Package org.biojava.nbio.survival.cox
Class SurvivalInfo
- java.lang.Object
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- org.biojava.nbio.survival.cox.SurvivalInfo
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- All Implemented Interfaces:
java.lang.Comparable<SurvivalInfo>
public class SurvivalInfo extends java.lang.Object implements java.lang.Comparable<SurvivalInfo>
Data class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable. The code handles figuring out if a variables is continuous or categorical. If categorical will convert to numerical values.- Author:
- Scooter Willis
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Constructor Summary
Constructors Constructor Description SurvivalInfo(double t, int e)
SurvivalInfo(double t, int e, java.lang.String variable, double d)
SurvivalInfo(double t, int e, java.util.LinkedHashMap<java.lang.String,java.lang.Double> d)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addContinuousVariable(java.lang.String variable, java.lang.Double value)
void
addUnknownDataTypeVariable(java.lang.String variable, java.lang.String value)
int
compareTo(SurvivalInfo o)
java.lang.String
getClusterValue()
java.lang.Double
getContinuousVariable(java.lang.String variable)
java.util.ArrayList<java.lang.String>
getDataVariables()
java.util.ArrayList<java.lang.String>
getGroupCategories(java.lang.String groupName)
java.lang.String
getId()
double
getLinearPredictor()
int
getNumberVariables()
double
getOffset()
int
getOrder()
java.lang.String
getOriginalMetaData(java.lang.String variable)
double
getResidual()
java.lang.Double
getResidualVariable(java.lang.String variable)
double
getScore()
int
getStatus()
int
getStrata()
double
getTime()
java.lang.String
getUnknownDataTypeVariable(java.lang.String variable)
java.lang.Double
getVariable(java.lang.String variable)
double
getWeight()
void
setClusterValue(java.lang.String clusterValue)
void
setId(java.lang.String id)
void
setLinearPredictor(double linearPredictor)
void
setOffset(double offset)
void
setOrder(int order)
void
setResidual(double residual)
void
setResidualVariable(java.lang.String variable, java.lang.Double value)
Set the residual value for the variable for this sample.void
setScore(double score)
void
setStatus(int status)
void
setStrata(int strata)
void
setTime(double time)
void
setWeight(double weight)
java.lang.String
toString()
void
updateContinousVariable(java.lang.String variable, java.lang.Double value)
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Constructor Detail
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SurvivalInfo
public SurvivalInfo(double t, int e)
- Parameters:
t
-e
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SurvivalInfo
public SurvivalInfo(double t, int e, java.util.LinkedHashMap<java.lang.String,java.lang.Double> d)
- Parameters:
t
-e
-d
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SurvivalInfo
public SurvivalInfo(double t, int e, java.lang.String variable, double d)
- Parameters:
t
-e
-variable
-d
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Method Detail
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setResidualVariable
public void setResidualVariable(java.lang.String variable, java.lang.Double value)
Set the residual value for the variable for this sample. Called from CoxScore.java- Parameters:
variable
-value
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getResidualVariable
public java.lang.Double getResidualVariable(java.lang.String variable)
- Parameters:
variable
-- Returns:
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getUnknownDataTypeVariable
public java.lang.String getUnknownDataTypeVariable(java.lang.String variable)
- Parameters:
variable
-- Returns:
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getOriginalMetaData
public java.lang.String getOriginalMetaData(java.lang.String variable)
- Parameters:
variable
-- Returns:
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addUnknownDataTypeVariable
public void addUnknownDataTypeVariable(java.lang.String variable, java.lang.String value)
- Parameters:
variable
-value
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updateContinousVariable
public void updateContinousVariable(java.lang.String variable, java.lang.Double value)
- Parameters:
variable
-value
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addContinuousVariable
public void addContinuousVariable(java.lang.String variable, java.lang.Double value)
- Parameters:
variable
-value
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getContinuousVariable
public java.lang.Double getContinuousVariable(java.lang.String variable)
- Parameters:
variable
-- Returns:
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getGroupCategories
public java.util.ArrayList<java.lang.String> getGroupCategories(java.lang.String groupName)
- Parameters:
groupName
-- Returns:
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getDataVariables
public java.util.ArrayList<java.lang.String> getDataVariables()
- Returns:
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getNumberVariables
public int getNumberVariables()
- Returns:
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getVariable
public java.lang.Double getVariable(java.lang.String variable)
- Parameters:
variable
-- Returns:
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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compareTo
public int compareTo(SurvivalInfo o)
- Specified by:
compareTo
in interfacejava.lang.Comparable<SurvivalInfo>
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getOffset
public double getOffset()
- Returns:
- the offset
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setOffset
public void setOffset(double offset)
- Parameters:
offset
- the offset to set
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getWeight
public double getWeight()
- Returns:
- the weight
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setWeight
public void setWeight(double weight)
- Parameters:
weight
- the weight to set
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getStrata
public int getStrata()
- Returns:
- the strata
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setStrata
public void setStrata(int strata)
- Parameters:
strata
- the strata to set
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getScore
public double getScore()
- Returns:
- the score
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setScore
public void setScore(double score)
- Parameters:
score
- the score to set
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getLinearPredictor
public double getLinearPredictor()
- Returns:
- the linearPredictor
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setLinearPredictor
public void setLinearPredictor(double linearPredictor)
- Parameters:
linearPredictor
- the linearPredictor to set
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getResidual
public double getResidual()
- Returns:
- the residual
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setResidual
public void setResidual(double residual)
- Parameters:
residual
- the residual to set
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getClusterValue
public java.lang.String getClusterValue()
- Returns:
- the clusterValue
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setClusterValue
public void setClusterValue(java.lang.String clusterValue)
- Parameters:
clusterValue
- the clusterValue to set
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getId
public java.lang.String getId()
- Returns:
- the id
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setId
public void setId(java.lang.String id)
- Parameters:
id
- the id to set
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getOrder
public int getOrder()
- Returns:
- the order
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setOrder
public void setOrder(int order)
- Parameters:
order
- the order to set
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getTime
public double getTime()
- Returns:
- the time
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setTime
public void setTime(double time)
- Parameters:
time
- the time to set
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getStatus
public int getStatus()
- Returns:
- the status
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setStatus
public void setStatus(int status)
- Parameters:
status
- the status to set
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