@@ -0,0 +1,834 @@
+package beast.evolution.substitutionmodel;%0A%0Aimport beast.core.Description;%0Aimport beast.core.Input;%0Aimport beast.core.Input.Validate;%0Aimport beast.core.parameter.BooleanParameter;%0A%0A@Description(%22Frequencies for ModelTest model, can switch between equal and empricial/estimated frequencies%22)%0Apublic class ModelFrequencies extends Frequencies %7B%0A%09public Input%3CBooleanParameter%3E hasEqualFreqslInput = new Input%3C%3E(%22hasEqualFreqs%22, %22flag to indicate equal frequencies shouldbe used%22, Validate.REQUIRED);%0A%0A%09%0A%09BooleanParameter hasEqualFreqs;%0A%09%0A%09@Override%0A%09public void initAndValidate() throws Exception %7B%0A%09%09hasEqualFreqs = hasEqualFreqslInput.get();%0A%09%09super.initAndValidate();%0A%09%7D%0A%0A%09@Override%0A%09public double%5B%5D getFreqs() %7B%0A%09%09if (hasEqualFreqs.getValue()) %7B%0A%09%09%09return new double%5B%5D%7B0.25, 0.25, 0.25, 0.25%7D;%0A%09%09%7D%0A%09%09return super.getFreqs();%0A%09%7D%0A%09%0A%7D%0A

add model frequencies