/**************************************************************************** * 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 "dna_seq_indexer.h" /********************************************************************** * * 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, const char* value) { index_t idx; if (obi_column_prepare_to_set_value(column, line_nb, element_idx) < 0) return -1; if (value == OBISeq_NA) { idx = OBIIdx_NA; } else { // Add the value in the indexer idx = obi_index_dna_seq(column->indexer, value); if (idx == -1) // An error occurred { if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR) { // If the error is that the indexer is read-only, clone it if (obi_clone_column_indexer(column) < 0) return -1; 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; } } // Add the value's index in the column *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx; return 0; } char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx) { index_t idx; if (obi_column_prepare_to_get_value(column, line_nb) < 0) return OBISeq_NA; idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx); // Check NA if (idx == OBIIdx_NA) return OBISeq_NA; return obi_retrieve_dna_seq(column->indexer, idx); } int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value) { index_t element_idx = obi_column_get_element_index_from_name(column, element_name); if (element_idx == OBIIdx_NA) return -1; return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value); } char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name) { index_t element_idx = obi_column_get_element_index_from_name(column, element_name); if (element_idx == OBIIdx_NA) return OBISeq_NA; return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx); }