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

G

Gene - interface edu.uconn.mcb.lineageevolver.Gene.

Common interface for models of genes.

GeneDuplicator - class edu.uconn.mcb.lineageevolver.GeneDuplicator.

GenomeVisitor subclass encapsulating gene duplication functionality.

GeneDuplicator() - Constructor for class edu.uconn.mcb.lineageevolver.GeneDuplicator

GeneKiller - class edu.uconn.mcb.lineageevolver.GeneKiller.

GenomeVisitor subclass encapsulating gene death functionality.

GeneKiller() - Constructor for class edu.uconn.mcb.lineageevolver.GeneKiller

Genome - class edu.uconn.mcb.lineageevolver.Genome.

Model of Genomes, composed of a collection of Genes.

Genome(String[], float[], float[][], float[]) - Constructor for class edu.uconn.mcb.lineageevolver.Genome

Constructor for objects of type Genome.

Genome(String[], float[][], float[]) - Constructor for class edu.uconn.mcb.lineageevolver.Genome

Genome.NoHGTProcessed - exception edu.uconn.mcb.lineageevolver.Genome.NoHGTProcessed.

Exception thrown when hgt was not processed within a reasonable timeframe.

Genome.NoHGTProcessed() - Constructor for class edu.uconn.mcb.lineageevolver.Genome.NoHGTProcessed

GenomeEvolver - class edu.uconn.mcb.lineageevolver.GenomeEvolver.

GenomeVisitor subclass encapsulating generic 'evolution'.

GenomeEvolver() - Constructor for class edu.uconn.mcb.lineageevolver.GenomeEvolver

Default constructor for Objects of type GenomeEvolver.

GenomeEvolver(int) - Constructor for class edu.uconn.mcb.lineageevolver.GenomeEvolver

Constructor specifying time for Objects of type GenomeEvolver

GenomeRearranger - class edu.uconn.mcb.lineageevolver.GenomeRearranger.

GenomeVisitor subclass encapsulating the rearrangement process.

GenomeRearranger() - Constructor for class edu.uconn.mcb.lineageevolver.GenomeRearranger

GenomeVisitor - class edu.uconn.mcb.lineageevolver.GenomeVisitor.

Abstract class for all visitors meant exclusively for Genomes.

GenomeVisitor() - Constructor for class edu.uconn.mcb.lineageevolver.GenomeVisitor

GraphEdge - interface edu.uconn.mcb.lineageevolver.graph.GraphEdge.

Common interface for all graph edge objects.

GraphNode - interface edu.uconn.mcb.lineageevolver.graph.GraphNode.

Common interface for all graph node objects.

GraphTopology - interface edu.uconn.mcb.lineageevolver.graph.GraphTopology.

Common interface for graph objects to be used as topologies.

GraphTopologyEvent - interface edu.uconn.mcb.lineageevolver.graph.GraphTopologyEvent.

Common interface for classes representing an event at some given moment on a branch.

genome - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.NodeData

The genome residing in this node.

getAdjacentNodes(GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Retrieves all nodes directly adjacent to the given node.

getAdjacentNodes(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getAminoAcid(int) - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

getAminoAcid(int) - Method in interface edu.uconn.mcb.lineageevolver.Gene

Returns the AminoAcid at the given index.

getByte(int) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the byte encoding for the AminoAcid encoded by the provided integer.

getByte(char) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the byte encoding for the AminoAcid encoded by the provided character.

getCategoryDifference(Genome, Genome) - Method in class edu.uconn.mcb.lineageevolver.Lineage

Returns the weighted difference in Lake's categories between two Genomes.

getChar(int) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the character encoding for the AminoAcid encoded by the provided integer.

getChar(byte) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the character encoding for the AminoAcid encoded by the provided byte.

getData(GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Returns the data stored inside a given node.

getData(GraphEdge) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Returns the data stored inside a given edge.

getData(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getData(GraphEdge) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getData(GraphEdge) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getData(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getEdge(GraphTopologyEvent) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getEdge(GraphTopologyEvent) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Returns the edge associated to a given event.

