Package 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.
Version:
$Id: Intervals.java 305 2006-04-26 00:22:30Z rambaut $
Author:
Andrew Rambaut, Alexei Drummond

  • Constructor Details

    • Intervals

      public Intervals(RootedTree tree)

    • Intervals

      public Intervals(int maxEventCount)

  • Method Details

    • 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