org.forester.phylogeny.data

Class BranchData

java.lang.Object

org.forester.phylogeny.data.BranchData

All Implemented Interfaces:

PhylogenyData

public class BranchData
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
BranchData()

Method Summary

Methods

Modifier and Type	Method and Description
void	addConfidence(Confidence confidence)
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
BranchColor	getBranchColor()
BranchWidth	getBranchWidth()
Confidence	getConfidence(int index)
java.util.List<Confidence>	getConfidences()
int	getNumberOfConfidences()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
boolean	isHasBranchColor()
boolean	isHasBranchWidth()
boolean	isHasConfidences()
void	setBranchColor(BranchColor branch_color)
void	setBranchWidth(BranchWidth branch_width)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.

Methods inherited from class java.lang.Object

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

Constructor Detail

BranchData

public BranchData()

Method Detail

addConfidence

public void addConfidence(Confidence confidence)

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public PhylogenyData copy()

Description copied from interface: PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getBranchColor

public BranchColor getBranchColor()

getBranchWidth

public BranchWidth getBranchWidth()

getConfidence

public Confidence getConfidence(int index)

getConfidences

public java.util.List<Confidence> getConfidences()

getNumberOfConfidences

public int getNumberOfConfidences()

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

isHasBranchColor

public boolean isHasBranchColor()

isHasBranchWidth

public boolean isHasBranchWidth()

isHasConfidences

public boolean isHasConfidences()

setBranchColor

public void setBranchColor(BranchColor branch_color)

setBranchWidth

public void setBranchWidth(BranchWidth branch_width)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException