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

E

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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