Package pal.coalescent
Class IntervalsExtractor
- java.lang.Object
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- pal.coalescent.IntervalsExtractor
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- 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
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Field Summary
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Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
Constructors Constructor Description IntervalsExtractor()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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.
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Method Detail
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extractFromClockTree
public static CoalescentIntervals extractFromClockTree(Tree tree)
extracts intervals from clock tree.
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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)
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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.
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extractFromTree
public static CoalescentIntervals extractFromTree(Tree tree)
extracts intervals from serial clock tree.
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