obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

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

Browse Source 
separate obiblob.c and obiblob.h files
This commit is contained in:
Celine Mercier
2016-04-12 11:21:14 +02:00
parent c225cfd8b6
commit 375bfcce8a
8 changed files with 304 additions and 249 deletions
Download Patch File Download Diff File Expand all files Collapse all files

105
src/encode.c
View File

@ -349,111 +349,6 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
}
Obi_byte_array_p obi_byte_array(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value)
{
Obi_byte_array_p byte_array;
// Allocate the memory for the byte array structure
byte_array = (Obi_byte_array_p) malloc(sizeof(Obi_byte_array_t) + length_encoded_value);
if (byte_array == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR); // TODO
obidebug(1, "\nError allocating memory for a byte array");
return NULL;
}
// Store the number of bits on which each element is encoded
byte_array->element_size = element_size;
// Store the length (in bytes) of the encoded value
byte_array->length_encoded_value = length_encoded_value;
// Store the initial length (in bytes) of the decoded value
byte_array->length_decoded_value = length_decoded_value;
// Store the encoded value
memcpy(byte_array->value, encoded_value, length_encoded_value);
return byte_array;
}
Obi_byte_array_p obi_str_to_obibytes(char* value)
{
Obi_byte_array_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_byte_array(value, ELEMENT_SIZE_STR, length, length);
if (value_b == NULL)
{
obidebug(1, "\nError encoding a character string in a byte array");
return NULL;
}
return value_b;
}
const char* obi_obibytes_to_str(Obi_byte_array_p value_b)
{
fprintf(stderr, "\n%s", value_b->value);
return value_b->value;
}
Obi_byte_array_p obi_seq_to_obibytes(char* seq)
{
Obi_byte_array_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_byte_array(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_byte_array(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
}
free(encoded_seq);
return value_b;
}
const char* obi_obibytes_to_seq(Obi_byte_array_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
///////////////////// FOR DEBUGGING ///////////////////////////
//NOTE: The first byte is printed the first (at the left-most).