Setting NA values is now handled properly for OBI_SEQ, OBI_STR and

OBI_QUAL columns

python/obitools3/obidms/_obidmscolumn_qual.pyx

@@ -58,26 +58,24 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
         cdef uint8_t* value_b
         cdef int      value_length
         if value is None :
-            value_b = OBIQual_int_NA
-            value_length = 0
+            if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
+                raise Exception("Problem setting a value in a column")
         else :
             value_length = len(value)
             value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
             for i in range(value_length) :
                 value_b[i] = <uint8_t>value[i]
-        if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
-            raise Exception("Problem setting a value in a column")
-        if value is not None :
+            if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
+                raise Exception("Problem setting a value in a column")
             free(value_b)
 
     cpdef set_str_line(self, index_t line_nb, object value):
-        cdef bytes value_b
         if value is None :
-            value_b = OBIQual_char_NA
+            if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
+                raise Exception("Problem setting a value in a column")
         else :
-            value_b = str2bytes(value)
-        if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
-            raise Exception("Problem setting a value in a column")
+            if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
+                raise Exception("Problem setting a value in a column")
 
 
 # TODO

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -31,13 +31,12 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        cdef bytes value_b
         if value is None :
-            value_b = OBISeq_NA
+            if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
+                raise Exception("Problem setting a value in a column")
         else :
-            value_b = str2bytes(value)
-        if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
-            raise Exception("Problem setting a value in a column")
+            if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
+                raise Exception("Problem setting a value in a column")
     
     # TODO choose alignment type (lcs or other) with supplementary argument
     cpdef align(self, 

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -26,13 +26,12 @@ cdef class OBIDMS_column_str(OBIDMS_column):
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        cdef bytes value_b
         if value is None :
-            value_b = OBIStr_NA
+            if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIStr_NA) < 0:
+                raise Exception("Problem setting a value in a column")
         else :
-            value_b = str2bytes(value)
-        if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
-            raise Exception("Problem setting a value in a column")
+            if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
+                raise Exception("Problem setting a value in a column")
 
 
 cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):

python/obitools3/obidms/_obiseq.pxd

@@ -4,35 +4,35 @@ from ._obidms cimport OBIView_line
 
 
 cdef class OBI_Seq(dict) :
-    cdef str id
-    cdef str definition
-    cdef str sequence
+    cdef object id
+    cdef object definition
+    cdef object sequence
 
-    cpdef set_id(self, str id)
-    cpdef get_id(self)
-    cpdef set_definition(self, str definition)
-    cpdef get_definition(self)
-    cpdef get_sequence(self)
+    cpdef set_id(self, object id)
+    cpdef object get_id(self)
+    cpdef set_definition(self, object definition)
+    cpdef object get_definition(self)
+    cpdef object get_sequence(self)
 
 
 cdef class OBI_Nuc_Seq(OBI_Seq) :
     cdef object quality
     
-    #cpdef str reverse_complement(self)    
-    cpdef set_sequence(self, str sequence)
+    #cpdef object reverse_complement(self)    
+    cpdef set_sequence(self, object sequence)
     cpdef set_quality(self, object quality)
-    cpdef get_quality(self)
+    cpdef object get_quality(self)
 
 
 cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
-    cpdef set_id(self, str id)
-    cpdef get_id(self)
-    cpdef set_definition(self, str definition)
-    cpdef get_definition(self)
-    cpdef set_sequence(self, str sequence)
-    cpdef get_sequence(self)
+    cpdef set_id(self, object id)
+    cpdef object get_id(self)
+    cpdef set_definition(self, object definition)
+    cpdef object get_definition(self)
+    cpdef set_sequence(self, object sequence)
+    cpdef object get_sequence(self)
     cpdef set_quality(self, object quality)
-    cpdef get_quality(self)
-    cpdef get_str_quality(self)
+    cpdef object get_quality(self)
+    cpdef object get_str_quality(self)
 
-   # cpdef str reverse_complement(self)
+   # cpdef object reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -9,20 +9,20 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
 
 cdef class OBI_Seq(dict) :
 
