--- /dev/null
+#include <time.h>
+#include <signal.h>
+#include <errno.h>
+#include <sys/times.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+
+
+typedef struct
+ {
+ char *name;
+ char *path;
+ char *suffix;
+ char *full;
+ }
+Fname;
+
+struct Tmpname
+ {
+ char *name;
+ struct Tmpname *next;
+ };
+/*********************************************************************/
+/* */
+/* DICHOTOMY */
+/* */
+/* */
+/*********************************************************************/
+double dichotomy (double value, double target_value, double middle, double *bottom,double *top);
+/*********************************************************************/
+/* */
+/* QSORT */
+/* */
+/* */
+/*********************************************************************/
+
+void qsort(void *base, size_t nmemb, size_t size, int (*compar)(const void *, const void *));
+/*int memcmp ( const void *a, const void * b, size_t size);
+void * memcpy ( void *a, void * b, size_t size);
+*/
+/*********************************************************************/
+/* */
+/* HEAPSORT */
+/* */
+/* */
+/*********************************************************************/
+FILE *hsort_file ( FILE *fp ,int n,int len, size_t size,int first_comp_field, int n_comp_fields,int (*compare)(const void *, const void*,int,int,size_t),void * (*copy)(void *,void*,size_t));
+void ** hsort_array ( void **ra,int n,int len, size_t size, int first_comp_field, int n_comp_fields,int (*compare)(const void *, const void*,int,int,size_t),void * (*copy)(void *,void*,size_t));
+/**********************************************************************/
+/* */
+/* HSORT WRAPPERS */
+/* */
+/* */
+/**********************************************************************/
+void **hsort_list_array ( void **L, int len, size_t size, int entry_len,int first_comp_field, int n_comp_fields);
+FILE *hsort_list_file ( FILE *fp, int len, size_t size, int entry_len,int first_comp_field, int n_comp_fields);
+int hsort_cmp ( const void *a, const void *b, int first, int clen, size_t size);
+void *hsort_cpy(void*to, void *from, size_t size);
+
+void test_hsort_list_array();
+
+/*********************************************************************/
+/* */
+/* CEDRIC BSEARCH */
+/* */
+/* */
+/*********************************************************************/
+void * bsearch_file ( const void *key,int *p,int comp_first,int comp_len, FILE *fp ,int len, int entry_len,size_t el_size, int (*compare)(const void *, const void*,int, int, size_t));
+void * bsearch_array( const void *key,int *p,int comp_first,int comp_len,void**list,int len, int entry_len,size_t el_size, int (*compare)(const void *, const void*,int, int, size_t));
+
+/*********************************************************************/
+/* */
+/* MY B_SEARCH_FILE FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+void **search_in_list_file ( void *key,int *p, int comp_len,FILE *fp, int len, size_t size, int entry_len);
+void **search_in_list_array ( void *key,int *p, int comp_len,void **L , int len, size_t size, int entry_len);
+
+/*********************************************************************/
+/* */
+/* SORT/COMPARE/SEARCH FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+
+int **search_in_list_int ( int *key, int k_len, int **list, int ne);
+void sort_float ( float **V,int N_F, int F, int left, int right);
+int cmp_float ( const float **a, const float **b);
+void sort_int_1D ( int *L, int n);
+char** sort_string_array (char **V, int n);
+
+void sort_int ( int **V,int N_F, int F, int left, int right);
+void sort_list_int ( int **V,int N_F, int F, int left, int right);
+void sort_list_int2 ( int **V,int *list,int N_F, int left, int right);
+void sort_int_inv ( int **V,int N_F, int F, int left, int right);
+void sort_list_int_inv ( int **V,int N_F, int F, int left, int right);
+int cmp_int ( const int**a, const int**b);
+int cmp_list_int (const int**a, const int**b);
+int cmp_list_int2 (const int**a, const int**b);
+
+int name_is_in_list ( char *name, char **name_list, int n_name, int len);
+char * check_list_for_dup ( char **list, int ne);
+FILE *get_number_list_in_file ( FILE *fp, int *list, int *n, int *max_len);
+
+
+/*********************************************************************/
+/* */
+/* QUANTILE */
+/* */
+/* */
+/*********************************************************************/
+int quantile ( int argc, char *argv[]);
+
+int quantile_rank (int **list,int field, int n, float p);
+/*********************************************************************/
+/* */
+/* DUPLICATION */
+/* */
+/* */
+/*********************************************************************/
+short * set_short ( short *, int n,...);
+char * set_char ( char *, int n,...);
+int * set_int ( int *, int n,...);
+float * set_float ( float *, int n,...);
+double * set_double( double*, int n,...);
+
+short * ga_memcpy_short ( short *array1, short *array2, int n);
+int * ga_memcpy_int ( int *array1, int *array2, int n);
+float * ga_memcpy_float ( float *array1, float *array2, int n);
+double * ga_memcpy_double( double *array1, double *array2, int n);
+
+short ** duplicate_short ( short **array , int len, int field);
+int ** duplicate_int ( int **array , int len, int field);
+char ** duplicate_char ( char **array , int len, int field);
+char * duplicate_string ( char *string);
+float ** duplicate_float ( float **array , int len, int field);
+double ** duplicate_double( double **array , int len, int field);
+
+short ** copy_short ( short **array1, short **array2, int len, int number_field);
+char ** copy_char ( char **array1, char **array2, int len, int number_field);
+int ** copy_int ( int **array1, int **array2, int len, int number_field);
+float ** copy_float ( float **array1, float **array2, int len, int number_field);
+double ** copy_double( double **array1, double **array2, int len, int number_field);
+
+/*********************************************************************/
+/* */
+/* CONCATENATION */
+/* */
+/* */
+/*********************************************************************/
+Alignment ** cat_aln_list ( Alignment **list_to_cat,int first, int end, Alignment **rec_list);
+
+/*********************************************************************/
+/* */
+/* NUMBER ARRAY ANALYSE */
+/* */
+/* */
+/*********************************************************************/
+int output_array_int (char *name, int **array);
+int **input_array_int (char *fname);
+short return_max_short (short ** array, int len_array, int field);
+char return_max_char( char ** array, int len_array, int field);
+int return_max_int( int ** array, int len_array, int field);
+float return_max_float( float ** array, int len_array, int field);
+double return_max_double( double** array, int len_array, int field);
+
+short return_min_short (short ** array, int len_array, int field);
+char return_min_char( char ** array, int len_array, int field);
+int return_min_int( int ** array, int len_array, int field);
+float return_min_float( float ** array, int len_array, int field);
+double return_min_double( double** array, int len_array, int field);
+
+short return_max_coor_short (short ** array, int len_array, int field, int *coor);
+char return_max_coor_char( char ** array, int len_array, int field, int *coor);
+int return_max_coor_int( int ** array, int len_array, int field, int *coor);
+float return_max_coor_float( float ** array, int len_array, int field, int *coor);
+double return_max_coor_double( double** array, int len_array, int field, int *coor);
+
+short return_min_coor_short (short ** array, int len_array, int field, int *coor);
+char return_min_coor_char( char ** array, int len_array, int field, int *coor);
+int return_min_coor_int( int ** array, int len_array, int field, int *coor);
+float return_min_coor_float( float ** array, int len_array, int field, int *coor);
+double return_min_coor_double( double** array, int len_array, int field, int *coor);
+
+short return_2Dmax_short (short ** array, int start, int len_array, int first_field, int number_field);
+char return_2Dmax_char( char ** array, int start, int len_array, int first_field, int number_field);
+int return_2Dmax_int( int ** array, int start, int len_array, int first_field, int number_field);
+float return_2Dmax_float( float ** array, int start, int len_array, int first_field, int number_field);
+double return_2Dmax_double( double** array, int start, int len_array, int first_field, int number_field);
+
+short return_2Dmin_short (short ** array, int start, int len_array, int first_field, int number_field);
+char return_2Dmin_char( char ** array, int start, int len_array, int first_field, int number_field);
+int return_2Dmin_int( int ** array, int start, int len_array, int first_field, int number_field);
+float return_2Dmin_float( float ** array, int start, int len_array, int first_field, int number_field);
+double return_2Dmin_double( double** array, int start, int len_array, int first_field, int number_field);
+
+short return_2Dmax_coor_short ( short ** array,int start1, int end1, int start2, int end2, int *i, int *j );
+char return_2Dmax_coor_char( char ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+int return_2Dmax_coor_int( int ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+float return_2Dmax_coor_float( float ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+double return_2Dmax_coor_double( double** array, int start1, int end1, int start2, int end2, int *i, int *j);
+
+short return_2Dmin_coor_short ( short ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+char return_2Dmin_coor_char( char ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+int return_2Dmin_coor_int( int ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+float return_2Dmin_coor_float( float ** array, int start1, int end1, int start2, int end2, int *i, int *j);
+double return_2Dmin_coor_double( double** array, int start1, int end1, int start2, int end2, int *i, int *j);
+
+double return_wmean_short ( short ** array, int len, int wfield, int field);
+double return_wmean_char ( char ** array, int len, int wfield, int field);
+double return_wmean_int ( int ** array, int len, int wfield, int field);
+double return_wmean_float ( float ** array, int len, int wfield, int field);
+double return_wmean_double( double** array, int len, int wfield, int field);
+
+double return_mean_short ( short ** array, int len, int field);
+double return_mean_char ( char ** array, int len, int field);
+double return_mean_int ( int ** array, int len, int field);
+double return_mean_float ( float ** array, int len, int field);
+double return_mean_double ( double** array, int len, int field);
+
+short return_sum_short ( short ** array, int len, int field);
+char return_sum_char ( char ** array, int len, int field);
+int return_sum_int ( int ** array, int len, int field);
+float return_sum_float ( float ** array, int len, int field);
+double return_sum_double( double** array, int len, int field);
+
+short return_sd_short ( short ** array, int len, int field, short mean);
+char return_sd_char ( char ** array, int len, int field, char mean);
+int return_sd_int ( int ** array, int len, int field, int mean);
+float return_sd_float ( float ** array, int len, int field, float mean);
+double return_sd_double( double** array, int len, int field, double mean);
+
+double return_z_score ( double x, double sum, double sum2, double n);
+double* return_r (double **list, int n);
+short* invert_list_short ( short * array, int len );
+char* invert_list_char ( char * array, int len );
+int* invert_list_int ( int * array, int len );
+float* invert_list_float ( float * array, int len );
+double* invert_list_double( double* array, int len );
+
+void swap_short ( short * array, short * array2,int len );
+void swap_char ( char * array, char * array2,int len );
+void swap_int ( int * array, int * array2,int len );
+void swap_float ( float * array, float * array2,int len );
+void swap_double( double* array, double* array2,int len );
+
+short return_max_short_hor (short ** array, int len_array, int field);
+char return_max_char_hor (char ** array, int len_array, int field);
+int return_max_int_hor (int ** array, int len_array, int field);
+float return_max_float_hor (float ** array, int len_array, int field);
+double return_max_double_hor(double ** array, int len_array, int field);
+
+short return_min_short_hor ( short ** array, int len_array, int field);
+char return_min_char_hor ( char ** array, int len_array, int field);
+int return_min_int_hor ( int ** array, int len_array, int field);
+float return_min_float_hor ( float ** array, int len_array, int field);
+double return_min_double_hor( double** array, int len_array, int field);
+
+short best_short (int n, ...);
+int best_int (int n, ...);
+char best_char (int n, ...);
+float best_float (int n, ...);
+double best_double(int n, ...);
+
+int is_defined_short (int n, ...);
+int is_defined_int (int n, ...);
+int is_defined_char (int n, ...);
+int is_defined_float (int n, ...);
+int is_defined_double(int n, ...);
+
+
+int max_int (int*i, ...);
+
+int return_maxlen ( char ** array, int number);
+int return_minlen ( char ** array, int number);
+
+float return_mean_diff_float ( float **array, int len, int field,float mean);
+
+
+void inverse_int ( int**array, int len, int field, int max, int min);
+void inverse_float ( float**array, int len, int field, int max, int min);
+void inverse_2D_float ( float **array, int start, int len, int start_field, int number_field, float max,float min);
+
+
+
+
+void **recycle (void **A, int l, int cycle);
+
+/*********************************************************************/
+/* */
+/* SHELL INTERFACES */
+/* */
+/* */
+/*********************************************************************/
