--- /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 a diagonal
+ *
+ */
+typedef struct
+{
+ ///Start of diagonal in seq1.
+ int x;
+ ///Start of diagonal in seq2.
+ int y;
+ ///Length of the diagonal.
+ int length;
+ ///expansion at the beginning;
+ int front_exp;
+ ///expansion at the end;
+ int end_exp;
+}
+Diagonal;
+
+
+
+
+/**
+ * \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;
+ ///number_of_sequences
+ int number_of_sequences;
+}
+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[256];
+ /// converting pos2char (for profile)
+ char pos2char[256];
+ /// gap opening costs
+ double gop;
+ /// gap extension costs
+ double gep;
+ /// nomatch???
+ int nomatch;
+ ///method to align profile
+ char method[20];
+ ///scoring Matrix;
+ int **M;
+ ///saves the diag method -> move to sparse!
+ char diag_method[30];
+}
+Fastal_param;
+
+/**
+ * \brief Struct to save the parameters and memory for the sparse dynamic programming algorithm.
+ */
+typedef struct
+{
+ /// saves the diagonals
+ int *diagonals;
+ /// saves ....
+ int *dig_length;
+ /// list of points to be considered during the alignment process
+ int **list;
+ /// number of points in \a list
+ int *list_length;
+ char *file_name1;
+ char *file_name2;
+ // static char *file_name1 = vtmpnam(NULL);
+// static char *file_name2 = vtmpnam(NULL);
+}
+Sparse_dynamic_param;
+
+
+typedef struct
+{
+ int window_length;
+ int step_legnth;
+ int threshold;
+ int oligo_length;
+ int distance;
+}
+Udisc_param;
+
+
+/**
+ * \brief Struct to save the parameters and memory for the needleman-wunsch algorithm.
+ */
+typedef struct
+{
+ /// dynamic programming matrix
+ double ** dyn_matrix;
+ /// length of dimension 1
+ int *length1;
+ /// length of dimension 2
+ int *length2;
+ /// summed up version of profile
+ int **sumup_prf;
+ /// number of entries in \a sumup_prf
+ int *sumup_length;
+}
+Nw_param;
+
+
+
+/**
+ * \brief Struct to save the parameters and memory for the Gotoh algorithm.
+ */
+typedef struct
+{
+ /// dynamic programming matrix
+ double ** m_matrix;
+ /// dynamic programming matrix
+ double ** i_matrix;
+ /// dynamic programming matrix
+ double ** d_matrix;
+ /// length of dimension 1
+ int *length1;
+ /// length of dimension 2
+ int *length2;
+ /// summed up version of profile
+ int **sumup_prf;
+ /// number of entries in \a sumup_prf
+ int *sumup_length;
+ /// log saver
+ double **log_saver;
+}
+Gotoh_param;
+
+
+
+
+typedef struct
+{
+ int diagonal;
+ int count;
+ int start;
+ int end;
+}
+Swift_diagonal;
+
+
+typedef struct
+{
+ int diagonal;
+ int count;
+}
+Diagonal_counter;
+
+//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, int num_sequences, Fastal_param *param_set);
+
+ //Gotoh
+ void free_gotoh(Gotoh_param* method_arguments_p, int alphabet_size);
+ void fill_arguments_gotoh(Gotoh_param* method_arguments_p, int alphabet_size);
+ int prf_gotoh(Fastal_profile *profile1, Fastal_profile *profile2, FILE *edit_file_name, Gotoh_param *arguments, Fastal_param *param_set);
+
+ //Sparse dynamic programming
+ void free_sparse(Sparse_dynamic_param* method_arguments_p);
+ void fill_arguments_sparse(Sparse_dynamic_param* method_arguments_p);
+ int **diagonals2int(int *diagonals, int num_diagonals, char *seq1, char *seq2, int *num_points, Fastal_param *param_set);
+ int seq_pair2blast_diagonal(char *seq_file_name1, char *seq_file_name2, int **diagonals, int *dig_length, int l1, int l2, int is_dna);
+ int sparse_dyn(Fastal_profile **profiles, Fastal_param *param_set, void *method_arguments_p, int is_dna, FILE *edit_file, FILE *prof_file, int number);
+ char *profile2consensus(Fastal_profile *profile, Fastal_param *param_set);
+ int ** diagonals2int_gap_test(int *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);
