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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/km_coffee/km_coffee.h b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_coffee.h
new file mode 100644 (file)
index 0000000..779cc80
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/km_coffee/km_coffee.h
@@ -0,0 +1,87 @@
+/******************************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*******************************/
+
+#include <stdlib.h>
+#include <time.h>
+
+#include "classes.h"
+#include "kmeans.h"
+#include "Vector.h"
+
+#include "Stack.h"
+
+#ifdef _OPENMP
+       #include<omp.h>
+#endif
+
+
+static char *km_tmp_dir = NULL;
+static char *km_cwd =NULL;
+
+
+typedef struct
+{
+       KM_node *node;
+       size_t id;
+}Node_pair;
+
+
+/**
+ * \brief Prints the generated tree to a given file
+
+ * The tree only contains the vector numbers so the vector set is needed to get the sequence names. The sequence set is needed to get the actual sequences.
+ * \param root The root note of the tree to print.
+ * \param vecs The vector set.
+ * \param seq_set The sequence set.
+ * \param out_f The file to write the file into.
+ *
+ */
+
+void
+print_km_tree(KM_node *root, int *vecs, const SeqSet *seq_set, char *out_f);
+
+
+/**
+ * \brief This function contains the code to produce a KM-Coffee alignment.
+ * \param seq_f The sequence file.
+ * \param k The maximum size of the profile clusters.
+ * \param k_leaf the maximum size of the leaf clusters.
+ * \param method The method to use for the alignment procedure.
+ * \param aln_f The output alignment file.
+ * \param n_core The number of cores to use (OPEN-MP for kmeans/fork in T-Coffee)
+ * \param gapopen The gapopening costs
+ * \param gapext The gapextension costs
+ * \param init The method to use to initialize the k-means prototypes.
+ * \return EXIT_SUCCESS on success else EXIT_FAILURE
+ */
+int
+km_coffee_align3(char *seq_f, int k, int k_leaf, char *method, char *aln_f, int n_cores, int gapopen, int gapext, char *init);
+
+
+
+
+