-    def __init__(self, str id, str seq, str definition=None) :
+    def __init__(self, object id, object seq, object definition=None) :
         self.set_id(id)
         self.set_sequence(seq)
         if definition is not None :
             self.set_definition(definition)
         
-    cpdef set_id(self, str id) :
+    cpdef set_id(self, object id) :
         self.id = id
         self[bytes2str(ID_COLUMN)] = id
         
     cpdef get_id(self) :
         return self.id
             
-    cpdef set_definition(self, str definition) :
+    cpdef set_definition(self, object definition) :
         self.definition = definition
         self[bytes2str(DEFINITION_COLUMN)] = definition
         
@@ -38,7 +38,7 @@ cdef class OBI_Seq(dict) :
 
 cdef class OBI_Nuc_Seq(OBI_Seq) :
     
-    cpdef set_sequence(self, str sequence) :
+    cpdef set_sequence(self, object sequence) :
         self.sequence = sequence
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
 
@@ -57,34 +57,34 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
 
     # TODO store the str version of column name macros
 
-    cpdef set_id(self, str id) :
+    cpdef set_id(self, object id) :
         self[bytes2str(ID_COLUMN)] = id
         
-    cpdef get_id(self) :
+    cpdef object get_id(self) :
         return self[bytes2str(ID_COLUMN)]
             
-    cpdef set_definition(self, str definition) :
+    cpdef set_definition(self, object definition) :
         self[bytes2str(DEFINITION_COLUMN)] = definition
 
-    cpdef get_definition(self) :
+    cpdef object get_definition(self) :
         return self[bytes2str(DEFINITION_COLUMN)]
 
-    cpdef set_sequence(self, str sequence) :
+    cpdef set_sequence(self, object sequence) :
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
 
-    cpdef get_sequence(self) :
+    cpdef object get_sequence(self) :
         return self[bytes2str(NUC_SEQUENCE_COLUMN)]
     
     cpdef set_quality(self, object quality) :
-        if type(quality) == list :
+        if (type(quality) == list) or (quality is None) :
             self[bytes2str(QUALITY_COLUMN)] = quality
         else :  # Quality is in str form
             (((self.view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self.index, quality)
 
-    cpdef get_quality(self) :
+    cpdef object get_quality(self) :
         return self[bytes2str(QUALITY_COLUMN)]
 
-    cpdef get_str_quality(self) :
+    cpdef object get_str_quality(self) :
         return ((self.view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self.index)
 
 #    def __str__(self) :

src/obidmscolumn_qual.c

@@ -33,18 +33,21 @@ int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t lin
 	int 	 i;
 	int		 ret_value;
 
-	// TODO NA
-
-	int_value_length = strlen(value);
-	int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
-
-	// Convert in uint8_t array to index in that format
-	for (i=0; i<int_value_length; i++)
-		int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
-
-	ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
-
-	free(int_value);
+	if (value == OBIQual_char_NA)
+	{
+		ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, OBIQual_int_NA, 0);
+	}
+	else
+	{
+		int_value_length = strlen(value);
+		int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
+
+		// Convert in uint8_t array to index in that format
+		for (i=0; i<int_value_length; i++)
+			int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
+		ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
+		free(int_value);
+	}
 
 	return ret_value;
 }
@@ -58,32 +61,38 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
 	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
-	// TODO NA
-
-	// Add the value in the indexer
-	idx = obi_index_uint8(column->indexer, value, value_length);
-	if (idx == -1)	// An error occurred
+	if (value == OBIQual_int_NA)
+	{
+		idx = OBIIdx_NA;
+	}
+	else
 	{
-		if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+		// Add the value in the indexer
+		idx = obi_index_uint8(column->indexer, value, value_length);
+		if (idx == -1)	// An error occurred
 		{
-			// TODO PUT IN A COLUMN FUNCTION
-			// If the error is that the indexer is read-only, clone it
-			new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
-			if (new_indexer_name == NULL)
-				return -1;
-			column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
-			strcpy((column->header)->indexer_name, new_indexer_name);
-			free(new_indexer_name);
-			obi_set_errno(0);
-
-			// Add the value in the new indexer
-			idx = obi_index_uint8(column->indexer, value, value_length);
-			if (idx == -1)
+			if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+			{
+				// TODO PUT IN A COLUMN FUNCTION
+				// If the error is that the indexer is read-only, clone it
+				new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
+				if (new_indexer_name == NULL)
+					return -1;
+				column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+				strcpy((column->header)->indexer_name, new_indexer_name);
+				free(new_indexer_name);
+				obi_set_errno(0);
+
+				// Add the value in the new indexer
+				idx = obi_index_uint8(column->indexer, value, value_length);
+				if (idx == -1)
+					return -1;
+			}
+			else
 				return -1;
 		}
-		else
-			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;
 
