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

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

diff --git a/binaries/src/tcoffee/t_coffee_source/km_coffee/classes.h b/binaries/src/tcoffee/t_coffee_source/km_coffee/classes.h
new file mode 100644 (file)
index 0000000..8b24ea9
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/km_coffee/classes.h
@@ -0,0 +1,88 @@
+/******************************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 CLASSES_H_
+#define CLASSES_H_
+
+#include <string.h>
+#include <stdio.h>
+
+// #include "km_util.h"
+
+// Single Seq
+/**
+ * \brief A stuct to save a sequence
+ */
+typedef struct
+{
+       char *name; /// The sequence name
+       char *seq; /// The sequence
+       size_t size; /// The size occupied by the sequence
+       size_t reserved; /// The reserved size
+}Seq;
+
+
+/**
+ * \brief initalizes a Sequence
+ * \param name The name of the sequence
+ * \param reserve The amount of memory to reserve
+ */
+Seq*
+init_Seq(char *name, int reserve);
+
+/**
+ * \brief Appends a piece of sequence to a Sequence.
+ * \param seq The sequence
+ * \param sequence The piece to append.
+ */
+void
+append(Seq *seq, char *sequence);
+
+
+/// Set of sequences
+typedef struct
+{
+       Seq **seqs; /// Array of pointers to sequences
+       size_t  n_seqs; /// number of sequence in the set
+       size_t reserved; /// reserved memory for seqs
+} SeqSet;
+
+/**
+ * \brief reads a fasta sequence
+ * \param seq_f The sequence file
+ * \return pointer to the sequence set
+ */
+SeqSet*
+read_fasta(char *seq_f);
+
+/**
+ * \brief frees all memory used by this set
+ * \param set The sequence set.
+ */
+void
+delSeqSet(SeqSet *set);
+
+#endif