From 83ee6fc8f03faa819a859919554a9d87963ab755 Mon Sep 17 00:00:00 2001
From: "ubjinn@gmail.com" <Qudepimu2@>
Date: Tue, 30 Oct 2018 23:18:24 +1100
Subject: [PATCH 01/11] Default complexities set to 1

---
 .../iconic/ea/operator/primitive/AbsoluteValue.java    |  2 +-
 .../org/iconic/ea/operator/primitive/Addition.java     |  2 +-
 .../java/org/iconic/ea/operator/primitive/And.java     |  2 +-
 .../java/org/iconic/ea/operator/primitive/ArcCos.java  |  2 +-
 .../java/org/iconic/ea/operator/primitive/ArcSin.java  |  2 +-
 .../java/org/iconic/ea/operator/primitive/ArcTan.java  |  2 +-
 .../ea/operator/primitive/ArithmeticPrimitive.java     |  4 ++++
 .../java/org/iconic/ea/operator/primitive/Ceiling.java |  2 +-
 .../org/iconic/ea/operator/primitive/Constant.java     | 10 +++++-----
 .../java/org/iconic/ea/operator/primitive/Cos.java     |  2 +-
 .../org/iconic/ea/operator/primitive/Division.java     |  2 +-
 .../java/org/iconic/ea/operator/primitive/EqualTo.java |  2 +-
 .../org/iconic/ea/operator/primitive/Exponential.java  |  2 +-
 .../java/org/iconic/ea/operator/primitive/Floor.java   |  2 +-
 .../ea/operator/primitive/FunctionalPrimitive.java     |  9 +++++++++
 .../iconic/ea/operator/primitive/GaussianFunction.java |  2 +-
 .../org/iconic/ea/operator/primitive/GreaterThan.java  |  2 +-
 .../ea/operator/primitive/GreaterThanOrEqual.java      |  2 +-
 .../org/iconic/ea/operator/primitive/IfThenElse.java   |  2 +-
 .../org/iconic/ea/operator/primitive/LessThan.java     |  2 +-
 .../iconic/ea/operator/primitive/LessThanOrEqual.java  |  2 +-
 .../iconic/ea/operator/primitive/LogisticFunction.java |  2 +-
 .../java/org/iconic/ea/operator/primitive/Maximum.java |  2 +-
 .../java/org/iconic/ea/operator/primitive/Minimum.java |  2 +-
 .../java/org/iconic/ea/operator/primitive/Modulo.java  |  2 +-
 .../iconic/ea/operator/primitive/Multiplication.java   |  2 +-
 .../org/iconic/ea/operator/primitive/NaturalLog.java   |  2 +-
 .../org/iconic/ea/operator/primitive/Negation.java     |  2 +-
 .../java/org/iconic/ea/operator/primitive/Not.java     |  2 +-
 .../main/java/org/iconic/ea/operator/primitive/Or.java |  2 +-
 .../java/org/iconic/ea/operator/primitive/Power.java   |  2 +-
 .../java/org/iconic/ea/operator/primitive/Root.java    |  2 +-
 .../org/iconic/ea/operator/primitive/SignFunction.java |  2 +-
 .../java/org/iconic/ea/operator/primitive/Sin.java     |  2 +-
 .../org/iconic/ea/operator/primitive/SquareRoot.java   |  2 +-
 .../org/iconic/ea/operator/primitive/StepFunction.java |  2 +-
 .../org/iconic/ea/operator/primitive/Subtraction.java  |  2 +-
 .../java/org/iconic/ea/operator/primitive/Tan.java     |  2 +-
 .../java/org/iconic/ea/operator/primitive/Tanh.java    |  2 +-
 .../org/iconic/ea/operator/primitive/TwoArcTan.java    |  2 +-
 .../java/org/iconic/ea/operator/primitive/Xor.java     |  2 +-
 41 files changed, 56 insertions(+), 43 deletions(-)

diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/AbsoluteValue.java b/api/src/main/java/org/iconic/ea/operator/primitive/AbsoluteValue.java
index 64945fb..a04efbc 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/AbsoluteValue.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/AbsoluteValue.java
@@ -19,7 +19,7 @@ public class AbsoluteValue extends ArithmeticPrimitive<Number> {
     public AbsoluteValue() {
         super(
                 args -> Math.abs(args.get(0)),
-                1, "ABS", "Returns the positive value of a.", 4
+                1, "ABS", "Returns the positive value of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Addition.java b/api/src/main/java/org/iconic/ea/operator/primitive/Addition.java
index 875de90..9ab844d 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Addition.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Addition.java
@@ -19,7 +19,7 @@ public class Addition extends ArithmeticPrimitive<Number> {
     public Addition() {
         super(
                 args -> args.stream().mapToDouble(Number::doubleValue).sum(),
-                2, "ADD", "Returns a + b.", 1
+                2, "ADD", "Returns a + b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/And.java b/api/src/main/java/org/iconic/ea/operator/primitive/And.java
index af6a0f9..b0901b9 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/And.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/And.java
@@ -19,7 +19,7 @@ public class And extends ArithmeticPrimitive<Number> {
     public And() {
         super(
                 args -> (args.get(0) > 0 && args.get(1) > 0) ? 1.d : 0.d,
-                2, "AND", "Returns 1 if both a and b are greater than 0, 0 otherwise.", 4
+                2, "AND", "Returns 1 if both a and b are greater than 0, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/ArcCos.java b/api/src/main/java/org/iconic/ea/operator/primitive/ArcCos.java
index 52d1c7d..e07bb13 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/ArcCos.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/ArcCos.java
@@ -19,7 +19,7 @@ public class ArcCos extends ArithmeticPrimitive<Number> {
     public ArcCos() {
         super(
                 args -> Math.acos(args.get(0)),
-                1, "ACOS", "Returns the inverse cosine function of a.", 4
+                1, "ACOS", "Returns the inverse cosine function of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/ArcSin.java b/api/src/main/java/org/iconic/ea/operator/primitive/ArcSin.java
index 966619b..002c3cd 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/ArcSin.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/ArcSin.java
@@ -19,7 +19,7 @@ public class ArcSin extends ArithmeticPrimitive<Number> {
     public ArcSin() {
         super(
                 args -> Math.asin(args.get(0)),
-                1, "ASIN", "Returns the inverse sine function of a.", 4
+                1, "ASIN", "Returns the inverse sine function of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/ArcTan.java b/api/src/main/java/org/iconic/ea/operator/primitive/ArcTan.java
index f64fd3c..ada76c7 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/ArcTan.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/ArcTan.java
@@ -19,7 +19,7 @@ public class ArcTan extends ArithmeticPrimitive<Number> {
     public ArcTan() {
         super(
                 args -> Math.atan(args.get(0)),
-                1, "ATAN", "Returns the inverse single argument tangent function of a.", 4
+                1, "ATAN", "Returns the inverse single argument tangent function of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/ArithmeticPrimitive.java b/api/src/main/java/org/iconic/ea/operator/primitive/ArithmeticPrimitive.java
index 6f9d980..d558181 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/ArithmeticPrimitive.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/ArithmeticPrimitive.java
@@ -22,4 +22,8 @@ public class ArithmeticPrimitive<T extends Number> extends FunctionalPrimitive<D
     public ArithmeticPrimitive(final Function<List<Double>, Double> lambda, final int arity, final String symbol, final String description, final Integer defaultComplexity) {
         super(lambda, arity, symbol, description, defaultComplexity);
     }
+
+    public ArithmeticPrimitive(final Function<List<Double>, Double> lambda, final int arity, final String symbol, final String description) {
+        super(lambda, arity, symbol, description);
+    }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Ceiling.java b/api/src/main/java/org/iconic/ea/operator/primitive/Ceiling.java
index b6a29b8..99f59d3 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Ceiling.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Ceiling.java
@@ -19,7 +19,7 @@ public class Ceiling extends ArithmeticPrimitive<Number> {
     public Ceiling() {
         super(
                 args -> Math.ceil(args.get(0)),
-                1, "CEIL", "Returns the integer of a rounded up.", 4
+                1, "CEIL", "Returns the integer of a rounded up."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java b/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
index 06f0bfb..749da56 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
@@ -1,12 +1,12 @@
 /**
  * Copyright 2018 Iconic
- *
+ * <p>
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -17,6 +17,6 @@
 
 public class Constant<T> extends FunctionalPrimitive<T, T> {
     public Constant(final T value) {
-        super(args -> value, 0, value.toString(), "A constant value.", 1);
+        super(args -> value, 0, value.toString(), "A constant value.");
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Cos.java b/api/src/main/java/org/iconic/ea/operator/primitive/Cos.java
index 9bbc04c..63646c4 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Cos.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Cos.java
@@ -19,7 +19,7 @@ public class Cos extends ArithmeticPrimitive<Number> {
     public Cos() {
         super(
                 args -> Math.cos(args.get(0)),
-                1, "COS", "Returns the cosine of a.", 3
+                1, "COS", "Returns the cosine of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Division.java b/api/src/main/java/org/iconic/ea/operator/primitive/Division.java
index 167c4ea..d7de19f 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Division.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Division.java
@@ -32,7 +32,7 @@ public Division() {
 
