binaries/src/tcoffee/t_coffee_source/fastal_lib_header.h

   1
   2
   3 #define ENLARGEMENT_PER_STEP 50
   4 #define PROFILE_ENLARGEMENT 550
   5
   6 // static char pos2aa[] = {'A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'};
   7
   8
   9 /**
  10  * \brief Struct to save all informations of a profile.
  11  *
  12  */
  13 typedef struct
  14 {
  15         /// Number of sequences in this profile
  16         int num_sequences;
  17         /// number of the profile
  18         int prf_number;
  19         ///0 = combination of two profiles, 1 = profile of a single sequence -> name1 = seq_name
  20         int is_leaf;
  21         ///length of the profile
  22         int length;
  23         ///weight of the sequence
  24         int weight;
  25         ///saves the amount of allocated memory
  26         int allocated_memory;
  27         ///the profile itself [alphabet_size][profile_length]
  28         int **prf;
  29 }
  30 Fastal_profile;
  31
  32 /**
  33  * \brief Struct to save all parameters for fastal.
  34  *
  35  */
  36 typedef struct
  37 {
  38         /// size of alphabet_size
  39         int alphabet_size;
  40         /// converting char2position (for profile)
  41         int char2pos[26];
  42         /// converting pos2char (for profile)
  43         char pos2char[26];
  44         /// gap opening costs
  45         int gop;
  46         /// gap extension costs
  47         int gep;
  48         /// nomatch???
  49         int nomatch;
  50         ///method to align profile
  51         char method[20];
  52         ///scoring Matrix;
  53         int **M;
  54 }
  55 Fastal_param;
  56
  57
  58
  59 //tree
  60 void generate_random_tree(int number);
  61
  62
  63 Fastal_profile* make_profile_of_sequence(char *seq_name, char *sequence, int number);
  64
  65
  66
  67 //Definite use
  68
  69 //*********************    input/output    **********************************
  70 void file2profile(FILE* profile_f, Fastal_profile *profile, int prf_number, Fastal_param *param_set);
  71 void file_pos2profile(FILE *seq_file, long off_set, Fastal_profile *profile, int prf_number, Fastal_param *param_set);
  72 void profile2file(Fastal_profile *profile, FILE* prf_f, Fastal_param *param_set);
  73
  74 //index
  75 int make_index_of_file(char *file_name, long **result);
  76
  77
  78 //*********************    pairwise alignment methods     ************************
  79
  80         //Needleman-Wunsch
  81         int prf_nw(Fastal_profile *profile1, Fastal_profile *profile2, double **prog_matrix, FILE *edit_file_name, int **sumup_prf, int *sumup_length, Fastal_param *param_set);
  82         int nw_matrix2edit_file(double **prog_matrix, Fastal_profile *profile1, Fastal_profile *profile2, FILE *edit_f, int **prf_field, int *field_length, Fastal_param *param_set);
  83         int** sumup_profile(Fastal_profile *profile, int **sumup_prf, Fastal_param *param_set);
  84         void write2file(int **sumup_prf, int length, FILE *file, int number, Fastal_param *param_set);
  85
  86
  87         //Sparse dynamic programming
  88         int seq_pair2blast_diagonal(char *seq_file_name1, char *seq_file_name2, int **diagonals, int *dig_length, int l1, int l2, int is_dna);
  89
  90
  91
  92
  93
  94
  95
  96
  97 //edit_files 2 alignment
  98         void edit2alignment(FILE *sequence_file, long *seq_positions, FILE *edit_file, long *edit_positions, int node_number, int number_of_sequences, char *aligned_sequence, int alignment_length, FILE *edit_seq_file, int offset, FILE* alignment_file);
  99 void edit_seq2aligned_seq(char *aligned_sequence, FILE *sequence_file, long sequence_position, FILE *alignment_file);
 100
 101
 102 //main
 103 int fastal(int argc, char **argv);
 104
 105 //toolbox
 106 void initiate_profile_files(FILE **profile_files);
 107 void initiate_profiles(Fastal_profile **profiles, Fastal_param *param_set);
 108 void free_fastal_profile(Fastal_profile *profile, int alphabet_size);
 109 double **resize_dyn_matrix(double **dyn_matrix, int *old_length1, int *old_length2, int length1, int length2);
 110 void free_dyn_matrix(int length1, double **dyn_matrix);
 111 void fill_parameters(int is_dna, Fastal_param *param_set, char *method);
