pal.coalescent
Class IntervalsExtractor

java.lang.Object
  pal.coalescent.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

Field Summary

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

IntervalsExtractor()

Method Summary

static CoalescentIntervals	extractFromClockTree(Tree tree) extracts intervals from clock tree.
static CoalescentIntervals	extractFromClockTree(Tree tree, double minSize) extracts intervals from clock tree.
static CoalescentIntervals	extractFromTree(Tree tree) extracts intervals from serial clock tree.
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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.