Character string indexer API

python/obitools3/obidms/_obidms.cfiles

@@ -1,5 +1,7 @@
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -2,6 +2,8 @@
 ../../../src/obidmscolumn_bool.h
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -2,6 +2,8 @@
 ../../../src/obidmscolumn_char.h
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_float.c
 ../../../src/obidmscolumn_float.h
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/crc64.h

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,5 +1,7 @@
 ../../../src/obidmscolumn_int.c
 ../../../src/obidmscolumn_int.h
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/crc64.h

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -2,6 +2,8 @@
 ../../../src/obidmscolumn_seq.h
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -2,6 +2,8 @@
 ../../../src/obidmscolumn_str.h
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obiseq.cfiles

@@ -1,5 +1,7 @@
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

python/obitools3/obidms/_obitaxo.cfiles

@@ -1,5 +1,7 @@
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h

src/char_str_indexer.c

@@ -0,0 +1,80 @@
+/****************************************************************************
+ * Character string indexing functions                                      *
+ ****************************************************************************/
+
+/**
+ * @file char_str_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of character strings.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_str_to_blob(const 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((byte_t*)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;
+}
+
+
+char* obi_blob_to_str(Obi_blob_p value_b)
+{
+	return value_b->value;
+}
+
+
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_str_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_char_str(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded character string
+	return obi_blob_to_str(value_b);
+}
+

src/char_str_indexer.h

@@ -0,0 +1,61 @@
+/****************************************************************************
+ * 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 CHAR_STR_INDEXER_H_
+#define CHAR_STR_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a character string to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_str_to_blob(char* value);
+
+
+/**
+ * @brief Converts a blob to a character string.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the character string contained in the blob.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_blob_to_str(Obi_blob_p value_b);
+
+
+// TODO doc
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value);
+
+char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* CHAR_STR_INDEXER_H_ */
+

src/obiblob.c

@@ -16,7 +16,6 @@
 #include <math.h>
 
 #include "obiblob.h"
-#include "encode.h"
 #include "obierrno.h"
 #include "obitypes.h"	// For byte_t type
 #include "obidebug.h"
@@ -56,31 +55,3 @@ Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_
 	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;
-}
-
-
-// TODO same for int
-

src/obiblob.h

@@ -50,34 +50,5 @@ typedef struct Obi_blob {
 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.
- *
- * @warning The blob must be freed by the caller.
- *
- * @param value The character string to convert.
- *
- * @returns A pointer to the blob created.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-Obi_blob_p obi_str_to_blob(char* value);
-
-
-/**
- * @brief Converts a blob to a character string.
- *
- * @param value_b The blob to convert.
- *
- * @returns A pointer to the character string contained in the blob.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_blob_to_str(Obi_blob_p value_b);
-
-
 #endif /* OBIBLOB_H_ */
 

src/obidmscolumn_str.c

@@ -18,7 +18,7 @@
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiblob_indexer.h"
+#include "char_str_indexer.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -32,7 +32,6 @@
 
 int obi_column_set_obistr_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
@@ -55,21 +54,14 @@ int obi_column_set_obistr_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
-	value_b = obi_str_to_blob(value);
-	if (value_b == NULL)
-		return -1;
-
 	// Add in the indexer
-	idx = obi_indexer_add(column->indexer, value_b);
+	idx = obi_index_char_str(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;
 }
 
@@ -104,17 +96,13 @@ int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
 			return -1;
 	}
 
-	if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
+	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
-		return -1;
-
-	return 0;
 }
 
 
 const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	index_t          idx;
-	Obi_blob_p value_b;
 
 	if ((line_nb+1) > ((column->header)->line_count))
 	{
@@ -129,9 +117,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return OBIStr_NA;
 
-	value_b = obi_indexer_get(column->indexer, idx);
+	return obi_retrieve_char_str(column->indexer, idx);
-
-	return obi_blob_to_str(value_b);
 }
 
 
@@ -157,8 +143,7 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
-	obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
+	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
-	return 0;
 }
 
 
@@ -168,8 +153,7 @@ int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
 	element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
-	obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
+	return obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
-	return 0;
 }