Package org.forester.phylogeny.data
Class Confidence
- java.lang.Object
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- org.forester.phylogeny.data.Confidence
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- All Implemented Interfaces:
java.lang.Comparable<Confidence>
,PhylogenyData
public class Confidence extends java.lang.Object implements PhylogenyData, java.lang.Comparable<Confidence>
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Field Summary
Fields Modifier and Type Field Description static int
CONFIDENCE_DEFAULT_VALUE
static java.text.NumberFormat
FORMATTER
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Constructor Summary
Constructors Constructor Description Confidence()
Confidence(double value, java.lang.String type)
Confidence(double value, java.lang.String type, double sd)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.StringBuffer
asSimpleText()
java.lang.StringBuffer
asText()
int
compareTo(Confidence confidence)
PhylogenyData
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.double
getStandardDeviation()
java.lang.String
getType()
double
getValue()
void
init()
boolean
isEqual(PhylogenyData confidence)
Compares this PhylogenyData to PhylogenyData data.void
setStandardDeviation(double sd)
void
setType(java.lang.String type)
void
setValue(double value)
java.lang.StringBuffer
toNHX()
void
toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation)
Writes a phyloXML representation of this phylogeny data.java.lang.String
toString()
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Field Detail
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CONFIDENCE_DEFAULT_VALUE
public static final int CONFIDENCE_DEFAULT_VALUE
- See Also:
- Constant Field Values
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FORMATTER
public static final java.text.NumberFormat FORMATTER
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Method Detail
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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compareTo
public int compareTo(Confidence confidence)
- Specified by:
compareTo
in interfacejava.lang.Comparable<Confidence>
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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 interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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getType
public java.lang.String getType()
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getValue
public double getValue()
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getStandardDeviation
public double getStandardDeviation()
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init
public void init()
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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 interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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setType
public void setType(java.lang.String type)
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setValue
public void setValue(double value)
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setStandardDeviation
public void setStandardDeviation(double sd)
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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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 interfacePhylogenyData
- Throws:
java.io.IOException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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