                         return identity;
                     },
-                2, "DIV", "Returns the division of a / b.", 2
+                2, "DIV", "Returns the division of a / b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/EqualTo.java b/api/src/main/java/org/iconic/ea/operator/primitive/EqualTo.java
index ce8bbba..e8af73c 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/EqualTo.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/EqualTo.java
@@ -19,7 +19,7 @@ public class EqualTo extends ArithmeticPrimitive<Number> {
     public EqualTo() {
         super(
                 args -> args.get(0).equals(args.get(1)) ? 1.d : 0.d,
-                2, "EQUAL", "Returns 1 if a is equal to b, 0 otherwise.", 4
+                2, "EQUAL", "Returns 1 if a is equal to b, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Exponential.java b/api/src/main/java/org/iconic/ea/operator/primitive/Exponential.java
index 11fb89b..e600a81 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Exponential.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Exponential.java
@@ -19,7 +19,7 @@ public class Exponential extends ArithmeticPrimitive<Number> {
     public Exponential() {
         super(
                 args -> Math.exp(args.get(0)),
-                1, "EXP", "Returns e^a.", 4
+                1, "EXP", "Returns e^a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Floor.java b/api/src/main/java/org/iconic/ea/operator/primitive/Floor.java
index 1cfd96b..0e8cae7 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Floor.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Floor.java
@@ -19,7 +19,7 @@ public class Floor extends ArithmeticPrimitive<Number> {
     public Floor() {
         super(
                 args -> Math.floor(args.get(0)),
-                1, "FLOOR", "Returns the integer of a rounded down.", 4
+                1, "FLOOR", "Returns the integer of a rounded down."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/FunctionalPrimitive.java b/api/src/main/java/org/iconic/ea/operator/primitive/FunctionalPrimitive.java
index 6b6d9ed..0603fd0 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/FunctionalPrimitive.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/FunctionalPrimitive.java
@@ -43,6 +43,15 @@ public FunctionalPrimitive(Function<List<T>, R> lambda, int arity, String symbol
         this.complexity = new SimpleIntegerProperty(defaultComplexity);
     }
 
