attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
}
}
// the missing symbol ("?") includes all others, including gap ("-")
UncertainCharacterState gap = xmlStateSet.createUncertainCharacterState("-", new HashSet<CharacterState>());
gap.setLabel("-");
xmlMissingStates.add(gap);
UncertainCharacterState missing = xmlStateSet.createUncertainCharacterState("?", xmlMissingStates);
missing.setLabel("?");
// then create the XML characters, assigning them all the same state set
List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
for ( int i = 0; i < tbColumns.size(); i++ ) {
MatrixColumn tbColumn = tbColumns.get(i);