A | |
| Abstract [Protein] |
Contains the lightweight, live internal representation of an
abstract protein.
|
| Assocext [] |
An assocext object is used to keep associations between
non-overlapping extents of integers and values.
|
B | |
| BMD [Protein.Abstract] |
Characteristics of the abstract Boolean Multiplexor Domain.
|
C | |
| Cell [] |
The main cell engine.
|
| Cell_options [] |
Generic command-line argument processing.
|
| CheatParseRep [] |
Temporary placeholder for a built-to-order cell genome for testing
purposes.
|
| Compact [Genome] | |
| Compartment [] |
Encapsulates the subdivisions within the Cytoplasm, along with the
transport mechanisms between them.
|
| Compile [Genome] | |
| Cytoplasm [] |
Implementation of the fourth layer of the Design Stack.
|
D | |
| Dllist [] |
Definitions for doubly-linked lists which allow for in-place
insertion and removal.
|
G | |
| Genome [] |
Contains the mapping from Monod genome to protein functional
domains.
|
| GenomeParser [] |
This plate should be moved to
plates.
|
H | |
| Hashnlist [] |
Extends the functionality of hash tables to map keys to lists
of values.
|
I | |
| Incubator [] |
Implementation of the Incubator design pattern, which coordinates
the interactions of ligands and processing units.
|
| Interact [] |
Definition of the generic interactive plate.
|
L | |
| LBDE [Protein.Abstract] |
Characteristics of the abstract Ligand Binding Domain with
Extraction.
|
| LBDR [Protein.Abstract] |
Characteristics of the abstract Ligand Binding Domain with
Remapping.
|
| LID [Protein.Abstract] |
Characteristics of the abstract Logical Integration Domain.
|
| Ligand [] |
Definitions for the ligand objects, the string-analogues living
within the Incubator layer of the design stack.
|
| Log [] |
The definitions for the event logger.
|
M | |
| Main [] |
Entry-point for the single-cell standalone executable.
|
| Matcher [Ligand] |
Contains the definitions for the objects which are used to find
binding regions on ligands.
|
O | |
| OldCompiled [Genome] | |
| Optimized [Protein] |
The implementation of this module contains the meat of the protein
execution model.
|
P | |
| PDMatcher [Protein.Abstract] |
Characteristics of the abstract Matcher Pseudo-Domain.
|
| Procunit [Incubator] |
Contains the definitions for the processing units appearing an an
Incubator.
|
| Protein [] |
The definitions for the proteins in the Cytoplasm layer.
|
S | |
| SLBD [Protein.Abstract] |
Characteristics of the abstract Simple Ligand Binding
Domain.
|
| SerializedSwarm [Swarm] |
A Swarm implementation - very inefficient, but simple.
|
| SingleCellHarness [] |
The control harness for a single Monod Cell.
|
| Skeleton [] |
Common definitions for the tectonic plates necessary at the Monod
Cell layer.
|
| Swarm [] |
Implementation of the Swarm design pattern, which serves to harbor
multiple interacting residents.
|
T | |
| Testinter [] |
The simplest Interactive tectonic plate - it's not interactive at
all.
|
U | |
| Util [] |
Contains miscellaneous functions which have general
usefulness.
|
W | |
| Wizard [Protein] |
Used to make abstract proteins with a table-driven interface.
|