New column type for DNA sequences. Only for those coded on 2 bits (only

'ATGCatgc') for now.

src/obidmscolumn_seq.c

@@ -0,0 +1,120 @@
+/****************************************************************************
+ * OBIDMS_column_seq functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_seq.c
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+#include "obiarray.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	byte_t* value_b;
+	index_t idx;
+
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
+	// Update lines used
+	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_seq_to_obibytes(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the obiarray
+	idx = obi_array_add(column->array, value_b);
+	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;
+}
+
+
+const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	index_t idx;
+	byte_t* value_b;
+
+	if ((line_nb+1) > (column->header)->lines_used)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return "\0";		// TODO
+	}
+
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+
+	// Check NA
+	if (idx == OBIIdx_NA)
+		return "\0";		// TODO
+
+	value_b = obi_array_get(column->array, idx);
+	return obi_obibytes_to_seq(value_b);
+}
+
+
+int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	if (obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+	return 0;
+}
+
+
+const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return "\0";
+	return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
+}
+