DNA_seq_indexer API

python/obitools3/obidms/_obidms.cfiles

@@ -2,6 +2,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -4,6 +4,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obiseq.cfiles

@@ -2,6 +2,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

python/obitools3/obidms/_obitaxo.cfiles

@@ -2,6 +2,8 @@
 ../../../src/bloom.c
 ../../../src/crc64.h
 ../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
 ../../../src/encode.h
 ../../../src/encode.c
 ../../../src/MurmurHash2.h

src/dna_seq_indexer.c

+/****************************************************************************
+ * DNA sequence indexing functions                                          *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidms.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_seq_to_blob(const 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;
+}
+
+
+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);
+}
+
+
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_seq_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+	char*		seq;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Decode sequence
+	seq = obi_blob_to_seq(value_b);
+
+	free(value_b);
+
+	return seq;
+}
+

src/dna_seq_indexer.h

+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef DNA_SEQ_INDEXER_H_
+#define DNA_SEQ_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a DNA sequence to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_seq_to_blob(const char* seq);
+
+
+/**
+ * @brief Converts a blob to a DNA sequence.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the blob.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_blob_to_seq(Obi_blob_p value_b);
+
+
+// TODO doc
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value);
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* DNA_SEQ_INDEXER_H_ */
+

src/encode.c

@@ -54,7 +54,7 @@ bool only_ATGC(const char* seq)
 }
 
 
-byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 {
 	byte_t*  seq_b;
 	uint8_t  modulo;
@@ -163,7 +163,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
 }
 
 
-byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 {
 	byte_t*  seq_b;
 	uint8_t  modulo;

src/encode.h

@@ -96,7 +96,7 @@ bool only_ATGC(const char* seq);
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
 
 
 /**
@@ -147,7 +147,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-byte_t* encode_seq_on_4_bits(char* seq, int32_t length);
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
 
 
 /**

src/obiblob.c

@@ -82,52 +82,5 @@ const char* obi_blob_to_str(Obi_blob_p value_b)
 }
 
 
-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
 

src/obiblob.h

@@ -45,6 +45,11 @@ typedef struct Obi_blob {
 } Obi_blob_t, *Obi_blob_p;
 
 
+
+// TODO doc
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value);
+
+
 /**
  * @brief Converts a character string to a blob.
  *
@@ -74,35 +79,5 @@ Obi_blob_p obi_str_to_blob(char* value);
 const char* obi_blob_to_str(Obi_blob_p value_b);
 
 
-/**
- * @brief Converts a DNA sequence to a blob with a header.
- *
- * @warning The blob must be freed by the caller.
- *
- * @param value The DNA sequence to convert.
- *
- * @returns A pointer to the blob created.
- * @retval NULL if an error occurred.
- *
- * @since November 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-Obi_blob_p obi_seq_to_blob(char* seq);
-
-
-/**
- * @brief Converts a blob to a DNA sequence.
- *
- * @param value_b The blob to convert.
- *
- * @returns A pointer to the DNA sequence contained in the blob.
- * @retval NULL if an error occurred.
- *
- * @since November 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_blob_to_seq(Obi_blob_p value_b);		// TODO move to encode source files
-
-
 #endif /* OBIBLOB_H_ */
 

src/obidmscolumn_seq.c

@@ -18,7 +18,7 @@
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiblob_indexer.h"
+#include "dna_seq_indexer.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -33,7 +33,6 @@
 
 int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
 {
-	Obi_blob_p value_b;
 	index_t    idx;
 
 	// Check that the line number is not greater than the maximum allowed
@@ -56,21 +55,13 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
 
-	// Encode the value on a byte array with a header	// TODO make function
-	value_b = obi_seq_to_blob(value);
-	if (value_b == NULL)
-		return -1;
-
-	// Add in the indexer
-	idx = obi_indexer_add(column->indexer, value_b);
+	idx = obi_index_dna_seq(column->indexer, value);
 	if (idx == -1)
 		return -1;
 
 	// Add the value's index in the column
 	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
 
-	free(value_b);
-
 	return 0;
 }
 
@@ -114,8 +105,7 @@ int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
 
 const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
-	index_t          idx;
-	Obi_blob_p       value_b;
+	index_t idx;
 
 	if ((line_nb+1) > ((column->header)->line_count))
 	{
@@ -130,9 +120,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBISeq_NA;
 
-	value_b = obi_indexer_get(column->indexer, idx);
-
-	return obi_blob_to_seq(value_b);
+	return obi_retrieve_dna_seq(column->indexer, idx);
 }