Package org.biojava.nbio.survival.cox
Class CoxInfo
- java.lang.Object
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- org.biojava.nbio.survival.cox.CoxInfo
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public class CoxInfo extends java.lang.Object
Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R- Author:
- Scooter Willis
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Field Summary
Fields Modifier and Type Field Description ExpressionFigure
ef
KaplanMeierFigure
kmf
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Constructor Summary
Constructors Constructor Description CoxInfo()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
dump()
static java.lang.String
fmt(java.lang.Double d, int precision, int pad)
java.lang.String
fmtpl(java.lang.String d, int pad)
Pad left a string with spacesjava.lang.String
fmtpr(java.lang.String d, int pad)
double
getChiSquare()
CoxCoefficient
getCoefficient(java.lang.String name)
java.util.LinkedHashMap<java.lang.String,CoxCoefficient>
getCoefficientsList()
java.lang.String
getCoefficientText(boolean header, java.lang.String beginLine, java.lang.String beginCell, java.lang.String endCell, java.lang.String endLine)
double
getDegreeFreedom()
double[][]
getImat()
java.util.LinkedHashMap<java.lang.String,java.lang.String>
getMetaDataFilter()
double[][]
getNaive_imat()
double[][]
getNaiveVariance()
int
getNumberCoefficients()
double
getOverallModelFitPvalue()
java.lang.Double
getRscore()
java.lang.Double
getRscoreLogrankTestpvalue()
java.lang.Double
getScoreLogrankTest()
java.lang.Double
getScoreLogrankTestpvalue()
java.util.ArrayList<SurvivalInfo>
getSurvivalInfoList()
double[][]
getVariableResiduals()
double[][]
getVariance()
WaldTestInfo
getWaldTestInfo()
double[]
getWeighted()
void
setCoefficient(java.lang.String name, CoxCoefficient coefficient)
void
setDegreeFreedom(double degreeFreedom)
void
setMetaDataFilter(java.util.LinkedHashMap<java.lang.String,java.lang.String> metaDataFilter)
void
setNaiveVariance(double[][] var)
void
setRscore(java.lang.Double rscore)
void
setRscoreLogrankTestpvalue(java.lang.Double rscoreLogrankTestpvalue)
void
setScoreLogrankTest(java.lang.Double scoreLogrankTest)
void
setScoreLogrankTestpvalue(java.lang.Double scoreLogrankTestpvalue)
void
setSurvivalInfoList(java.util.ArrayList<SurvivalInfo> data)
void
setVariableResiduals(double[][] rr)
void
setVariance(double[][] var)
void
setWaldTestInfo(WaldTestInfo waldTestInfo)
java.lang.String
toString()
java.lang.String
toString(java.lang.String beginLine, java.lang.String del, java.lang.String endLine)
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Field Detail
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kmf
public KaplanMeierFigure kmf
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ef
public ExpressionFigure ef
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Method Detail
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getSurvivalInfoList
public java.util.ArrayList<SurvivalInfo> getSurvivalInfoList()
- Returns:
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setVariance
public void setVariance(double[][] var) throws java.lang.Exception
- Parameters:
var
-- Throws:
java.lang.Exception
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getVariance
public double[][] getVariance()
- Returns:
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setNaiveVariance
public void setNaiveVariance(double[][] var) throws java.lang.Exception
- Parameters:
var
-- Throws:
java.lang.Exception
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getNaiveVariance
public double[][] getNaiveVariance()
- Returns:
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setSurvivalInfoList
public void setSurvivalInfoList(java.util.ArrayList<SurvivalInfo> data)
- Parameters:
data
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getWeighted
public double[] getWeighted()
- Returns:
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getVariableResiduals
public double[][] getVariableResiduals()
- Returns:
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setVariableResiduals
public void setVariableResiduals(double[][] rr)
- Parameters:
rr
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getNumberCoefficients
public int getNumberCoefficients()
- Returns:
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getCoefficient
public CoxCoefficient getCoefficient(java.lang.String name)
- Parameters:
name
-- Returns:
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setCoefficient
