--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*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*******************************/
+#include <time.h>
+#include <signal.h>
+#include <errno.h>
+#include <sys/times.h>
+#include <sys/types.h>
+#include <sys/wait.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;
+ };
+/*********************************************************************/
+/* */
+/* SANDBOX
+/* */
+/* */
+/*********************************************************************/
+void sb();
+/*********************************************************************/
+/* */
+/* 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);
+
+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);
+int * flash_sort_int_inv ( int **V,int N_F, int F, int left, int right);
+int * flash_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_double_inv ( double **V,int N_F, int F, int left, int right);
+void sort_float_inv ( float **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_double ( const double**a, const double**b);
+int cmp_float ( const float **a, const float**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 (const 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);
+float atofgetenv(const char *x);
+int atoigetenv(const char *x);
+void setenv_func ( char *string_name, char *string_value);
+char *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, ...);
+int strim (const char *s1, const char *s2);
+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 HERE2 (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 printf_system_direct_check (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 **list2expanded_flist (char **list, int *n, char *tag);
+char **expand_flist (char *file, char **list,int i,int *n, char *tag);
+
+char ***file2list (char *name, char *sep);
+char ** file2lines (char *name);
+char * file2string (char *name);
+int file2size (char *name);
+int string2file ( char *file, char *mode, char *string,...);
+char *chomp (char *name);
+int get_cl_param (int argc, char **argv, FILE **fp, const char para_name[], int *set_flag, const char type[], int optional, int max_n_val,const 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 (const char var[], char* v);
+char* get_string_variable (const char var[]);
+char* unset_string_variable (char *var);
+char* store_string_variable (char *var, char * v, int mode);
+
+int int_variable_isset (const char var[]);
+int set_int_variable (char *var, int v);
+int get_int_variable (const char var[]);
+int unset_int_variable (const 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);
+int vtmpnam_size ();
+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 (int);
+void clean_exit();
+void signal_exit(int);
+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_n ( char *fname, char *token, int nlines);
+int token_is_in_file (char *fname, char *token);
+
+int check_file_for_token ( char *file , 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_url_exists ( 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
+
+///////////////////////////////////////////////////////////////////////////////
+// //
+// //
+// Kmeans //
+///////////////////////////////////////////////////////////////////////////////
+
+
+
+void km_output_data ( double **data, int n, int dim, int len, char *infile, char *outfile);
+int km_kmeans(double **data, int n, int m, int k, double t, double **centroids);
+float km_make_kmeans(double **d, int n, int dim, int k,double t, double **centroids, int nrounds);
+double ** km_read_data ( char *file, int n, int dim, int len, char **field_list);
+int km_file2dim ( char *file, int *n,int *dim, int *len);
+double** km_shuffle_data (double **d, double **sd, int n, int r);
+void km_display_data (double **d, int n, int dim);
+double km_data2evaluate ( double **d, int n, int dim);
+double km_kmeans_bs (double **data, int n, int dim, int k,double t, double **centroids, int nrounds);
git://source.jalview.org / jabaws.git / blobdiff