+    public FunctionalPrimitive(Function<List<T>, R> lambda, int arity, String symbol, String description) {
+        this.lambda = lambda;
+        this.arity = arity;
+        this.symbol = symbol;
+        this.description = description;
+        this.defaultComplexity = 1;
+        this.complexity = new SimpleIntegerProperty(this.defaultComplexity);
+    }
+
     @Override
     public R apply(List<T> args) {
         assert (args.size() >= getArity());
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/GaussianFunction.java b/api/src/main/java/org/iconic/ea/operator/primitive/GaussianFunction.java
index 72a1e8b..98fe5a2 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/GaussianFunction.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/GaussianFunction.java
@@ -21,7 +21,7 @@ public class GaussianFunction extends ArithmeticPrimitive<Number> {
     public GaussianFunction() {
         super(
                 args -> Math.exp(-Math.pow(args.get(0),2)),
-                1, "GAUSS", "Returns exp(-x^2), providing a normal distribution.", 4
+                1, "GAUSS", "Returns exp(-x^2), providing a normal distribution."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThan.java b/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThan.java
index 001ec38..a128977 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThan.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThan.java
@@ -19,7 +19,7 @@ public class GreaterThan extends ArithmeticPrimitive<Number> {
     public GreaterThan() {
         super(
                 args -> args.get(0) > args.get(1) ? 1.d : 0.d,
-                2, "GREATER", "Returns 1 if a > b, 0 otherwise.", 4
+                2, "GREATER", "Returns 1 if a > b, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThanOrEqual.java b/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThanOrEqual.java
index 990cc55..6c55d93 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThanOrEqual.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/GreaterThanOrEqual.java
@@ -19,7 +19,7 @@ public class GreaterThanOrEqual extends ArithmeticPrimitive<Number> {
     public GreaterThanOrEqual() {
         super(
                 args -> args.get(0) >= args.get(1) ? 1.d : 0.d,
-                2, "GREATER_EQUAL", "Returns 1 if a >= b, 0 otherwise.", 4
+                2, "GREATER_EQUAL", "Returns 1 if a >= b, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/IfThenElse.java b/api/src/main/java/org/iconic/ea/operator/primitive/IfThenElse.java
index 7b58cac..aaff365 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/IfThenElse.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/IfThenElse.java
@@ -19,7 +19,7 @@ public class IfThenElse extends ArithmeticPrimitive<Number> {
     public IfThenElse() {
         super(
                 args -> args.get(0) > 0 ? args.get(1) : args.get(2),
-                3, "IF", "Returns returns b if a > 0, c otherwise.", 5
+                3, "IF", "Returns returns b if a > 0, c otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/LessThan.java b/api/src/main/java/org/iconic/ea/operator/primitive/LessThan.java
index 4ccf148..051608d 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/LessThan.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/LessThan.java
@@ -19,7 +19,7 @@ public class LessThan extends ArithmeticPrimitive<Number> {
     public LessThan() {
         super(
                 args -> args.get(0) < args.get(1) ? 1.d : 0.d,
-                2, "LESS", "Returns 1 if a < b, 0 otherwise.", 4
+                2, "LESS", "Returns 1 if a < b, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/LessThanOrEqual.java b/api/src/main/java/org/iconic/ea/operator/primitive/LessThanOrEqual.java
index 320749f..67c2211 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/LessThanOrEqual.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/LessThanOrEqual.java
@@ -19,7 +19,7 @@ public class LessThanOrEqual extends ArithmeticPrimitive<Number> {
     public LessThanOrEqual() {
         super(
                 args -> args.get(0) <= args.get(1) ? 1.d : 0.d,
-                2, "LESSEQUAL", "Returns 1 if a <= b, 0 otherwise.", 4
+                2, "LESSEQUAL", "Returns 1 if a <= b, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/LogisticFunction.java b/api/src/main/java/org/iconic/ea/operator/primitive/LogisticFunction.java
index de81b1a..232fe8b 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/LogisticFunction.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/LogisticFunction.java
@@ -21,7 +21,7 @@ public class LogisticFunction extends ArithmeticPrimitive<Number> {
     public LogisticFunction() {
         super(
                 args -> 1/(1+Math.exp(args.get(0))),
-                1, "LOGISTIC", "Returns (1 / 1 + exp(-a)).\nThis is a common sigmoid squashing function.", 4
+                1, "LOGISTIC", "Returns (1 / 1 + exp(-a)).\nThis is a common sigmoid squashing function."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Maximum.java b/api/src/main/java/org/iconic/ea/operator/primitive/Maximum.java
index 68d9642..8086641 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Maximum.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Maximum.java
@@ -19,7 +19,7 @@ public class Maximum extends ArithmeticPrimitive<Number> {
     public Maximum() {
         super(
                 args -> Math.max(args.get(0),args.get(1)),
-                2, "MAX", "Returns the maximum value of a and b.", 4
+                2, "MAX", "Returns the maximum value of a and b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Minimum.java b/api/src/main/java/org/iconic/ea/operator/primitive/Minimum.java
index f72a95f..f505a76 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Minimum.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Minimum.java
@@ -19,7 +19,7 @@ public class Minimum extends ArithmeticPrimitive<Number> {
     public Minimum() {
         super(
                 args -> Math.min(args.get(0),args.get(1)),
-                2, "MIN", "Returns the minimum value of a and b.", 4
+                2, "MIN", "Returns the minimum value of a and b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Modulo.java b/api/src/main/java/org/iconic/ea/operator/primitive/Modulo.java
index adcc9f9..3dd032e 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Modulo.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Modulo.java
@@ -19,7 +19,7 @@ public class Modulo extends ArithmeticPrimitive<Number> {
     public Modulo() {
         super(
                 args -> args.get(0) % args.get(1),
-                2, "MOD", "Returns the remainder of a / b.", 4
+                2, "MOD", "Returns the remainder of a / b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Multiplication.java b/api/src/main/java/org/iconic/ea/operator/primitive/Multiplication.java
index 13a9105..7e2e106 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Multiplication.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Multiplication.java
@@ -19,7 +19,7 @@ public class Multiplication extends ArithmeticPrimitive<Number> {
     public Multiplication() {
         super(
                 args -> args.stream().reduce(1.d, (a, b) -> a * b),
-                2, "MUL", "Returns a * b.", 1
+                2, "MUL", "Returns a * b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/NaturalLog.java b/api/src/main/java/org/iconic/ea/operator/primitive/NaturalLog.java
index 0563618..8254ffa 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/NaturalLog.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/NaturalLog.java
@@ -19,7 +19,7 @@ public class NaturalLog extends ArithmeticPrimitive<Number> {
     public NaturalLog() {
         super(
                 args -> Math.log(args.get(0)),
-                1, "LN", "Returns the natural logarithm (base e) of a.", 4
+                1, "LN", "Returns the natural logarithm (base e) of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Negation.java b/api/src/main/java/org/iconic/ea/operator/primitive/Negation.java
index ec79e00..ad88114 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Negation.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Negation.java
@@ -19,7 +19,7 @@ public class Negation extends ArithmeticPrimitive<Number>  {
     public Negation() {
         super(
                 args -> -args.get(0),
-                1, "NEG", "Returns - a.", 1
+                1, "NEG", "Returns - a."
         );
 
