diff --git a/src/build_reference_db.c b/src/build_reference_db.c index f1bb222..e8ddcb9 100755 --- a/src/build_reference_db.c +++ b/src/build_reference_db.c @@ -352,11 +352,11 @@ int build_reference_db(const char* dms_name, // Read alignment score score = obi_get_float_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_score_column, i, 0); - ///////////////// Compute for first sequence \\\\\\\\\\\\\\\\\\\\\\\ + ///////////////// Compute for first sequence \\\\\\\\\\\\\\\\\\\\\\\ (TODO function) // Read arrays - lca_taxid_array = (obiint_t*) obi_column_get_array(final_lca_taxid_a_column, idx1, &taxid_array_length); - score_array = (obifloat_t*) obi_column_get_array(final_score_a_column, idx1, &score_array_length); + lca_taxid_array = (obiint_t*) obi_get_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, &taxid_array_length); + score_array = (obifloat_t*) obi_get_array_with_col_p_in_view(o_view, final_score_a_column, idx1, &score_array_length); taxid_array_writable_length = taxid_array_length; score_array_writable_length = score_array_length; @@ -371,12 +371,12 @@ int build_reference_db(const char* dms_name, // If empty, add values if (taxid_array_length == 0) { - if (obi_column_set_array(final_lca_taxid_a_column, idx1, &taxid_lca, (uint8_t) obi_sizeof(OBI_INT), 1) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0) { obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database"); return -1; } - if (obi_column_set_array(final_score_a_column, idx1, &score, (uint8_t) obi_sizeof(OBI_FLOAT), 1) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_score_a_column, idx1, &score, (uint8_t) (obi_sizeof(OBI_FLOAT) * 8), 1) < 0) { obidebug(1, "\nError setting a score array in a column when building a reference database"); return -1; @@ -482,12 +482,12 @@ int build_reference_db(const char* dms_name, // Write new arrays if (modified) { - if (obi_column_set_array(final_lca_taxid_a_column, idx1, lca_taxid_array_writable, (uint8_t) obi_sizeof(OBI_INT), taxid_array_writable_length) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, lca_taxid_array_writable, (uint8_t) (obi_sizeof(OBI_INT) * 8), taxid_array_writable_length) < 0) { obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database"); return -1; } - if (obi_column_set_array(final_score_a_column, idx1, score_array_writable, (uint8_t) obi_sizeof(OBI_FLOAT), score_array_writable_length) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_score_a_column, idx1, score_array_writable, (uint8_t) (obi_sizeof(OBI_FLOAT) * 8), score_array_writable_length) < 0) { obidebug(1, "\nError setting a score array in a column when building a reference database"); return -1; @@ -495,11 +495,11 @@ int build_reference_db(const char* dms_name, } } - ///////////////// Compute for second sequence \\\\\\\\\\\\\\\\\\\\\\\ + ///////////////// Compute for second sequence \\\\\\\\\\\\\\\\\\\\\\\ (TODO function) // Read arrays - lca_taxid_array = (obiint_t*) obi_column_get_array(final_lca_taxid_a_column, idx2, &taxid_array_length); - score_array = (obifloat_t*) obi_column_get_array(final_score_a_column, idx2, &score_array_length); + lca_taxid_array = (obiint_t*) obi_get_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx2, &taxid_array_length); + score_array = (obifloat_t*) obi_get_array_with_col_p_in_view(o_view, final_score_a_column, idx2, &score_array_length); taxid_array_writable_length = taxid_array_length; score_array_writable_length = score_array_length; @@ -514,12 +514,12 @@ int build_reference_db(const char* dms_name, // If empty, add values if (taxid_array_length == 0) { - if (obi_column_set_array(final_lca_taxid_a_column, idx2, &taxid_lca, (uint8_t) obi_sizeof(OBI_INT), 1) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx2, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0) { obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database"); return -1; } - if (obi_column_set_array(final_score_a_column, idx2, &score, (uint8_t) obi_sizeof(OBI_FLOAT), 1) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_score_a_column, idx2, &score, (uint8_t) (obi_sizeof(OBI_FLOAT) * 8), 1) < 0) { obidebug(1, "\nError setting a score array in a column when building a reference database"); return -1; @@ -626,12 +626,12 @@ int build_reference_db(const char* dms_name, // Copy arrays for modification (can't edit in place, as it is stored in indexer data file) if (modified) { - if (obi_column_set_array(final_lca_taxid_a_column, idx2, lca_taxid_array_writable, (uint8_t) obi_sizeof(OBI_INT), taxid_array_writable_length) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx2, lca_taxid_array_writable, (uint8_t) (obi_sizeof(OBI_INT) * 8), taxid_array_writable_length) < 0) { obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database"); return -1; } - if (obi_column_set_array(final_score_a_column, idx2, score_array_writable, (uint8_t) obi_sizeof(OBI_FLOAT), score_array_writable_length) < 0) + if (obi_set_array_with_col_p_in_view(o_view, final_score_a_column, idx2, score_array_writable, (uint8_t) (obi_sizeof(OBI_FLOAT) * 8), score_array_writable_length) < 0) { obidebug(1, "\nError setting a score array in a column when building a reference database"); return -1;