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Class Summary |
| AffectorTemplate |
|
| BetterTokenizer |
The BetterTokenizer class takes an input stream and
* parses it into "tokens", allowing the tokens to be
* read one at a time. |
| CalculatorNode |
a CalculatorNode is a wrapper useful for doing arithmetic on a group of Nodes,
like treating a group of similar Nodes as if it were a single pool. |
| Cell |
This class represents a single cell in the model. |
| Experiment |
This class is supposed to be able to conduct experiments on the currently loaded net. |
| GeneNet |
GeneNet.java
The MainClass. |
| GeneralInput |
|
| GlobalIO |
|
| Globals |
Contains all the global parameters of our model which |
| Model |
|
| ModelRunner |
|
| MoreMath |
This class includes a bunch of extra mathematical functions and other math
tidbits that are useful to have around. |
| NetInput |
|
| Network |
|
| NetworkFile |
|
| Node |
A node is one of the state variables in the model: an mRNA, protein, protein complex, protein
at a membrane, etc. |
| NodeSpecifier |
|
| NodeTemplate |
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| NoiseGenerator |
|