Added different cross immunity functions to SequencePhenotype

Description

Updated riskOfInfection() in SequencePhenotype.java. There are 3 options for crossImmunityFunction

"linear"
- standard linear mapping function
"exponential"
- from Erick's comment on #3
"exponentialSimplified"
- simplified equation Erick wrote

The function used to calculate the return value of riskOfInfection() can be changed by updating crossImmunityFunction in parameters.yml.

Closes #3

Tests

Added testRiskOfInfection() to TestSequencePhenotype.java, which passes for all the options of crossImmunityFunction.

Edge cases we tested:

We compared sequences that

resulted intestRiskOfInfection() returning 0

shared the same base in half the indices

hamming distance == 0.5 * this.sequence.length())

were completely different

hamming distance == this.sequence.length()

The main use was tested as well.

Checklist:

[x] The code uses informative and accurate variable and function names
[x] The functionality is factored out into functions and methods with logical interfaces
[x] Comments are up to date, document intent, and there are no commented-out code blocks
[x] Commenting and/or documentation is sufficient for others to be able to understand intent and implementation
[x] TODOs have been eliminated from the code
[x] The corresponding issue number (e.g. #278) has been searched for in the code to find relevant notes
[ ] Documentation has been redeployed

(Sorry about all the whitespace. I'm trying to work it out, but IntelliJ isn't cooperating right now)

matsengrp / antigen