The array will be initialized to false when you allocate it.
All arrays in Java are initialized to the default value for the type. This means that arrays of ints are initialised to 0, arrays of booleans are initialised to false and arrays of reference types are initialised to null.
They will be initialized to false by default. In Java arrays are created on heap and every element of the array is given a default value depending on its type. For boolean data type the default value is 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.