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Class Summary |
| AlgorithmicNucleicAcid |
This class represents a nucleic acid whose bases are algorithmically
and randomly generated. |
| AminoAcid |
This class represents an amino acid object. |
| Base |
This class represents a Base object, as in the base purines and
pyrimidines which form DNA and RNA. |
| BioEngine |
This class represents the Java Bean representing all of the
BioScope engine. |
| BioEngineBeanInfo |
This class contains the information necessary for a Java Beans
builder (e.g. |
| BioLogicaSpecies |
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| Branch |
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| Characteristic |
This class represents a characteristic of a trait of a species. |
| ChromosomeSpecification |
This class represents the specification of a particular chromosome for use in
creating an organism. |
| Codon |
This class represents a Codon object, groups of 3 bases
which code for particular amino acids. |
| CrossOver |
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| Debug |
Debug contains useful code and constants for debugging. |
| ElementContext |
This class represents a context for an XML element during the
process of reading that element in from a BioLogica XML file. |
| Elements |
This class contains the name strings and ids for engine XML elements. |
| EngineObject |
This abstract class is the base for all BioScope engine classes and defines
the basic API's that all engine classes must implement. |
| EngineProp |
This class contains definitions for BioLogica engine simple and
vector property names. |
| EngineStrings |
This class contains the strings for the engine package. |
| Environment |
This class represents an environment. |
| Family |
This class represents a family of diploid organisms consisting of a female
parent organism, a male parent organism and a set of child organisms. |
| Gene |
This class represents a gene. |
| GenotypeToPhenotypeRule |
This class represents a rule for choosing a phenotype from a genotype. |
| ImportContext |
This class represents a context for a set of objects being imported
into an active BioLogica process. |
| NucleicAcid |
This class represents a container nucleic acid, which is little more than
a collection of other nucleic acids, some of which are alleles, some
algorithmic sequences, some containers, etc. |
| Organism |
This class represents an organism. |
| OrganismAllele |
This class represents an organism allele - an allele within
one organism. |
| OrganismAllelePair |
This class represents a pair of organism alleles or, in the case of sex chromosomes,
it can represent a single allele on a single chromosome. |
| OrganismChromosome |
This class represents an organism chromosome - a chromosome which has a
length and some organism alleles. |
| OrganismChromosomePair |
This class represents a pair of organism chromosomes, either a pair of autosomes or
a pair of sex chromosomes. |
| OrganismImage |
This class represents a portion of the image used to draw an
organism. |
| PathStrings |
PathStrings is a class containing static references to path strings
used in various parts of BioLogica, including the engine. |
| RawNucleicAcid |
This class represents a nucleic acid stored as a sequence of base values. |
| Species |
This class represents a species. |
| SpeciesAllele |
This class represents a species allele - a known, fixed variation of a species gene. |
| SpeciesChromosome |
This class represents a species chromosome - a chromosome which has a
length, some genes and their alleles, etc. |
| SpeciesImage |
This class represents an image containing some of the graphics for drawing
the organisms of a particular species. |
| SpeciesImageColumn |
This class represents a column of a SpeciesImage. |
| SpeciesImageRow |
This class represents a row of a SpeciesImage. |
| Terrain |
This class represents a type of terrain in a world. |
| Trait |
This class represents a trait of a species. |
| World |
This class represents a BioLogica world. |