Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / tcoffee / t_coffee_source / fast_tree_header.h

diff --git a/website/archive/binaries/mac/src/tcoffee/t_coffee_source/fast_tree_header.h b/website/archive/binaries/mac/src/tcoffee/t_coffee_source/fast_tree_header.h
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/tcoffee/t_coffee_source/fast_tree_header.h
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+/*!
+ * 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*******************************/