From f1c5b292ed7caf06b99ed8a8f50508e704960ad4 Mon Sep 17 00:00:00 2001
From: Joel Therrien <joelt@sfu.ca>
Date: Fri, 2 Aug 2019 15:10:48 -0700
Subject: [PATCH] Add serialVersionUID to Serializable classes

This makes forests between versions more compatible if only method definitions changed.
---
 .../randomforest/CovariateRow.java            |  2 +
 .../covariates/bool/BooleanCovariate.java     |  4 +
 .../covariates/bool/BooleanSplitRule.java     |  2 +
 .../covariates/factor/FactorCovariate.java    |  4 +
 .../covariates/factor/FactorSplitRule.java    |  2 +
 .../covariates/numeric/NumericCovariate.java  |  4 +
 .../covariates/numeric/NumericSplitRule.java  |  2 +
 .../competingrisk/CompetingRiskFunctions.java |  2 +
 .../competingrisk/CompetingRiskResponse.java  |  2 +
 .../CompetingRiskResponseWithCensorTime.java  |  3 +
 .../CompetingRiskFunctionCombiner.java        |  2 +
 .../CompetingRiskResponseCombiner.java        |  2 +
 .../splitfinder/GrayLogRankSplitFinder.java   |  1 +
 .../splitfinder/LogRankSplitFinder.java       |  1 +
 .../regression/MeanResponseCombiner.java      |  1 +
 .../WeightedVarianceSplitFinder.java          |  1 +
 .../randomforest/tree/SplitNode.java          |  1 +
 .../randomforest/tree/TerminalNode.java       |  1 +
 .../joeltherrien/randomforest/tree/Tree.java  |  1 +
 .../randomforest/utils/Point.java             |  2 +
 .../utils/RightContinuousStepFunction.java    |  2 +
 .../utils/VeryDiscontinuousStepFunction.java  | 80 -------------------
 22 files changed, 42 insertions(+), 80 deletions(-)
 delete mode 100644 library/src/main/java/ca/joeltherrien/randomforest/utils/VeryDiscontinuousStepFunction.java

diff --git a/library/src/main/java/ca/joeltherrien/randomforest/CovariateRow.java b/library/src/main/java/ca/joeltherrien/randomforest/CovariateRow.java
index 3e053bf..89b6c27 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/CovariateRow.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/CovariateRow.java
@@ -27,6 +27,8 @@ import java.util.stream.Collectors;
 @RequiredArgsConstructor
 public class CovariateRow implements Serializable, Cloneable {
 
+    private static final long serialVersionUID = 1L;
+
     private final Covariate.Value[] valueArray;
 
     @Getter
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanCovariate.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanCovariate.java
index 797378b..824c5eb 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanCovariate.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanCovariate.java
@@ -28,6 +28,8 @@ import java.util.Random;
 
 public final class BooleanCovariate implements Covariate<Boolean> {
 
+    private static final long serialVersionUID = 1L;
+
     @Getter
     private final String name;
 
@@ -84,6 +86,8 @@ public final class BooleanCovariate implements Covariate<Boolean> {
 
     public class BooleanValue implements Value<Boolean>{
 
+        private static final long serialVersionUID = 1L;
+
         private final Boolean value;
 
         private BooleanValue(final Boolean value){
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanSplitRule.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanSplitRule.java
index 813d13a..dfdf2fd 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanSplitRule.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/bool/BooleanSplitRule.java
@@ -21,6 +21,8 @@ import ca.joeltherrien.randomforest.covariates.SplitRule;
 
 public class BooleanSplitRule implements SplitRule<Boolean> {
 
+    private static final long serialVersionUID = 1L;
+
     private final int parentCovariateIndex;
 
     public BooleanSplitRule(BooleanCovariate parent){
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorCovariate.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorCovariate.java
index b3eb245..63db922 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorCovariate.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorCovariate.java
@@ -26,6 +26,8 @@ import java.util.*;
 
 public final class FactorCovariate implements Covariate<String> {
 
+    private static final long serialVersionUID = 1L;
+
     @Getter
     private final String name;
 
@@ -122,6 +124,8 @@ public final class FactorCovariate implements Covariate<String> {
     @EqualsAndHashCode
     public final class FactorValue implements Covariate.Value<String>{
 
+        private static final long serialVersionUID = 1L;
+
         private final String value;
 
         private FactorValue(final String value){
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorSplitRule.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorSplitRule.java
index 7fb4b4c..56b613f 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorSplitRule.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/factor/FactorSplitRule.java
@@ -25,6 +25,8 @@ import java.util.Set;
 @EqualsAndHashCode
 public final class FactorSplitRule implements SplitRule<String> {
 
+    private static final long serialVersionUID = 1L;
+
     private final int parentCovariateIndex;
     private final Set<String> leftSideValues;
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericCovariate.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericCovariate.java
index 6c1c490..9b65187 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericCovariate.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericCovariate.java
@@ -37,6 +37,8 @@ import java.util.stream.Stream;
 @ToString
 public final class NumericCovariate implements Covariate<Double> {
 
