/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.survival.cox;
import java.util.ArrayList;
import java.util.LinkedHashMap;
/**
* 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 <willishf at gmail dot com>
*/
public class SurvivalInfo implements Comparable<SurvivalInfo> {
private String id = "";
private double time;
private int status;
private int order = 0; //not really used but included to keep track of original position if sorting.
private double offset = 0; //offsets for linear predictor ????
private double weight = 1; //used to set weight of survivor for over sampling.
private int strata = 0; // this should be a boolean but leaving as an int
private double score = 0.0;
private double linearPredictor = 0.0;
private double residual = 0.0;
private String clusterValue = "";
LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<String,Double>();
LinkedHashMap<String, Double> data = new LinkedHashMap<String, Double>();
// LinkedHashMap<String, Double> discreteData = new LinkedHashMap<String, Double>();
LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<String, String>();
LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<String,String>();
/**
*
* @param t
* @param e
*/
public SurvivalInfo(double t, int e) {
time = t;
status = e;
}
/**
*
* @param t
* @param e
* @param d
*/
public SurvivalInfo(double t, int e, LinkedHashMap<String, Double> d) {
time = t;
status = e;
data = d;
for(String key : d.keySet()){
Double value = d.get(key);
originalMetaData.put(key, value + "");
}
}
/**
*
* @param t
* @param e
* @param variable
* @param d
*/
public SurvivalInfo(double t, int e, String variable, double d) {
time = t;
status = e;
data.put(variable, d);
originalMetaData.put(variable, String.valueOf(d));
}
/**
* Set the residual value for the variable for this sample. Called from CoxScore.java
* @param variable
* @param value
*/
public void setResidualVariable(String variable, Double value){
residualVariableMap.put(variable, value);
}
/**
*
* @param variable
* @return
*/
public Double getResidualVariable(String variable){
return residualVariableMap.get(variable);
}
/**
*
* @param variable
* @return
*/
public String getUnknownDataTypeVariable(String variable){
return unknownDataType.get(variable);
}
/**
*
* @param variable
* @return
*/
public String getOriginalMetaData(String variable){
return originalMetaData.get(variable);
}
/**
*
* @param variable
* @param value
*/
public void addUnknownDataTypeVariable(String variable, String value) {
originalMetaData.put(variable, value);
unknownDataType.put(variable, value);
}
/**
*
* @param variable
* @param value
*/
public void updateContinousVariable(String variable, Double value){
data.put(variable, value);
}
/**
*
* @param variable
* @param value
*/
public void addContinuousVariable(String variable, Double value) {
originalMetaData.put(variable, value + "");
data.put(variable, value);
}
/**
*
* @param variable
* @return
*/
public Double getContinuousVariable(String variable) {
return data.get(variable);
}
/**
*
* @param groupName
* @return
*/
public ArrayList<String> getGroupCategories(String groupName) {
ArrayList<String> groupNameList = new ArrayList<String>();
for (String key : data.keySet()) {
if (key.startsWith(groupName + "_")) {
groupNameList.add(key);
}
}
return groupNameList;
}
// public void addDiscreteVariable(String variable, double value) {
// discreteData.put(variable, value);
// }
// public Double getDiscreteVariable(String variable) {
// return discreteData.get(variable);
// }
/**
*
* @return
*/
public ArrayList<String> getDataVariables(){
ArrayList<String> v = new ArrayList<String>();
v.addAll(data.keySet());
v.addAll(unknownDataType.keySet());
return v;
}
/**
*
* @return
*/
public int getNumberVariables(){
return data.size();
}
/**
*
* @param variable
* @return
*/
public Double getVariable(String variable) {
Double value = data.get(variable);
return value;
}
@Override
public String toString() {
return "t=" + time + " e=" + status + " o=" + order;
}
// double CompNum4Sort(double[] a, double[] b) {
//(time - time - (status -status) /1024)
// return (a[0] - b[0] - (a[1] - b[1]) / 1024);
// }
@Override
public int compareTo(SurvivalInfo o) {
// return (int) (this.time - o.time - (this.status - o.status) / 1024);
if (time < o.time) {
return -1;
} else if (time > o.time) {
return 1;
} else {
if (this.status == o.status) {
return 0;
} else if (status == 1) {
return -1;
} else {
return 1;
}
}
}
/**
* @return the offset
*/
public double getOffset() {
return offset;
}
/**
* @param offset the offset to set
*/
public void setOffset(double offset) {
this.offset = offset;
}
/**
* @return the weight
*/
public double getWeight() {
return weight;
}
/**
* @param weight the weight to set
*/
public void setWeight(double weight) {
this.weight = weight;
}
/**
* @return the strata
*/
public int getStrata() {
return strata;
}
/**
* @param strata the strata to set
*/
public void setStrata(int strata) {
this.strata = strata;
}
/**
* @return the score
*/
public double getScore() {
return score;
}
/**
* @param score the score to set
*/
public void setScore(double score) {
this.score = score;
}
/**
* @return the linearPredictor
*/
public double getLinearPredictor() {
return linearPredictor;
}
/**
* @param linearPredictor the linearPredictor to set
*/
public void setLinearPredictor(double linearPredictor) {
this.linearPredictor = linearPredictor;
}
/**
* @return the residual
*/
public double getResidual() {
return residual;
}
/**
* @param residual the residual to set
*/
public void setResidual(double residual) {
this.residual = residual;
}
/**
* @return the clusterValue
*/
public String getClusterValue() {
return clusterValue;
}
/**
* @param clusterValue the clusterValue to set
*/
public void setClusterValue(String clusterValue) {
this.clusterValue = clusterValue;
}
/**
* @return the id
*/
public String getId() {
return id;
}
/**
* @param id the id to set
*/
public void setId(String id) {
this.id = id;
}
/**
* @return the order
*/
public int getOrder() {
return order;
}
/**
* @param order the order to set
*/
public void setOrder(int order) {
this.order = order;
}
/**
* @return the time
*/
public double getTime() {
return time;
}
/**
* @param time the time to set
*/
public void setTime(double time) {
this.time = time;
}
/**
* @return the status
*/
public int getStatus() {
return status;
}
/**
* @param status the status to set
*/
public void setStatus(int status) {
this.status = status;
}
}