A B C D E F G H I J K L M N O P R S T V _

A

AATranslator - class edu.uconn.mcb.lineageevolver.AATranslator.
Serves as a translator between AminoAcid naming schemes.
AATranslator() - Constructor for class edu.uconn.mcb.lineageevolver.AATranslator
 
AATranslator.InvalidAminoAcid - exception edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.
Base class for exceptions generated during amino acid encoding/decoding.
AATranslator.InvalidAminoAcid() - Constructor for class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid
 
AATranslator.InvalidAminoAcid.InvalidAminoAcidByte - exception edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidByte.
Exception thrown when a byte value outside the AminoAcid range was used as an encoded AminoAcid.
AATranslator.InvalidAminoAcid.InvalidAminoAcidByte(byte) - Constructor for class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidByte
Constructor for InvalidAminoAcidByte objects given a non-AminoAcid-coding byte.
AATranslator.InvalidAminoAcid.InvalidAminoAcidChar - exception edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidChar.
Exception thrown when a character value outside the AminoAcid range was used as an encoded AminoAcid.
AATranslator.InvalidAminoAcid.InvalidAminoAcidChar(char) - Constructor for class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidChar
Constructor for InvalidAminoAcidChar objects given a non-AminoAcid-coding character.
AATranslator.InvalidAminoAcid.InvalidAminoAcidInt - exception edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidInt.
Exception thrown when an integer value outside the AminoAcid range (0-19) was used as an encoded AminoAcid.
AATranslator.InvalidAminoAcid.InvalidAminoAcidInt(int) - Constructor for class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidInt
Constructor for InvalidAminoAcidInt objects given a non-AminoAcid-coding integer.
ASRVByteAAGene - class edu.uconn.mcb.lineageevolver.ASRVByteAAGene.
Gene implementation using ByteAminoAcid and Simple Among Site Rate Variation (ASRV).
ASRVByteAAGene() - Constructor for class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
Default constructor for objects of type ASRVByteAAGene.
ASRVByteAAGene(float, int, int, float[], String) - Constructor for class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
Constructor for objects of type ASRVByteAAGene that generates a new gene given a character sequence in the form of a String.
ASRVByteAAGene(float, int, int, float[], byte[]) - Constructor for class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
Constructor for objects of type ASRVByteAAGene that generates a new gene given a byte sequence.
ASRVByteAAGene(float, int, int) - Constructor for class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
Constructor for objects of type ASRVByteAAGene that sets characteristic properties of gene instances.
ASRV_MUTLENGTH_MEAN - Static variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
The average length of sites that mutate their substitution rates in a given mutation event.
ASRV_MUTLENGTH_STDEV - Static variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
The standard deviation of sites that mutate their substitution rates in a given mutation event.
ASRV_MUT_FREQ - Static variable in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene
The number of substitutions undergone before each ASRV mutation.
AminoAcid - interface edu.uconn.mcb.lineageevolver.AminoAcid.
Common interface for models of amino acids.
aa - Variable in class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidByte
The bad byte that was used as an encoded AminoAcid.
aa - Variable in class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidChar
The bad character that was used as an encoded AminoAcid.
aa - Variable in class edu.uconn.mcb.lineageevolver.AATranslator.InvalidAminoAcid.InvalidAminoAcidInt
The bad integer that was used as an encoded AminoAcid.
addEdge(Object, GraphNode, GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph
Adds an edge to this graph.
addEdge(Object, GraphNode, GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph
 
addEdge(Object, GraphNode, GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology
 
addEvent(GenomeVisitor, GraphEdge, int) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology
 
addEvent(GenomeVisitor, GraphEdge, int) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology
Adds an event to a given edge, provided a time interval and a GenomeVisitor.
addNode(Object) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph
Adds a node to this graph.
addNode(Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph
 
addNode(Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology
 
applyEvent(GraphTopologyEvent, Lineage) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology
 
applyEvent(GraphTopologyEvent, Lineage) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology
Applies an event to a Lineage.
applyTo(Visitable) - Method in class edu.uconn.mcb.lineageevolver.GenomeVisitor
Initiates a handshake with the provided Visitable.
applyTo(Visitable) - Method in class edu.uconn.mcb.lineageevolver.LineageVisitor
 
applyTo(Visitable) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.Event
Applies this Event to a Visitable object.
applyTo(Visitable) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.GenomeEvent
 
applyTo(Visitable) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData.LineageEvent
Applies the visitor for this Event onto the provided Visitable, which should always be a Lineage.
applyTo(Visitable) - Method in interface edu.uconn.mcb.lineageevolver.misc.Visitor
Applies this Visitor to the given Visitable object.
applyToGenome(Genome) - Method in class edu.uconn.mcb.lineageevolver.GeneDuplicator
Processes gene duplication on the provided genome.
applyToGenome(Genome) - Method in class edu.uconn.mcb.lineageevolver.GeneKiller
Processes gene death on the provided genome.
applyToGenome(Genome) - Method in class edu.uconn.mcb.lineageevolver.GenomeEvolver
Induces 'evolution' on the given genome.
applyToGenome(Genome) - Method in class edu.uconn.mcb.lineageevolver.GenomeRearranger
Applies rearrangement on the given genome.
applyToGenome(Genome) - Method in class edu.uconn.mcb.lineageevolver.GenomeVisitor
Applies this visitor to the given Genome.
applyToLineage(ArrayList, GraphTopology) - Method in class edu.uconn.mcb.lineageevolver.LineageFork
 
applyToLineage(ArrayList, GraphTopology) - Method in class edu.uconn.mcb.lineageevolver.LineageVisitor
Applies this visitor to a given Lineage.

A B C D E F G H I J K L M N O P R S T V _