C D E I K N P R S T X

C

compareTo(Entry) - Method in class DelaySim.Entry
compare two Entry objects on their 'time' value

D

DDA - Class in DelaySim
A class describing a reaction-based system to be simulated by the Delay Stochastic Simulation Algorithm where reactions follow the delay-as-duration approach.
DDA(Reaction[], int[]) - Constructor for class DelaySim.DDA
Constructor for a DDA object.
delay - Variable in class DelaySim.Reaction
the delay
DelaySim - package DelaySim
 

E

Entry - Class in DelaySim
A class describing entries in the scheduling lists of the simulation algorithms.
Entry(double, int) - Constructor for class DelaySim.Entry
Create an event-object happening at time 'time' and involving reaction 'reaction'

I

idx - Variable in class DelaySim.Entry
reaction involved in the event
insert_producs(int[]) - Method in class DelaySim.Reaction
Perform insertion of the products in the state vector given as parameter.
is_applicable(int[]) - Method in class DelaySim.Reaction
Check if reaction is applicable in the state vector given as parameter.

K

k - Variable in class DelaySim.Reaction
the kinetic constant

N

name - Variable in class DelaySim.Reaction
the reaction name
nu_p - Variable in class DelaySim.Reaction
the stoichiometry vector for products
nu_r - Variable in class DelaySim.Reaction
the stoichiometry vector for reactants

P

PDA - Class in DelaySim
A class describing a reaction-based system to be simulated by the Delay Stochastic Simulation Algorithm where reactions follow the purely delayed approach.
PDA(Reaction[], int[]) - Constructor for class DelaySim.PDA
Constructor for a PDA object.
print() - Method in class DelaySim.DDA
Print a summary on this system.
print() - Method in class DelaySim.PDA
Print a summary on this system.

R

R - Variable in class DelaySim.DDA
the set of reactions both delayed and non-delayed
R - Variable in class DelaySim.PDA
the set of reactions both delayed and non-delayed
rate - Variable in class DelaySim.Reaction
 
rate(int[]) - Method in class DelaySim.Reaction
Evaluate the propensity function for the reaction in the state described by the vector used as parameter.
Reaction - Class in DelaySim
A class describing a generic reaction.
Reaction(String, int[], int[], double, double) - Constructor for class DelaySim.Reaction
Constructor for a Reaction object.
remove_reactants(int[]) - Method in class DelaySim.Reaction
Perform removal of the reactants from the state vector given as parameter.

S

simulate(double, double) - Method in class DelaySim.DDA
Execute a DDA simulation for this system starting at time t0 up to time T.
simulate(double, double) - Method in class DelaySim.PDA
Execute a PDA simulation for this system starting at time t0 up to time T.

T

time - Variable in class DelaySim.Entry
time of the event
toString() - Method in class DelaySim.Entry
Return a string representation of this event
toString() - Method in class DelaySim.Reaction
 

X

x - Variable in class DelaySim.DDA
the simulation state
x - Variable in class DelaySim.PDA
the simulation state

C D E I K N P R S T X