+    private static final long serialVersionUID = 1L;
+
     @Getter
     private final String name;
 
@@ -122,6 +124,8 @@ public final class NumericCovariate implements Covariate<Double> {
     @EqualsAndHashCode
     public class NumericValue implements Covariate.Value<Double>{
 
+        private static final long serialVersionUID = 1L;
+
         private final Double value; // may be null
 
         private NumericValue(final Double value){
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericSplitRule.java b/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericSplitRule.java
index 43b0c95..dd7e4a3 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericSplitRule.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/covariates/numeric/NumericSplitRule.java
@@ -23,6 +23,8 @@ import lombok.EqualsAndHashCode;
 @EqualsAndHashCode
 public class NumericSplitRule implements SplitRule<Double> {
 
+    private static final long serialVersionUID = 1L;
+
     private final int parentCovariateIndex;
     private final double threshold;
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
index 7dcddfb..7b1218d 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
@@ -26,6 +26,8 @@ import java.util.List;
 @Builder
 public class CompetingRiskFunctions implements Serializable {
 
+    private static final long serialVersionUID = 1L;
+
     private final List<RightContinuousStepFunction> causeSpecificHazards;
     private final List<RightContinuousStepFunction> cumulativeIncidenceCurves;
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponse.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponse.java
index afdc4bf..2a94ecd 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponse.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponse.java
@@ -23,6 +23,8 @@ import java.io.Serializable;
 @Data
 public class CompetingRiskResponse implements Serializable {
 
+    private static final long serialVersionUID = 1L;
+
     private final int delta;
     private final double u;
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponseWithCensorTime.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponseWithCensorTime.java
index a2fcc7e..e1086b4 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponseWithCensorTime.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponseWithCensorTime.java
@@ -26,6 +26,9 @@ import lombok.EqualsAndHashCode;
 @EqualsAndHashCode(callSuper = true)
 @Data
 public final class CompetingRiskResponseWithCensorTime extends CompetingRiskResponse {
+
+    private static final long serialVersionUID = 1L;
+
     private final double c;
 
     public CompetingRiskResponseWithCensorTime(int delta, double u, double c) {
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
index ee8292a..89d55f5 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
@@ -29,6 +29,8 @@ import java.util.List;
 @RequiredArgsConstructor
 public class CompetingRiskFunctionCombiner implements ResponseCombiner<CompetingRiskFunctions, CompetingRiskFunctions> {
 
+    private static final long serialVersionUID = 1L;
+
     private final int[] events;
     private final double[] times; // We may restrict ourselves to specific times.
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
index 0ff9ef8..8f2515b 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
@@ -35,6 +35,8 @@ import java.util.List;
  */
 public class CompetingRiskResponseCombiner implements ResponseCombiner<CompetingRiskResponse, CompetingRiskFunctions> {
 
+    private static final long serialVersionUID = 1L;
+
     private final int[] events;
 
     public CompetingRiskResponseCombiner(final int[] events){
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/GrayLogRankSplitFinder.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/GrayLogRankSplitFinder.java
index b6eed13..c34e975 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/GrayLogRankSplitFinder.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/GrayLogRankSplitFinder.java
@@ -28,6 +28,7 @@ import java.util.List;
  *
  */
 public class GrayLogRankSplitFinder extends CompetingRiskSplitFinder<CompetingRiskResponseWithCensorTime> {
+    private static final long serialVersionUID = 1L;
 
     private final int[] eventsOfFocus;
     private final int[] events;
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder.java
index c31bb84..b0787b2 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder.java
@@ -28,6 +28,7 @@ import java.util.List;
  *
  */
 public class LogRankSplitFinder extends CompetingRiskSplitFinder<CompetingRiskResponse> {
+    private static final long serialVersionUID = 1L;
 
     private final int[] eventsOfFocus;
     private final int[] events;
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/MeanResponseCombiner.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/MeanResponseCombiner.java
index 137c02c..a6a65d0 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/MeanResponseCombiner.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/MeanResponseCombiner.java
@@ -25,6 +25,7 @@ import java.util.List;
  *
  */
 public class MeanResponseCombiner implements ResponseCombiner<Double, Double> {
+    private static final long serialVersionUID = 1L;
 
