// use the following regex to decide an annotations (whole) line is NOT an RNA
// SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
public static final int REGEX_NOT_RNASS = 2;
// use the following regex to decide an annotations (whole) line is NOT an RNA
// SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
public static final int REGEX_NOT_RNASS = 2;
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);