+char* getenv4debug ( const char *var);
+char* get_env_variable ( const char *var, int mode);
+int atoigetenv(const char *x);
+void setenv_func ( char *string_name, char *string_value);
+void get_pwd ( char *name);
+char *pg2path (char *pg);
+int pg_is_installed ( char *pg);
+/*********************************************************************/
+/* */
+/* MISC */
+/* */
+/*********************************************************************/
+char *num2plot (int value, int max, int line_len);
+int perl_strstr ( char *string, char *pattern);
+float grep_function ( char *pattern, char *file);
+void crash_if ( int val, char *s);
+void crash ( char *s);
+int ** make_recursive_combination_table ( int tot_n_param, int *n_param, int *nc, int**table, int field);
+/*********************************************************************/
+/* */
+/* STRING PROCESSING */
+/* */
+/* */
+/*********************************************************************/
+char *strnrchr ( char *s,char x, int n);
+int intlen (int n);
+char * update_string (char *string1, char *string2);
+char* strcatf (char *string1,char *string2, ...);
+char *vcat (char *v1, char *v2);
+
+int strget_param ( char *string, char *param_name, char *param_value, char *format, ...);
+char * lstrstr ( char *in, char *token);
+char * vstrstr ( char *in, char *token);
+char * estrstr ( char *in, char *token,...);
+char * festrstr ( char *in, char *token,...);
+
+int strscanf (char *in, char *token, char *format, ...);
+int strfcanf (char *file, char *token, char *format, ...);
+
+int match_motif ( char *string, char **motif);
+
+char *after_strstr (char *string, char *token);
+
+char ** push_string (char *val, char **stack, int *nval, int mode);
+int vsrand (int val);
+int *randomize_list (int *list, int len, int ncycle);
+int vstrcmp (const char *s1, const char *s2);
+int vstrncmp (const char *s1, const char *s2, int n);
+FILE *print_array_char (FILE *out, char **array, int n, char *sep);
+
+char *extract_suffixe ( char *array);
+char * path2filename ( char *array);
+char *filename2path (char *name);
+Fname* parse_fname ( char *array);
+
+void string_array_convert ( char **array, int n_strings, int ns, char **sl);
+void string_convert( char *string, int ns, char **sl);
+int convert ( char c, int ns, char **sl);
+int convert2 ( char c, char *list);
+
+void string_array_upper ( char **string, int n);
+void string_array_lower ( char **string, int n);
+char *upper_string ( char *string);
+char *lower_string ( char *string);
+char * substitute_double ( char *string, char *token);
+char * substitute ( char *string, char *token, char *replacement);
+char * substitute_char ( char *string, char token, char replacement);
+char * substituteN ( char *string, char *token, char *replacement, int N);
+char * tild_substitute ( char *string, char *token, char *replacement);
+
+
+char ** clean_string ( int n, char **string);
+
+int str_overlap ( char *string1, char *string2, char x);
+int get_string_line ( int start, int n_lines, char *in, char *out);
+FILE * output_string_wrap ( int wrap,char *string, FILE *fp);
+char * extract_char ( char * array, int first, int len);
+int check_cl4t_coffee (int argv, char **argc);
+
+char** break_list ( char **argv, int *argc, char *separators);
+char** merge_list ( char **argv, int *argc);
+int *name_array2index_array ( char **list1, int n1, char **list2, int n2);
+char ** get_list_of_tokens ( char *string, char *separators, int *n_tokens);
+char **ungap_array(char ** array, int n);
+void ungap ( char *seq);
+int seq2len (char *seq, char *pset, char *nset);
+int seq2res_len (char *seq);
+void remove_charset ( char *seq, char *set);
+char *remove_charset_from_file (char *fname, char *set);
+char *mark_internal_gaps(char *seq, char symbol);
+
+char *list2string (char **list, int n);
+char *list2string2 (char **list, int n, char* sep);
+
+char ** string2list (char *string);
+char ** string2list2(char *string, char *separators);
+int * string2num_list( char *string);
+int * string2num_list2( char *string, char *separators);
+char **char_array2number ( char ** array, int n);
+char *char2number ( char * array);
+long atop(char *);
+char *invert_string (char *string);
+char *invert_string2 (char *string);
+char *string2inverted_string (char *string);
+/* Analyse and Compare Strings*/
+int isblanc ( char *buf);
+/*int islower (char c);
+int isupper (char c);
+*/
+void splice_out ( char *seq, char x);
+char* splice_out_seg ( char *seq,int pos, int len);
+
+int is_number ( char *buf);
+int is_alpha_line ( char *buf);
+int is_alnum_line ( char *buf);
+int case_insensitive_strcmp ( char *string1, char *string2);
+int get_string_sim ( char *string1, char *string2, char *ignore);
+
+int is_gap ( char x);
+int is_gop (int p, char *s);
+
+int is_aa ( char x);
+int is_dna ( char x);
+int is_rna ( char x);
+int haslower (char *s);
+int hasupper (char *s);
+
+
+char * get_alphabet ( char *seq, char *alphabet);
+int is_in_set ( char r, char *list);
+int array_is_in_set (char *array, char *set);
+char * generate_void ( int x);
+char * generate_null ( int x);
+char * generate_string ( int x, char y);
+
+
+char * translate_string (char *string, char *in, char*out);
+int get_longest_string (char **array,int n, int *len, int *index);
+int get_shortest_string (char **array,int n, int *len, int *index);
+/*EDIT STRING*/
+char **pad_string_array ( char **array, int n, int len, char pad);
+char * crop_string (char *string, int start, int end);
+int get_distance2char ( char *x, char *list);
+
+/*********************************************************************/
+/* */
+/* TIME FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+FILE *print_program_information (FILE *fp, char *comment);
+FILE* print_cpu_usage (FILE *fp, char *comment);
+void print_exit_success_message ();
+void print_exit_failure_message ();
+
+int get_time ();
+int get_ctime ();
+int reset_time();
+int increase_ref_time(int increase);
+/*********************************************************************/
+/* */
+/* SYSTEM CALLS */
+/* */
+/* */
+/*********************************************************************/
+int has_error_lock();
+int is_rootpid();
+int is_shellpid(int pid);
+int shift_lock (int from, int to, int from_type,int to_type, int action);
+char *lock2name (int pid, int type);
+int release_all_locks (int pid);
+char *lock (int pid, int type, int action, char *value, ...);
+int check_process (const char *com,int pid,int r, int failure_handling);
+int assert_pid (pid_t p);
+pid_t **declare_pidtable ();
+pid_t set_pid (pid_t p);
+pid_t vvfork(char *mode);
+pid_t vwait (pid_t *p);
+int vwait_npid (int submited, int max, int min);
+int kill_child_pid(int pid);
+
+int safe_system (const char * commande);
+pid_t vwaitpid (pid_t p, int *status, int options);
+
+int evaluate_sys_call_io ( char *out_file, char *com, char *fonc);
+//char *cvsprintf (char *r,char *format, va_list arg_ptr,... );
+void HERE (char *string, ...);
+void printf_exit (int exit_code, FILE *fp, char *string, ...);
+int printf_file ( char *file, char *mode, char *string, ...);
+int printf_fork ( FILE *fp,char *string,...);
+int printf_system (char *string, ...);
+int printf_system_direct (char *string, ...);
+int my_system_cl (int argc, char *argv[]);
+int my_system ( char *command);
+int unpack_perl_script (char *name, char ***unpacked, int n);
+void unpack_all_perl_script (char *script);
+/*********************************************************************/
+/* */
+/* IO FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+void set_command_line (char *s);
+FILE * print_command_line (FILE *fp );
+int getpid_ref();
+char ** standard_initialisation ( char **in_argv, int *in_argc);
+char ** standard_initialisation_start ( char **in_argv, int *in_argc);
+char ** standard_initialisation_end ( char **in_argv, int *in_argc);
+/*
+by default : dir_4_tcoffee: $HOME/.t_coffee
+tmp: dir_4_tcoffee/tmp OR TMP_4_TCOFFEE
+cache: idem
+methods: idem
+mcoffee: idem
+*/
+int get_nproc ();
+char *get_os();
+char *get_lockdir_4_tcoffee ();
+char *get_plugins_4_tcoffee ();
+char *get_home_4_tcoffee();
+char *get_dir_4_tcoffee();
+char *get_tmp_4_tcoffee();
+char *get_cache_4_tcoffee();
+char *get_methods_4_tcoffee();
+char *get_mcoffee_4_tcoffee();
+
+
+
+void myexit (int signal);
+FILE *fatal_exit ( FILE *fp, int exit_signal, char *string, ...);
+int set_warning_mode ( int mode);
+FILE *add_warning (FILE *fp, char *string, ...);
+FILE *add_information (FILE *fp, char *string, ...);
+int fprintf_error( FILE *fp, char *string, ...);
+
+void output_warning_list();
+
+int count_n_res_in_array (char *array, int len);
+int count_n_gap_in_array (char *array, int len);
+int count_n_symbol_in_array ( char *array, char *array_list, int len);
+char* count_strings_in_file ( char *in, char *out);
+char** count_strings ( char **array, int len);
+int ** count_int_strings ( int **array, int len, int s);
+
+int get_first_non_white_char (char *name);
+int count_n_char_x_in_file(char *name, char x);
+int count_n_char_in_file(char *name);
+int count_n_line_in_file(char *name);
+int measure_longest_line_in_file ( char *name );
+int file_cat ( char *fname1, char *fname2);
+FILE* display_file_content (FILE *output, char *name);
+int cat_file (char *file1, char *file2);
+char ***file2list (char *name, char *sep);
+char ** file2lines (char *name);
+char * file2string (char *name);
+int string2file ( char *file, char *mode, char *string,...);
+char *chomp (char *name);
+int get_cl_param (int argc, char **argv, FILE **fp,char *para_name, int *set_flag, char *type, int optional, int max_n_val,char *usage, ...);
+char ** get_parameter ( char *para_name, int *np, char *fname);
+
+char *get_t_coffee_environement (char *file);
+char *set_path_4_plugins (char *);
+int add_package2_tcoffee_env (char *package);
+
+void dump (char *dump_file, char *dump_nature);
+void dump_error_file();
+void update_error_dir();
+
+FILE* stack_msg(FILE *fp);
+FILE* install_msg(FILE *fp);
+FILE* proxy_msg(FILE *fp);
+FILE* email_msg(FILE *fp);
+FILE* error_msg(FILE *fp);
+FILE *proxy_msg(FILE *fp);
+
+char *get_proxy();
+char *get_proxy_from_env();
+int set_proxy (char *proxy);
+
+char *input_name ();
+char *Email4cl(int input_mode, int set_mode);
+char *Email(int input_mode, int set_mode);
+char *input_email ();
+char *get_email_from_env ();
+char *get_email ();
+int set_email (char *email);
+int cputenv4path (char*);
+int cputenv (char*, ...);
+int fcputenv (char *,char *, char*, ...);
+char *file_putenv (char *file);
+int check_dir_getenv ( char *string);
+
+char* set_string_variable (char *var, char* v);
+char* get_string_variable (char *var);
+char* unset_string_variable (char *var);
+char* store_string_variable (char *var, char * v, int mode);
+
+int int_variable_isset (char *var);
+int set_int_variable (char *var, int v);
+int get_int_variable (char *var);
+int unset_int_variable (char *var);
+int store_int_variable (char *var, int v, int mode);
+
+void check_vtmpnam ();
+int flag_file2remove_is_on ();
+void set_file2remove_off();
+void set_file2remove_on();
+char *set_file2remove_extension(char *extension, int mode);
+char * add2file2remove_list ( char *name);
+
+
+
+FILE * vtmpfile();
+void initiate_vtmpnam (char *s);
+char * vtmpnam ( char *s);
+char * tmpnam_2 (char *s);
+void safe_remove(char*s);
+char * vremove ( char *s);
+char * vremove2 ( char *s);
+void error_exit ();
+void clean_exit();
+void signal_exit();
+void main_exit ();
+int log_function (char *fname);
+
+void clean_function ( );
+void sig_clean_function ( int x);
+char * prepare_cache ( const char *mode);
+char * get_cache_dir();
+void update_cache ();
+void ignore_cache();
+
+FILE * vfopen ( char *name, char *mode);
+FILE * vfclose (FILE *fp);
+int echo ( char *string, char *fname);
+
+int **get_file_block_pattern (char *fname, int *n_blocks, int max_n_line);
+
+int token_is_in_file (char *fname, char *token);
+
+FILE * find_token_in_file_nlines ( char *fname, FILE * fp, char *token, int n_line);
+FILE * find_token_in_file ( char *fname, FILE * fp, char *token);
+FILE * quick_find_token_in_file (FILE *fp, char *token);
+
+char * vfgets (char *buf, FILE *fp);
+
+FILE * set_fp_after_char ( FILE *fp, char x);
+FILE * set_fp_id ( FILE *fp, char *id);
+FILE * skip_commentary_line_in_file ( char com, FILE *fp);
+char * strip_file_from_comments (char *com, char *in_file);
+
+int check_for_update ( char *web_address);
+int url2file (char *address, char *out);
+int wget (char *address, char *out);
+int curl (char *address, char *out);
+
+
+int simple_check_internet_connection (char *address);
+int check_internet_connection (int mode);
+int check_environement_variable_is_set ( char *variable, char *description, int fatal);
+int check_program_is_installed ( char *program_name, char *current_path, char *path_variable, char *where2getit, int fatal);
+FILE * display_output_filename ( FILE *io, char *type, char *format, char *name, int check_output);
+FILE * display_input_filename ( FILE *io, char *type, char *format, char *name, int check_output);
+int filename_is_special ( char *fname);
+char *check_file_exists ( char *fname);
+int my_mkdir ( char *dir);
+int my_rmdir ( char *dir);
+
+int file_is_empty(char *fname);
+int file_exists (char *path,char *fname);
+int isexec (char *fname);
+int isdir (char *fname);
+int isdir4path (char *fname);
+int rrmdir (char *fname);
+char * ls_l(char *path,char *fname);
+
+void create_file ( char *name);
+void delete_file ( char *fname);
+int util_rename ( char* from, char *to);
+int util_copy ( char* from, char *to);
+FILE * output_completion4halfmat ( FILE *fp,int n, int tot, int n_eports, char *s);
+FILE * output_completion ( FILE *fp,int n, int tot, int n_eports, char *s);
+void * null_function (int a, ...);
+int btoi ( int nc,...);
