org.forester.phylogeny.data
Class Confidence

java.lang.Object
  extended by org.forester.phylogeny.data.Confidence
All Implemented Interfaces:
Comparable<Confidence>, PhylogenyData

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


Field Summary
static double CONFIDENCE_DEFAULT_VALUE
           
 
Constructor Summary
Confidence()
           
Confidence(double value, String type)
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 int compareTo(Confidence confidence)
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 String getType()
           
 double getValue()
           
 void init()
           
 boolean isEqual(PhylogenyData confidence)
          Compares this PhylogenyData to PhylogenyData data.
 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 double CONFIDENCE_DEFAULT_VALUE
See Also:
Constant Field Values
Constructor Detail

Confidence

public Confidence()

Confidence

public Confidence(double value,
                  String type)
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()

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)

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