C++ (Cpp) new_INTEGER_from_IntAE Examples

Example #1

File: XStringSet_io.c Project: nw328/Biostrings

static SEXP make_fasta_index_data_frame(const IntAE *recno_buf,
					const IntAE *fileno_buf,
					const LLongAE *offset_buf,
					const CharAEAE *desc_buf,
					const IntAE *seqlength_buf)
{
	SEXP df, colnames, tmp;
	int i;

	PROTECT(df = NEW_LIST(5));

	PROTECT(colnames = NEW_CHARACTER(5));
	PROTECT(tmp = mkChar("recno"));
	SET_STRING_ELT(colnames, 0, tmp);
	UNPROTECT(1);
	PROTECT(tmp = mkChar("fileno"));
	SET_STRING_ELT(colnames, 1, tmp);
	UNPROTECT(1);
	PROTECT(tmp = mkChar("offset"));
	SET_STRING_ELT(colnames, 2, tmp);
	UNPROTECT(1);
	PROTECT(tmp = mkChar("desc"));
	SET_STRING_ELT(colnames, 3, tmp);
	UNPROTECT(1);
	PROTECT(tmp = mkChar("seqlength"));
	SET_STRING_ELT(colnames, 4, tmp);
	UNPROTECT(1);
	SET_NAMES(df, colnames);
	UNPROTECT(1);

	PROTECT(tmp = new_INTEGER_from_IntAE(recno_buf));
	SET_ELEMENT(df, 0, tmp);
	UNPROTECT(1);

	PROTECT(tmp = new_INTEGER_from_IntAE(fileno_buf));
	SET_ELEMENT(df, 1, tmp);
	UNPROTECT(1);

	PROTECT(tmp = NEW_NUMERIC(LLongAE_get_nelt(offset_buf)));
	for (i = 0; i < LENGTH(tmp); i++)
		REAL(tmp)[i] = (double) offset_buf->elts[i];
	SET_ELEMENT(df, 2, tmp);
	UNPROTECT(1);

	PROTECT(tmp = new_CHARACTER_from_CharAEAE(desc_buf));
	SET_ELEMENT(df, 3, tmp);
	UNPROTECT(1);

	PROTECT(tmp = new_INTEGER_from_IntAE(seqlength_buf));
	SET_ELEMENT(df, 4, tmp);
	UNPROTECT(1);

	/* list_as_data_frame() performs IN-PLACE coercion */
	list_as_data_frame(df, IntAE_get_nelt(recno_buf));
	UNPROTECT(1);
	return df;
}

Example #2

File: match_reporting.c Project: zachcp/Biostrings

SEXP _MatchBuf_which_asINTEGER(const MatchBuf *match_buf)
{
	SEXP ans;
	int i;

	PROTECT(ans = new_INTEGER_from_IntAE(match_buf->PSlink_ids));
	sort_int_array(INTEGER(ans), LENGTH(ans), 0);
	for (i = 0; i < LENGTH(ans); i++)
		INTEGER(ans)[i]++;
	UNPROTECT(1);
	return ans;
}

Example #3

File: match_reporting.c Project: zachcp/Biostrings

SEXP _reported_matches_asSEXP()
{
	SEXP start, width, ans;

	switch (internal_match_buf.ms_code) {
	    case MATCHES_AS_NULL:
		return R_NilValue;
	    case MATCHES_AS_COUNTS:
	    case MATCHES_AS_WHICH:
		return ScalarInteger(_get_match_count());
	    case MATCHES_AS_RANGES:
		PROTECT(start = new_INTEGER_from_IntAE(
		  internal_match_buf.match_starts->elts[active_PSpair_id]));
		PROTECT(width = new_INTEGER_from_IntAE(
		  internal_match_buf.match_widths->elts[active_PSpair_id]));
		PROTECT(ans = new_IRanges("IRanges", start, width, R_NilValue));
		UNPROTECT(3);
		return ans;
	}
	error("Biostrings internal error in _reported_matches_asSEXP(): "
	      "invalid 'internal_match_buf.ms_code' value %d",
	      internal_match_buf.ms_code);
	return R_NilValue;
}

Example #4

File: match_reporting.c Project: zachcp/Biostrings

SEXP _MatchBuf_counts_asINTEGER(const MatchBuf *match_buf)
{
	return new_INTEGER_from_IntAE(match_buf->match_counts);
}