+/*********************************************************************/
+/* */
+/* Geometric FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+
+float get_geometric_distance ( float ** matrix, int ncoor, int d1, int d2, char *mode);
+/*********************************************************************/
+/* */
+/* MATHEMATICAL FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+double log_addN ( int N, double *L);
+double log_add6 (double a, double b, double c, double d, double e, double f );
+double log_add5 (double a, double b, double c, double d, double e);
+double log_add4 (double a, double b, double c, double d);
+double log_add3 (double a, double b, double c);
+double log_add2 (double a, double b);
+
+float factorial_log ( int start, int end);
+float M_chooses_Nlog ( int m, int N);
+double factorial ( int start, int end);
+double M_chooses_N ( int m, int N);
+float my_int_log(int a);
+/*********************************************************************/
+/* */
+/* Fast Log Additions (adapted from Probcons)*/
+/* */
+/* */
+/*********************************************************************/
+double EXP(double x);
+float LOOKUP (float x);
+void LOG_PLUS_EQUALS (float *x, float y);
+float LOG_ADD (float x, float y);
+float LOG_ADD3 (float x1, float x2, float x3);
+float LOG_ADD4 (float x1, float x2, float x3, float x4);
+float LOG_ADD5 (float x1, float x2, float x3, float x4, float x5);
+float LOG_ADD6 (float x1, float x2, float x3, float x4, float x5, float x6);
+float LOG_ADD7 (float x1, float x2, float x3, float x4, float x5, float x6, float x7);
+///////////////////////////////////////////////////////////////////////////////////////////
+// Hash function
+////////////////////////////////////////////////////////////////////////////////////////////
+unsigned long hash_file(char* file); //returns the hash value for key
+///////////////////////////////////////////////////////////////////////////////////////////
+// Generating lists through recirsive exploration
+////////////////////////////////////////////////////////////////////////////////////////////
+int **generate_array_int_list (int len, int min, int max, int step, int *n, char *filename);
+char ***generate_array_string_list (int len, char ***alp, int *alp_size, int *n, char *file, int mode);
+float *display_accuracy (float *count, FILE *fp);
+float *counts2accuracy (float *count);
+
+float rates2sensitivity (int tp, int tn, int fp, int fn, float *sp, float *sn, float *sen2, float *best);
+float profile2sensitivity (char *pred, char *ref, float *sp, float *sn, float *sen2, float *b);
+float profile2evalue (char *pred, char *ref);
+//isexec lib
+#include <stdio.h>
+
+unsigned long linrand(unsigned long r);
+unsigned long addrand(unsigned long r);
+void addrandinit(unsigned long s);
+
+unsigned long mult(unsigned long p,unsigned long q);
+
+
+struct Job_TC
+ {
+ int jobid;
+ int status;
+
+ struct Job_TC *c;
+ struct Job_TC *p;
+ struct Job_io_TC *io;
+ struct Job_control_TC *control;
+
+ struct Job_param_TC *param;
+
+ /*memory mangement*/
+ char **pl;
+ int np;
+};
+typedef struct Job_TC Job_TC;
+
+struct Job_control_TC
+ {
+
+ struct Job_TC* (*submitF) (struct Job_TC*);
+ struct Job_TC* (*retrieveF)(struct Job_TC*);
+ char *mode;
+};
+typedef struct Job_control_TC Job_control_TC;
+
+struct Job_io_TC
+ {
+ char *in;
+ char *out;
+ struct Constraint_list *CL;
+ struct Alignment *A;
+};
+typedef struct Job_io_TC Job_io_TC;
+
+struct Job_param_TC
+{
+ char *method;
+ struct TC_method *TCM;
+ char *temp_c;
+ char *aln_c;
+ char *seq_c;
+ char *aln_mode;
+};
+typedef struct Job_param_TC Job_param_TC;
+
+Job_TC* print_lib_job ( Job_TC *job,char *string, ...);
+Job_TC *print_lib_job2 ( Job_TC* job, int n, char **name, char **value);
+
+
+/*Stack Manipulation*/
+Job_TC *free_queue (Job_TC *job);
+Job_TC *free_job (Job_TC *job);
+Job_TC * queue2heap (Job_TC*job);
+Job_TC * queue2last (Job_TC*job);
+int queue2n (Job_TC*job);
+Job_TC * descend_queue (Job_TC*job);
+Job_TC *queue_cat (Job_TC *P, Job_TC *C);
+Job_TC *delete_job (Job_TC *job);
+/*Job Control*/
+struct Job_TC* submit_job ( Job_TC *job);
+struct Job_TC* retrieve_job ( Job_TC *job);
+Job_TC*** split_job_list (Job_TC *job, int ns);
+int **n2splits (int nsplits, int nelements);
+struct Dps_result
+ {
+ int njobs;
+ struct Dps_job **dps_job;
+};
+typedef struct Dps_result Dps_result;
+
+struct Dps_job
+ {
+ int JobId;
+ struct Constraint_list *CL;
+ char *input_file;
+ char *output_file;
+};
+typedef struct Dps_job Dps_job;
+
+struct Dps_result *seq2list_DPS (struct Constraint_list *CL,char *method, char *aln_command, char *seq_command, char *weight, Dps_result *dps_result);
+struct Constraint_list * gather_results_DPS ( Dps_result *DPS, struct Constraint_list *CL);
+Dps_result *declare_dps_result ( int naln, Dps_result *dps);
+
+#define SEQ2 0
+#define R2 1
+#define WE 2
+#define CONS 3
+#define MISC 4
+#define SEQ1 5
+#define R1 6
+#define INDEX 7
+
+#define ICHUNK 5
+
+#define LIST_N_FIELDS 7
+#define CLIST_TYPE int
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS Typedef */
+/* */
+/*********************************************************************************************/
+typedef int (*Profile_cost_func) (int*, int *,struct Constraint_list *);
+typedef int (*Col_cost_func)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+typedef int (*Pair_cost_func)(struct Constraint_list *, int, int, int, int);
+typedef int (*Pwfunc) (Alignment *, int*, int **,struct Constraint_list *);
+
+/*********************************************************************************************/
+/* */
+/* STRUCTURES FOR PDB ANALYSIS */
+/* */
+/*********************************************************************************************/
+typedef struct
+ {
+ char *use_seqan;
+}
+TC_param;
+typedef struct
+ {
+ char blast_server[FILENAMELEN+1];
+ char db[FILENAMELEN+1];
+ int min_cov;
+ int min_id;
+ int max_id;
+}
+Blast_param;
+
+typedef struct
+ {
+ int n_excluded_nb;
+
+ float similarity_threshold;
+ float rmsd_threshold;
+ float md_threshold;
+ int distance_on_request;
+ char *comparison_io;
+ int print_rapdb;
+ float maximum_distance;/*Diameter of the bubble used to identify the Calpha Neighborhood*/
+ int N_ca; /*Number of Calpha to be looked at on both side*/
+ float max_delta ; /*Maximum value for delta to be positive*/
+ char *local_mode;
+ int scale; /*Value substracted to the pdb score in the bubble mode*/
+ int n_extra_param;
+ char **extra_param;
+ char *evaluate_mode;
+ char *color_mode;
+ float filter;
+ int filter_aln;
+ int irmsd_graph;
+ int nirmsd_graph;
+
+
+ }
+Pdb_param;
+
+typedef struct
+ {
+ int num;
+ int res_num;/*Residue number from 1 to N*/
+ char res[4];
+ char type[4];
+ float x;
+ float y;
+ float z;
+ }
+Atom;
+
+typedef struct
+ {
+
+ Atom*CA;
+ Atom *C;
+ Atom *N;
+ Atom *CB;
+ }
+Amino_acid;
+
+
+typedef struct
+ {
+ /*Distances used for the Neighbour mode*/
+ int **nb; /*Neighbors of each Ca ( sorted by distance) given as atoms*/
+ /*nb[x][0] contains the number of neighbor atoms*/
+ float **d_nb; /* contains the distances between atom y=nb[x][5] and Ca x*/
+ /* !!!d_nb[x][0] is empty, the array starts at +1 to folow nb*/
+ int max_nb; /* Largest neigborhood*/
+}
+Struct_nb;
+
+typedef struct
+ {
+
+ int len; /*Number of Calpha Carbons*/
+ int n_atom; /*Number of atoms*/
+ char *name; /*Name of the sequence*/
+ char *seq; /*Sequence ( Complete)*/
+ Atom **structure; /*Atoms*/
+ Atom **ca; /*List of pointers to the Calpha Atoms from 0 to N-1*/
+ Amino_acid **peptide_chain;/*List of pointers to the Calpha Atoms from 0 to N-1*/
+
+
+ Struct_nb *Chain;
+ Struct_nb *Bubble;
+ Struct_nb *Transversal;
+
+ float ** ca_dist;
+ Pdb_param *pdb_param;
+}
+
+Ca_trace;
+/*********************************************************************************************/
+/* */
+/* MOCA: Data structure for domains and alignments */
+/* */
+/*********************************************************************************************/
+struct Moca
+{
+ /*Normalisation factor: value by which each constraint weight is decreased*/
+ int moca_scale;
+ /*Functions used for domain extraction:*/
+ /*Function for evaluating the score of a domain: returns 0 if not acceptable, value if OK*/
+ int (*evaluate_domain)(Alignment*,struct Constraint_list *);
+ int moca_threshold;
+
+ /*Function for hiding previously used residues*/
+ int ** (*cache_cl_with_domain)(Alignment*, struct Constraint_list *);
+ int **forbiden_residues; /*List of residues already used for domain construction*/
+
+
+ /*Function for trunkating the result into a non-overlapping alignment*/
+ Alignment* (*make_nol_aln)(Alignment*, struct Constraint_list *);
+
+ /*Parameters Coordinates of the first motif to extract*/
+ int moca_start;
+ int moca_len;
+ int moca_interactive;
+
+};
+typedef struct Moca Moca;
+/*********************************************************************************************/
+/* */
+/* CONSTRAINT LISTS */
+/* */
+/*********************************************************************************************/
+struct Distance_matrix
+{
+ char mode[100];
+ char sim_mode[100];
+ char nseq;
+ int **similarity_matrix; /*Pairwise ID levels: 1-10000*/
+ int **score_similarity_matrix; /*Pairwise ID levels: 1-10000*/
+ int **distance_matrix; /*Pairwise ID levels: 1-10000*/
+};
+typedef struct Distance_matrix Distance_matrix;
+struct Constraint_list
+ {
+ /*In Case of Modif, synchronize with:
+ util_declare/declare_constraint_list
+ util_declare/cache_dp_value4constraint_list
+ util_declare/duplicate_constraint_list
+ util_declare/free_constraint_list
+ */
+
+ //Generic parameters
+ TC_param *TC;
+
+ int copy_mode;
+ struct Constraint_list *pCL;
+ Sequence *S; /*Total sequences*/
+ int *master; //Sequences used as master sequences
+ int o2a_byte; // number of one to all provided in one go.
+ Sequence *STRUC_LIST; /*Name of the sequences with a Structure*/
+ char align_pdb_param_file[FILENAMELEN+1];
+ char align_pdb_hasch_mode[FILENAMELEN+1];
+
+
+ Weights *W; /*Sequence Weights*/
+ Distance_matrix *DM; /*Accurate Distance Matrix*/
+ Distance_matrix *ktupDM; /*Fast Distance Matrix*/
+ Fname *RunName;
+
+ int *translation;
+ char ** out_aln_format;
+ int n_out_aln_format;
+
+
+ /*Packing Sequence: To use with domain analysis*/
+ int **packed_seq_lu;
+
+ /*DATA*/
+ FILE *fp; /*File used for i/o if disk being used*/
+ //int *L; /*Array used for storing Lib if mem being used*/
+ int **M; /*substitution matrix*/
+ char rna_lib[FILENAMELEN+1]; /*name of a file containing the RNA libraries*/
+
+ /*List Information*/
+ int ne; /*Number of elements in the list*/
+ char list_name[1000]; /*Name of the list*/
+ int entry_len; /*Size of an entry in el_size*/
+ size_t el_size; /*Size of each elements in an entry in bytes*/
+
+ /*Normalisation information*/
+ int normalise;
+ int max_ext_value;
+ int max_value;
+ int overweight;
+ int filter_lib;
+
+ /*Pair wise alignment method*/
+ int pw_parameters_set;
+ int gop;
+ int gep;
+ int f_gop;
+ int f_gep;
+ int nm_gop;
+ int nm_gep;
+
+ int nomatch;
+
+ int TG_MODE;
+ int F_TG_MODE;
+
+ char dp_mode[FILENAMELEN+1];
+ int reverse_seq;//Used for HoT
+ int extend_seq; //Used for RNA or Promoter Alignments
+ int maximise;
+ char matrix_for_aa_group[FILENAMELEN+1];
+ char method_matrix[FILENAMELEN+1];
+ float diagonal_threshold;
+ int ktup;
+ int use_fragments;
+ int fasta_step;
+ int lalign_n_top;
+ int sw_min_dist;
+ char **matrices_list;
+ int n_matrices;
+ char tree_mode[FILENAMELEN+1];
+
+ char distance_matrix_mode[FILENAMELEN+1];
+ char distance_matrix_sim_mode[FILENAMELEN+1];
+
+ Alignment *tree_aln;
+
+ /*Functions used for dynamic programming and Evaluation*/
+ int no_overaln;
+ /*1 Function for evaluating the cost of a column*/
+ Col_cost_func get_dp_cost;
+ Profile_cost_func profile_mode;
+ char profile_comparison [FILENAMELEN+1];
+
+ /*2 Function for evaluating the cost of a pair of residues*/
+ Pair_cost_func evaluate_residue_pair;
+ /*3 Function for making dynamic programming*/
+ Pwfunc pair_wise;
+
+ /*
+ int (*get_dp_cost)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+ int (*evaluate_residue_pair)(struct Constraint_list *, int, int, int, int);
+ int (*pair_wise)(Alignment *, int*, int **,struct Constraint_list *);
+ */
+
+ int weight_field;
+ int max_n_pair; /*maximum number of pairs when aligning two profiles*/
+
+ /*Extend a sequence against itself*/
+
+ /*Threading parameters*/
+ Blast_param *Prot_Blast;
+ Blast_param *Pdb_Blast;
+ Blast_param *DNA_Blast;
+ /*Split parameters*/
+ int split;
+ int split_nseq_thres;
+ int split_score_thres;
+ /*Check Structural Status*/
+ int check_pdb_status;
+ /*log*/
+ char method_log[1000];
+ char evaluate_mode[1000];
+ char method_evaluate_mode[100];
+ /*Gene Prediction Parameter*/
+ char genepred_score[100];
+
+ /*Parameters for domain extraction*/
+ Moca *moca;
+ /*Functions for hiding forbiden pairs of residues*/
+ int ****forbiden_pair_list; /* pair_list[S1][S2][L1][L2]=1 ->forbiden*/
+ /* pair_list[S1][S2][L1][L2]=0 ->allowed*/
+ /* pair_list[S1][S2][L1]=NULL ->all pairs S1L1, S2 allowed */
+ /* S-> sequences, 0..N */
+ /* L-> residues , 1..L-1 */
+
+ /*extention properties: copy*/
+ int *seq_for_quadruplet;
+ int nseq_for_quadruplet;
+
+ /*extention properties: Do Not copy*/
+ int extend_jit; /*Extend only on request*/
+ int extend_threshold; /*Do not extend pairs below the Theshold*/
+ int do_self; /*Extend a sequence against itself*/
+ char extend_clean_mode[100];
+ char extend_compact_mode[100];
+
+ /*Lookup table parameteres*/
+ /*!!!!!do not copy in duplication*/
+ /*Residue Index contains residue_index[nseq][seq_len][0]->number of links*/
+ /*[seq][res][x ]->target seq (0->N-1)*/
+ /*[seq][res][x+1]->traget res (1->len*/
