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

S

StrResultVisitor - interface edu.uconn.mcb.lineageevolver.misc.StrResultVisitor.

Common interface for Visitors that store a string as a result.

Substitutable - interface edu.uconn.mcb.lineageevolver.Substitutable.

Common interface for modelling substitutable elements.

SubstitutionMatrix - interface edu.uconn.mcb.lineageevolver.SubstitutionMatrix.

Common interface for all substitution matrices.

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

Checks if an integer encodes for a given amino acid.

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

Checks if a byte encodes for a given amino acid.

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

Checks if a character encodes for a given amino acid.

select() - Method in class edu.uconn.mcb.lineageevolver.RandomSelection

Returns a random selection, weighted according to the probabilities.

setData(GraphNode, Object) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Sets the data for a given node.

setData(GraphEdge, Object) - Method in interface edu.uconn.mcb.lineageevolver.graph.DirectedGraph

Sets the data for a given edge.

setData(GraphNode, Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

setData(GraphEdge, Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraph

setData(GraphEdge, Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

setData(GraphNode, Object) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

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

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

Sets the evolution speed for this Gene.

setGenome(GraphNode, Genome) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

setGenome(GraphNode, Genome) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Sets the genome for a given node.

setHGTCounts(int[]) - Method in class edu.uconn.mcb.lineageevolver.config.Configuration

setName(GraphNode, String) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

setName(GraphNode, String) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Sets the name for a given node.

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

Sets the root genome.

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

Sets the substitution probability of this amino acid.

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

setSubstitutions(int) - Method in class edu.uconn.mcb.lineageevolver.GenomeEvolver

Sets the duration of evolution for this visitor.

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

Sets the number of substitutions to be processed during this substitution event.

setSubstitutions(GraphEdge, int) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

setSubstitutions(GraphEdge, int) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Sets the branch length for the given edge.

setTime(GraphEdge, int) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

setTime(GraphEdge, int) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Sets the time associated to the given edge.

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

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

Sets the type of this amino acid.

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

Sets the type of this amino acid given a new type encoded as a character.

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

Sets the type of this amino acid given a new type encoded as a byte..

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

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

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

Processes substitution according to the currently employed substitution matrix for this Gene.

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

Induces substitution in this substitutable object.

substitute(GraphEdge, int) - Method in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology

substitute(GraphEdge, int) - Method in interface edu.uconn.mcb.lineageevolver.graph.GraphTopology

Processes substitution on a given edge for a given amount of time.

substitutionEvent - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData

The substitution event to run when substitution should occur.

substitutions - Variable in class edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData

The number of substitutions along this branch.

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

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

Returns the number of substitutions per time interval for the given edge.

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

Processes a reversal event such that the reversal is symmetric about the origin or terminus of replication.