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ExperimentFile

ExperimentFile

Section: Staden Package (3) Updated:
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NAME

exp_read_info, exp_fread_info, exp_create_info, exp_destroy_info, exp_create_range, exp_extract_range, exp_get_feature_index, exp_get_int, exp_get_rng, exp_get_str, exp_put_int, exp_put_rng, exp_put_str, exp_print_line, exp_print_seq, exp_print_file, opos2str, str2opos, conf2str, str2conf - Manipulations of the Experiment File format

 

SYNOPSIS

#include <expFileIO.h>

Exp_info *exp_read_info(
        char *file);

Exp_info *exp_fread_info(
        FILE *fp);

Exp_info *exp_create_info();

void exp_destroy_info(
        Exp_info *e);

char *exp_create_range(
        char *str,
        int start,
        int end);

int exp_extract_range(
        char *str,
        int *start,
        int *end);

int exp_get_feature_index(
        char *e);

int exp_get_int(
        Exp_info *e,
        int id,
        int *val);

int exp_get_rng(
        Exp_info *e,
        int id,
        int *from,
        int *to);

int exp_get_str(
        Exp_info *e,
        int id,
        char *s,
        f_implicit s_l);

int exp_put_int(
        Exp_info *e,
        int id,
        int *val);

int exp_put_rng(
        Exp_info *e,
        int id,
        int *from,
        int *to);

int exp_put_str(
        Exp_info *e,
        int id,
        char *s,
        f_implicit s_l);

int exp_print_line(
        FILE *fp,
        Exp_info *e,
        int eflt,
        int i);

int exp_print_seq(
        FILE *fp,
        Exp_info *e,
        int eflt,
        int i);

void exp_print_file(
        FILE *fp,
        Exp_info *e);

char *opos2str(
        int2 *opos,
        int len,
        char *buf);

int str2opos(
        int2 *opos,
        char *buf);

char *conf2str(
        int1 *conf,
        int len,
        char *buf);

int str2conf(
        int1 *conf,
        char *buf);

 

DESCRIPTION

These functions manipulate Experiment Files. They include functions for reading, writing, and editing the files. The principle structure used by the routines is the Exp_info structure. This is as follows. #define MAXIMUM_EFLT_LENGTH 4 #define MAXIMUM_EFLTS 48 #define EXP_FILE_LINE_LENGTH 128

typedef Array Exp_entries;

typedef struct {
    Array entries[MAXIMUM_EFLTS]; /* array of array of entries */
    int Nentries[MAXIMUM_EFLTS];  /* array of number of entries */
    FILE *fp; } Exp_info;

#define NULL_Exp_info ( (Exp_info *) NULL )

For the purposes of simple and efficient coding, each line on an experiment file must be smaller than the defined EXP_FILE_LINE_LENGTH, which is 128 characters.

Many functions take an experiment file line type identifier as an argument. These functions are listed in the prototypes as taking int id. Here id should be specified using one of the macros defining in the header file. They take the form of EFLT_XX where XX is the line type. For instance, the ID line type identifier should be written as EFLT_ID.

The C functions available follow. Some FORTRAN interfaces are also available, but these are not documented. See the include file for their prototypes.

exp_read_info and exp_fread_info read an experiment file into an allocated Exp_info structure. If successful, the structure pointer is return. Otherwise the null pointer is returned.

exp_create_info allocates and initialises a new, blank, Exp_info structure. If successful, the structure pointer is return. Otherwise the null pointer is returned.

exp_destroy_info deallocates an Exp_info structure.

exp_create_range creates a string using the experiment file range format of "start..stop". This format is used by the AQ, ON, TG and TC line types. The buffer specified should be large enough to hold the string. The function returns the str pointer supplied as an argument.

exp_extract_range extracts the start and end values from the string representation of a range; "start..stop". The values are stored in the integer pointers sent as arguments. If successful, the function returns 0. Otherwise -1 is returned.

exp_get_feature_index converts from a string representation of an experiment file line type to the integer value. For example, exp_get_feature_index("SQ") returns the integer 22, which is the same as the EFLT_SQ definition.

exp_get_int obtains the integer value held in a specific line type. The value is stored in the integer pointer val. If successful, the function returns 0. Otherwise 1 is returned.

exp_get_rng obtains the range values held in a specific line type. The values are stored in the integer pointers from and to. If successful, the function returns 0. Otherwise 1 is returned.

exp_get_str obtains the string value held in a specific line type. The value is stored in the string s. At most s_l characters are copied. If successful, the function returns 0. Otherwise 1 is returned.

exp_put_int writes the integer pointed to by val to the specified line type. If successful, the function returns 0. Otherwise 1 is returned.

exp_put_rng writes the range pointed to by from and to to the specified line type. If successful, the function returns 0. Otherwise 1 is returned.

exp_put_str writes the string s of length s_l to the specified line type. If successful, the function returns 0. Otherwise 1 is returned.

exp_print_line outputs all entries of the specified type to the specified file pointer.

exp_print_seq

exp_print_file outputs all entries of all line types to the specified file pointer.

opos2str converts an array of original positions held in opos with len elements to a string suitable for use in the ON line type. The buf should be large enough to hold the string, which in the worst case will be 4 * sequence length. Returns buf.

str2opos converts the experiment file original position string held in buf to an array of original positions to be stored in opos. opos must be large enough to hold the data, hence it should be of the same length as the sequence. Returns the number of elements written to the opos array.

conf2str converts an array of confidence values helf in confR with len elements to a string suitable for use in the AV line type. The buf should be large enough to hold the string, which in the worst case will be 4 * sequence length. Returns buf.

str2conf convers the experiment file confidence values string held in buf to an array of confidence values to be stored in conf. conf must be large enough to hold the data, hence it should be of the same length as the sequence. Returns the number of elements written to the conf array.

 

SEE ALSO

ExperimentFile(4)


 

Index

NAME
SYNOPSIS
DESCRIPTION
SEE ALSO

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Time: 21:45:46 GMT, April 16, 2011