public void setCoefficient(java.lang.String name, CoxCoefficient coefficient)
- Parameters:
name
-coefficient
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getCoefficientText
public java.lang.String getCoefficientText(boolean header, java.lang.String beginLine, java.lang.String beginCell, java.lang.String endCell, java.lang.String endLine)
- Parameters:
header
-beginLine
-beginCell
-endCell
-endLine
-- Returns:
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fmt
public static java.lang.String fmt(java.lang.Double d, int precision, int pad)
- Parameters:
d
-precision
-pad
-- Returns:
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dump
public void dump()
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fmtpr
public java.lang.String fmtpr(java.lang.String d, int pad)
- Parameters:
d
-pad
-- Returns:
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fmtpl
public java.lang.String fmtpl(java.lang.String d, int pad)
Pad left a string with spaces- Parameters:
d
-pad
-- Returns:
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toString
public java.lang.String toString(java.lang.String beginLine, java.lang.String del, java.lang.String endLine)
- Parameters:
beginLine
-del
-endLine
-- Returns:
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getChiSquare
public double getChiSquare()
- Returns:
- the scoreLogrankTest
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getDegreeFreedom
public double getDegreeFreedom()
- Returns:
- the degreeFreedom
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getOverallModelFitPvalue
public double getOverallModelFitPvalue()
- Returns:
- the scoreLogrankTestpvalue
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getRscore
public java.lang.Double getRscore()
- Returns:
- the rscore
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setRscore
public void setRscore(java.lang.Double rscore)
- Parameters:
rscore
- the rscore to set
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getRscoreLogrankTestpvalue
public java.lang.Double getRscoreLogrankTestpvalue()
- Returns:
- the rscoreLogrankTestpvalue
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setRscoreLogrankTestpvalue
public void setRscoreLogrankTestpvalue(java.lang.Double rscoreLogrankTestpvalue)
- Parameters:
rscoreLogrankTestpvalue
- the rscoreLogrankTestpvalue to set
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getScoreLogrankTest
public java.lang.Double getScoreLogrankTest()
- Returns:
- the scoreLogrankTest
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setScoreLogrankTest
public void setScoreLogrankTest(java.lang.Double scoreLogrankTest)
- Parameters:
scoreLogrankTest
- the scoreLogrankTest to set
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getScoreLogrankTestpvalue
public java.lang.Double getScoreLogrankTestpvalue()
- Returns:
- the scoreLogrankTestpvalue
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setScoreLogrankTestpvalue
public void setScoreLogrankTestpvalue(java.lang.Double scoreLogrankTestpvalue)
- Parameters:
scoreLogrankTestpvalue
- the scoreLogrankTestpvalue to set
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getMetaDataFilter
public java.util.LinkedHashMap<java.lang.String,java.lang.String> getMetaDataFilter()
- Returns:
- the metaDataFilter
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setMetaDataFilter
public void setMetaDataFilter(java.util.LinkedHashMap<java.lang.String,java.lang.String> metaDataFilter)
- Parameters:
metaDataFilter
- the metaDataFilter to set
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getCoefficientsList
public java.util.LinkedHashMap<java.lang.String,CoxCoefficient> getCoefficientsList()
- Returns:
- the coefficientsList
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getWaldTestInfo
public WaldTestInfo getWaldTestInfo()
- Returns:
- the waldTestInfo
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getImat
public double[][] getImat()
- Returns:
- the imat
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getNaive_imat
public double[][] getNaive_imat()
- Returns:
- the naive_imat
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setDegreeFreedom
public void setDegreeFreedom(double degreeFreedom)
- Parameters:
degreeFreedom
- the degreeFreedom to set
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setWaldTestInfo
public void setWaldTestInfo(WaldTestInfo waldTestInfo)
- Parameters:
waldTestInfo
- the waldTestInfo to set
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