+ int ** diagonals2int_euclidf(int *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);
+ int ** diagonals2int_dot(int *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);
+ int seq_pair2blastz_diagonal(char *seq_file_name1, char *seq_file_name2, int **diagonals, int *dig_length, int l1, int l2, int is_dna);
+ int list2linked_pair_wise_fastal(Fastal_profile *prf1, Fastal_profile *prf2, Fastal_param *param_set, int **list, int n, FILE *edit_f, FILE *prof_f, int node_number);
+
+//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);
+void alignment2files(Fastal_profile **profiles, Fastal_param *param_set,int **alignment, int alignment_length, FILE *edit_f, FILE *prof_f, int node_number);
+
+//toolbox
+double calculate_sum_of_pairs_score_affine(char *alignment_file_name, int **score_matrix, double gop, double gep);
+double calculate_sum_of_pairs_score_affine_test(char *alignment_file_name, int **score_matrix, double gop, double gep);
+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, char *diag_method, char *mat);
+
+
+int seq_pair2diagonal_own(char *seq1, char *seq2, int **diagonals, int *dig_length, int l1, int l2, int is_dna, int word_length);
+
+
+
+
+
+
+
+typedef struct
+{
+ ///field saving the positions [x1,y1,l1,x2,y2,l2,...]
+ int *segments;
+ /// points to the current used segment
+ int *current_pos;
+ /// saves the previous diagonal position.
+ int prev_position;
+ /// diagonal number
+// int diagonal_num;
+}
+Segment;
+
+
+Segment* extend_diagonals(Diagonal *diagonals, int *num_diagonals, int l1, int l2);
+int seq_pair2blast_diagonal2(char *seq_file_name1, char *seq_file_name2, Diagonal **diagonals, int *dig_length, int l1, int l2, int is_dna);
+
+int ** segments2int(Segment *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);
+// #include "string.h"
+
+struct Fastal_arguments
+{
+// char *args[2];
+ //IO
+
+
+ char *sequence_file;
+ char *tree_file;
+ char *output_file;
+ int tree_out;
+
+ char *method;
+ int is_dna;
+ double gop;
+ double gep;
+
+
+
+ char *diag_method;
+// Tree Computation
+// int retree;
+ int gap_iterate;
+ int tree_only;
+ char *tree_method;
+ int tree_param1;
+ int tree_param2;
+
+
+ //Scoring
+ char *mat;
+ int agreement_score;
+ int evaluate;
+ int score;
+ int num_ref_aln;
+ int num_seq_in_ref;
+ char *aln_ref;
+ char *aln2test;
+};
+
+
+
+
+void tree_parse(struct Fastal_arguments *arguments, char* param);
+
+
+
+void arg_parse (int argc, char **argv, struct Fastal_arguments *arguments);
+
+
+
+//sum of pairs score
+double calculate_sum_of_pairs_score_affine(char *alignment_file_name, int **score_matrix, double gop, double gep);
+
+
+//compare with reference alignment
+void make_ref_alignment(char *seq_file_name, char *tree_file_name, char *ref_aln_name, int num_seq_in_ref);
+double agreement_score(char *ref_file_name, char *aln_file_name);
+
+
+void seq2profile2(char *seq, Fastal_profile *prf, int *char2pos);
+void split_set(FILE *aln_file_name, Fastal_profile *gap_prf, Fastal_profile *no_gap_prf, char *seq, int index, int *char2pos, char* split_file_name);
+void iterate(Fastal_param *param, void *method_arguments_p, char *aln_file_name, char *out_file_name, int iteration_number);
+
+void edit2seq_pattern(FILE *edit_file, char *seq1, char *seq2);
+int *del_gap_from_profile(Fastal_profile *prf, int alphabet_size, int *gap_list, int *gap_list_length, int *num_gaps);
+
+void write_iterated_aln(char* old_aln_file_name, char* new_aln_file_name, char *gap_file_name, char *seq1, int *gap_list1, int num_gap1, char *seq2, int *gap_list2, int num_gap2);
+/******************************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*******************************/
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