jebl.evolution.trees
Class CalculateSplitRates

java.lang.Object
  extended by jebl.evolution.trees.CalculateSplitRates

public class CalculateSplitRates
extends java.lang.Object

Created by IntelliJ IDEA. User: msuchard Date: Dec 18, 2006 Time: 1:13:51 PM To change this template use File | Settings | File Templates.


Field Summary
 double edgeFraction
           
 java.lang.String INDICATOR
           
 int numRateBoxes
           
 int numTimeBoxes
           
 java.lang.String RATE
           
 
Constructor Summary
CalculateSplitRates(NexusImporter importer)
           
 
Method Summary
 void addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap, RootedTree tree)
           
 void displayIntervals()
           
 void displayStatistics()
           
 void findTimeIntervals()
           
 void loadTrees(int maxTrees, int burnIn)
           
static void main(java.lang.String[] args)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

INDICATOR

public final java.lang.String INDICATOR
See Also:
Constant Field Values

RATE

public final java.lang.String RATE
See Also:
Constant Field Values

numRateBoxes

public int numRateBoxes

numTimeBoxes

public int numTimeBoxes

edgeFraction

public double edgeFraction
Constructor Detail

CalculateSplitRates

public CalculateSplitRates(NexusImporter importer)
Method Detail

loadTrees

public void loadTrees(int maxTrees,
                      int burnIn)
               throws java.io.IOException,
                      ImportException
Throws:
java.io.IOException
ImportException

displayStatistics

public void displayStatistics()

addTreeToDensityMap

public void addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap,
                                RootedTree tree)

displayIntervals

public void displayIntervals()

findTimeIntervals

public void findTimeIntervals()

main

public static void main(java.lang.String[] args)
Parameters:
args - args[0] = Beast tree log, args[1] = max number of trees to read args[2] = number of burnin trees to discard args[3] = proportion file name, args[4] = density map filename


http://code.google.com/p/jebl2/