Package pal.coalescent
Class IntervalsExtractor
java.lang.Object
pal.coalescent.IntervalsExtractor
- All Implemented Interfaces:
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
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 -
Method Summary
Modifier and TypeMethodDescriptionstatic 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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Constructor Details
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IntervalsExtractor
public IntervalsExtractor()
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Method Details
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extractFromClockTree
extracts intervals from clock tree. -
extractFromClockTree
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
extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model. -
extractFromTree
extracts intervals from serial clock tree.
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