org.forester.phylogeny.data

Class Confidence

java.lang.Object

org.forester.phylogeny.data.Confidence

All Implemented Interfaces:

Comparable<Confidence>, PhylogenyData

public class Confidence
extends Object
implements PhylogenyData, Comparable<Confidence>

Field Summary

Fields

Modifier and Type	Field and Description
static int	CONFIDENCE_DEFAULT_VALUE
static NumberFormat	FORMATTER

Constructor Summary

Constructors

Constructor and Description
Confidence()
Confidence(double value, String type)
Confidence(double value, String type, double sd)

Method Summary

Modifier and Type	Method and Description
StringBuffer	asSimpleText()
StringBuffer	asText()
int	compareTo(Confidence confidence)
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
double	getStandardDeviation()
String	getType()
double	getValue()
void	init()
boolean	isEqual(PhylogenyData confidence) Compares this PhylogenyData to PhylogenyData data.
void	setStandardDeviation(double sd)
void	setType(String type)
void	setValue(double value)
StringBuffer	toNHX()
void	toPhyloXML(Writer writer, int level, String indentation) Writes a phyloXML representation of this phylogeny data.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

CONFIDENCE_DEFAULT_VALUE

public static final int CONFIDENCE_DEFAULT_VALUE

See Also:

Constant Field Values

FORMATTER

public static final NumberFormat FORMATTER

Constructor Detail

Confidence

public Confidence()

Confidence

public Confidence(double value,
                  String type)

Confidence

public Confidence(double value,
                  String type,
                  double sd)

Method Detail

asSimpleText

public StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()

Specified by:

asText in interface PhylogenyData

compareTo

public int compareTo(Confidence confidence)

Specified by:

compareTo in interface Comparable<Confidence>

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

getType

public String getType()

getValue

public double getValue()

getStandardDeviation

public double getStandardDeviation()

init

public void init()

isEqual

public boolean isEqual(PhylogenyData confidence)

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

setType

public void setType(String type)

setValue

public void setValue(double value)

setStandardDeviation

public void setStandardDeviation(double sd)

toNHX

public StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object