Package jebl.evolution.coalescent
Class Intervals
- java.lang.Object
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- jebl.evolution.coalescent.Intervals
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- All Implemented Interfaces:
IntervalList
public class Intervals extends java.lang.Object implements IntervalList
A concrete class for a set of coalescent intevals.- Version:
- $Id: Intervals.java 305 2006-04-26 00:22:30Z rambaut $
- Author:
- Andrew Rambaut, Alexei Drummond
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.evolution.coalescent.IntervalList
IntervalList.IntervalType, IntervalList.Utils
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Constructor Summary
Constructors Constructor Description Intervals(int maxEventCount)
Intervals(RootedTree tree)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 intervaldouble
getInterval(int i)
Gets an interval.int
getIntervalCount()
get number of intervalsIntervalList.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()
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Constructor Detail
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Intervals
public Intervals(RootedTree tree)
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Intervals
public Intervals(int maxEventCount)
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Method Detail
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copyIntervals
public void copyIntervals(Intervals source)
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resetEvents
public void resetEvents()
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addSampleEvent
public void addSampleEvent(double time)
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addCoalescentEvent
public void addCoalescentEvent(double time)
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addMigrationEvent
public void addMigrationEvent(double time, int destination)
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addNothingEvent
public void addNothingEvent(double time)
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getSampleCount
public int getSampleCount()
Description copied from interface:IntervalList
get the total number of sampling events.- Specified by:
getSampleCount
in interfaceIntervalList
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getIntervalCount
public int getIntervalCount()
Description copied from interface:IntervalList
get number of intervals- Specified by:
getIntervalCount
in interfaceIntervalList
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getInterval
public double getInterval(int i)
Description copied from interface:IntervalList
Gets an interval.- Specified by:
getInterval
in interfaceIntervalList
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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 interfaceIntervalList
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getCoalescentEvents
public int getCoalescentEvents(int i)
Description copied from interface:IntervalList
Returns the number coalescent events in an interval- Specified by:
getCoalescentEvents
in interfaceIntervalList
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getIntervalType
public IntervalList.IntervalType getIntervalType(int i)
Description copied from interface:IntervalList
Returns the type of interval observed.- Specified by:
getIntervalType
in interfaceIntervalList
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getTotalDuration
public double getTotalDuration()
Description copied from interface:IntervalList
get the total duration of these intervals.- Specified by:
getTotalDuration
in interfaceIntervalList
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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 interfaceIntervalList
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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 interfaceIntervalList
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