Branch to refactor and debug (AVLs bugged)

src/encode.h

@@ -10,6 +10,10 @@
  */
 
 
+#ifndef ENCODE_H_
+#define ENCODE_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <stdint.h>
@@ -18,8 +22,31 @@
 #include "obitypes.h"
 
 
-#define NUC_MASK_2B 0x3   /**< Binary: 11 to use when decoding 2 bits sequences */
-#define NUC_MASK_4B 0xF  /**< Binary: 1111 to use when decoding 4 bits sequences */
+#define NUC_MASK_2B 0x3   									/**< Binary: 11 to use when decoding 2 bits sequences
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define NUC_MASK_4B 0xF  									/**< Binary: 1111 to use when decoding 4 bits sequences
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define ELEMENT_SIZE_STR (8)								/**< The size of an element from a value of type character string.
+                              	  	 	 	 	 	 	 	 */
+#define ELEMENT_SIZE_SEQ_2 (2)								/**< The size of an element from a value of type DNA sequence encoded on 2 bits.
+                              	  	 	 	 	 	 	 	 */
+#define ELEMENT_SIZE_SEQ_4 (4)								/**< The size of an element from a value of type DNA sequence encoded on 4 bits.
+                              	  	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief Byte array structure.
+ */
+typedef struct Obi_byte_array {
+	uint8_t  element_size;		 	/**< Size in bits of one element from the value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_encoded_value;	/**< Length in bytes of the encoded value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_decoded_value;	/**< Length in bytes of the decoded value.
+	 	 	 	 	 	 	 	 	 */
+	byte_t   value[];				/**< Encoded value.
+	 	 	 	 	 	 	 	 	 */
+} Obi_byte_array_t, *Obi_byte_array_p;
 
 
 /**
@@ -174,8 +201,70 @@ byte_t* encode_seq_on_4_bits(char* seq, int32_t length);
 char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
 
 
+/**
+ * @brief Converts a character string to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_byte_array_p obi_str_to_obibytes(char* value);
+
+
+/**
+ * @brief Converts a byte array to a character string.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the character string contained in the byte array.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_str(Obi_byte_array_p value_b);
+
+
+/**
+ * @brief Converts a DNA sequence to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_byte_array_p obi_seq_to_obibytes(char* seq);
+
+
+/**
+ * @brief Converts a byte array to a DNA sequence.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the byte array.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_seq(Obi_byte_array_p value_b);		// TODO move to encode source files
+
+
 ////////// FOR DEBUGGING ///////////
 
 // little endian
 void print_bits(void* ptr, int32_t length);
 
+
+#endif /* ENCODE_H_ */
+