--- 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;