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info.bioinfweb.treegraph.document.io.newick
Class BranchLengthsScaler

java.lang.Object
  info.bioinfweb.treegraph.document.io.newick.BranchLengthsScaler

public class BranchLengthsScaler
extends Object

Sets the branch lengths scale of a tree so that the contained branched have a specific average length. Additionally the small interval of the scale bar is set in a way that it equals about a specified value.

Since:

2.0.24

Author:

Ben Stöver

Field Summary

private int	count
private static BranchLengthsScaler	sharedInstance
private double	sum

Constructor Summary

BranchLengthsScaler()

Method Summary

private void	calculateAverage(Node root)
static BranchLengthsScaler	getSharedInstance()
void	setAverageScale(Tree tree, double averageLength, float smallIntervalLength) Sets the branch lengths scale of a tree so that the contained branched have the specified average length.
void	setDefaultAverageScale(Tree tree) Sets the branch lengths scale of a tree so that the contained branched have BranchFormats.DEFAULT_MIN_LENGTH as their average length.

Methods inherited from class java.lang.Object

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

Field Detail

sharedInstance

private static BranchLengthsScaler sharedInstance

count

private int count

sum

private double sum

Constructor Detail

BranchLengthsScaler

public BranchLengthsScaler()

Method Detail

getSharedInstance

public static BranchLengthsScaler getSharedInstance()

calculateAverage

private void calculateAverage(Node root)

setAverageScale

public void setAverageScale(Tree tree,
                            double averageLength,
                            float smallIntervalLength)

Sets the branch lengths scale of a tree so that the contained branched have the specified average length. Additionally the small interval of the scale bar is set in a way that it equals about a specified value.

Parameters:

tree -

averageLength - the average length in millimeters

smallIntervalLength - the approximate desired length of a small interval of the scale bar in millimeters

setDefaultAverageScale

public void setDefaultAverageScale(Tree tree)

Sets the branch lengths scale of a tree so that the contained branched have BranchFormats.DEFAULT_MIN_LENGTH as their average length. Additionally the small interval of the scale bar is set in a way that it equals about ScaleBarFormats.DEFAULT_SMALL_INTERVAL_IN_MM.

Parameters:

tree -

Since:

2.0.41