Add abstract T cell classes and modules

[allison-li-1016]

Addresses #40

Estimated Time: XLarge

Overview of major changes:
This PR is meant to set the stage for the incoming CART agents and actions from CARCADE.

• Added switch statements to setState() function for PatchCellCART to accommodate for T cell specific states
• Added antigens to cancer and tissue cells
• Added PatchCellCART abstract class
• Added PatchProcessInflammation abstract class
• Added CART metabolism

Detailed breakdown of changes

Patch Cell Classes

PatchCell class:

• moved step() method down a level to subclasses. The purpose of this is to allow for non-tissue agents to have unique rules that does not necessarily follow existing rule set.
• some fields are now protected instead of private to allow subclass visibility since step() function is now in subclasses.
• addition of inflammation module option when assigning processes
• addition of isStopped() method that returns whether or not this cell has stopped stepping. This is important for the kill and reset action in subsequent PRs.

PatchCellTissue class:

• Addition of CAR antigens field that represents the number of CAR antigens on the cell.
• Addition of PDL1 antigens field that represents the number of PDL1 antigens on the cell.
• Binding field that stores the binding status of this cell (ex. bound, unbound, etc.)
• step() method has moved from PatchCell class to this class. Everything inside the step() method remains the same as before.

PatchCellCancer class:

• Addition of CAR antigens field that represents the number of CAR antigens on the cell.

PatchCellTest class:

• Moved step() function related tests down to PatchCellTissueTest class

PatchCellTissueTest class:

• refactored unit tests that relate to the step() function

CART Agents and associated classes

PatchCellCART

• Abstract class for T cells
• Has bindTarget() method that determines if the cell can bind to a target depending on target cell surface antigens, and number of receptors on T cell

PatchCellCARTTest

• added unit tests for aforementioned agents

Files changed to accommodate new agent:

PatchModuleProliferation

• While splitting added update to inflammation module for new T cells

PatchEnums

• Added T cell states to state enums
• Added inflammation to domain enums
• Added new AntigenFlag enum to record cell binding status

PatchEnumsTest

• added a test for fetching antigen enum

Inflammation Modules

PatchProcessInflammation class:

• Abstract class for inflammation process
• Implementation of inflammation ODEs in which IL-2 is taken up by T cells, and T cell can undertake cytotoxic or stimulatory functions

PatchProcessInflammationTest class:

• added unit tests for each class to verify functionality

Metabolism Modules

PatchProcess Metabolism class:

• added CART option in make() method to allow for new metabolism type

PatchProcessMetabolismCART class:

• As implemented in original CARCADE model
• There is an up-regulated glucose uptake rate and metabolic preference depending on the activation status of the cell. The activation status of the cell is determined by the inflammation process.

PatchProcessMetabolismCARTTest class:

• added unit tests to verify functionality of the CART metabolism class

Parameters

parameter.patch.xml

• T cell agent parameter values
• CART metabolism rates
• Inflammation module default values
• Treat action default values