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.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
IntervalsExtractor
public IntervalsExtractor()
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.