Class IntervalsExtractor

java.lang.Object
pal.coalescent.IntervalsExtractor
All Implemented Interfaces:
Units

public class IntervalsExtractor extends Object implements Units
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
Version:
$Id: IntervalsExtractor.java,v 1.12 2001/07/12 12:17:43 korbinian Exp $
Author:
Alexei Drummond, Korbinian Strimmer
  • Constructor Details

    • IntervalsExtractor

      public IntervalsExtractor()
  • Method Details

    • extractFromClockTree

      public static CoalescentIntervals extractFromClockTree(Tree tree)
      extracts intervals from clock tree.
    • extractFromClockTree

      public static CoalescentIntervals extractFromClockTree(Tree tree, double minSize)
      extracts intervals from clock tree. Leafs are assumed to have height zero. Starting at time zero, small (invalid input: '<'= minSize) intervals are pooled with the next non-small interval (if this does not exist then with the previous non-small interval)
    • extractFromTree

      public static CoalescentIntervals extractFromTree(Tree tree, MutationRateModel muModel)
      extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.
    • extractFromTree

      public static CoalescentIntervals extractFromTree(Tree tree)
      extracts intervals from serial clock tree.