boolCell.m

classdef boolCell < matlab.mixin.Copyable
    %   Boolean cell: this object models a cell with a boolean network
    
    properties
        % Set by the caller
        numGenes    % The number of genes in the cell
        k           % The number of connections each node has
        p           % Probability of function value taking on value of 1
        bandwidth   % The number of external connections the cell makes
        Ttable      % The truth table for the network
        varF        % Which intracellular connections a cell makes
        outCells    % Which cells produce intercellular output
        inCells     % Which cells receive intercellular input
        perturb     % Perturbation
        
        
        % Generated if a grid is set up
        neighbors   % The neighbors of the cell
        cellPos     % Position of the cell
        
        % Generated every step
        states
    end
    
    methods
        
        % Constructor
        function obj = boolCell(numGenes,k,p,bandwidth,Ttable,varF,outCells,inCells, perturb)
            % Set some defaults
            if  nargin == 0
                obj.numGenes  = 15;
                obj.k         = 0;
                obj.p         = 0;
                obj.bandwidth = 0;
                obj.Ttable    = [];
                obj.varF      = [];
                obj.outCells  = [];
                obj.inCells   = [];
                obj.perturb   = [];
            else
                obj.numGenes  = numGenes;
                obj.k         = k;
                obj.p         = p;
                obj.bandwidth = bandwidth;
                obj.Ttable    = Ttable;
                obj.varF      = varF;
                obj.outCells  = outCells;
                obj.inCells   = inCells;
                obj.perturb   = perturb;
            end
        end
        
        function thisCell = setPos(thisCell, cellPos)
            thisCell.cellPos = cellPos;
        end
        
        function setState(thisCell, state, timestep)
            %Used to set the initial state
            thisCell.states(:,timestep) = state;
        end 

        function perturb_genes(thisCell, timestep)
            %------------ Perturbation Update for all cells -------------%
            perturbProb = thisCell.perturb;
            
            % Add gamma 
            newRand = rand;
            if ((1-(1-perturbProb)^(thisCell.numGenes)) > newRand);
                
                % Creating the perturbation gamma array
                gamma = zeros(1, thisCell.numGenes);
                for gene = 1:length(gamma)
                    r = rand;
                    if (perturbProb > rand)
                        gamma(gene) = 1;
                    else
                        % do nothing
                    end
                end
                thisCell.states(:,timestep) = mod(thisCell.states(:,timestep)+gamma',2);
            else
                % No perturbation      
            end          
        end
        
        function page_rank(thisCell, timestep)
            %------------ Page Rank Update for all cells -------------%

            thisCell.states(:,timestep) = randi([0,1],thisCell.numGenes,1);
        end

        function update_genes(thisCell,timestep)
            %-------------- Boolean update for all cells ------------%

            for genecol = 1:thisCell.numGenes
                tempVarf = [];
                for generow = 1:size(thisCell.varF,1)
                    if (thisCell.varF(generow, genecol) == -1)
                        % do nothing
                    else
                        %This is the list of nodes we will be making
                        %   connections to
                        tempVarf = [tempVarf, thisCell.varF(generow,genecol)];
                    end
                end

                if (isempty(tempVarf) == 0)
                    wiringnode = 0;
                    for wire = 1:length(tempVarf)
                        % The wiring of input nodes to compute
                        %   thisCell's state at t+1
                        wiringnode = wiringnode + 2^(length(tempVarf)-wire) * thisCell.states(tempVarf(wire),timestep-1);
                    end
                    thisCell.states(genecol,timestep) = thisCell.Ttable(wiringnode+1, genecol);
                end
            end   
        end       
    end
end