 
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Not.java b/api/src/main/java/org/iconic/ea/operator/primitive/Not.java
index 8da2d00..cd53e3d 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Not.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Not.java
@@ -19,7 +19,7 @@ public class Not extends ArithmeticPrimitive<Number> {
     public Not() {
         super(
                 args -> (args.get(0) > 0) ? 0.d : 1.d,
-                1, "NOT", "Returns 0 if a is greater than 0, 1 otherwise.", 4
+                1, "NOT", "Returns 0 if a is greater than 0, 1 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Or.java b/api/src/main/java/org/iconic/ea/operator/primitive/Or.java
index f680c77..2a7d2c7 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Or.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Or.java
@@ -19,7 +19,7 @@ public class Or extends ArithmeticPrimitive<Number> {
     public Or() {
         super(
                 args -> (args.get(0) > 0 || args.get(1) > 0) ? 1.d : 0.d,
-                2, "OR", "Returns 1 if either a or b are greater than 0, 0 otherwise.", 4
+                2, "OR", "Returns 1 if either a or b are greater than 0, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Power.java b/api/src/main/java/org/iconic/ea/operator/primitive/Power.java
index 0fb8217..8afb72d 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Power.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Power.java
@@ -19,7 +19,7 @@ public class Power extends ArithmeticPrimitive<Number> {
     public Power() {
         super(
                 args -> Math.pow(args.get(0), args.get(1)),
-                2, "POW", "Returns a^b.", 5
+                2, "POW", "Returns a^b."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Root.java b/api/src/main/java/org/iconic/ea/operator/primitive/Root.java
index b8bc1b9..e9432f4 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Root.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Root.java
@@ -31,7 +31,7 @@ public Root() {
                     }
                     return Double.NaN;
                 },
-                2, "ROOT", "Returns the b-th root of a if a is greater than 0, NaN otherwise.", 5
+                2, "ROOT", "Returns the b-th root of a if a is greater than 0, NaN otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/SignFunction.java b/api/src/main/java/org/iconic/ea/operator/primitive/SignFunction.java
index e80a0d9..111ce3f 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/SignFunction.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/SignFunction.java
@@ -21,7 +21,7 @@ public class SignFunction extends ArithmeticPrimitive<Number> {
     public SignFunction() {
         super(
                 args -> Math.signum(args.get(0)),
-                1, "SGN", "Returns -1 if a is negative, 1 if a is positive, 0 otherwise.", 4
+                1, "SGN", "Returns -1 if a is negative, 1 if a is positive, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Sin.java b/api/src/main/java/org/iconic/ea/operator/primitive/Sin.java
index 20c9cfd..06f921a 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Sin.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Sin.java
@@ -19,7 +19,7 @@ public class Sin extends ArithmeticPrimitive<Number> {
     public Sin() {
         super(
                 args -> Math.sin(args.get(0)),
-                1, "SIN","Returns the sine of a.", 3
+                1, "SIN","Returns the sine of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/SquareRoot.java b/api/src/main/java/org/iconic/ea/operator/primitive/SquareRoot.java
index 0dded20..3219a9a 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/SquareRoot.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/SquareRoot.java
@@ -19,7 +19,7 @@ public class SquareRoot extends ArithmeticPrimitive<Number> {
     public SquareRoot() {
         super(
                 args -> Math.sqrt(args.get(0)),
-                1, "SQRT","Returns the square root of a.", 4
+                1, "SQRT","Returns the square root of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/StepFunction.java b/api/src/main/java/org/iconic/ea/operator/primitive/StepFunction.java
index d7e914b..653d19e 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/StepFunction.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/StepFunction.java
@@ -20,7 +20,7 @@ public class StepFunction extends ArithmeticPrimitive<Number> {
     public StepFunction() {
         super(
                 args -> args.get(0) > 0 ? 1.d : 0.d,
-                1, "STEP","Returns 1 if x is positive, 0 otherwise.", 4
+                1, "STEP","Returns 1 if x is positive, 0 otherwise."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Subtraction.java b/api/src/main/java/org/iconic/ea/operator/primitive/Subtraction.java
index d131791..7a79523 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Subtraction.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Subtraction.java
@@ -27,7 +27,7 @@ public Subtraction() {
 
