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/* (C) Copyright 1993, 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. */
/* sequences.h: sequence manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef SEQUENCES_H_
#define SEQUENCES_H_
#include "strutil.h"
/*
* Exported variables and data structures
*/
#define AA_SEQ 0 /* Amino acid sequence designator */
#define NA_SEQ 1 /* Nucleic acid sequence designator */
#define UNKNOWN_SEQ 2 /* Unknown sequence designator */
#define NA_FREQ 0.85 /* the percent of 'A', 'C', 'G'. & 'T' in */
/* the sequence to consider it a NA_SEQ */
/* the Residue type */
typedef unsigned char Residue;
struct sequence_struct {
char name[SMALL_BUFF_LENGTH]; /* the name of the sequence */
char info[SMALL_BUFF_LENGTH]; /* the info line of the sequence */
int position; /* the position of the subsequence (if */
/* is one) in the sequence */
int length; /* the length of the sequence */
int max_length; /* the maximum length of memory allocated */
int type; /* type of sequence: AA_SEQ or NA_SEQ */
double weight; /* the weight of the sequence if the */
/* sequence is in a block */
double undefined; /* for future use */
double undefined_dbl; /* for future use */
void *undefined_ptr; /* for future use */
Residue *sequence; /* the sequence of either protein or DNA */
};
typedef struct sequence_struct Sequence;
/* Sequence Database types */
/*--------Sequence database format structure -------------------------*/
#define MAXDB 10 /* Max. # database formats */
#define GB 0 /* GenBank type */
#define PIR 1 /* PIR type */
#define EMBL 2 /* EMBL type. SwissProt is the same. */
#define GCG 3 /* plain GCG type */
#define GCG_GB 4 /* GCG with GenBank header */
#define GCG_PIR 5 /* GCG with PIR header */
#define GCG_EMBL 6 /* GCG with EMBL/SwissProt header */
#define FASTA 7 /* FASTA type */
#define UNI 8 /* UNIVERSAL type */
#define FLAT 9 /* FLAT, no title, just sequence */
/*#define VMS 3*/ /* PIR/VMS type */
/* NOTE: VMS must be the the last type and UNI must be just before it. See */
/* the code in type_dbs for the reason */
/* NOTE: Fasta and Universa (and VMS) formats are very similar. The */
/* only difference between Fasta and Universa is that there is a */
/* '*' at the end of the Universa format. The reason for the */
/* Universa format is that there was a time when patmat needed */
/* the '*' end-of-sequence delimiter. There is no longer a */
/* need with blimps, but the universa format handling is being */
/* kept around for backward compatibility. */
/* NOTE: The GCG formats consists of a header file of the format of the */
/* originating database and the sequence protion in the GCG */
/* format. This obviously can lead to confusion, especially */
/* since the characters in the second line of the GCG sequence */
/* format will signal that the sequence is an amino acid */
/* sequence (bad when the GCG sequence is from a DNA database). */
/* NOTE: The plain GCG format is a kludge. There is code to handle */
/* it, but since it is one of the formats that does not have an */
/* end delimiter there is the possibility that there will be */
/* junk added to the sequence if there is more than one */
/* sequence in the file. */
struct db_info { /* Sequence Database format info */
char *type;
char *start;
char *desc;
char *seq;
char *end;
int title_offset;
int seq_offset;
};
extern struct db_info DbInfo[MAXDB];
/*
* Exported functions
*/
/*
* read_a_sequence
* reads a sequence from the data base and returns a pointer to the new
* Sequence data structure
* Parameters:
* FILE *sfp: the sequence file pointer
* int db: the database type of the file
* int type: the type of sequences in the file
* Error codes: Returns NULL if there was no sequence to read.
*/
extern Sequence *read_a_sequence();
/*
* read_sequence
* read_sequence reads from the string the sequence of the given type into
* the passed in Sequence data structure
* Parameters:
* Sequence *seq: the Sequence data structure to put the data in
* int seq_type: the type of sequence (amino acid or nucleic acid)
* int start_pos: the position in the sequence to start entering the data
* char *str: the string that has the sequence (NULL terminated)
* Note: The entire string up to the NULL character is considered the
* sequence.
