
*/
extern Block *read_a_block ();
extern Block *read_a_block_faster ();
extern Boolean read_to_block();
/*
* block_comparison
* Compares two blocks. It compares by the value in the id
* field if it exists.
* Parameters:
* BlockListEntry a, b: the entries to compare
* Return codes: a return value < 0 if a < b, a return value = 0 if a == b,
* and a return value > 0 if a > b
* Error codes: none
*/
extern int block_comparison();
/*
* free_block
* Frees the block and the sub elements.
* Parameters:
* Score *score: the score to free
* Return code: none
* Error code: none
*/
extern void free_block() ;
extern int read_block_header();
extern void read_block_body();
extern void next_cluster();
/*
* resize_block_sequences
* Increases the memory for the storage of the sequences of a block.
* Parameter:
* Block *block: the block to resize
* Error codes: none
*/
extern void resize_block_sequences();
extern void resize_block_clusters();
/*
* print_block
* Prints a block data structure. Primarily for debugging purposes.
* Parameters:
* Block *block: the block to print
* Error Codes: none
*/
extern void print_block();
/*
* ouput_block
* Outputs a block data structure to the given file.
* Parameters:
* Block *block: the block to print
* FILE *obfp: the ouput block file pointer
* Error Codes: none
*/
extern void output_block();
/*
* ouput_block_s
* Outputs a block data structure to the given file with the
* specified style of data.
* Parameters:
* Block *block: the block to print
* FILE *obfp: the ouput block file pointer
* int style: the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
* Error Codes: none
*/
extern void output_block_s();
/*
* new_block
* Creates a new empty Block structrue
* Parameters:
* ncols: Number of columns = sequence length
* nrows: Number of rows = number of sequences
*/
extern Block *new_block();
#endif /* BLOCKS_H_ */
/* Change log information follows. */
/*
* Changes since 3.3.2:
12/15/99 Added double undefined_dbl field.
12/17/99 Added family field, MINAC, MAXAC
* Changes since 3.2.5:
2/11/99 Added min_prev & max_prev fields to the blocks structure;
rename block->sequence_length to block_width.
* Changes since 3.2.2:
1/29/98 Added resize_block_clusters(), etc.
* Changes since 3.2:
4/16/97 Added resize_block_sequences()
* Changes since 3.1:
2/14/97 Added new_block().
*
*/
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