Package edu.uconn.mcb.lineageevolver.graph

Provides graph data structure interface and implementation.

See:
Description

Interface Summary

DirectedGraph	Common interface for all graph objects.
GraphEdge	Common interface for all graph edge objects.
GraphNode	Common interface for all graph node objects.
GraphTopology	Common interface for graph objects to be used as topologies.
GraphTopologyEvent	Common interface for classes representing an event at some given moment on a branch.

Class Summary

EdgeListEdge	GraphEdge implementation for use with EdgeListGraph objects.
EdgeListGraph	Comment for this type goes here.
EdgeListGraphTopology	Implementation of a GraphTopology using an EdgeListGraph
EdgeListNode	Implementation of GraphNode interface for use with EdgeListGraph objects.

Package edu.uconn.mcb.lineageevolver.graph Description

Provides graph data structure interface and implementation. The graph data structure was chosen (for representation of topologies) to accomodate LineageEvolver's event-centric take on evolution. All Events must be associated to an edge in a graph, and fall under one of two categories:

• Manually Generated Events
  This type of event is generated manually by a driver class. Events such as gene deletion or horizontal gene transfer fall under this category.
• Automatically Generated Events
  This type of event is generated automatically by the Graph data structure upon request. All events of this type are inferred by other data present in the Graph data structure, and thus manual generation of these events is redundant. Events such as forkation (generated when all time intervals along an edge have been processed) and substitution (generated based on branch length in number of substitutions) fall under this category.