 112
 113 struct fastal_arguments
 114 {
 115 //      char *args[2];
 116         char *method;
 117         char *sequence_file;
 118         char *tree_file;
 119         char *output_file;
 120         int is_dna;
 121         int gop;
 122         int gep;
 123 };
 124
 125 // static char fastal_doc[] = "Fastal -- a program to align sequences with little memory";
 126 // // static char args_doc[] = "ARG1 ARG2";
 127 // static void* fastal_options[]=
 128 // {
 129 //      {"in",          'i', "FILE", 0, "Sequence file (FASTA format)" },
 130 //      {"output",  'o', "FILE", 0, "Output to FILE" },
 131 //      {"tree",        't', "FILE", 0, "Tree file" },
 132 //      {"method",      'm', "METHOD", 0, "Methods:\n   fast (sparse dynamic),\n   nw (Needleman-Wunsch) "},
 133 //      {"is_dna",      'd', 0, 0, "Sequences are DNA"},
 134 //      {"is_aa",       'a', 0, 0, "Sequences are AminoAcids"},
 135 //      {"gop",         'g', "VALUE", 0, "Gap opening costs"},
 136 //      {"gep",         'e', "VALUE", 0, "Gap extension costs"},
 137 //      { 0 }
 138 // };
 139
 140
 141
 142
 143
 144 /*
 145 void
 146 fastal_parse_opt (int key, char *arg)
 147 {
 148 //      struct fastal_arguments *arguments = state->input;
 149
 150         switch (key)
 151         {
 152                 case 'o':
 153                         arguments->output_file = arg;
 154                         break;
 155                 case 't':
 156                         arguments->tree_file = arg;
 157                         break;
 158                 case 'i':
 159                         arguments->sequence_file = arg;
 160                         break;
 161                 case 'm':
 162                         arguments->method = arg;
 163                         break;
 164                 case 'g':
 165                         arguments->gop = atoi(arg);
 166                         break;
 167                 case 'e':
 168                         arguments->gep = atoi(arg);
 169                         break;
 170                 case 'd':
 171                         arguments->is_dna = 1;
 172                         break;
 173                 case 'a':
 174                         arguments->is_dna = 0;
 175                         break;
 176                 default:
 177                         printf("UNKNOWN OPTION key");
 178                         exit(1);
 179         }
 180         return 0;
 181 }*/
 182 //
 183 //
 184 // static struct argp argp = { fastal_options, fastal_parse_opt,/* fastal_args_doc,*/ fastal_doc};
 185 /*********************************COPYRIGHT NOTICE**********************************/
 186 /*© Centro de Regulacio Genomica */
 187 /*and */
 188 /*Cedric Notredame */
 189 /*Tue Oct 27 10:12:26 WEST 2009. */
 190 /*All rights reserved.*/
 191 /*This file is part of T-COFFEE.*/
 192 /**/
 193 /*    T-COFFEE is free software; you can redistribute it and/or modify*/
 194 /*    it under the terms of the GNU General Public License as published by*/
 195 /*    the Free Software Foundation; either version 2 of the License, or*/
 196 /*    (at your option) any later version.*/
 197 /**/
 198 /*    T-COFFEE is distributed in the hope that it will be useful,*/
 199 /*    but WITHOUT ANY WARRANTY; without even the implied warranty of*/
 200 /*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the*/
 201 /*    GNU General Public License for more details.*/
 202 /**/
 203 /*    You should have received a copy of the GNU General Public License*/
 204 /*    along with Foobar; if not, write to the Free Software*/
 205 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA*/
 206 /*...............................................                                                                                      |*/
 207 /*  If you need some more information*/
 208 /*  cedric.notredame@europe.com*/
 209 /*...............................................                                                                                                                                     |*/
 210 /**/
 211 /**/
 212 /*      */
 213 /*********************************COPYRIGHT NOTICE**********************************/