+++ /dev/null
-
-
-#define ENLARGEMENT_PER_STEP 50
-#define PROFILE_ENLARGEMENT 550
-
-// static char pos2aa[] = {'A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'};
-
-
-/**
- * \brief Struct to save all informations of a profile.
- *
- */
-typedef struct
-{
- /// Number of sequences in this profile
- int num_sequences;
- /// number of the profile
- int prf_number;
- ///0 = combination of two profiles, 1 = profile of a single sequence -> name1 = seq_name
- int is_leaf;
- ///length of the profile
- int length;
- ///weight of the sequence
- int weight;
- ///saves the amount of allocated memory
- int allocated_memory;
- ///the profile itself [alphabet_size][profile_length]
- int **prf;
-}
-Fastal_profile;
-
-/**
- * \brief Struct to save all parameters for fastal.
- *
- */
-typedef struct
-{
- /// size of alphabet_size
- int alphabet_size;
- /// converting char2position (for profile)
- int char2pos[26];
- /// converting pos2char (for profile)
- char pos2char[26];
- /// gap opening costs
- int gop;
- /// gap extension costs
- int gep;
- /// nomatch???
- int nomatch;
- ///method to align profile
- char method[20];
- ///scoring Matrix;
- int **M;
-}
-Fastal_param;
-
-
-
-//tree
-void generate_random_tree(int number);
-
-
-Fastal_profile* make_profile_of_sequence(char *seq_name, char *sequence, int number);
-
-
-
-//Definite use
-
-//********************* input/output **********************************
-void file2profile(FILE* profile_f, Fastal_profile *profile, int prf_number, Fastal_param *param_set);
-void file_pos2profile(FILE *seq_file, long off_set, Fastal_profile *profile, int prf_number, Fastal_param *param_set);
-void profile2file(Fastal_profile *profile, FILE* prf_f, Fastal_param *param_set);
-
-//index
-int make_index_of_file(char *file_name, long **result);
-
-
-//********************* pairwise alignment methods ************************
-
- //Needleman-Wunsch
- 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);
- 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);
- int** sumup_profile(Fastal_profile *profile, int **sumup_prf, Fastal_param *param_set);
- void write2file(int **sumup_prf, int length, FILE *file, int number, Fastal_param *param_set);
-
-
- //Sparse dynamic programming
- int seq_pair2blast_diagonal(char *seq_file_name1, char *seq_file_name2, int **diagonals, int *dig_length, int l1, int l2, int is_dna);
-
-
-
-
-
-
-
-
-//edit_files 2 alignment
- 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);
-void edit_seq2aligned_seq(char *aligned_sequence, FILE *sequence_file, long sequence_position, FILE *alignment_file);
-
-
-//main
-int fastal(int argc, char **argv);
-
-//toolbox
-void initiate_profile_files(FILE **profile_files);
-void initiate_profiles(Fastal_profile **profiles, Fastal_param *param_set);
-void free_fastal_profile(Fastal_profile *profile, int alphabet_size);
-double **resize_dyn_matrix(double **dyn_matrix, int *old_length1, int *old_length2, int length1, int length2);
-void free_dyn_matrix(int length1, double **dyn_matrix);
-void fill_parameters(int is_dna, Fastal_param *param_set, char *method);
-
-struct fastal_arguments
-{
-// char *args[2];
- char *method;
- char *sequence_file;
- char *tree_file;
- char *output_file;
- int is_dna;
- int gop;
- int gep;
-};
-
-// static char fastal_doc[] = "Fastal -- a program to align sequences with little memory";
-// // static char args_doc[] = "ARG1 ARG2";
-// static void* fastal_options[]=
-// {
-// {"in", 'i', "FILE", 0, "Sequence file (FASTA format)" },
-// {"output", 'o', "FILE", 0, "Output to FILE" },
-// {"tree", 't', "FILE", 0, "Tree file" },
-// {"method", 'm', "METHOD", 0, "Methods:\n fast (sparse dynamic),\n nw (Needleman-Wunsch) "},
-// {"is_dna", 'd', 0, 0, "Sequences are DNA"},
-// {"is_aa", 'a', 0, 0, "Sequences are AminoAcids"},
-// {"gop", 'g', "VALUE", 0, "Gap opening costs"},
-// {"gep", 'e', "VALUE", 0, "Gap extension costs"},
-// { 0 }
-// };
-
-
-
-
-
-/*
-void
-fastal_parse_opt (int key, char *arg)
-{
-// struct fastal_arguments *arguments = state->input;
-
- switch (key)
- {
- case 'o':
- arguments->output_file = arg;
- break;
- case 't':
- arguments->tree_file = arg;
- break;
- case 'i':
- arguments->sequence_file = arg;
- break;
- case 'm':
- arguments->method = arg;
- break;
- case 'g':
- arguments->gop = atoi(arg);
- break;
- case 'e':
- arguments->gep = atoi(arg);
- break;
- case 'd':
- arguments->is_dna = 1;
- break;
- case 'a':
- arguments->is_dna = 0;
- break;
- default:
- printf("UNKNOWN OPTION key");
- exit(1);
- }
- return 0;
-}*/
-//
-//
-// static struct argp argp = { fastal_options, fastal_parse_opt,/* fastal_args_doc,*/ fastal_doc};
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/
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