     @Override
     public Double combine(List<Double> responses) {
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder.java b/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder.java
index 9fb4d43..f903d65 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder.java
@@ -27,6 +27,7 @@ import java.util.List;
 import java.util.stream.Collectors;
 
 public class WeightedVarianceSplitFinder implements SplitFinder<Double> {
+    private static final long serialVersionUID = 1L;
 
     private Double getScore(Set leftHand, Set rightHand) {
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/tree/SplitNode.java b/library/src/main/java/ca/joeltherrien/randomforest/tree/SplitNode.java
index f3bd170..8dedaae 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/tree/SplitNode.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/tree/SplitNode.java
@@ -29,6 +29,7 @@ import java.util.List;
 @ToString
 @Getter
 public class SplitNode<Y> implements Node<Y> {
+    private static final long serialVersionUID = 1L;
 
     private final Node<Y> leftHand;
     private final Node<Y> rightHand;
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/tree/TerminalNode.java b/library/src/main/java/ca/joeltherrien/randomforest/tree/TerminalNode.java
index 17c6249..06ad951 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/tree/TerminalNode.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/tree/TerminalNode.java
@@ -27,6 +27,7 @@ import java.util.List;
 @RequiredArgsConstructor
 @ToString
 public class TerminalNode<Y> implements Node<Y> {
+    private static final long serialVersionUID = 1L;
 
     private final Y responseValue;
 
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/tree/Tree.java b/library/src/main/java/ca/joeltherrien/randomforest/tree/Tree.java
index fdf4919..baab407 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/tree/Tree.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/tree/Tree.java
@@ -23,6 +23,7 @@ import java.util.Arrays;
 import java.util.List;
 
 public class Tree<Y> implements Node<Y> {
+    private static final long serialVersionUID = 1L;
 
     @Getter
     private final Node<Y> rootNode;
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/utils/Point.java b/library/src/main/java/ca/joeltherrien/randomforest/utils/Point.java
index 75fad2f..754a4fc 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/utils/Point.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/utils/Point.java
@@ -26,6 +26,8 @@ import java.io.Serializable;
  */
 @Data
 public class Point implements Serializable {
+    private static final long serialVersionUID = 1L;
+
     private final double time;
     private final double y;
 }
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunction.java b/library/src/main/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunction.java
index 5cc673e..2ae8056 100644
--- a/library/src/main/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunction.java
+++ b/library/src/main/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunction.java
@@ -30,6 +30,8 @@ import java.util.function.DoubleUnaryOperator;
  */
 public final class RightContinuousStepFunction extends StepFunction {
 
+    private static final long serialVersionUID = 1L;
+
     private final double[] y;
 
     /**
diff --git a/library/src/main/java/ca/joeltherrien/randomforest/utils/VeryDiscontinuousStepFunction.java b/library/src/main/java/ca/joeltherrien/randomforest/utils/VeryDiscontinuousStepFunction.java
deleted file mode 100644
index ce6827c..0000000
--- a/library/src/main/java/ca/joeltherrien/randomforest/utils/VeryDiscontinuousStepFunction.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright (c) 2019 Joel Therrien.
- *     This program is free software: you can redistribute it and/or modify
- *     it under the terms of the GNU General Public License as published by
- *     the Free Software Foundation, either version 3 of the License, or
- *     (at your option) any later version.
- *
- *     This program is distributed in the hope that it will be useful,
- *     but WITHOUT ANY WARRANTY; without even the implied warranty of
- *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *     GNU General Public License for more details.
- *
- *     You should have received a copy of the GNU General Public License
- *     along with this program.  If not, see <https://www.gnu.org/licenses/>.
- */
-
-package ca.joeltherrien.randomforest.utils;
-
-/**
- * Represents a step function represented by discrete points. However, there may be individual time values that has
- * a y value that doesn't belong to a particular 'step'.
- */
-public final class VeryDiscontinuousStepFunction implements MathFunction {
-
-    private final double[] x;
-    private final double[] yAt;
-    private final double[] yRight;
-
-    /**
-     * Represents the value that should be returned by evaluate if there are points prior to the time the function is being evaluated at.
-     *
-     * Map be null.
-     */
-    private final double defaultY;
-
-    public VeryDiscontinuousStepFunction(double[] x, double[] yAt, double[] yRight, double defaultY) {
-        this.x = x;
-        this.yAt = yAt;
-        this.yRight = yRight;
-        this.defaultY = defaultY;
-    }
-
-    @Override
-    public double evaluate(double time){
-        int index = Utils.binarySearchLessThan(0, x.length, x, time);
-        if(index < 0){
-            return defaultY;
-        }
-        else{
-            if(x[index] == time){
-                return yAt[index];
-            }
-            else{ // time > x[index]
-                return yRight[index];
-            }
-        }
-    }
-
-
-    @Override
-    public String toString(){
-        final StringBuilder builder = new StringBuilder();
-        builder.append("Default point: ");
-        builder.append(defaultY);
-        builder.append("\n");
-
-        for(int i=0; i<x.length; i++){
-            builder.append("x:");
-            builder.append(x[i]);
-            builder.append("\tyAt:");
-            builder.append(yAt[i]);
-            builder.append("\tyRight:");
-            builder.append(yRight[i]);
-            builder.append("\n");
-        }
-
-        return builder.toString();
-    }
-
-}