+ /*[seq][res][x+2]->target weight */
+ /*It is automatically recomputed when L residue_indexed is set to 0*/
+ int residue_indexed;
+ int ***residue_index;
+ int ** freeze;
+ int residue_field;
+
+ /*Index of the pairs of sequences within L*/
+ int seq_indexed;
+ int **start_index;
+ int **end_index;
+ int max_L_len;
+ int chunk;
+
+
+
+ /*PDB STRUCTURE ALIGNMENTS*/
+ Ca_trace ** T; /*This structure contains the PDB trace for sequences with a known Struc T[Nseq]*/
+
+ /*MISC*/
+ int cpu;
+ FILE *local_stderr;
+ char multi_thread[100];
+ char lib_list[FILENAMELEN+1];
+};
+
+typedef struct Constraint_list Constraint_list;
+
+struct TC_method
+{
+
+ char executable[FILENAMELEN+1];
+ char executable2[FILENAMELEN+1];
+ char in_flag[FILENAMELEN+1];
+ char in_flag2[FILENAMELEN+1];
+ char out_flag[FILENAMELEN+1];
+ char aln_mode[FILENAMELEN+1];
+ char out_mode[FILENAMELEN+1];
+ char seq_type[FILENAMELEN+1];
+ char weight[FILENAMELEN+1];
+ char matrix[FILENAMELEN+1];
+ int gop;
+ int gep;
+ int minid;
+ int maxid;
+ char param[1000];
+ char param1[1000];
+ char param2[1000];
+ int extend_seq;
+ int reverse_seq;
+ Constraint_list *PW_CL;
+};
+typedef struct TC_method TC_method;
+
+/*********************************************************************/
+/* */
+/* PRODUCE IN LIST */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode);
+Job_TC* method2job_list ( char *method, Sequence *S,char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL);
+
+Job_TC *job_list2multi_thread_job_list (Job_TC* ojob, char *mt, Constraint_list *CL);
+Job_TC *retrieve_lib_job ( Job_TC *job);
+Job_TC *submit_lib_job ( Job_TC *job);
+int add_method_output2method_log (char *l, char *command,Alignment *A, Constraint_list *CL, char *iofile);
+
+int check_seq_type (TC_method *M, char *slist,Sequence *S);
+int check_profile_seq_type (Sequence *S, int i, char t);
+char **method_list2method4dna_list ( char **list, int n);
+int is_in_pre_set_method_list (char *fname);
+char *** display_method_names (char *mode, FILE *fp);
+
+char *method_name2method_file (char *method);
+char *make_aln_command(TC_method *m, char *seq, char *aln);
+struct TC_method* method_file2TC_method ( char *fname);
+char *method_file_tag2value (char *method, char *tag);
+int TC_method2method_file( struct TC_method*, char *fname );
+/*********************************************************************/
+/* */
+/* WRITE IN LIST */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * empty_constraint_list (Constraint_list *CL);
+Constraint_list * unfreeze_constraint_list (Constraint_list *CL);
+Constraint_list * freeze_constraint_list (Constraint_list *CL);
+Constraint_list * undump_constraint_list (Constraint_list *CL, char *file);
+int dump_constraint_list (Constraint_list *CL, char *file,char *mode);
+int safe_dump_constraint_list (Constraint_list *CL, char *file,char *mode, Sequence *RS);
+FILE* display_constraint_list (Constraint_list *CL, FILE *fp, char *tag);
+
+
+Constraint_list *index_constraint_list ( Constraint_list *CL);
+Constraint_list *index_res_constraint_list ( Constraint_list *CL, int field);
+Constraint_list * progressive_index_res_constraint_list ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+char ** reindex_constraint_list (char **profile, int np,char **list, int *inL, Sequence *S);
+/*********************************************************************/
+/* */
+/* ENTRY MANIPULATION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * add_list_entry2list (Constraint_list *CL, int n_para, ...);
+Constraint_list * evaluate_constraint_list_reference ( Constraint_list *CL);
+
+int CLisCompacted (Constraint_list *CL, char *t);
+int checkCL( Constraint_list *CL, char *t);
+Constraint_list *add_entry2list ( CLIST_TYPE *entry, Constraint_list *CL);
+Constraint_list *add_entry2list2 ( CLIST_TYPE *entry, Constraint_list *CL);
+int *extract_entry (Constraint_list *CL);
+/*********************************************************************/
+/* */
+/* LIST EXTENTION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *extend_list_pair (Constraint_list *CLin,char *store_mode, int s1, int s2);
+Constraint_list *extend_list (Constraint_list *CLin, char *store_mode,char *clean_mode, char *compact_mode,int do_self, Sequence *SUBSET);
+void get_bounds (Constraint_list *CL, int s1, int s2, int *start, int *end);
+int ** fill_pos_matrix (Constraint_list *CL, int beg, int end, int slen, int **pos, int *len, int mirrored);
+
+/*********************************************************************/
+/* */
+/* SEARCH IN LIST (ARRAY AND FILE) */
+/* */
+/* */
+/*********************************************************************/
+FILE * compare_list (FILE *OUT, Constraint_list *CL1,Constraint_list *CL2);
+//CLIST_TYPE *search_in_list_constraint(int *key, int k_len, int **L, int ne, int ***start_index, int ***end_index);
+CLIST_TYPE *main_search_in_list_constraint ( int *key,int *p,int k_len,Constraint_list *CL);
+Constraint_list *sort_constraint_list_inv (Constraint_list *CL, int start, int len);
+Constraint_list *invert_constraint_list (Constraint_list *CL, int start,int len);
+Constraint_list * sort_constraint_list (Constraint_list *CL, int start, int len);
+Constraint_list * sort_constraint_list_on_n_fields (Constraint_list *CL, int start, int len, int first_field, int n_fields);
+
+/*********************************************************************/
+/* */
+/* INPUT/OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list* read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode,char *type, FILE *local_stderr, Constraint_list *CL, char *seq_source);
+Constraint_list* read_constraint_list(Constraint_list *CL,char *fname,char *in_mode,char *mem_mode,char *weight_mode);
+Constraint_list * read_constraint_list_raw_file(Constraint_list *CL, char *fname);
+
+int read_cpu_in_n_list(char **fname, int n);
+int read_seq_in_list ( char *fname, int *nseq, char ***sequences, char ***seq_name);
+
+Sequence * read_seq_in_n_list(char **fname, int n, char *type, char *SeqMode);
+
+int read_cpu_in_list ( char *fname);
+int ** read_list ( char *fname, int **list,int *ne, int *nseq, int *cpu, char ***sequences, char ***seq_name);
+
+char * expand_constraint_list_file ( char *file);
+Constraint_list * read_constraint_list_file(Constraint_list *CL, char *fname);
+Constraint_list * fast_read_constraint_list_file(Constraint_list *CL, char *fname);
+
+/*********************************************************************/
+/* */
+/* EXTENDED LIST OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+FILE * save_extended_constraint_list ( Constraint_list *CL, char *mode, FILE *fp) ;
+FILE * save_extended_constraint_list_pair ( Constraint_list *CL, char *mode, char* seq1, char * seq2,FILE *fp);
+
+/*********************************************************************/
+/* */
+/* LIST OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+int constraint_list2raw_file ( Constraint_list *CL, char *fname, char *fmode);
+FILE * save_raw_constraint_list ( FILE *fp,Constraint_list *CL, int start,int len, int *translation);
+FILE * save_constraint_list ( Constraint_list *CL,int start, int len, char *fname, FILE *fp,char *mode,Sequence *S);
+FILE * save_sub_list_header ( FILE *OUT, int n, char **name, Constraint_list *CL);
+FILE * save_list_header ( FILE *OUT,Constraint_list *CL);
+FILE * save_list_footer (FILE *OUT,Constraint_list *CL);
+FILE * save_constraint_list_ascii ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation);
+FILE * save_constraint_list_bin ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation);
+
+/*********************************************************************/
+/* */
+/* LIST CONVERTION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * expand_constraint_list (Constraint_list *CL, int T);
+Constraint_list * shrink_constraint_list_indexed (Constraint_list *CL, int T);
+Constraint_list * shrink_constraint_list (Constraint_list *CL);
+Constraint_list * extend_constraint_list ( Constraint_list *CL);
+Constraint_list * relax_constraint_list (Constraint_list *CL);
+Constraint_list * relax_constraint_list_4gp (Constraint_list *CL);
+
+Constraint_list * expand_constraint_list_4gp (Constraint_list *CL, int T);
+
+Constraint_list * filter_constraint_list (Constraint_list *CL, int field, int T);
+int constraint_list_is_connected ( Constraint_list *CL);
+int constraint_list2avg ( Constraint_list *CL);
+float constraint_list2connectivity ( Constraint_list *CL);
+
+int constraint_list2fraction_covered ( Constraint_list *CL);
+
+int *seqpair2weight (int s1, int s2, Alignment *A,Constraint_list *CL, char *weight_mode, int *weight);
+Constraint_list *aln_file2constraint_list (char *alname, Constraint_list *CL,char *weight_mode);
+Constraint_list *aln2constraint_list (Alignment *A, Constraint_list *CL,char *weight_mode);
+
+double **list2mat (Constraint_list *CL,int s1,int s2, double *min, double *max);
+Constraint_list * constraint_list2bin_file(Constraint_list *clist);
+FILE * bin_file2constraint_list ( Constraint_list *CL, FILE *fp, char *name);
+
+int **list2residue_total_weight ( Constraint_list *CL);
+int **list2residue_total_extended_weight ( Constraint_list *CL);
+int **list2residue_partial_extended_weight ( Constraint_list *CL);
+/*******************************************************************************************/
+/* */
+/* */
+/* clean functions */
+/* */
+/* */
+/* */
+/*******************************************************************************************/
+Constraint_list *clean ( char *clean_mode,Constraint_list *C,int start, int len);
+Constraint_list * clean_shadow ( Constraint_list *CL, int start, int len);
+
+/*********************************************************************/
+/* */
+/* LIST FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode);
+CLIST_TYPE return_max_constraint_list ( Constraint_list *CL, int field);
+Constraint_list *modify_weight( Constraint_list *CL,int start, int end, char *modify_mode);
+Constraint_list *compact_list (Constraint_list *CL, char *compact_mode);
+Constraint_list *rescale_list_simple (Constraint_list *CL,int start, int len,int new_min, int new_max);
+Constraint_list *rescale_list (Constraint_list *CL,int start, int len,int max1, int max2);
+Constraint_list* filter_list (Constraint_list *CL, int start, int len,int T);
+Constraint_list *undefine_list (Constraint_list *CL);
+int ** seq2defined_residues ( Sequence *S, Constraint_list *CL);
+int ** aln2defined_residues ( Alignment *A, Constraint_list *CL);
+/*********************************************************************/
+/* DEBUG */
+/* */
+/*********************************************************************/
+void print_CL_mem(Constraint_list *CL, char *function);
+int constraint_list_is_sorted ( Constraint_list *CL);
+void check_seq_pair_in_list(Constraint_list *CL,int seq1, int seq2);
+/******************************************************************/
+/* NEW METHODS */
+/* */
+/* */
+/******************************************************************/
+
+Constraint_list * align_coding_nucleotides (char *seq, char *method, char *weight, char *mem_mode, Constraint_list *CL);
+/*********************************************************************************************/
+/* */
+/* FUNCTION FOR PRUNING THE LIST */
+/* */
+/*********************************************************************************************/
+char * list2prune_list (Sequence *S, int **sm);
+/*********************************************************************************************/
+/* */
+/* FUNCTION FOR WEIGHTING THE LIST */
+/* */
+/*********************************************************************************************/
+Constraint_list *weight_constraint_list(Constraint_list * CL, char *seq_weight);
+Weights* compute_t_coffee_weight(Constraint_list * CL);
+Constraint_list *re_weight_constraint_list(Constraint_list * CL,Weights *W);
+Constraint_list *set_weight4constraint_list(Constraint_list * CL,int w);
+
+Distance_matrix *cl2distance_matrix (Constraint_list *CL, Alignment *A, char *mode, char *sim_mode, int print);
+Distance_matrix *seq2distance_matrix (Constraint_list *CL, Alignment *A, char *mode, char *sim_mode, int print);
+
+/*********************************************************************************************/
+/* */
+/* MULTI_THREAD */
+/* */
+/*********************************************************************************************/
+int run_multi_thread_file (char *fname, char *config);
+/*********************************************************************/
+/* */
+/* RNA FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+char * seq2rna_lib ( Sequence *S, char *name);
+Constraint_list *read_rna_lib ( Sequence *S, char *fname);
+Constraint_list *rna_lib_extension ( Constraint_list *CL, Constraint_list *R);
+char *** produce_method_file ( char *method);
+typedef struct
+ {
+ int p1;
+ int p2;
+ int p3;
+ int p4;
+ int t;
+ int f;
+ char mode[20];//lower, unalign
+ char model[20];//fsa1 fsa2
+}
+OveralnP;
+
+//RNA
+
+int ** alifold_list2cov_list (Alignment *A, int **list);
+int ** update_RNAfold_list (Alignment *A, int **pos, int s, int **l);
+int ** vienna2list ( char *seq);
+Alignment *compare_RNA_fold ( Alignment *A, Alignment *B);
+
+Alignment *alifold2analyze (Alignment *A, Alignment *ST, char *mode);
+Alignment *alifold2cov_aln (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_stat (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_list (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_cache (Alignment *inA, int **l, int ug);
+
+
+Alignment *add_alifold2aln (Alignment *A, Alignment *ST);
+Alignment *aln2alifold(Alignment *A);
+
+//end
+Alignment * aln2bootstrap (Alignment *A, int n);
+Alignment * aln2sample (Alignment *A, int n);
