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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.
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