+++ /dev/null
-/*!
- * Node of a Tree
- */
-typedef struct
-{
- ///number of this node
- int name;
- ///left child
- int left;
- ///right child
- int right;
-// ///weight of the node
-// double weight;
- ///position of the leafs during construction
- int *index;
- ///position of...
- int *index2;
- ///number of leafes below this node
- int num_leafs;
-}
-Tree_fastal;
-
-
-
-/*!
- * Saves all important paramters for the PartTree algorithm
- *
- */
-typedef struct
-{
- ///Size of the ktup
- short ktup;
- ///power
- short ng;
- ///number of possible ktup
- int tsize;
- ///subgroup size
- int subgroup;
- ///File with the ktup tables
- FILE *ktup_table_f;
- ///Index of the positions in the ktup file
- long *ktup_positions;
- ///number of sequences
- int num_sequences;
- ///length of the sequences
- int *seq_lengths;
- ///threshold for filter
- double threshold;
- /*! \brief An Integer array to save the tree
- *
- * Always three fields in this array belong together. The first two denote the number of the children the third one the number of the current node.
- */
- Tree_fastal *tree;
- /// Current position in the tree
- int pos_tree;
-}
-PartTree_param;
-
-
-
-//******************************* METHODS ***********************************
-
-
-//*********** ktup-distance ***************
-void makepointtable_fast(int *coded_seq, int ktup, int ng, int length);
-void makecompositiontable_fastal(FILE* tables_f, int *table, int *pointt, int length);
-void get_table(short *table, FILE *tables, long index);
-
-
-
-void make_fast_tree(char *file_name, int n, int ktup);
-int make_pos_len_index_of_file(char *file_name, char *ktable_f, long **file_positions, int **seq_lengths, int ktup, int is_dna);
-int make_pos_len_index_of_file_retree(char *file_name, long **file_positions, int **seq_lengths);
-// void ktup_one2all(FILE *seq_f, int* file_positions, int *least_similar);
-
-
-int **make_distance_matrix(FILE *table_f, long *file_positions, int *sequence_group, int number, int **dist_mat);
-int euclidean_dist(FILE* ktup_f, long pos1, long pos2, short *table1, short *table2, int length);
-int euclidean_dist_half(FILE* ktup_f, long pos2, short *table1, short *table2, int length);
-
-void partTree_r(PartTree_param *param_set);
-void partTree_retree(PartTree_param *param_set);
-void make_partTree(char *sequence_f, char *tree_f, int ktup, int subgroup, int is_dna, int retree);
-
-int filter(int *sequence_group, int **dist_mat, int *seed_set_cleaned, PartTree_param *param_set);
-int fast_aln2sim_mat2 (char *seq1, char *seq2);
-
-
-
-
-
-
-
-/**
- * \brief Struct to save the features for a set of sequences.
- *
- */
-typedef struct
-{
- /// The number of this sequence.
- int seq_number;
- /// The feature to use in qsort.
- int *elem_2_compare;
- /// An element of features.
- double *features;
-}
-Cluster_info;
-
-
-int cluster_recursive(int start, int end, Cluster_info* matrix, int dim, double *mean, double *variance, int *elem_2_compare, FILE* tree_f, int *node);
-int* recode_sequence(char * seq, int seq_length, int *char2value, int alphabet_size, int word_length);
-double* get_features(int *recoded_seq, int seq_length, int k_tup, int max_coding, int max_dist, int num_features);
-Cluster_info* feature_extract(char *seq_file_name, int max_dist, int k_tup, int *char2value, int alphabet_size, int *elem_2_compare, int *num_seq_p, int num_features);
-void compute_oligomer_distance_tree(char *seq_file_name, int* char2value, char *tree_file_name, int max_dist, int word_length, int alphabet_size);
-
-/******************************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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