+Alignment * aln2random_aln (Alignment *A, char *mode);
+Alignment *aln2scale (Alignment *A, char *offset);
+Alignment* aln2case_aln (Alignment *A, char *upper, char *lower);
+Alignment*aln2gap_cache (Alignment *A, int val);
+Alignment *score_aln2score_ascii_aln (Alignment *A, Alignment *C);
+int **aln2resindex ( Alignment *A, Alignment *B, FILE *fp);
+int **index_seq_res ( Sequence *S1, Sequence *S2, int **name_index);
+int **index_seq_name ( Sequence *S1, Sequence *S2);
+int *get_name_index (char **l1, int n1, char **l2, int n2);
+
+int* get_res_index (char *seq1, char *seq2);
+int * pos2list (int * pos, int len, int *nl);
+ int *list2pos (int *list, int nl, int len);
+
+
+int change_residue_coordinate ( char *in_seq1, char *in_seq2, int v);
+
+int ** minimise_repeat_coor (int **coor, int nseq, Sequence *S);
+int ** get_nol_seq( Constraint_list *CL,int **coor, int nseq, Sequence *S);
+
+
+int compare_pos_column( int **pos1,int p1, int **pos2,int p2, int nseq);
+
+
+
+char * seq2alphabet (Sequence *S);
+char *aln2alphabet (Alignment *A);
+char *array2alphabet (char **array, int n, char *forbiden);
+
+//TM Predictions
+char* alnpos2hmmtop_pred (Alignment *A, Alignment *Pred, int pos, int mode);
+Alignment * aln2hmmtop_pred (Alignment *A);
+char * seq2tmstruc ( char *seq);
+
+char * set_blast_default_values();
+char * seq2pdb ( Sequence *S);
+Alignment * seq2blast ( Sequence *S);
+
+Sequence * seq2unique_name_seq ( Sequence *S);
+Alignment * aln2unique_name_aln ( Alignment *S);
+int name_list2unique_name_list (int n, char **name);
+Sequence *seq2clean_seq ( Sequence *S, char *alp);//remove all alp characters from seq
+char**gene2exons (char **seq, int nseq);
+
+int ** seq2aln_pos (Alignment *A, int *n, int **ls);
+Alignment *padd_aln ( Alignment *A);
+char **padd_string ( char **string, int n,char pad);
+
+Alignment *local_maln2global_maln (char *seq, Alignment *A);
+
+Alignment * seq2profile (Sequence *S, int index);
+
+Sequence *remove_empty_sequence (Sequence *S);
+Alignment * aln2profile (Alignment * A);
+Alignment * aln2collapsed_aln (Alignment * A, int n, char **string);
+Alignment* remove_seq_from_aln (Alignment *A, char *seq);
+
+Alignment* aln2sub_aln_file (Alignment *A, int n, char **string);
+Alignment* aln2sub_seq (Alignment *A, int n, char **string);
+
+int ** aln2inv_pos (Alignment *A);
+int * seq2inv_pos ( char *seq);
+int ** aln2pos_simple (Alignment *A, int n_nseq, ...);
+int ** aln2pos_simple_2 (Alignment *A);
+Alignment ** split_seq_in_aln_list ( Alignment **aln, Sequence *S, int l_seq, char **seq_list);
+
+Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name);
+
+int seq_list2in_file ( TC_method *M, Sequence *S, char *list, char *file);
+int seq_list2fasta_file( Sequence *S, char *list, char *file, char *outmode);
+Structure * seq2struc ( Sequence *S, Structure *ST);
+Alignment *strings2aln (int nseq,...);
+
+Alignment * seq2aln ( Sequence *S, Alignment *A,int rm_gap);
+Alignment *seq_coor2aln ( Sequence *S, Alignment *A, int **coor, int nseq);
+
+Alignment *stack_aln (Alignment *A, Alignment *B);
+Alignment *chseqIaln(char *name, int seq_n, int start,int len,Sequence *S, int seqIaln, Alignment *A);
+
+
+char *dna_aln2cons_seq ( Alignment *A);
+char *aln2cons_seq ( Alignment *A, int ns, int *ls, int n_groups, char **group_list);
+char *aln2cons_maj ( Alignment *A, int ns, int *ls, int n_groups, char **group_list);
+Alignment *aln2conservation ( Alignment *A, int threshold,char *seq);
+
+char *sub_aln2cons_seq_mat ( Alignment *A,int ns, int *ls, char *mat_name);
+char *aln2cons_seq_mat ( Alignment*A, char *mat_name);
+Alignment *aln2short_aln( Alignment *A, char *list, char *new, int spacer);
+Sequence *keep_residues_in_seq ( Sequence *S,char *list, char replacement);
+Alignment *keep_residues_in_aln ( Alignment *A,char *list, char replacement);
+Alignment *filter_keep_residues_in_aln ( Alignment *A,Alignment *ST, int use_cons, int value, char *list, char replacement);
+
+Alignment *aln_convert (Alignment *A, Alignment *ST, int use_cons, int value,int n, ...);
+Alignment *aln2number (Alignment *A);
+Alignment * filter_aln ( Alignment *A, Alignment *ST, int value);
+Alignment * filter_aln_lower_upper ( Alignment *A, Alignment *ST,int use_cons, int value);
+Alignment * filter_aln_upper_lower ( Alignment *A, Alignment *ST, int use_cons,int value);
+Alignment * filter_aln_switchcase ( Alignment *A, Alignment *ST, int use_cons, int value);
+
+Alignment * STseq2STaln ( Alignment *A, Alignment *ST);
+Alignment * merge_annotation ( Alignment *A, Alignment *ST, char *seq);
+Alignment * filter_aln_convert ( Alignment *A, Alignment *ST, int use_cons,int value, int n_symbol,char** symbol_list);
+int aln2ngap (Alignment *A);
+
+int * count_in_aln ( Alignment *A, Alignment *ST, int value, int n_symbol,char **symbol_list, int *table);
+void count_misc (Alignment*A, Alignment *B);
+
+Alignment * trim_aln_with_seq ( Alignment *S, Alignment *P);
+Alignment * add_align_seq2aln ( Alignment *A, char *seq, char *seq_name);
+Sequence * aln2seq ( Alignment *A);
+Sequence * aln2seq_main ( Alignment *A, int mode);
+Alignment * thread_profile_files2aln (Alignment *A, char *template_file, Fname *F);
+Alignment * expand_aln (Alignment *A);
+Alignment * aln2expanded_aln (Alignment *A);
+Alignment * expand_number_aln (Alignment *A,Alignment *EA);
+Alignment * remove_gap_column ( Alignment *A, char *mode);
+Alignment* ungap_sub_aln ( Alignment *A, int nseq, int *ls);
+Sequence * ungap_seq ( Sequence *A);
+Alignment * insert_gap_col (Alignment *A, int p, int l);
+Alignment * unalign_residues (Alignment *A, int i1, int i2);
+Alignment * unalign_aln_2 (Alignment *A, Alignment *C, int t);
+Alignment * unalign_aln (Alignment *A, Alignment *C, int t);
+Alignment * unalign_aln_pos (Alignment *A, int s, int p, int l);
+
+Alignment *degap_aln (Alignment *A);
+
+Alignment * ungap_aln_n ( Alignment *A, int n);
+Alignment * ungap_aln ( Alignment *A);
+void compress_aln ( Alignment *A);
+Alignment* condense_aln (Alignment *A);
+
+Alignment * probabilistic_rm_aa ( Alignment *A, int pos, int len);
+Alignment * aln_gap2random_aa(Alignment *A);
+Alignment * make_random_aln(Alignment *A,int nseq, int len, char *alphabet);
+Alignment * add_random_sequence2aln( Alignment *A, char *alphabet);
+
+int ** trim_aln_borders ( char **seq1, char **seq2, int nseq);
+Sequence * trim_aln_seq ( Alignment *A, Alignment *B);
+Sequence * trim_aln_seq_name ( Alignment *A, Alignment *B);
+Sequence *get_defined_residues( Alignment *A);
+
+
+Alignment *thread_defined_residues_on_aln ( Alignment *A, Sequence *S1);
+Sequence *seq2number (Sequence *S);
+Sequence * merge_seq ( Sequence *IN, Sequence *OUT);
+char * seq_name2coor ( char *s, int *start, int *end, char sep);
+Alignment *seq_name2removed_seq_name(Sequence *S, Alignment *NA, float **diff);
+int seq_name2index (char *name, Sequence *S);
+
+Sequence *extract_one_seq(char *n,int start, int end, Alignment *S,int keep_name);
+Sequence * extract_sub_seq( Sequence *COOR, Sequence *S);
+
+
+Sequence * add_prf2seq (char *alnfile, Sequence *S);
+int prf_in_seq ( Sequence *S);
+Sequence * add_sequence ( Sequence *IN, Sequence *OUT, int i);
+Sequence * trim_seq ( Sequence *A, Sequence *B);
+Sequence * reorder_seq ( Sequence *A, char **name, int nseq);
+Sequence * reorder_seq_2 ( Sequence *A, int **name,int field, int nseq);
+
+char * concatenate_seq ( Sequence *S, char *conc, int *order);
+Sequence * swap_header ( Sequence *S, Sequence *H);
+
+Alignment *aln2jacknife (Alignment *A, int nseq, int len);
+char ** name2random_subset (char **in_name, int n_in, int n_out);
+Alignment * aln2random_order ( Alignment *A);
+Alignment * aln2scramble_seq ( Alignment *A);
+
+Alignment * reorder_aln ( Alignment *A, char **name, int nseq);
+
+char ** rm_name_tag (char **name, int nseq, char *tag);
+
+/******************************************************************************/
+/* TEMPLATE MANAGEMENENT */
+/******************************************************************************/
+char * string_contains_template_tag (char *string);
+Sequence * seq2template_type(Sequence *Seq);
+
+Sequence * vremove_seq_template_files (Sequence *S);
+Sequence * display_seq_template_files (Sequence *S);
+Sequence * handle_seq_template_file (Sequence *S, char *mode);
+int handle_X_template_files ( X_template *T, char *mode);
+
+
+Sequence * seq2template_seq ( Sequence *S, char *template_file, Fname *F);
+char * seq2template_file (Sequence *S, char *file);
+int seq2template_file2 (Sequence *S, char *file, char *mode);
+
+Sequence * profile_seq2template_seq ( Sequence *S, char *template_file, Fname *F);
+int seq2n_X_template ( Sequence *S, char *type);
+
+struct X_template *fill_X_template (char *name, char *p, char *type);
+FILE * display_seq_template (Sequence *S, FILE *io);
+char *template_type2type_name (char *type);
+char *template_type2short_type_name (char *type);
+
+
+FILE * display_sequence_templates ( Sequence *S, int i, FILE *io);
+FILE * display_X_template (struct X_template *X, FILE *io);
+
+struct X_template* free_X_template ( struct X_template *X);
+
+struct X_template *fill_P_template (char *name, char *p, Sequence *S);
+struct X_template *fill_F_template (char *name, char *p, Sequence *S);
+struct X_template *fill_S_template ( char *name,char *p, Sequence *S);
+struct X_template *fill_R_template (char *name, char *p, Sequence *S);
+struct X_template *fill_G_template (char *name, char *p, Sequence *S);
+struct X_template *fill_T_template (char *name, char *p, Sequence *S);
+struct X_template *fill_E_template (char *name, char *p, Sequence *S);
+struct X_template *fill_U_template (char *name, char *p, Sequence *S);
+
+char *seq2T_value ( Sequence *S, int i, char *param_name, char *template_type);
+char *profile2P_template_file (Sequence *S, int n);
+Alignment * seq2R_template_profile (Sequence *S, int n);
+char *seq2P_pdb_id (Sequence *S, int n);
+char * seq2P_template_file (Sequence *S, int n);
+char * seq2T_template_string (Sequence *S, int n);
+char * seq2E_template_string (Sequence *S, int n);
+int * seq2U_template (Sequence *S, int n);
+
+struct X_template * seq_has_template ( Sequence *S, int n, char *type);
+
+/******************************************************************************/
+/* ALIGNMENT MANIPULATION */
+/******************************************************************************/
+
+char *aln_column2string (Alignment *A, int p);
+int **fix_seq_aln (Sequence *S, Alignment*A, int **cache);
+int **fix_seq_seq ( Sequence *S1, Sequence *S2);
+int **fix_aln_seq_new (Alignment *S1, Sequence *S2);
+
+Alignment * fix_aln_seq ( Alignment *A, Sequence *S);
+Alignment * rotate_aln ( Alignment *A, char *name);
+Alignment * invert_aln ( Alignment *A);
+char * complement_string (char *s);
+Alignment * complement_aln ( Alignment *A);
+Alignment * extract_nol_local_aln( Alignment *A, int start, int max_end);
+Alignment * aln2block (Alignment *A, int start, int end, Alignment *B);
+Alignment * alnpos2block (Alignment *A, int*pos, Alignment *B);
+
+Alignment * extract_aln ( Alignment *A, int start, int end);
+Alignment * extract_aln2 ( Alignment *A, int start, int end, char *seq_name);
+Alignment * extract_aln3 ( Alignment *A, char *filename);
+Alignment * alnpos_list2block (Alignment *A, int n, char **in_list);
+
+Alignment * trunkate_local_aln ( Alignment *A);
+int get_nol_aln_border ( Alignment *A, int start, int direction);
+Alignment ** trim_local_aln ( Alignment *A, int **List, int ne, int **residue_list, Sequence *S);
+
+Alignment * aln_cat ( Alignment *A, Alignment *B);
+Alignment * concatenate_aln ( Alignment *A, Alignment *B, char *sep);
+char * extract_defined_seq ( char *in, int in_of, int in_start, int *aa_def, int dir, int *out_start, char *out_seq);
+int verify_aln ( Alignment *A, Sequence *S, char * error);
+Alignment * remove_end (Alignment *A);
+Alignment * orthologous_concatenate_aln (Alignment *A, Sequence *S, char *mode);
+Alignment * aln2N_replicate (Alignment *A, char *nn, char *name);
+FILE *aln2replicate (Alignment *A, FILE *fp);
+
+Alignment * voronoi_concatenate_aln (Alignment *A, Sequence *S);
+
+Alignment *adjust_est_aln ( Alignment *PW, Alignment *M, int s);
+Alignment * rename_seq_in_aln (Alignment *A, char ***list);
+Sequence * rename_seq_in_seq (Sequence *A, char ***list);
+/********************************************************************/
+/* */
+/* FLOAT SIMILARITIES */
+/* */
+/* */
+/* */
+/********************************************************************/
+float get_seq_fsim ( char *string1, char *string2, char *ignore, char *similarity_groups, int **matrix, int mode);
+float get_seq_fsim2 ( char *string1, char *string2, char *ignore, char *in_mode);
+float ** get_fsim_aln_array ( Alignment *A, char *mode);
+/********************************************************************/
+/* */
+/* ALIGNMENT ANALYSES */
+/* */
+/* */
+/* */
+/********************************************************************/
+int **sim_array2dist_array ( int **p, int max);
+int **dist_array2sim_array ( int **p, int max);
+int **normalize_array (int **p, int max, int norm);
+
+int aln2most_similar_sequence ( Alignment *A, char *mode);
+int aln2coverage ( Alignment *A, int ref_seq);
+
+double aln2entropy (Alignment *A, int *in_ls, int in_ns, float gap_threshold);
+int sub_aln2sim ( Alignment *A, int *ns, int **ls, char *mode);
+int sub_aln2max_sim ( Alignment *A, int *ns, int **ls, char *mode);
+int aln2sim ( Alignment *A, char *mode);
+int seq2idscore_sim ( char *seq1, char *seq2);
+
+int aln_is_aligned ( Alignment *A);
+int* get_cdna_seq_winsim ( int *cache, char *string1, char *string2, char *ignore, char *mode, int *w);
+int get_cdna_seq_sim ( int *cache, char *string1, char *string2, char *ignore, char *mode);
+
+int seq2aln2sim (char *seq1, char *seq2, char *mode_aln, char *mode_id);
