At the beginning of the simulation, make sure that viruses are initiated with the input sequence instead of a random sequence

[Haddox]

I think there is a bug in the way that we initialize the simulation. Specifically, when we initialize a virus object at the start of the simulation:

antigen/Parameters.java

Line 121 in 9add838

urVirus = new Virus();

... we create a new GeometricSeqPhenotype object without providing an input sequence:

antigen/PhenotypeFactory.java

Line 19 in 9add838

if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) { p = new GeometricSeqPhenotype(); }

The result is that the code generates a random sequence that is the same length as the input sequence:

antigen/GeometricSeqPhenotype.java

Line 72 in 9add838

startingSequenceGenerator();

I think that we need to make the following two changes:

1. update the code so that line 71 of GeometricSeqPhenotype.java sets this.nucleotideSequence to be equal to Paramters.startingSequence.
2. remove line 72, so that we don't call startingSequenceGenerator, which generates a random sequence that is the same length as the input sequence.