Class IntervalsExtractor

  • All Implemented Interfaces:
    Units

    public class IntervalsExtractor
    extends java.lang.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 Detail

      • IntervalsExtractor

        public IntervalsExtractor()
    • Method Detail

      • 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 (<= 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.