+int* get_seq_winsim( char *string1, char *string2, char *ignore, char *mode, int *w);
+int get_seq_sim ( char *string1, char *string2, char *ignore, char *mode);
+int get_seq_sim_2 ( char *string1, char *string2, char *ignore, char **gr, int ng);
+int get_seq_sim_3 ( char *string1, char *string2, char *ignore, int **mat);
+
+
+int *** get_winsim_aln_array ( Alignment *A, char *mode, int ***w);
+int ** get_sim_master_aln_array ( Alignment *A,int n, char *mode);
+
+int ** seq2sim_mat (Sequence *S, char *mode);
+int ** seq2cov_mat (Sequence *S, char *mode);
+int ** seq2comp_mat (Sequence *S, char *mode, char *comp_mode);
+
+int logid_score (int sim, int len);
+int ** fast_aln2sim_mat (Alignment *A, char *mode);
+int ** fast_aln2sim_list (Alignment *A, char *mode, int *ns, int **ls);
+
+int ** aln2sim_mat (Alignment *A, char *mode);
+int **aln2cov (Alignment *A);
+int ** get_dist_aln_array ( Alignment *A, char *mode);
+int ** get_raw_sim_aln_array ( Alignment *A, char *mode);
+int ** get_sim_aln_array ( Alignment *A, char *mode);
+int generic_get_seq_sim ( char *seq1, char *seq2, int *cache, char *mode);
+Alignment * grep_seq (Alignment *S,char *field, char *mode, char *string);
+Alignment* modify_seq (Alignment *S,char *field, char *string1, char *string2);
+
+Sequence * seq2filter (Sequence *S_in, int min, int max);
+int ** get_cov_aln_array ( Alignment *A, char *mode);
+int ** get_cov_master_aln_array ( Alignment *A,int n, char *mode);
+
+
+int * get_aln_col_weight ( Alignment *A, char *mode);
+int analyse_aln_column ( Alignment *B, int col);
+
+int sub_aln2nseq_prf ( Alignment *A, int ns, int *ls);
+int **aln2count_mat (Alignment *A);
+int **sub_aln2count_mat2 (Alignment *A, int ns, int *ls);
+int **sub_aln2count_mat3 (char **al, int n);
+int **aln2count_mat2 (Alignment *A);
+char *aln2random_seq (Alignment *A, int noise1, int noise2, int noise3, int gap_noise);
+
+Alignment * master_trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment * trimseq( Alignment *A, Sequence *S, char *mode);
+Alignment *simple_trimseq (Alignment *A,Alignment*K, char *mode, char *seq, int **sim);
+Alignment *sim_filter (Alignment *A, char *in_mode, char *seq_list);
+
+Sequence * seq_weight2species_weight (Alignment *A, Sequence *S);
+Alignment * aln2voronoi_weights (Alignment *A);
+float ** get_weight ( Alignment *A, Sequence *S, char *mode);
+float **seq2pwsim ( Alignment *A, Sequence *S, char *mode);
+Alignment * trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment * tc_trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment* seq2subseq3( Alignment *A, Sequence *S,int use_aln, int lower_sim,int upper_sim, int min_nseq, int trim_direction, char *weight_mode, float ***sim_weight, int *seq_list);
+Alignment* seq2subseq2( Alignment *A, Sequence *S,int use_aln, int lower_sim,int upper_sim, int max_nseq, int trim_direction, char *weight_mode, float ***weight_table, int *seq_list);
+float extreme_seq (int direction, Alignment *A,float **sim_weight,int *seq_list, int *seq_index);
+
+
+Alignment* seq2subseq1( Alignment *A, Sequence *S,int use_aln, int percent,int max_nseq,int max_diff, char *weight_mode);
+/********************************************************************/
+/* */
+/* AMINO ACID FUNCTIONS */
+/* */
+/* */
+/* */
+/********************************************************************/
+char** string2alphabet (char *string, int depth, int *falp_size);
+int is_in_same_group_aa ( char r1, char r2, int n_group, char **gl, char *mode);
+int find_group_aa_distribution (char *col, int nseq,int n_group, char **gl, int *distrib, char *mode );
+char** make_group_aa (int *ngroup, char *mode);
+char** make_group_aa_upgma (char *mat, int max_size);
+
+
+char * test_gene2prot (Constraint_list *CL, int s1);
+Alignment* gene2prot (Alignment *A);
+Alignment * dna_aln2_3frame_cdna_aln(Alignment *A,int *ns,int **l_s);
+
+int ** get_sim_aln_array_normal_distribution ( Alignment *A, char *mode, int *STD, int *CENTER);
+double normal(double x, double mean, double std);
+int generic_get_seq_sim_normal_distribution ( char *seq1, char *seq2, int*cache, char *mode, int *STD, int *CENTER);
+int get_seq_sim_distribution ( char *string1, char *string2, char *ignore, char *in_mode, int *STD, int *CENTER);
+
+Alignment *aln2clean_pw_aln (Alignment *A,OveralnP *F);
+char **pw_aln2clean_pw_aln (char ** aln,OveralnP *F);
+int * pw_aln2clean_aln_weight ( char *seq1, char *seq2, int w, OveralnP *F);
+
+float* aln2pred ( Alignment *A, Alignment*B, char *mode);
+float* analyze_overaln ( Alignment *A, Alignment *B, char *mode, int f,int p1,int p2, int p3,int filter);
+
+
+Alignment * mark_exon_boundaries (Alignment *A, Alignment *E);
+
+struct orp
+{
+ char name[100];
+ char mode[100];
+ int ncomp;
+ int nseq;
+ int len;
+
+ Alignment *A;
+ Alignment *P;
+ Alignment *S;
+
+ int *pos;
+ char ***motif;
+ float sp;
+ float sn;
+ float sen2;
+ float best;
+ int tp;
+ int tn;
+ int fp;
+ int fn;
+
+ int offset;
+ float evalue;
+ struct orp *PR;
+};
+
+typedef struct orp ORP;
+
+typedef Alignment * (*filter_func) (Alignment *, Alignment*, int,int, char *);
+/************************************************************************************/
+/* ALIGNMENT ANALYZE : SAR */
+/************************************************************************************/
+int display_simple_sar_analyze_pair_col (Alignment *A, Alignment *SAR, char *mode);
+int **simple_sar_analyze_pair_col ( Alignment *inA, Alignment *SAR, char *mode);
+int ***simple_sar_predict ( Alignment *inA, Alignment *SAR, char *mode);
+int display_simple_sar_analyze_col ( Alignment *inA, Alignment *SAR, char *mode);
+Alignment *sar_analyze4 (Alignment *A, Alignment *SAR, char *name);/*28/08/06*/
+Alignment *sar_analyze3 (Alignment *A, Alignment *SAR, char *name);
+Alignment *sar_analyze2 (Alignment *A, Alignment *SAR, char *name);
+Alignment *sar_analyze (Alignment *A, Alignment *SAR, char *name);
+int aln2sar_column_list ( Alignment *A, char *filter);
+float get_sar_sim (char *seq1, char *seq2);
+float get_sar_sim2 (char *seq1, char *seq2);
+Alignment *aln2weighted_sar_score ( Alignment *A,Alignment *B, char *weight_file, char *compound);
+float seq2weighted_sar_score ( char *seq, int **weight);
+
+int sarset2subsarset ( Alignment *A, Alignment *S, Alignment **subA, Alignment **subS, Alignment *SUB);
+int sar2subsar (Alignment *A, Alignment *S, Alignment **subA, Alignment **subS, char **slist, int nl);
+int sar2subsar_file ( Alignment *A, Alignment *S, char *aln, char *sar);
+
+Alignment *weight2sar (Alignment *A, Alignment *SAR, char *weight_file, int limit);
+Alignment * sar2simpred (Alignment *A, Alignment *SAR, char *pos, char *compound, int L,int U );
+Alignment * sar2simpred2 (Alignment *A, Alignment *SAR, char *seqlist, char *posfile, char *compound, int L1 );
+
+Alignment *display_sar ( Alignment *A, Alignment *SAR, char *compound);
+NT_node sar2tree (Alignment *A, char *mode);
+/************************************************************************************/
+/* ALIGNMENT ANALYZE : SAR FOR OR */
+/************************************************************************************/
+
+Alignment * or_scan (Alignment *A, Alignment *B, char *param);
+Alignment * or_sar (Alignment *A, Alignment *B, char *param, int print);
+ORP * or_loo ( Alignment *inA, Alignment *inS, char *mode, int *pos,int print);
+
+
+ORP * combine_n_predictions (ORP **R,Alignment *A, Alignment *B);
+ORP* combine_2_predictions ( ORP *IN, ORP *TO,Alignment *A, Alignment *B);
+ORP * display_or_summary (ORP *CP, char *mode, FILE *fp, int print);
+
+Alignment * or_comp_loo ( Alignment *inA, Alignment *inS, char *mode, int *pos,int print);
+int * or_comp_pos ( Alignment *inA, Alignment *inS, char *mode,int print);
+float or_id_evaluate ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+char* or_id_evaluate2 ( Alignment *A, Alignment *S, char *mode, int *pos, int print, float *score);
+float or_loo_evaluate ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+float or_loo_evaluate2 ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+
+Alignment * or_test ( Alignment *inA, Alignment *inS, char *mode);
+Alignment * or_jack(Alignment *A, Alignment *S, char *param);
+Alignment * or_predict(Alignment *A, Alignment *S, char *mode);
+Alignment * or_aln2pos_aln (Alignment *A, Alignment *S, char *mode);
+ORP* or_self_predict(Alignment *inA, Alignment *inS, char *mode, int *pos, int print);
+Alignment * or_sim(Alignment *A, Alignment *S, char *mode);
+
+Alignment *display_pos (Alignment *A, Alignment *B, int *pos, char *mode);
+
+float evaluate_prediction (Alignment *R, Alignment *P, char *mode, int print);
+ORP* new_evaluate_prediction (ORP *P, char *mode, int print);
+
+Alignment * aln2prediction (Alignment *A,char ***motif, int *pos);
+int * aln2predictive_positions (Alignment *A, Alignment *B, char *mode, int print);
+int * aln2predictive_positions_mat (Alignment *A, Alignment *B, char *mode, int print);
+int * aln2predictive_positions_scan (Alignment *A, Alignment *B, char *mode, int print);
+char *** compounds2motifs (Alignment *A, Alignment *B, int *pos, int depth, char *mode, int print);
+char ** compound2motif (Alignment *A, Alignment *B, int *pos, int depth, int c, char *mode, int print);
+double pos2sim (Alignment *A, Alignment *B, int *pos);
+double sar_aln2r (Alignment *A, Alignment *B, int *pos, int print);
+double sar_aln2delta (Alignment *A, Alignment *B, int *pos, int print);
+Alignment * jack_sar(Alignment *A, Alignment *S, char *param);
+Alignment *set_sar (Alignment *A, Alignment *S, char *param);
+char * get_compound_name (int c, char *mode);
+Alignment *get_prediction_target (Alignment *A, Alignment *S, char *param);
+int * file2pos_list (Alignment *A, char *posfile);
+ORP * declare_or_prediction ( int ncomp, int nseq, int len);
+void free_orp_list ( ORP**P);
+void free_orp ( ORP*P);
+double evaluate_sar_score1 ( int len, int n11, int n1a, int n1b);
+double evaluate_sar_score2 ( int len, int n11, int n1a, int n1b);
+
+Sequence * compare_sar_sequence( Sequence *S1, Sequence *S2, int depth);
+Constraint_list * mask_list_with_aln (Alignment *A,int start, int len,Constraint_list *CL, int new_value);
+Constraint_list* mask_list_with_aln_pair (Alignment *A,int start, int end,Constraint_list *CL,int new_value);
+Constraint_list *mask_entry( Constraint_list *CL, int p, int new_value);
+Constraint_list *prepare_list_and_seq4sw(Constraint_list *I, int n_seq, char **seq_name);
+int ** get_undefined_list (Constraint_list *CL);
+int is_never_undefined (Constraint_list *CL,int r);
+int* do_analyse_list ( Constraint_list *CL);
+
+
+
+void print_list(Constraint_list *CL);
+void print_pair (Constraint_list *CL,int p);
+int** bin_list (Constraint_list *CL,int field, int Threshold);
+void save_full_list (Constraint_list *CL, char*fname);
+FILE * output_list ( Constraint_list *CL, FILE *fp);
+FILE * output_pair (Constraint_list *CL,int p, FILE *fp);
+NT_node ** seq2cw_tree ( Sequence *S, char *file);
+NT_node ** make_nj_tree ( Alignment *A,int **distances,int gop, int gep, char **out_seq, char **out_seq_name, int out_nseq, char *tree_file, char *tree_mode);
+NT_node ** make_upgma_tree ( Alignment *A,int **distances,int gop, int gep, char **out_seq, char **out_seq_name, int out_nseq, char *tree_file, char *tree_mode);
+
+NT_node ** int_dist2nj_tree (int **distances, char **out_seq_name, int out_nseq, char *tree_file);
+NT_node ** float_dist2nj_tree (float **distances, char **out_seq_name, int out_nseq, char *tree_file);
+NT_node ** dist2nj_tree (double **distances, char **out_seq_name, int out_nseq, char *tree_file);
+
+NT_node ** int_dist2upgma_tree (int **mat, Alignment *A, int nseq, char *fname);
+NT_node upgma_merge (int **mat, NT_node *NL, int *used, int *n, int N);
+
+void nj_tree(char **tree_description, int nseq);
+void fast_nj_tree(char **tree_description);
+void slow_nj_tree(char **tree_description);
+
+void print_phylip_tree(char **tree_description, FILE *tree, int bootstrap);
+void two_way_split(char **tree_description, FILE *tree, int start_row, int flag, int bootstrap);
+void guide_tree(char *fname, double **saga_tmat, char **sag_seq_name, int saga_nseq);
+
+
+
+NT_node split2upgma_tree (Split **S, Alignment *A, int nseq, char *fname);
+NT_node split_upgma_merge (Alignment *A, Split **S, NT_node *NL, int *used, int *n, int N);
+float get_split_dist ( Alignment *A, NT_node L, NT_node R, Split **S) ;
+
+Alignment * upgma_tree_aln (Alignment*A, int nseq, Constraint_list *CL);
+int ** dist_mat2best_split (int **mat, int nseq);
+int upgma_node_heap (NT_node X);typedef struct Tmpname Tmpname;
+struct Memcontrol
+ {
+ size_t size;
+ size_t size_element;
+ char check[3];
+ struct Memcontrol *p;
+ struct Memcontrol *n;
+ };
+typedef struct Memcontrol Memcontrol;
+void free_pair_wise();//Frees static memory in the pair_wise functions
+/************************************************************************/
+/* */
+/* CONSTRAINT_LIST */
+/* */
+/* */
+/************************************************************************/
+int *** duplicate_residue_index (int ***r);
+int *** declare_residue_index (Sequence *S);
+
+Constraint_list *free_constraint_list4lib_computation (Constraint_list *CL);
+Constraint_list *duplicate_constraint_list4lib_computation (Constraint_list *CL);
+Constraint_list * declare_constraint_list_simple ( Sequence *S);
+Constraint_list * declare_constraint_list ( Sequence *S, char *name, int *L, int ne,FILE *fp, int **M);
+Constraint_list *cache_dp_value4constraint_list ( char mode[],Constraint_list *CL);
+Constraint_list *duplicate_constraint_list_soft (Constraint_list *CL);
+Constraint_list *duplicate_constraint_list (Constraint_list *CL);
+Constraint_list *copy_constraint_list (Constraint_list *CL, int mode);