@@ -100,7 +109,9 @@ char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t l
 
 	int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length);
 
-	// TODO NA
+	// Check NA
+	if (int_value == OBIQual_int_NA)
+		return OBIQual_char_NA;
 
 	value = (char*) malloc((int_value_length + 1) * sizeof(char));
 

src/obidmscolumn_seq.c

@@ -32,32 +32,38 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
-	// TODO NA
-
-	// Add the value in the indexer
-	idx = obi_index_dna_seq(column->indexer, value);
-	if (idx == -1)	// An error occurred
+	if (value == OBISeq_NA)
+	{
+		idx = OBIIdx_NA;
+	}
+	else
 	{
-		if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+		// Add the value in the indexer
+		idx = obi_index_dna_seq(column->indexer, value);
+		if (idx == -1)	// An error occurred
 		{
-			// TODO PUT IN A COLUMN FUNCTION
-			// If the error is that the indexer is read-only, clone it
-			new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
-			if (new_indexer_name == NULL)
-				return -1;
-			column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
-			strcpy((column->header)->indexer_name, new_indexer_name);
-			free(new_indexer_name);
-			obi_set_errno(0);
-
-			// Add the value in the new indexer
-			idx = obi_index_dna_seq(column->indexer, value);
-			if (idx == -1)
+			if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+			{
+				// TODO PUT IN A COLUMN FUNCTION
+				// If the error is that the indexer is read-only, clone it
+				new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
+				if (new_indexer_name == NULL)
+					return -1;
+				column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+				strcpy((column->header)->indexer_name, new_indexer_name);
+				free(new_indexer_name);
+				obi_set_errno(0);
+
+				// Add the value in the new indexer
+				idx = obi_index_dna_seq(column->indexer, value);
+				if (idx == -1)
+					return -1;
+			}
+			else
 				return -1;
 		}
-		else
-			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;
 

src/obidmscolumn_str.c

@@ -32,31 +32,36 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
-	// TODO NA
-
-	// Add the value in the indexer
-	idx = obi_index_char_str(column->indexer, value);
-	if (idx == -1)	// An error occurred
+	if (value == OBIStr_NA)
+	{
+		idx = OBIIdx_NA;
+	}
+	else
 	{
-		if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+		// Add the value in the indexer
+		idx = obi_index_char_str(column->indexer, value);
+		if (idx == -1)	// An error occurred
 		{
-			// TODO PUT IN A COLUMN FUNCTION
-			// If the error is that the indexer is read-only, clone it
-			new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
-			if (new_indexer_name == NULL)
-				return -1;
-			column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
-			strcpy((column->header)->indexer_name, new_indexer_name);
-			free(new_indexer_name);
-			obi_set_errno(0);
-
-			// Add the value in the new indexer
-			idx = obi_index_char_str(column->indexer, value);
-			if (idx == -1)
+			if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
+			{
+				// TODO PUT IN A COLUMN FUNCTION
+				// If the error is that the indexer is read-only, clone it
+				new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
+				if (new_indexer_name == NULL)
+					return -1;
+				column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+				strcpy((column->header)->indexer_name, new_indexer_name);
+				free(new_indexer_name);
+				obi_set_errno(0);
+
+				// Add the value in the new indexer
+				idx = obi_index_char_str(column->indexer, value);
+				if (idx == -1)
+					return -1;
+			}
+			else
 				return -1;
 		}
-		else
-			return -1;
 	}
 
 	// Add the value's index in the column