Package jebl.evolution.coalescent

Class Intervals

  • 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

    • 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

      • 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

      • 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