1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
|
/* (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. */
/* matrix.h: Matrix datatype and matrix manipulation functions */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef MATRIX_H_
#define MATRIX_H_
#include "pattern.h"
/*
* Exported variables and data structures
*/
typedef double MatType; /* so we can easily change to double if */
/* needed. NOTE: read_matrix_body will */
/* need to be changed to reflect any changes */
/* to the type of MatType. */
/* and convert.c it rounds values to an int */
/* before storing */
/* WARNING!!! in convert.c there is a LOT of */
/* rounding! (and I mean a LOT). */
#define NUMBER_WIDTH 20
#define DESC_WIDTH 80
#define MATRIX_AA_WIDTH 26 /* 20 aa, 3 ambig, 1 stop, 1 gap, and */
/* 1 for non-codes J, O, U. */
/* the +2 to account for the gap and */
/* codes that are not defined ( - and */
/* J, O, U ) */
struct matrix_struct {
Block *block; /* the block that this matrix is from */
char id[SMALL_BUFF_LENGTH]; /* Matrix ID string */
char ac[SMALL_BUFF_LENGTH]; /* Matrix AC string */
char de[DESC_WIDTH]; /* Matrix DE string */
char ma[SMALL_BUFF_LENGTH]; /* Matrix MA string */
char number[NUMBER_WIDTH]; /* the number of this matrix */
char motif[20]; /* motif */
int width; /* the length of the sequence/matrix */
int num_sequences; /* the number of sequences that were in the */
/* generating data. */
int percentile; /* the block/matrix percentile */
int strength; /* the block/matrix strength */
int max_length; /* max length when reading in */
Pattern **patterns; /* the patterns for this PSSM, an array
of ptrs to Patterns, NULL */
int undefined; /* for future use */
void *undefined_ptr; /* for future use */
MatType *weights[MATRIX_AA_WIDTH]; /* the weight matrix */
};
typedef struct matrix_struct Matrix;
/*
* Exported functions
*/
/*
* read_a_matrix
* reads a matrix from the data base and returns a pointer to the new
* matrix data structure
* Parameters:
* FILE *mfp: a pointer to the database file with the matrix.
* Error codes: NULL if a matrix was not read
*/
extern Matrix *read_a_matrix ();
/*
* matrix_comparison
* Compares two matricies. It compares by the value in the block->id
* field if it exists.
* Parameters:
* MatrixListEntry 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 matrix_comparison();
/*
* new_matrix
* allocates space for a matrix of length len, sets up the data structure
* and returns a pointer to the Matrix.
* Parameters:
* int len: the length of the sequence/matrix
* Error codes:
*/
extern Matrix *new_matrix();
/*
* free_matrix
* Deletes the matrix and the sub elements.
* Parameters:
* Matrix *matrix: the matrix to free
* Return code: none
* Error code: none
*/
extern void free_matrix();
/*
* print_matrix
* Prints a Matrix data structure. Primarily for debugging purposes.
* Parameters:
* Matrix *matrix: the matrix to print
* Error Codes: none
*/
extern void print_matrix();
/*
* output_matrix
* Outputs a matrix data structure to the given file.
* Parameters:
* Matrix *matrix: the matrix to output
* FILE *omfp: the output matrix file pointer
* Return code: none
* Error code: none
*/
extern void output_matrix();
/*
* output_matrix_s
* Outputs a matrix data structure to the given file with the
* specified style of data.
* Parameters:
* Matrix *matrix: the matrix to output
* FILE *omfp: the output matrix file pointer
* int style: the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
* Return code: none
* Error code: none
*/
extern void output_matrix_s();
/*
* output_matrix_st
* Outputs a matrix data structure to the given file with the
* specified style of data. Optionally only outputs ACTG.
* Parameters:
* Matrix *matrix: the matrix to output
* FILE *omfp: the output matrix file pointer
* int style: the kind of output (INT_OUTPUT, FLOAT_OUTPUT)
* int type: the type of matrix (AA_SEQ, NA_SEQ)
* Return code: none
* Error code: none
*/
extern void output_matrix_st();
#endif /* MATRIX_H_ */
/* Change log information follows. */
/*
Changes since 3.2.5:
2/11/99 Renamed Matrix->length to Matrix->width.
Changes since 3.1:
2/14/97 Added output_matrix_st().
Changes since 3.0.0:
3/25/96 Changed MatType from int to double. JGH
*/
|
