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

src/sse_banded_LCS_alignment.h

@@ -0,0 +1,23 @@
+/*
+ * sse_banded_LCS_alignment.h
+ *
+ *  Created on: november 29, 2012
+ *      Author: mercier
+ */
+
+#ifndef SSE_BANDED_LCS_ALIGNMENT_H_
+#define SSE_BANDED_LCS_ALIGNMENT_H_
+
+
+#include <stdint.h>
+#include <stdbool.h>
+
+#define ALILEN (0)	// TODO enum
+#define MAXLEN (1)
+#define MINLEN (2)
+
+// TODO doc
+int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool lcsmode);
+double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode);
+
+#endif