JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / km_coffee / Vector.h

diff --git a/binaries/src/tcoffee/t_coffee_source/km_coffee/Vector.h b/binaries/src/tcoffee/t_coffee_source/km_coffee/Vector.h
new file mode 100644 (file)
index 0000000..39402e7
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/km_coffee/Vector.h
@@ -0,0 +1,135 @@
+/******************************COPYRIGHT NOTICE*******************************/
+/*  (c) Centro de Regulacio Genomica                                                        */
+/*  and                                                                                     */
+/*  Cedric Notredame                                                                        */
+/*  12 Aug 2014 - 22:07.                                                                    */
+/*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*******************************/
+#ifndef VECTOR_H_
+#define VECTOR_H_
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <float.h>
+#include <limits.h>
+// #include "classes.h"
+// #include "km_util.h"
+
+
+typedef struct
+{
+       size_t x;
+       double y;
+} id_pair;
+
+typedef struct
+{
+       double *data;
+       size_t seq_len;
+       size_t id;
+       size_t assignment;
+       double val;
+} Vector;
+
+
+typedef struct
+{
+       Vector **vecs;
+       size_t n_vecs;
+       size_t used;
+       size_t dim;
+} VectorSet;
+
+
+/**
+ * \brief Turns a sequence into a vector
+ * \param seq The sequence to use
+ * \param k The kmer size
+ * \param factor The multiplication factor for the coding
+ * \param vec_len The length of the new vector
+ * \param vec_num The vector id to set
+ * \param alphabet The alphabet coding to use
+ * \param used shifting of the entries
+ * \return A pointer to to the vector encoding the given sequence
+ */
+Vector *
+seq2vec_kmer(const Seq *seq, short k, unsigned int *factor, size_t vec_len, size_t vec_num, short *alphabet, int *used);
+
+
+VectorSet*
+seqset2vecs_dist(SeqSet *seq_set, char *groups[], size_t n_groups);
+
+VectorSet*
+seqset2vecs_whatever(SeqSet *seq_set, char *groups[], size_t n_groups);
+
+/**
+ * \brief Turns as sequence set into a set of vectors
+ * \param seq_set The sequence set
+ * \param k The size of the kmers
+ * \param alphabet_size The size of the alphbet to use
+ * \param alphabet The encoding of the alphabet
+ * \return A pointer to the created vector set
+ */
+VectorSet*
+seqset2vecs_kmer(SeqSet *seq_set, short k, short alphabet_size, short *alphabet);
+
+/**
+ * \brief Calculates the squared distance between two vectors.
+ * \param vec1 The first vector.
+ * \param vec2 The second vector.
+ * \param dim The length of the two vectors.
+ */
+double
+km_sq_dist(const Vector *vec1, const Vector *vec2, size_t dim);
+
+/**
+ * \brief Calculated the angle between two vectors
+ * \param vec1 The first vector.
+ * \param vec2 The second vector.
+ * \param dim The length of the two vectors.
+ */
+double
+km_angle_dist(const Vector *vec1, const Vector *vec2, size_t dim);
+
+double
+km_muscle_dist(const Vector *vec1, const Vector *vec2, size_t dim, int k);
+
+void
+delVecSet(VectorSet *set);
+
+Vector *
+new_vec(Vector *vec, int vec_len);
+
+Vector *
+new_vec_nodata(Vector *vec, int vec_len);
+
+void
+print_vecs(VectorSet *set, char *out_f);
+
+void
+read_vecs(VectorSet *set, char *in_f);
+
+SeqSet *
+find_distant(SeqSet *seq_set, VectorSet *set);
+
+#endif