* Preconditions: seq.length must have a the value of the size allocated to
* the residues
* Postconditions: the residues from start_pos to either seq.length or
* return value + start_pos in the seq.sequence have been
* updated to the residues passed in by the string
* seq.type is set to seq_type
* Return codes: returns the number of residues added to the sequence
* Error codes: returns the negative value of the number of residues left
* over after the sequence has been filled.
* Note: A return value of zero is means that no residues were
* added to the sequence.
*/
extern int read_sequence();
/*
* sequence_type
* tries to guess the type of the sequence passed in the string.
* Note: if the sequence can not be matched to an NA_SEQ, it falls through
* to being a AA_SEQ.
* Parameters:
* char *str: the sequence string, no more than SMALL_BUFF_LENGTH long
* Return Codes: Returns either AA_SEQ or NA_SEQ depending on
* if the sequence is an Amino Acid or Nucleic Acid.
* Error Codes: none
*/
extern int sequence_type();
/*
* sequence_comparison
* Compares two sequences. It compares by the value in the name
* field if it exists.
* Parameters:
* SequenceListEntry 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 sequence_comparison();
/*
* free_sequence
* Deletes the sequence and the sub elements.
* Parameters:
* Sequence *sequence: the sequence to free
* Return code: none
* Error code: none
*/
extern void free_sequence();
/*
* translate_sequence
* Given a frame (1, 2, 3, -1, -2, or -3), translates the DNA sequence
* (NA_SEQ) into an amino acid sequence.
* Parameters:
* Sequence *seq: the DNA sequence
* int frame: the frame to read
* unsigned char gcode[64]: the genetic code (forward).
* for frames 1, 2, 3
* unsigned char revgcode[64]: the genetic code (reverse complement)
* for frames -1, -2, -3
* Return code: a pointer to the new translated sequence
* Error codes: returns the original sequence if the sequence is not a
* NA_SEQ or the translation frame is incorrect.
*/
extern Sequence *translate_sequence();
/* untranslate an amino acid sequence to a degenerate DNA sequence */
extern Sequence *untranslate_sequence();
/* NOTE: These should only be used in config.c when determining the */
/* database types. These should be used to set the values in the */
/* file lists. */
/*
* type_dbs
* Figures out the type of the database to be read.
* This is from motomisc.c used in the universa conversion program.
* Parameters:
* FILE *fin: the database file
* struct db_info dbs[]: the information of the structure of the db's
* Return codes: the type of database the file is.
* Error code: the database number -1 is returned if the type of database
* cannot be figured out
*/
extern int type_dbs();
/*
* seq_type_dbs
* Finds the type or the database given.
* Parameters:
* FILE *fin: the database file
* struct db_info dbs[]: the information of the structure of the db's
* int db: the number of this database (indexes into dbs)
* Return codes: Returns the type of sequence of the first entry in the
* database. This assumes that the entire database is of this
* type.
* Error codes: none
*/
extern int seq_type_dbs();
/*
* print_sequence
* Prints a Sequence data structure. Primarily for debugging purposes.
* Parameters:
* Sequence *seq: the sequence to print
* Error Codes: none
*/
extern void print_sequence();
/*
* output_sequence
* Outputs a Sequence data structure to the given file.
* Parameters:
* Sequence *seq: the sequence to print
* FILE *osfp: the output sequence file pointer
* Error Codes: none
*/
extern void output_sequence();
/*
* resize_sequence
* Adds more memory for the storage of the residues of a sequence.
* Parameter:
* Sequence *seq: the sequence to resize
* Error codes: none
*/
extern void resize_sequence();
#endif /* SEQUENCES_H_ */
/* Change log information follows. */
/*
Changes since version 3.3.2:
12/15/99 Added double undefined_dbl field.
Changes since version 3.2:
11/24/97 Made resize_sequence() external.
Changes since version 3.1:
1/20/97 Added untranslate_sequence()
Changes since version 2.x:
3/20/96 Lowered NA_FREQ from 0.90 to 0.85 after user complaints. JGH
*
*/
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