char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
+ // DEBUG System.out.println(i + ": " + annotations[i]);
if (annotations[i] == null)
{
continue;
if (annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'E')
{
+ // DEBUG System.out.println( "/H|E/ '" +
+ // annotations[i].secondaryStructure + "'");
hasIcons |= true;
}
else
// Check for RNA secondary structure
{
- // System.out.println(annotations[i].secondaryStructure);
+ // DEBUG System.out.println( "/else/ '" +
+ // annotations[i].secondaryStructure + "'");
// TODO: 2.8.2 should this ss symbol validation check be a function in
// RNA/ResidueProperties ?
if (annotations[i].secondaryStructure == '('
|| annotations[i].secondaryStructure == 'B'
|| annotations[i].secondaryStructure == 'C'
|| annotations[i].secondaryStructure == 'D'
- || annotations[i].secondaryStructure == 'E'
+ // || annotations[i].secondaryStructure == 'E'
|| annotations[i].secondaryStructure == 'F'
|| annotations[i].secondaryStructure == 'G'
- || annotations[i].secondaryStructure == 'H'
+ // || annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'I'
|| annotations[i].secondaryStructure == 'J'
|| annotations[i].secondaryStructure == 'K'
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
- && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '(' && firstChar != '[' && firstChar != '<'
&& firstChar != '{' && firstChar != 'A' && firstChar != 'B'
&& firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
&& firstChar != 'F' && firstChar != 'G' && firstChar != 'H'