+Sequence * free_constraint_list (Constraint_list *CL);
+Constraint_list * free_constraint_list_full (Constraint_list *CL);
+Distance_matrix * free_distance_matrix ( Distance_matrix *DM);
+Distance_matrix * duplicate_distance_matrix ( Distance_matrix *DMin);
+/************************************************************************/
+/* */
+/* Blast_param Functions */
+/* */
+/* */
+/************************************************************************/
+Blast_param * duplicate_blast_param ( Blast_param*B);
+Blast_param * free_blast_param ( Blast_param*B);
+/************************************************************************/
+/* */
+/* TC_param Functions */
+/* */
+/* */
+/************************************************************************/
+TC_param * duplicate_TC_param ( TC_param*B);
+TC_param * free_TC_param ( TC_param*B);
+/************************************************************************/
+/* */
+/* MOCA Functions */
+/* */
+/* */
+/************************************************************************/
+Moca * duplicate_moca ( Moca *m);
+Moca * free_moca ( Moca *m);
+/************************************************************************/
+/* */
+/* PDB Functions */
+/* */
+/* */
+/************************************************************************/
+Structure * declare_structure ( int n, char **array);
+Structure * extend_structure ( Structure *S);
+/************************************************************************/
+/* */
+/* Weights Functions */
+/* */
+/* */
+/************************************************************************/
+Weights* declare_weights ( int nseq);
+Weights* duplicate_weights (Weights *W);
+Weights* free_weights ( Weights* W);
+
+FILE* print_mem_usage (FILE *fp, char *comment);
+void set_max_mem (int m);
+int verify_memory (int s);
+int my_assert ( void *p, int index);
+
+void * vmalloc ( size_t size);
+void * vcalloc ( size_t nobj, size_t size);
+void * vcalloc_nomemset ( size_t nobj, size_t size);
+void * sub_vcalloc ( size_t nobj, size_t size, int MODE);
+
+void * vrealloc ( void *p, size_t size);
+void vfree2 ( void **p);
+void vfree ( void *p);
+void * free_arrayN (void *p, int ndim);
+void vfree_all ();
+/*********************************************************************/
+/* */
+/* SIZES */
+/* */
+/* */
+/*********************************************************************/
+void write_size_short (int x, short *array, int offset);
+void write_size_char (int x, char *array, int offset);
+void write_size_int (int x, int *array, int offset);
+void write_size_float (int x, float *array, int offset);
+void write_size_double(int x, double *array, int offset);
+
+int read_size_short ( void *array, size_t size );
+int read_size_char ( void *array, size_t size );
+int read_size_int ( void *array, size_t size );
+int read_size_float ( void *array, size_t size );
+int read_size_double( void *array, size_t size );
+int read_array_size_new ( void *array);
+int read_array_size ( void *array, size_t size );
+int read_array_new ( void *array);
+int is_dynamic_memory ( void *array);
+
+/*********************************************************************/
+/* */
+/* REALLOCATION */
+/* */
+/* */
+/*********************************************************************/
+void **realloc_arrayN(int ndim,void **main_array,size_t size, ...);
+void **realloc_arrayN2 ( int ndim, void ** p, int *A, size_t size);
+
+
+void ** realloc_array (void **array,size_t size, int first, int second, int ext1, int ext2);
+short ** realloc_short ( short **array, int first, int second, int ext1, int ext2);
+char ** realloc_char ( char **array, int first, int second, int ext1, int ext2);
+int ** realloc_int ( int **array, int first, int second, int ext1, int ext2);
+float ** realloc_float ( float **array, int first, int second, int ext1, int ext2);
+double ** realloc_double ( double **array, int first, int second, int ext1, int ext2);
+Alignment ** realloc_aln_array ( Alignment **array, int ext1);
+/*The new realloc is recommended*/
+short ** new_realloc_short ( short **array, int ext1, int ext2);
+char ** new_realloc_char ( char **array, int ext1, int ext2);
+int ** new_realloc_int ( int **array, int ext1, int ext2);
+float ** new_realloc_float ( float **array, int ext1, int ext2);
+double ** new_realloc_double ( double **array, int ext1, int ext2);
+
+
+void * declare_arrayNnomemset (int ndim, size_t size, ...);
+void *declare_arrayN2nomemset ( int ndim, int *A, size_t size);
+
+void * declare_arrayN (int ndim, size_t size, ...);
+void *declare_arrayN2 ( int ndim, int *A, size_t size);
+
+
+void ** declare_array (int first, int second, size_t size);
+short ** declare_short ( int first, int second);
+char ** declare_char ( int first, int second);
+int ** declare_int ( int first, int second);
+int ** declare_int2 ( int first, int *second, int delta);
+
+float ** declare_float ( int first, int second);
+double ** declare_double ( int first, int second);
+
+void ** declare_array_nomemset (int first, int second, size_t size);
+short ** declare_short_nomemset ( int first, int second);
+char ** declare_char_nomemset ( int first, int second);
+int ** declare_int_nomemset ( int first, int second);
+float ** declare_float_nomemset ( int first, int second);
+double ** declare_double_nomemset ( int first, int second);
+
+
+Alignment ** declare_aln_array ( int first);
+
+short ** free_short ( short **array, int first);
+int ** free_int ( int **array, int first);
+char ** free_char ( char **array, int first);
+double ** free_double ( double **array, int first);
+float ** free_float ( float **array, int first);
+Alignment ** free_aln_array ( Alignment **array);
+Alignment *free_data_in_aln (Alignment *A);
+
+long aln_stack (Alignment *A, int mode);
+
+Sequence *free_Alignment ( Alignment *A);
+Sequence *free_aln ( Alignment *A);
+Alignment *declare_Alignment ( Sequence *S);
+Alignment *realloc_alignment ( Alignment *A, int new_len);
+Alignment *realloc_alignment2 ( Alignment *A, int new_nseq, int new_len);
+
+Alignment *declare_aln ( Sequence *S);
+Alignment *declare_aln2 (int nseq, int len);
+Alignment *realloc_aln ( Alignment *A, int new_len);
+Alignment *realloc_aln2 ( Alignment *A, int new_nseq, int new_len);
+Alignment *update_aln_random_tag (Alignment *A);
+
+Alignment *copy_aln ( Alignment *A, Alignment *B);
+Alignment* extract_sub_aln2 ( Alignment *A, int nseq, char **list);
+Alignment* extract_sub_aln ( Alignment *A, int nseq, int *list);
+Alignment* shrink_aln ( Alignment *A, int nseq, int *list);
+
+Profile *copy_profile (Profile *P1);
+Profile *declare_profile(char *alphabet, int len);
+Profile * free_profile ( Profile *P);
+
+Sequence * reset_sequence_len (Sequence *S);
+Sequence * declare_sequence ( int min, int max, int nseq);
+Sequence * realloc_sequence (Sequence *OUT, int new_nseq, int max_len);
+Sequence * duplicate_sequence (Sequence *S );
+Sequence * add_sequence ( Sequence *IN, Sequence *OUT, int i);
+void free_sequence ( Sequence *LS, int nseq);
+
+
+
+Fname *declare_fname ();
+Fname *free_fname ( Fname *F);
+/*********************************************************************************************/
+/* */
+/* STRUCTURES FOR HSEARCH */
+/* */
+/*********************************************************************************************/
+#define FIND 0
+#define ADD 1
+#define REMOVE 2
+#define DECLARE 3
+#define MARK 4
+#define UNMARK 5
+#define FREE 6
+#define FREE_STACK 7
+#define FREE_ALL 8
+#define FREE_MARK 9
+#define INFO 10
+
+struct HaschT
+{
+ int ne;
+ struct Hasch_entry **p;
+};
+typedef struct HaschT HaschT;
+
+struct Hasch_entry
+{
+ struct Hasch_entry *n;
+ struct Hasch_entry *p;
+ int k;
+ struct Hasch_data *data;
+ struct Hasch_data * (*free_data)(struct Hasch_data *);
+ struct Hasch_data * (*declare_data)(struct Hasch_entry*);
+ int tag;
+};
+typedef struct Hasch_entry Hasch_entry;
+struct Char_node
+{
+ struct Char_node **c;
+ int key;
+
+};
+typedef struct Char_node Char_node;
+
+HaschT * hcreate ( int n_elements,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+HaschT *hdestroy (HaschT *T,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+Hasch_entry* hsearch (HaschT *T, int k, int action, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+Hasch_entry * extract_hasch_entry_from_list (Hasch_entry *e, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+Hasch_entry * insert_hasch_entry_in_list (Hasch_entry *p, Hasch_entry *e, Hasch_entry *n, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+Hasch_entry * allocate_hasch_entry (Hasch_entry *e, int action,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) );
+
+
+
+
+
+int string2key (char *s, Char_node *n);
+Char_node * declare_char_node (int action);
+char * process_repeat (char *aln, char *seq, char *pdb);
+char * normalize_pdb_file (char *name, char *seq,char *out_file);
+Ca_trace * trim_ca_trace (Ca_trace *st, char *seq );
+
+Ca_trace * read_ca_trace (char *file, char *seq_field );
+Ca_trace * simple_read_ca_trace (char *file );
+Ca_trace * hasch_ca_trace ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_nb ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_bubble ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_transversal ( Ca_trace *TRACE);
+
+float get_atomic_distance ( Atom *A, Atom*B);
+float ** measure_ca_distances(Ca_trace *T);
+
+float** print_contacts ( char *file1, char *file2, float T);
+char * map_contacts ( char *file1, char *file2, float T);
+int * identify_contacts (Ca_trace *ST1,Ca_trace *ST2, float T);
+Sequence *seq2contacts ( Sequence *S, float T);
+char *string2contacts (char *seq,char *name,char *comment, float T);
+char **struc2nb (char *name,char *seq, char *comment, float Threshold, char *atom_list, char *output);
+char **struclist2nb (char *name,char *seq, char *comment, float Threshold, char *atom_list, char *output);
+
+typedef struct
+{ Alignment *A;
+ Alignment *B;
+ Alignment *sim_A;
+ Sequence *S;
+ Structure *ST;
+/*PARAMETERS*/
+ char ***grep_list;
+ int n_greps;
+
+ char *sim_aln;
+ char *alignment1_file;
+ char *alignment2_file;
+
+ char *io_format;
+
+ int n_structure;
+ char **struct_file;
+ char **struct_format;
+ int *n_symbol;
+ char ***symbol_list;
+
+/*LIST VARIABLES*/
+ int **code_A;
+ int **code_B;
+ int n_elementsA;
+ int n_elementsB;
+
+ int **end_index;
+ int **start_index;
+/*RESULTS_VARIABLES*/
+ int **tot_count;
+ int **pos_count;
+ int ***pw_tot_count;
+ int ***pw_pos_count;
+ int *glob;
+ int **pw_glob;
+/*IO VARIABLES*/
+ int n_categories;
+ char ***category;
+ char *category_list;
+ int *n_sub_categories;
+ char sep_l;
+ char sep_r;
+/*Sims VARIABLES*/
+ float **sim;
+ float **sim_param;
+ char *sim_matrix;
+
+ int sim_n_categories;
+ char ***sim_category;
+ char *sim_category_list;
+ int *sim_n_sub_categories;
+}Result;
+
+
+#define MAX_N_CATEGORIES 100
+#define MAX_N_STRUC 100
+
+
+
+
+int aln_compare (int argc, char *argv[]);
+int **analyse_distance ( Alignment *A, int **dis);
+
+Structure * read_structure (char *fname, char *format, Alignment *A,Alignment *B, Structure *ST, int n_symbols, char **symbol_table);
+
+
+int is_in_struct_category ( int s1, int s2, int r1, int r2, Structure *ST, char **cat, int n_sub_cat);
+char * get_structure_residue (int s, int r, Structure *S);
+int parse_category_list ( char *category_list, char ***category, int *sub_n_categories);
+int struc_matches_pattern ( char *struc, char *pattern);
+float **get_aln_compare_sim ( Alignment *A, Structure *S, char **cat, int n_cat, char *matrix);
+float **analyse_sim ( Alignment *A, float **dis);
+
+/*Output*/
+FILE *output_format (char *iof, FILE *fp, Result *R);
+FILE *output_pair_wise_sequence_results (FILE *fp, Result *R);
+FILE *output_sequence_results (FILE *fp, Result *R);
+FILE *output_total_results (FILE *fp, Result *R);
+FILE *output_header (FILE *fp, Result *R);
+FILE *output_large_header ( FILE *fp, Result *R);
+
+/*Parameter Checking*/
+int is_a_struc_format (char *format);
+void get_separating_char ( char s, char *l, char *r);
+void output_informations ();
+
+int check_configuration4program();
+typedef struct
+ {
+ Alignment *A;
+ Weights *W;
+ Sequence *S;
+ int **M;
+ Structure *RNA_ST;
+ NT_node T;
+ Constraint_list *CL;
+ char format[100];
+ char file[100];
+ int rm_gap;
+
+}Sequence_data_struc;
+
+typedef struct
+ {
+ char **symbol_list;
+ int n_symbol;
+ char *coor_file;
+ int rm_gap;
+ int keep_case;
+ int keep_name;
+ int use_consensus;
+}Action_data_struc;
+
+/*Control of alignment sizes*/
+int set_landscape_msa (int len);
+int get_msa_line_length (int line, int aln_len);
+
+int seq_reformat (int argc, char **argv);
+
+Sequence_data_struc *read_data_structure ( char *in_format, char *in_file,Action_data_struc *RAD);
+Alignment * main_read_aln ( char *name, Alignment *A);
+Sequence * read_sequences ( char *name);
+Sequence * read_alifold ( char *name);
+Alignment *alifold2aln ( char *name);
+Sequence * main_read_seq ( char *mname);
+int output_format_aln ( char *format, Alignment *A, Alignment *EA,char *name);
+int main_output ( Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char *out_format, char *out_file);
+
+char * identify_seq_format ( char *file);
+char * name2type_name ( char *name);
+char identify_format (char **fname);
+char **identify_list_format ( char **list, int n);
+
+int type_is_exon_boundaries(char **seq, int n);
+
+int format_is_oligo ( char *file);
+int format_is_msf ( char *file);
+int format_is_fasta( char *file);
+int format_is_fasta_aln( char *file);
+int format_is_fasta_seq( char *file);
+int is_pir_name (char *name);
+int format_is_pir ( char *file);
+int format_is_pir_aln( char *file);
+int format_is_pir_seq( char *file);
+int pir_name (char *name);
+int format_is_conc_aln (char *file);
