Renamed "Obi_byte_arrays" to "Obiblobs" and moved Obiblob functions to

separate obiblob.c and obiblob.h files

src/obiblob.c

@@ -0,0 +1,130 @@
+/****************************************************************************
+ * Obiblob functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obiblob.c
+ * @author Celine Mercier
+ * @date April 11th 2016
+ * @brief Functions handling Obiblob structures.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "obierrno.h"
+#include "obitypes.h"	// For byte_t type
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO: endianness problem?
+
+
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value)
+{
+	Obi_blob_p blob;
+
+	// Allocate the memory for the blob structure
+	blob = (Obi_blob_p) malloc(sizeof(Obi_blob_t) + length_encoded_value);
+	if (blob == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a blob");
+		return NULL;
+	}
+
+	// Store the number of bits on which each element is encoded
+	blob->element_size = element_size;
+
+	// Store the length (in bytes) of the encoded value
+	blob->length_encoded_value = length_encoded_value;
+
+	// Store the initial length (in bytes) of the decoded value
+	blob->length_decoded_value = length_decoded_value;
+
+	// Store the encoded value
+	memcpy(blob->value, encoded_value, length_encoded_value);
+
+	return blob;
+}
+
+
+Obi_blob_p obi_str_to_blob(char* value)
+{
+	Obi_blob_p 		 value_b;
+	int32_t 		 length;
+
+	// Compute the number of bytes on which the value will be encoded
+	length = strlen(value) + 1;		// +1 to store \0 at the end (makes retrieving faster)
+
+	value_b = obi_blob(value, ELEMENT_SIZE_STR, length, length);
+	if (value_b == NULL)
+	{
+		obidebug(1, "\nError encoding a character string in a blob");
+		return NULL;
+	}
+
+	return value_b;
+}
+
+
+const char* obi_blob_to_str(Obi_blob_p value_b)
+{
+	return value_b->value;
+}
+
+
+Obi_blob_p obi_seq_to_blob(char* seq)
+{
+	Obi_blob_p 		 value_b;
+	int32_t          length_encoded_seq;	// length of the encoded sequence in bytes
+	int32_t          seq_length;
+	byte_t*          encoded_seq;
+
+	seq_length = strlen(seq);
+
+	// Check if just ATGC and encode accordingly
+	if (only_ATGC(seq))
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 4.0);
+		// Encode
+		encoded_seq = encode_seq_on_2_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_2, length_encoded_seq, seq_length);
+	}
+	else
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 2.0);
+		// Encode
+		encoded_seq = encode_seq_on_4_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
+	}
+
+	free(encoded_seq);
+
+	return value_b;
+}
+
+
+const char* obi_blob_to_seq(Obi_blob_p value_b)
+{
+	// Decode
+	if (value_b->element_size == 2)
+		return decode_seq_on_2_bits(value_b->value, value_b->length_decoded_value);
+	else
+		return decode_seq_on_4_bits(value_b->value, value_b->length_decoded_value);
+}
+
+
+// TODO same for int
+