edu.uconn.mcb.lineageevolver.graph
Class EdgeListGraphTopology.EdgeData

java.lang.Object
  edu.uconn.mcb.lineageevolver.graph.EdgeListGraphTopology.EdgeData

Enclosing class:

EdgeListGraphTopology

protected class EdgeListGraphTopology.EdgeData

extends java.lang.Object

Encapsulation class used for storing multiple items inside an edge for EdgeListGraphTopology objects. Every EdgeData object must be associated to an Edge.

Author:

Hasan Khalil

Nested Class Summary

(package private) class	EdgeListGraphTopology.EdgeData.Event Encapsulation class used for storing Event information inside an EdgeData object.
protected class	EdgeListGraphTopology.EdgeData.ForkEvent Event produced for carryout out a forkation on the topology.
protected class	EdgeListGraphTopology.EdgeData.GenomeEvent Common abstract class for all events dealing directly with Genomes, as a GenomeVisitor.
protected class	EdgeListGraphTopology.EdgeData.LineageEvent Common abstract class for all events dealing with Lineages.
protected class	EdgeListGraphTopology.EdgeData.SubstitutionEvent Event produced for carrying out substitution.

Field Summary

(package private) int	cur The current number of time units traversed along this branch.
(package private) java.lang.Object	data The data stored in this edge.
(package private) EdgeListEdge	edge The edge that we're bound to.
(package private) java.util.ArrayList	events Our list of events, in order.
(package private) EdgeListGraphTopology.EdgeData.SubstitutionEvent	substitutionEvent The substitution event to run when substitution should occur.
(package private) int	substitutions The number of substitutions along this branch.
(package private) int	time The number of time units along this branch.

Constructor Summary

EdgeListGraphTopology.EdgeData(int substitutions, int time, java.lang.Object data, EdgeListEdge edge)
Constructor for EdgeData objects, specifying all instance variables.

Method Summary

(package private) EdgeListGraphTopology.EdgeData.SubstitutionEvent	getSubstitutionEvent(int subsitiutions) Returns a SubstitutionEvent with appropriate configuration given a number of substitutions.
(package private) EdgeListGraphTopology.EdgeData.Event	nextEvent() Returns the next event on this edge according to this.cur.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

substitutions

int substitutions

The number of substitutions along this branch.

time

int time

The number of time units along this branch.

cur

int cur

The current number of time units traversed along this branch.

events

java.util.ArrayList events

Our list of events, in order.

edge

EdgeListEdge edge

The edge that we're bound to.

data

java.lang.Object data

The data stored in this edge.

substitutionEvent

EdgeListGraphTopology.EdgeData.SubstitutionEvent substitutionEvent

The substitution event to run when substitution should occur.

Constructor Detail

EdgeListGraphTopology.EdgeData

public EdgeListGraphTopology.EdgeData(int substitutions,
                                      int time,
                                      java.lang.Object data,
                                      EdgeListEdge edge)

Constructor for EdgeData objects, specifying all instance variables.

Parameters:

substitutions - the branch length in substitutions.

time - the branch length in time intervals.

data - any extra data that this EdgeData should store.

edge - the Edge that this EdgeData should belong to.

Method Detail

getSubstitutionEvent

EdgeListGraphTopology.EdgeData.SubstitutionEvent getSubstitutionEvent(int subsitiutions)

Returns a SubstitutionEvent with appropriate configuration given a number of substitutions. Each EdgeData stores with it a SubstitutionEvent, which is re-used with each call of this method. As such, this is not thread safe.

Parameters:

subsitiutions - the number of substitutions that the returned SubstitutionEvent should be configured for.

Returns:

the configured SubstitutionEvent.

nextEvent

EdgeListGraphTopology.EdgeData.Event nextEvent()

Returns the next event on this edge according to this.cur. If no events after this.cur are found, and there are children, the fork event is returned. Otherwise, null is returned.

Returns:

the next event on this edge.