+int format_is_saga ( char *file);
+int format_is_swissprot (char *name);
+
+int is_seq ( char *name);
+int is_aln ( char *name);
+int has_pdb (char *name);
+int is_stockhom_aln ( char *name);
+int is_blast_file (char *name);
+int is_sap_file (char *name);
+int is_pdb_file ( char *name);
+int is_simple_pdb_file ( char *name);
+char *fix_pdb_file (char *name);
+
+int is_pdb_name ( char *name);
+char* get_pdb_id(char *name);
+char* get_pdb_struc(char *name, int start, int end);
+char* seq_is_pdb_struc ( Sequence *S, int i);
+char* is_pdb_struc ( char *name); /*Returns NULL if not a PDB structure Or a the name of a file containing a PDB structure*/
+int is_matrix (char *name);
+
+int is_lib (char *name);
+int is_lib_01 (char *name);
+int is_lib_02 (char *name);
+int is_lib_list ( char *name);
+int is_single_seq_weight_file (char *fname);
+int is_newick (char *name);
+
+int is_method ( char *file);
+
+char *format_name2aln_format_name (char *name);
+int is_in_format_list ( char *name);
+int is_out_format_list ( char *name);
+int is_struc_in_format_list ( char *name);
+int is_struc_out_format_list ( char *name);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT MISC */
+/* */
+/***************************************************************************************** */
+
+char *** read_rename_file ( char *fname, int mode);
+void get_barton_list_tc_seq ( char *in_file);
+int process_barton_entry (char *buf, char *name);
+
+Structure *read_rna_struc_number ( Alignment *A, char *fname);
+char ** read_lib_list (char *name, int *n);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT WEIGHTS */
+/* */
+/***************************************************************************************** */
+Weights* get_amps_sd_scores ( char *fname);
+Weights *read_seq_weight (char **name, int nseq, char* seq_weight);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT SEQUENCES */
+/* */
+/***************************************************************************************** */
+char ***read_group ( char *file);
+Sequence* get_pdb_sequence ( char *fname);
+Sequence* get_struc_gor ( char *fname);
+Sequence* get_dialign_sequence ( char *fname);
+Sequence* get_pima_sequence ( char *fname);
+Sequence* get_sequence_dali ( char *fname);
+Sequence* get_pir_sequence ( char *fname, char *comment_name);
+Sequence* perl_reformat2fasta ( char *perl_script, char *file);
+
+Sequence* get_fasta_tree ( char *fname, char *comment_name);
+Sequence* get_fasta_sequence ( char *fname, char *comment_name);
+Sequence* get_fasta_sequence_num ( char *fname, char *comment_name);
+Sequence* get_fasta_sequence_raw ( char *fname, char *comment_name);
+Sequence *get_file_list ( char *fname);
+Sequence *get_tree_file_list ( char *fname);
+
+Sequence* get_gor_sequence ( char *fname, char *comment_name);
+Sequence* get_swissprot_sequence ( char *fname, char *comment_name);
+int fscanf_seq_name ( FILE *fp, char *sname);
+
+void read_check ( Alignment *A, char *check_file);
+void read_stockholm_aln ( char *fname, Alignment *A);
+void read_aln ( char *fname, Alignment *A);
+void read_number_aln ( char *fname, Alignment *A);
+Alignment *read_blast_aln ( char *fname, Alignment *A);
+void read_msf_aln ( char *fname, Alignment *A);
+void read_amps_aln ( char *in_file, Alignment *A);
+int get_amps_seq_name ( char **name, char* fname);
+Alignment *read_gotoh_aln ( char *fname, Alignment *A);
+
+void undump_msa ( Alignment *A, char *tmp);
+void dump_msa ( char *file,Alignment *A, int nseq, int *lseq);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT MATRICES */
+/* */
+/***************************************************************************************** */
+int output_freq_mat ( char *outfile, Alignment *A);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT P-Values */
+/* */
+/***************************************************************************************** */
+float output_maln_pval ( char *outfile, Alignment *A);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT WEIGHTS */
+/* */
+/***************************************************************************************** */
+void output_similarities (char *file, Alignment *A, char *mode);
+void output_similarities_pw (char *file, Alignment *A, Alignment *B, char *mode);
+Alignment * similarities_file2aln ( char *file);
+int** input_similarities (char *file, Alignment *A, char *mode);
+
+void output_statistics (char *file, Alignment *A, char *mode);
+void output_pw_weights4saga ( Weights *W, float **w_list, char *wfile);
+int output_seq_weights ( Weights *W, char *wfile);
+FILE * display_weights (Weights *W, FILE *fp);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT SEQ */
+/* */
+/***************************************************************************************** */
+char** clean_seq_names (char **names, int n, int mode);
+char *clean_seq_name (char *name, int mode);
+
+
+void output_pir_seq1 (char *fname, Alignment*A );
+void output_pir_seq (char *fname, Alignment*A );
+void output_gor_seq (char *fname, Alignment*A );
+void output_mult_fasta_seq (char *fname, Alignment*A, int n );
+
+void main_output_fasta_seq ( char *fname, Alignment *A, int header);
+void output_fasta_tree ( char *fname, Alignment *A);
+void output_fasta_seqS (char *fname, Sequence *S );
+void output_fasta_seq1 (char *fname, Alignment*A );
+char *output_fasta_seqX (char *name, char *mode, Sequence *S, Alignment *A, int i);
+
+void output_pir_check (char *fname,int nseq, char **A );
+void output_fasta_seq (char *fname, Alignment*A );
+void output_gotoh_seq (char *fname, Alignment*A );
+void output_est_prf (char *fname, Alignment *A);
+void output_gor_seq (char *fname, Alignment*A );
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT ALN */
+/* */
+/***************************************************************************************** */
+void output_pir_aln ( char *fname,Alignment*A);
+void output_model_aln ( char *fname,Alignment*A );
+char * output_fasta_sub_aln (char *fname, Alignment*A, int ns, int *ls );
+char * output_fasta_sub_aln2 (char *fname, Alignment*A, int *ns, int **ls );
+
+void ouput_suchard_aln ( char *fname,Alignment*A);
+void output_fasta_aln ( char *fname,Alignment*A);
+void output_msf_aln ( char *fname,Alignment*B);
+FILE * output_generic_interleaved_aln (FILE *fp, Alignment *B, int line, char gap, char *mode);
+void output_stockholm_aln (char *file, Alignment *A, Alignment *ST);
+void output_clustal_aln( char *name, Alignment*B);
+void output_strict_clustal_aln( char *name, Alignment*B);
+void output_generic_clustal_aln( char *name, Alignment*B, char *format);
+void output_saga_aln ( char *name, Alignment*B);
+void output_phylip_aln ( char *name, Alignment*B);
+void output_mocca_aln ( char *name, Alignment*B,Alignment*S);
+void output_rnalign (char *out_file, Alignment*A,Sequence *STRUC);
+void output_pw_lib_saga_aln (char *lib_name, Alignment *A );
+void output_lib (char *lib_name, Alignment *A );
+void output_compact_aln( char *name, Alignment *B);
+
+void print_sub_aln ( Alignment *B, int *ns, int **ls);
+void print_aln ( Alignment *B);
+FILE * output_aln( Alignment *B, FILE *fp);
+
+
+FILE * output_aln_score ( Alignment *B, FILE *fp);
+FILE * output_aln_with_res_number ( Alignment *B, FILE *fp);
+
+
+FILE* output_Alignment ( Alignment *B, FILE *fp);
+FILE* output_Alignment_without_header ( Alignment *B, FILE *fp);
+FILE * output_Alignment_score ( Alignment *B, FILE *fp);
+FILE * output_Alignment_with_res_number ( Alignment *B, FILE *fp);
+void output_constraints ( char *fname, char *mode, Alignment *A);
+
+Alignment *input_conc_aln ( char *name, Alignment *A);
+void output_conc_aln ( char *name, Alignment *B);
+void output_glalign ( char *name, Alignment *B, Alignment *S);
+void output_lalign_header( char *name, Alignment *B);
+void output_lalign ( char *name, Alignment *B);
+void output_lalign_aln ( char *name, Alignment *B);
+
+/**************************************************************************************************/
+/* */
+/* */
+/* INPUT/OUTPUT MATRICES */
+/* */
+/**************************************************************************************************/
+int is_blast_matrix (char *fname);
+int is_pavie_matrix (char *fname);
+int is_clustalw_matrix (char *fname);
+
+int is_distance_matrix_file (char *name);
+int is_similarity_matrix_file (char *name);
+
+void aln2mat (Sequence *S);
+void aln2mat_diaa (Sequence *S);
+int **seq2latmat ( Sequence *S, char *fname);
+int output_mat (int **mat, char *fname, char *alp, int offset);
+int ** read_blast_matrix ( char *mat_name);
+int output_blast_mat (int **mat, char *fname);
+double* mat2cmp (int **mat1, int **mat2);
+
+void output_pavie_mat (int **mat, char *fname, double gep, char *alp);
+int ** read_pavie_matrix ( char *mat_name);
+
+/****************************************************************************************************/
+/*************************** *************************************/
+/*************************** PROCESSING *************************************/
+/*************************** *************************************/
+/*******************************************************************************************/
+/* */
+/* */
+/* THREADING */
+/***************************************************************************************** */
+
+
+
+
+Structure * declare_rna_structure_num (Sequence *SA);
+
+char *thread_aa_seq_on_dna_seq( char *s);
+void thread_seq_struc2aln ( Alignment *A, Sequence *ST);
+Alignment *thread_dnaseq_on_prot_aln (Sequence *S, Alignment *A);
+void cache_id ( Alignment *A);
+
+
+
+int process_est_sequence ( Sequence *S, int *cluster_list);
+char * invert_seq ( char *seq);
+int get_best_match ( char *seq1, char *seq2);
+int** extract_m_diag_streches ( int ** m, int l1, int l2,char *seq1, char *seq2, int *n_mdiag);
+int is_strech ( char *AA, char *seq1, char *seq2, int len, int x, int y);
+
+int search_for_cluster ( int seq, int cluster_number, int *cluster_list, int T, int nseq, int **S);
+int * SHC ( int nseq, int **NST, int **ST);
+int mutate_sol (int *sol, int nseq);
+int evaluate_sol ( int*sol, int nseq, int **ST, int **NST);
+
+
+
+char **make_symbols ( char *name, int *n);
+Alignment *code_dna_aln (Alignment *A);
+char* back_translate_dna_codon ( char aa, int deterministic);
+int translate_dna_codon ( char *seq, char stop);
+char* mutate_amino_acid ( char aa, char *mode);
+Alignment * mutate_aln ( Alignment *A, char *r);
+
+int extend_seqaln (Sequence *S, Alignment *A);
+int unextend_seqaln (Sequence *S, Alignment *A);
+char *extend_seq (char *seq);
+char *unextend_seq (char *seq);
+
+Sequence * transform_sequence ( Sequence *S, char *mode);
+Alignment *translate_splice_dna_aln (Alignment *A,Alignment *ST );
+Alignment * mutate_cdna_aln ( Alignment *A);
+
+char *test_dna2gene (char *dna, int *w);
+Sequence *dnaseq2geneseq (Sequence *S, int **w);
+
+int ** shift_res_weights ( Sequence *R, int **w, int shift);
+int res_weights2min(Sequence *R, int **w);
+int res_weights2max(Sequence *R, int **w);
+int res_weights2avg(Sequence *R, int **w);
+int output_wexons (char *name, Alignment *A);
+int scan_res_weights4ac (Sequence *R, int **w, int start, int end, int step);
+float *res_weights2accuracy_counts ( Sequence *R, int **w,int T, float *result);
+float* genepred_seq2accuracy_counts (Sequence *R, Sequence *T,float *result);
+void genepred_seq2accuracy_counts4all (Sequence *R, Sequence *Ts); //JM
+float* genepred2accuracy_counts (char *ref, char *target , float *result);
+
+char *dna2gene (char *dna, int *w);
+char * translate_dna_seq_on3frame ( char *dna_seq, char stop, char *prot);
+
+char * translate_dna_seq ( char *dna_seq, int frame, char stop, char *prot);
+int is_stop (char r1, char r2, char r3);
+int seq2tblastx_db (char *file,Sequence *S, int strand);
+
+char * back_translate_dna_seq ( char *in_seq,char *out_seq, int mode);
+Alignment *back_translate_dna_aln (Alignment *A);
+Sequence *translate_dna_seqS (Sequence *S, int frame, int stop);
+Alignment *translate_dna_aln (Alignment *A, int frame);
+char *dna_seq2pep_seq (char *seq, int frame);
+
+Alignment *clean_gdna_aln (Alignment *A);
+Alignment *clean_cdna_aln (Alignment *A);
+Alignment *clean_est (Alignment *A);
+/**************************************************************************************************/
+/******************************** ********************************************/
+/******************************** PROCESSING ********************************************/
+/*************** **************** ********************************************/
+void modify_data (Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char **action_list,int n_actions, Action_data_struc *RAD);
+
+//
+// Name MAnipulation
+//
+
+Alignment *clean_aln (Alignment *A);
+Sequence *clean_sequence ( Sequence *S);
+char ** translate_names (int n, char **name);
+char * translate_name ( char *name);
+char *decode_name (char *name, int mode);
+FILE * display_sequences_names (Sequence *S, FILE *fp, int check_pdb_status, int print_templates);
+Sequence *add_file2file_list (char *name, Sequence *S);
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE is free software; you can redistribute it and/or modify*/
+/* it under the terms of the GNU General Public License as published by*/
+/* the Free Software Foundation; either version 2 of the License, or*/
+/* (at your option) any later version.*/
+/**/
+/* T-COFFEE is distributed in the hope that it will be useful,*/
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
+/* GNU General Public License for more details.*/
+/**/
+/* You should have received a copy of the GNU General Public License*/
+/* along with Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
git://source.jalview.org / jabaws.git / blobdiff