getEdges(GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Retrieves all edges outgoing from a given node.

getEdges(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getEvent(GraphEdge) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getEvent(GraphEdge) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Returns the next event on the given edge corresponding to the current position on that edge.

getEvolutionSpeed() - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

getEvolutionSpeed() - Method in interface edu.uconn.mcb.lineageevolver.Gene

Returns the currently employed evolution speed for this Gene

getGene(int) - Method in class edu.uconn.mcb.lineageevolver.Genome

Returns the Gene at a given index in this Genome.

getGeneEvolutionSpeeds() - Method in class edu.uconn.mcb.lineageevolver.Genome

Returns an array containing the evolution speeds for each gene in this Genome.

getGenome(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getGenome(GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Returns genome stored in the given node.

getHGTCounts() - Method in class edu.uconn.mcb.lineageevolver.config.Configuration

getID() - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

getID() - Method in interface edu.uconn.mcb.lineageevolver.Gene

Return the ID number for this gene.

getInt(char) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the integer encoding for the AminoAcid encoded by the provided character.

getInt(byte) - Static method in class edu.uconn.mcb.lineageevolver.AATranslator

Returns the integer encoding for the AminoAcid encoded by the provided byte.

getLakeCategory(int) - Method in class edu.uconn.mcb.lineageevolver.Genome

Returns the lake category value specified.

getName(GraphNode) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

getName(GraphNode) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Returns the name of the given node.

getNodes(GraphEdge) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Retrieves the two nodes connected by a given edge.

getNodes() - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Retrieves all nodes in this graph.

getNodes(GraphEdge) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getNodes() - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

getParalogID() - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

getParalogID() - Method in interface edu.uconn.mcb.lineageevolver.Gene

Returns the paralog number for this gene.

getResult() - Method in interface edu.uconn.mcb.lineageevolver.misc.StrResultVisitor

Returns the string stored as a result of a successful visit.

getRootGenome() - Method in class edu.uconn.mcb.lineageevolver.config.Configuration

Returns the root Genome.

getSize() - Method in class edu.uconn.mcb.lineageevolver.ASRVByteAAGene

getSize() - Method in interface edu.uconn.mcb.lineageevolver.Gene

Returns the number of AminoAcids in this Gene.

getSize() - Method in class edu.uconn.mcb.lineageevolver.Genome

Returns the number of genes in this genome.

getSubstitution(Substitutable) - Method in class edu.uconn.mcb.lineageevolver.JTT

getSubstitution(Substitutable) - Method in interface edu.uconn.mcb.lineageevolver.SubstitutionMatrix

Returns a suitable substitution for the provided substitutable according to this substitution matrix.

getSubstitutionEvent(int) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData

Returns a SubstitutionEvent with appropriate configuration given a number of substitutions.

getSubstitutionProbability() - Method in interface edu.uconn.mcb.lineageevolver.AminoAcid

Returns the substitution probability for this amino acid.

getSubstitutionProbability() - Method in class edu.uconn.mcb.lineageevolver.ByteAminoAcid

getTopLevel() - Method in class edu.uconn.mcb.lineageevolver.Lineage

Returns the top level of genomes in this lineage.

getTotalTime() - Method in class edu.uconn.mcb.lineageevolver.config.Configuration

getTree() - Method in class edu.uconn.mcb.lineageevolver.config.Configuration

getType() - Method in interface edu.uconn.mcb.lineageevolver.AminoAcid

Returns the type of this amino acid.

getType() - Method in class edu.uconn.mcb.lineageevolver.ByteAminoAcid

Returns the type of this amino acid.

gneDestination - Variable in class edu.uconn.mcb.lineageevolver.Recombiner.NoRecombineRegion

The destination Gene for which recombination failed.

gneSource - Variable in class edu.uconn.mcb.lineageevolver.Recombiner.NoRecombineRegion

The source Gene for which recombination failed.