First version of alignment functions (imported from suma* programs)

src/obi_align.h

@@ -0,0 +1,37 @@
+/****************************************************************************
+ * Sequence alignment functions header file	                                *
+ ****************************************************************************/
+
+/**
+ * @file obi_align.h
+ * @author Celine Mercier
+ * @date May 11th 2016
+ * @brief Header file for the functions handling the alignment of DNA sequences.
+ */
+
+
+#ifndef OBI_ALIGN_H_
+#define OBI_ALIGN_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+#include "obidmscolumn.h"
+#include "obitypes.h"
+
+
+
+/**
+ * @brief
+ *
+ * TODO
+ *
+ */
+int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode);
+
+
+#endif /* OBI_ALIGN_H_ */
+