jebl.evolution.coalescent
Class Intervals

java.lang.Object
  jebl.evolution.coalescent.Intervals

All Implemented Interfaces:

IntervalList

public class Intervals
extends Object
implements IntervalList

A concrete class for a set of coalescent intevals.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.evolution.coalescent.IntervalList

IntervalList.IntervalType, IntervalList.Utils

Constructor Summary

Intervals(int maxEventCount)

Intervals(RootedTree tree)

Method Summary

void	addCoalescentEvent(double time)
void	addMigrationEvent(double time, int destination)
void	addNothingEvent(double time)
void	addSampleEvent(double time)
void	copyIntervals(Intervals source)
int	getCoalescentEvents(int i) Returns the number coalescent events in an interval
double	getInterval(int i) Gets an interval.
int	getIntervalCount() get number of intervals
IntervalList.IntervalType	getIntervalType(int i) Returns the type of interval observed.
int	getLineageCount(int i) Returns the number of uncoalesced lineages within this interval.
int	getSampleCount() get the total number of sampling events.
double	getTotalDuration() get the total duration of these intervals.
boolean	isBinaryCoalescent() Checks whether this set of coalescent intervals is fully resolved (i.e.
boolean	isCoalescentOnly() Checks whether this set of coalescent intervals coalescent only (i.e.
void	resetEvents()

Methods inherited from class java.lang.Object

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

Constructor Detail

Intervals

public Intervals(RootedTree tree)

Intervals

public Intervals(int maxEventCount)

Method Detail

copyIntervals

public void copyIntervals(Intervals source)

resetEvents

public void resetEvents()

addSampleEvent

public void addSampleEvent(double time)

addCoalescentEvent

public void addCoalescentEvent(double time)

addMigrationEvent

public void addMigrationEvent(double time,
                              int destination)

addNothingEvent

public void addNothingEvent(double time)

getSampleCount

public int getSampleCount()

Description copied from interface: IntervalList

get the total number of sampling events.

Specified by:

getSampleCount in interface IntervalList

getIntervalCount

public int getIntervalCount()

Description copied from interface: IntervalList

get number of intervals

Specified by:

getIntervalCount in interface IntervalList

getInterval

public double getInterval(int i)

Description copied from interface: IntervalList

Gets an interval.

Specified by:

getInterval in interface IntervalList

getLineageCount

public int getLineageCount(int i)

Description copied from interface: IntervalList

Returns the number of uncoalesced lineages within this interval. Required for s-coalescents, where new lineages are added as earlier samples are come across.

Specified by:

getLineageCount in interface IntervalList

getCoalescentEvents

public int getCoalescentEvents(int i)

Description copied from interface: IntervalList

Returns the number coalescent events in an interval

Specified by:

getCoalescentEvents in interface IntervalList

getIntervalType

public IntervalList.IntervalType getIntervalType(int i)

Description copied from interface: IntervalList

Returns the type of interval observed.

Specified by:

getIntervalType in interface IntervalList

getTotalDuration

public double getTotalDuration()

Description copied from interface: IntervalList

get the total duration of these intervals.

Specified by:

getTotalDuration in interface IntervalList

isBinaryCoalescent

public boolean isBinaryCoalescent()

Description copied from interface: IntervalList

Checks whether this set of coalescent intervals is fully resolved (i.e. whether is has exactly one coalescent event in each subsequent interval)

Specified by:

isBinaryCoalescent in interface IntervalList

isCoalescentOnly

public boolean isCoalescentOnly()

Description copied from interface: IntervalList

Checks whether this set of coalescent intervals coalescent only (i.e. whether is has exactly one or more coalescent event in each subsequent interval)

Specified by:

isCoalescentOnly in interface IntervalList