org.biojava.nbio.survival.cox

Class SurvivalInfo

java.lang.Object

org.biojava.nbio.survival.cox.SurvivalInfo

All Implemented Interfaces:

Comparable<SurvivalInfo>

public class SurvivalInfo
extends Object
implements 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

Constructor Summary

Constructors

Constructor and Description
SurvivalInfo(double t, int e)
SurvivalInfo(double t, int e, LinkedHashMap<String,Double> d)
SurvivalInfo(double t, int e, String variable, double d)

Method Summary

Modifier and Type	Method and Description
void	addContinuousVariable(String variable, Double value)
void	addUnknownDataTypeVariable(String variable, String value)
int	compareTo(SurvivalInfo o)
String	getClusterValue()
Double	getContinuousVariable(String variable)
ArrayList<String>	getDataVariables()
ArrayList<String>	getGroupCategories(String groupName)
String	getId()
double	getLinearPredictor()
int	getNumberVariables()
double	getOffset()
int	getOrder()
String	getOriginalMetaData(String variable)
double	getResidual()
Double	getResidualVariable(String variable)
double	getScore()
int	getStatus()
int	getStrata()
double	getTime()
String	getUnknownDataTypeVariable(String variable)
Double	getVariable(String variable)
double	getWeight()
void	setClusterValue(String clusterValue)
void	setId(String id)
void	setLinearPredictor(double linearPredictor)
void	setOffset(double offset)
void	setOrder(int order)
void	setResidual(double residual)
void	setResidualVariable(String variable, 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)
String	toString()
void	updateContinousVariable(String variable, Double value)

Methods inherited from class java.lang.Object

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

Constructor Detail

SurvivalInfo

public SurvivalInfo(double t,
                    int e)

Parameters:

t -

e -

SurvivalInfo

public SurvivalInfo(double t,
                    int e,
                    LinkedHashMap<String,Double> d)

Parameters:

t -

e -

d -

SurvivalInfo

public SurvivalInfo(double t,
                    int e,
                    String variable,
                    double d)

Parameters:

t -

e -

variable -

d -

Method Detail

setResidualVariable

public void setResidualVariable(String variable,
                                Double value)

Set the residual value for the variable for this sample. Called from CoxScore.java

Parameters:

variable -

value -

getResidualVariable

public Double getResidualVariable(String variable)

Parameters:

variable -

Returns:

getUnknownDataTypeVariable

public String getUnknownDataTypeVariable(String variable)

Parameters:

variable -

Returns:

getOriginalMetaData

public String getOriginalMetaData(String variable)

Parameters:

variable -

Returns:

addUnknownDataTypeVariable

public void addUnknownDataTypeVariable(String variable,
                                       String value)

Parameters:

variable -

value -

updateContinousVariable

public void updateContinousVariable(String variable,
                                    Double value)

Parameters:

variable -

value -

addContinuousVariable

public void addContinuousVariable(String variable,
                                  Double value)

Parameters:

variable -

value -

getContinuousVariable

public Double getContinuousVariable(String variable)

Parameters:

variable -

Returns:

getGroupCategories

public ArrayList<String> getGroupCategories(String groupName)

Parameters:

groupName -

Returns:

getDataVariables

public ArrayList<String> getDataVariables()

Returns:

getNumberVariables

public int getNumberVariables()

Returns:

getVariable

public Double getVariable(String variable)

Parameters:

variable -

Returns:

toString

public String toString()

Overrides:

toString in class Object

compareTo

public int compareTo(SurvivalInfo o)

Specified by:

compareTo in interface Comparable<SurvivalInfo>

getOffset

public double getOffset()

Returns:

the offset

setOffset

public void setOffset(double offset)

Parameters:

offset - the offset to set

getWeight

public double getWeight()

Returns:

the weight

setWeight

public void setWeight(double weight)

Parameters:

weight - the weight to set

getStrata

public int getStrata()

Returns:

the strata

setStrata

public void setStrata(int strata)

Parameters:

strata - the strata to set

getScore

public double getScore()

Returns:

the score

setScore

public void setScore(double score)

Parameters:

score - the score to set

getLinearPredictor

public double getLinearPredictor()

Returns:

the linearPredictor

setLinearPredictor

public void setLinearPredictor(double linearPredictor)

Parameters:

linearPredictor - the linearPredictor to set

getResidual

public double getResidual()

Returns:

the residual

setResidual

public void setResidual(double residual)

Parameters:

residual - the residual to set

getClusterValue

public String getClusterValue()

Returns:

the clusterValue

setClusterValue

public void setClusterValue(String clusterValue)

Parameters:

clusterValue - the clusterValue to set

getId

public String getId()

Returns:

the id

setId

public void setId(String id)

Parameters:

id - the id to set

getOrder

public int getOrder()

Returns:

the order

setOrder

public void setOrder(int order)

Parameters:

order - the order to set

getTime

public double getTime()

Returns:

the time

setTime

public void setTime(double time)

Parameters:

time - the time to set

getStatus

public int getStatus()

Returns:

the status

setStatus

public void setStatus(int status)

Parameters:

status - the status to set