I just need to initialize all the array elements to Boolean false.
Either use boolean[] instead so that all values defaults to false:
boolean[] array = new boolean[size];
Or use Arrays#fill() to fill the entire array with Boolean.FALSE:
Boolean[] array = new Boolean[size];
Arrays.fill(array, Boolean.FALSE);
Also note that the array index is zero based. The freq[Global.iParameter[2]] = false; line as you’ve there would cause ArrayIndexOutOfBoundsException. To learn more about arrays in Java, consult this basic Oracle tutorial.