                     return identity;
                 },
-                2, "SUB", "Returns a - b.", 1
+                2, "SUB", "Returns a - b."
         );
 
 
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Tan.java b/api/src/main/java/org/iconic/ea/operator/primitive/Tan.java
index 2cab2e2..baf74ce 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Tan.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Tan.java
@@ -19,7 +19,7 @@ public class Tan extends ArithmeticPrimitive<Number> {
     public Tan() {
         super(
                 args -> Math.tan(args.get(0)),
-                1, "TAN","Returns the tangent of a.", 4
+                1, "TAN","Returns the tangent of a."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Tanh.java b/api/src/main/java/org/iconic/ea/operator/primitive/Tanh.java
index e747b3c..36ad5ac 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Tanh.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Tanh.java
@@ -21,7 +21,7 @@ public class Tanh extends ArithmeticPrimitive<Number> {
     public Tanh() {
         super(
                 args -> Math.tanh(args.get(0)),
-                1, "TANH","Returns the hyperbolic tangent of a.\nThis is a common squashing function returning a value between -1 and 1.", 4
+                1, "TANH","Returns the hyperbolic tangent of a.\nThis is a common squashing function returning a value between -1 and 1."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/TwoArcTan.java b/api/src/main/java/org/iconic/ea/operator/primitive/TwoArcTan.java
index 2ce3e37..eff5598 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/TwoArcTan.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/TwoArcTan.java
@@ -19,7 +19,7 @@ public class TwoArcTan extends ArithmeticPrimitive<Number> {
     public TwoArcTan() {
         super(
                 args -> Math.atan2(args.get(0),args.get(1)),
-                2, "ATAN2","Returns the two argument inverse tangent function.", 4
+                2, "ATAN2","Returns the two argument inverse tangent function."
         );
     }
 }
diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Xor.java b/api/src/main/java/org/iconic/ea/operator/primitive/Xor.java
index 87550e7..d4e6601 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Xor.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Xor.java
@@ -19,7 +19,7 @@ public class Xor extends ArithmeticPrimitive<Number> {
     public Xor() {
         super(
                 args -> (args.get(0) > 0 ^ args.get(1) > 0) ? 1.d : 0.d,
-                2, "XOR","Returns 1 if (a <= 0 and b > 0) or (a > 0 and b <= 0), 0 otherwise.", 4
+                2, "XOR","Returns 1 if (a <= 0 and b > 0) or (a > 0 and b <= 0), 0 otherwise."
         );
     }
 }

From 7482b05fc286cc2129fc2b1b2f43dd70c5c4060d Mon Sep 17 00:00:00 2001
From: "ubjinn@gmail.com" <Qudepimu2@>
Date: Wed, 31 Oct 2018 04:49:38 +1100
Subject: [PATCH 02/11] Enable/Disable all primitive button. Added check to
 start search for atleast 1 primitive, however there is still funky stuff
 going on. The program will crash after the alert (Previously it would just
 crash, we weren't checking at all) If you select which dataset you wish to
 use, while having no primitives enabled it will crash.

