jebl.evolution.coalescent
Interface IntervalList

All Known Implementing Classes:

Intervals

public interface IntervalList

An interface for a set of coalescent intevals.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

static class	IntervalList.IntervalType
static class	IntervalList.Utils

Method Summary

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.

Method Detail

getIntervalCount

int getIntervalCount()

get number of intervals

getSampleCount

int getSampleCount()

get the total number of sampling events.

getInterval

double getInterval(int i)

Gets an interval.

getLineageCount

int getLineageCount(int i)

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

getCoalescentEvents

int getCoalescentEvents(int i)

Returns the number coalescent events in an interval

getIntervalType

IntervalList.IntervalType getIntervalType(int i)

Returns the type of interval observed.

getTotalDuration

double getTotalDuration()

get the total duration of these intervals.

isBinaryCoalescent

boolean isBinaryCoalescent()

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

isCoalescentOnly

boolean isCoalescentOnly()

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