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EVOLRATE_MUTATION_MEAN
- Static variable in class edu.uconn.mcb.lineageevolver.
ASRVByteAAGene
The average rate at which this gene's fltEvolutionSpeed mutations.
EVOLRATE_MUTATION_STDEV
- Static variable in class edu.uconn.mcb.lineageevolver.
ASRVByteAAGene
The standard deviation for this gene's fltEvolutionSpeed mutation.
EdgeListEdge
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListEdge
.
GraphEdge implementation for use with EdgeListGraph objects.
EdgeListEdge()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListEdge
Default constructor for EdgeListEdge objects.
EdgeListGraph
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraph
.
Comment for this type goes here.
EdgeListGraph()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraph
Default constructor for objects of type EdgeListGraph.
EdgeListGraphTopology
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology
.
Implementation of a GraphTopology using an EdgeListGraph
EdgeListGraphTopology()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology
EdgeListGraphTopology.EdgeData
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData
.
Encapsulation class used for storing multiple items inside an edge for EdgeListGraphTopology objects.
EdgeListGraphTopology.EdgeData(int, int, Object, EdgeListEdge)
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData
Constructor for EdgeData objects, specifying all instance variables.
EdgeListGraphTopology.EdgeData.Event
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.Event
.
Encapsulation class used for storing Event information inside an EdgeData object.
EdgeListGraphTopology.EdgeData.Event()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.Event
Default constructor for Events (should called only by subclasses).
EdgeListGraphTopology.EdgeData.ForkEvent
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.ForkEvent
.
Event produced for carryout out a forkation on the topology.
EdgeListGraphTopology.EdgeData.ForkEvent(EdgeListGraphTopology.EdgeData)
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.ForkEvent
Constructor for ForkEvent objects given an EdgeData belonging to the edge on which the newly created ForkEvent should reside.
EdgeListGraphTopology.EdgeData.GenomeEvent
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.GenomeEvent
.
Common abstract class for all events dealing directly with Genomes, as a GenomeVisitor.
EdgeListGraphTopology.EdgeData.GenomeEvent()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.GenomeEvent
EdgeListGraphTopology.EdgeData.LineageEvent
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.LineageEvent
.
Common abstract class for all events dealing with Lineages.
EdgeListGraphTopology.EdgeData.LineageEvent()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.LineageEvent
EdgeListGraphTopology.EdgeData.SubstitutionEvent
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.SubstitutionEvent
.
Event produced for carrying out substitution.
EdgeListGraphTopology.EdgeData.SubstitutionEvent()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.SubstitutionEvent
Default constructor for objects of type SubstitutionEvent.
EdgeListGraphTopology.NodeData
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.NodeData
.
Encapuslation class used for storing multiple items inside a node for EdgeListGraphTopology objects.
EdgeListGraphTopology.NodeData(String, Genome, Object, EdgeListNode)
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.NodeData
Default constructor for objects of type NodeData.
EdgeListNode
- class edu.uconn.mcb.lineageevolver.graph.
EdgeListNode
.
Implementation of GraphNode interface for use with EdgeListGraph objects.
EdgeListNode()
- Constructor for class edu.uconn.mcb.lineageevolver.graph.
EdgeListNode
Default constructor for objects of type EdgeListNode.
edge
- Variable in class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData
The edge that we're bound to.
edgeData
- Variable in class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData.Event
The EdgeData object corresponding to the edge on which this event resides.
edges
- Variable in class edu.uconn.mcb.lineageevolver.graph.
EdgeListNode
The edges outgoing from this node, AKA our edge list.
edu.uconn.mcb.lineageevolver
- package edu.uconn.mcb.lineageevolver
Provides all basic, universal LineageEvolver classes directly, and serves as a parent for all other LineageEvolver packages.
edu.uconn.mcb.lineageevolver.config
- package edu.uconn.mcb.lineageevolver.config
This package provides configuration interfaces and classes.
edu.uconn.mcb.lineageevolver.graph
- package edu.uconn.mcb.lineageevolver.graph
Provides graph data structure interface and implementation.
edu.uconn.mcb.lineageevolver.misc
- package edu.uconn.mcb.lineageevolver.misc
Provides miscellaneous/general classes, commonly part of a design paradigm, etc.
edu.uconn.mcb.lineageevolver.parsing
- package edu.uconn.mcb.lineageevolver.parsing
Provides classes for parsing data files into respective LineageEvolver objects.
equals(Object)
- Method in class edu.uconn.mcb.lineageevolver.
ASRVByteAAGene
Checks for equality between two ASRVByteAAGenes.
equals(Object)
- Method in class edu.uconn.mcb.lineageevolver.
ByteAminoAcid
events
- Variable in class edu.uconn.mcb.lineageevolver.graph.
EdgeListGraphTopology.EdgeData
Our list of events, in order.
evolve(int)
- Method in class edu.uconn.mcb.lineageevolver.
Genome
Induces evolution in this Genome by causing genes selected according to random calculations on the evolution speed of each gene to undergo 'evolution'.
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