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--- a/src/alig_graph_closure.c
+++ b/src/alig_graph_closure.c
@@ -27,7 +27,7 @@
void init_seq(CLOSURE *clos, int nbreseq, int *longseq);
void desinit_seq(CLOSURE *clos);
-int print_aligSets(CLOSURE *clos, int nseq, int i);
+void print_aligSets(CLOSURE *clos, int nseq, int i);
char DEBUG=0;
@@ -309,7 +309,7 @@
}
-int print_aligSets(CLOSURE *clos, int nseq, int i)
+void print_aligSets(CLOSURE *clos, int nseq, int i)
{
char nouveau_, terminer;
int n, ng, nd, nn, k;
@@ -395,7 +395,7 @@
liberer(clos);
}
-int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j)
+void addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j)
{
char nouveau_, terminer;
int n, n1, n2, ng1, ng2, nd1, nd2, nn, k;
@@ -623,7 +623,7 @@
return(!path(clos, y, j, x, i));
}
-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
+void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
{
int k;
--- a/src/alig_graph_closure.h
+++ b/src/alig_graph_closure.h
@@ -43,13 +43,13 @@
void freeAligGraphClosure(CLOSURE *clos);
-int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j);
+void addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j);
int alignablePositions(CLOSURE *clos, int x, int i, int y, int j);
int alignedPositions(CLOSURE *clos, int x, int i, int y, int j);
-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
+void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
--- a/src/anchor.c
+++ b/src/anchor.c
@@ -17,6 +17,7 @@
#include "define.h"
#include "dialign.h"
#include "alig_graph_closure.h"
+#include "pratique.h"
extern int anc_num, *seqlen ;
@@ -24,6 +25,8 @@
extern char *seq[MAX_SEQNUM];
extern struct multi_frag *anchor_frg ;
+extern int word_count( char *seq );
+
void anchor_check( int s1, int s2, int b1, int b2, int l , float scr ) {
if(
@@ -101,7 +104,7 @@
}
-int multi_anc_read( char *file_name ) {
+void multi_anc_read( char *file_name ) {
char anc_file_name[ NAME_LEN ] ;
FILE *fp;
--- a/src/dialign.c
+++ b/src/dialign.c
@@ -218,7 +218,7 @@
extern void subst_mat(char *file_name, int fragno , struct multi_frag *smp );
extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ;
extern int anc_read( char *file_name ) ;
- extern int multi_anc_read( char *file_name ) ;
+ extern void multi_anc_read( char *file_name ) ;
extern void randomize( int r_numb , FILE *fp1 );
extern int mini2(int a, int b);
extern int maxi2(int a, int b);
@@ -250,6 +250,9 @@
extern void av_tree_print();
extern void matrix_read( FILE *fp_mat ) ;
extern void mem_alloc( ) ;
+ extern void regex_parse( char *mot_regex ) ;
+ extern void seq_parse( char *mot_regex ) ;
+ extern void exclude_frg_read( char *file_name , int ***exclude_list) ;
/******************************/
@@ -258,7 +261,7 @@
-main(int argc, char **argv)
+int main(int argc, char **argv)
{
int k, anc1, dia_counter, tmpi1, tmpi2 ;
--- a/src/functions.c
+++ b/src/functions.c
@@ -853,7 +853,7 @@
}
}
-wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) {
int i, dc, pc, s1, pos;
@@ -882,7 +882,7 @@
-plot_calc( int num , int e_len, float *w_count, float *pl,
+void plot_calc( int num , int e_len, float *w_count, float *pl,
struct multi_frag *dia , FILE *fp_csc )
{
int i, dc, pc, s1, pos;
--- a/src/input.c
+++ b/src/input.c
@@ -17,6 +17,7 @@
#include "define.h"
#include "dialign.h"
#include "alig_graph_closure.h"
+#include "pratique.h"
extern int max_dia , self_comparison ;
extern int sim_score[21][21];
@@ -370,8 +371,11 @@
}
- if ( fgets( line , MLINE , fp ) == NULL )
- erreur("\n\n problem with file %s \n\n", file_name );
+ if ( fgets( line , MLINE , fp ) == NULL ) {
+ char buffer [500];
+ snprintf ( buffer, 500, "\n\n problem with file %s \n\n", file_name );
+ erreur( buffer );
+ }
else
if( w_type % 2 )
av_sim_score_nuc = atof( line );
--- a/src/output.c
+++ b/src/output.c
@@ -61,9 +61,9 @@
extern void mini(int *a, int b);
extern void maxi(int *a, int b);
extern int int_test(float f);
- extern plot_calc( int num , int e_len, float *w_count, float *pl,
+ extern void plot_calc( int num , int e_len, float *w_count, float *pl,
struct multi_frag *dia , FILE *fp_csc ) ;
- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ;
--- a/src/pratique.c
+++ b/src/pratique.c
@@ -4,7 +4,7 @@
/* ------------------------------------------------------------*/
-void erreur(char *message)
+_Noreturn void erreur(char *message)
{
printf("%s\n", message);
exit(1);
--- a/src/pratique.h
+++ b/src/pratique.h
@@ -12,7 +12,7 @@
#define TAILLE_MAX_LIGNE_FICHIER 10000
-void erreur(char *message);
+_Noreturn void erreur(char *message);
void *allouer(size_t taille);
void *reallouer(void *pointeur, size_t taille);
--- a/src/regex.c
+++ b/src/regex.c
@@ -151,7 +151,7 @@
}
-seq_parse( char *mot_regex ) {
+void seq_parse( char *mot_regex ) {
int sn, ok , i ;
int sp, ap, rp, hv, match;
max_mot_offset = sqrt ( - log ( 0.1 ) * 10 / mot_factor ) * mot_offset_factor;
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