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
|
Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252
https://bugs.gentoo.org/show_bug.cgi?id=570252
In addition, fixed multiple -Wformat= warnings, such as
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
^
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
--- DIALIGN-TX_1.0.2/source/alig.c
+++ DIALIGN-TX_1.0.2/source/alig.c
@@ -10,9 +10,9 @@
extern void error(char *message);
extern void merror(char *msg1, char *msg2);
-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
struct prob_dist *pdist);
-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
struct prob_dist *pdist);
//extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2,
@@ -520,7 +520,7 @@
* datastructure (i.e. frontiers). The given diag must be consistent
* to the given alignment !
*/
-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
char alignedSomething = 0;
int i,j,k;
--- DIALIGN-TX_1.0.2/source/assemble.c
+++ DIALIGN-TX_1.0.2/source/assemble.c
@@ -10,9 +10,9 @@
extern void error(char *message);
extern void merror(char *msg1, char *msg2);
-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
struct prob_dist *pdist);
-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
struct prob_dist *pdist);
//extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
extern long double** create_tmp_pdist(struct prob_dist *pdist);
@@ -22,7 +22,7 @@
int n2, struct seq* sq2, unsigned int sp2,
int dlength);
extern void free_diag(struct diag* dg);
-extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
+extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
struct prob_dist *pdist,
struct gt_node* n1,
struct gt_node* n2,
@@ -34,10 +34,10 @@
extern struct alignment* create_empty_alignment(struct seq_col *scol);
extern void free_alignment(struct alignment *algn);
-extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
+extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
//extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
//extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
//extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
--- DIALIGN-TX_1.0.2/source/diag.c
+++ DIALIGN-TX_1.0.2/source/diag.c
@@ -183,7 +183,7 @@
* omitScore = 0: normal
* omitScore = 1: no score calculation
*/
-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) {
if(dg->multi_dg) {
@@ -302,7 +302,7 @@
}
}
-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
struct prob_dist *pdist) {
real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL);
}
--- DIALIGN-TX_1.0.2/source/io.c
+++ DIALIGN-TX_1.0.2/source/io.c
@@ -267,7 +267,7 @@
for( c=r; c<length; c++) {
// check whether it is a regular acid or a special character like '$',...
if( (r<length-additional) && (c<length-additional)) {
- fscanf( fp, "%i", &is);
+ if( fscanf( fp, "%i", &is) ){};
} else {
is = 0;
}
@@ -279,7 +279,7 @@
// ensure symmetry of the weight matrix
data[length*c+r] = is;
}
- fscanf(fp, "%s\n", rline);
+ if( fscanf(fp, "%s\n", rline) ){};
}
fclose(fp);
@@ -368,7 +368,7 @@
}
for(scr=0;scr<=mxscr;scr++) {
dist[i][scr]=1.0;
- fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
+ if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){};
//if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename);
scr = tscr;
if(weight==0.0) weight = 1.0;
@@ -532,7 +532,7 @@
sdcol->data = malloc(sizeof (struct diag*)*alloc_size);
sdcol->length=0;
- while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
+ while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
if(sdcol->length >= alloc_size) {
alloc_size+=16;
sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size);
|
GitWeb