---
 .../definition/DefineSearchController.java    | 24 +++++++++++++++----
 .../project/search/StartSearchController.java |  9 +++++++
 .../views/workspace/DefineSearchView.fxml     |  5 +++-
 3 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/client/src/main/java/org/iconic/project/definition/DefineSearchController.java b/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
index 28859bf..7eb411b 100644
--- a/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
+++ b/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
@@ -1,12 +1,12 @@
 /**
  * Copyright 2018 Iconic
- *
+ * <p>
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -24,6 +24,8 @@
 import javafx.beans.value.ObservableValue;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.event.ActionEvent;
+import javafx.event.EventHandler;
 import javafx.fxml.Initializable;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
@@ -76,6 +78,9 @@ public class DefineSearchController implements Initializable, DefineSearchServic
     @FXML
     public TableView<Map.Entry<FunctionalPrimitive<Double, Double>, SimpleBooleanProperty>> blockDisplayTableView;
 
+    @FXML
+    public Button enableAll;
+
     @FXML
     public TextArea selectedBlockDisplayDescription;
 
@@ -129,6 +134,15 @@ public void initialize(URL location, ResourceBundle resources) {
 
         blockDisplayTableView.getColumns().addAll(enabledCol, nameCol, complexityCol);
 
+        enableAll.setOnAction(event -> {
+            boolean setBoolean = enableAll.getText().compareTo("Enable All") == 0;
+            for (Map.Entry<FunctionalPrimitive<Double, Double>, SimpleBooleanProperty> item :
+                    blockDisplayTableView.getItems()) {
+                item.getValue().set(setBoolean);
+            }
+            enableAll.setText(setBoolean?"Disable All":"Enable All");
+        });
+
         // Listener for the description pane
         blockDisplayTableView.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
             if (newValue != null) {
@@ -367,7 +381,7 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
 
                 String functionDefinition = tfTargetExpression.getText();
 
-                if(dataset.isPresent()) {
+                if (dataset.isPresent()) {
                     setFunction();
                     dataset.get().defineFunction(functionDefinition);
                 }
diff --git a/client/src/main/java/org/iconic/project/search/StartSearchController.java b/client/src/main/java/org/iconic/project/search/StartSearchController.java
index 6272150..828a775 100644
--- a/client/src/main/java/org/iconic/project/search/StartSearchController.java
+++ b/client/src/main/java/org/iconic/project/search/StartSearchController.java
@@ -294,6 +294,15 @@ private void validateConfiguration(SearchConfigurationModel search) {
             return;
         }
 
+        if(search.getEnabledPrimitives().size() < 1){
+            Alert alert = new Alert(Alert.AlertType.INFORMATION);
+            alert.setTitle("Search Invalid");
+            alert.setHeaderText("Missing Primitives");
+            alert.setContentText("The Defined Search has no enabled primitives to use! Please visit the 'Define Search' tab and enable at least one primitive.");
+            alert.showAndWait();
+            return;
+        }
+
         // Get the dataset Model - Check that the dataset doesn't have any missing values
         if (search.getDatasetModel().isPresent()) {
             DatasetModel datasetModel = search.getDatasetModel().get();
diff --git a/client/src/main/resources/views/workspace/DefineSearchView.fxml b/client/src/main/resources/views/workspace/DefineSearchView.fxml
index 000abe2..2c1e4cd 100644
--- a/client/src/main/resources/views/workspace/DefineSearchView.fxml
+++ b/client/src/main/resources/views/workspace/DefineSearchView.fxml
@@ -81,7 +81,10 @@
 
             <HBox spacing="10">
                 <VBox spacing="10">
-                    <Label labelFor="$blockDisplayTableView" text="Enabled Building Blocks"/>
+                    <HBox spacing="10">
+                        <Label labelFor="$blockDisplayTableView" text="Enabled Building Blocks"/>
+                        <Button fx:id="enableAll" text="Enable All"/>
+                    </HBox>
                     <TableView fx:id="blockDisplayTableView"/>
                 </VBox>
                 <VBox spacing="10">

From a0b9b87e91098d82561ee00b62f5ef6dbeaca027 Mon Sep 17 00:00:00 2001
From: Jasbir Shah <JasbirShah@outlook.com>
Date: Wed, 31 Oct 2018 17:28:02 +1100
Subject: [PATCH 03/11] Add enabled primitives self-validation to search
 configuration models

---
 .../org/iconic/ea/operator/primitive/Constant.java |  8 ++++----
 .../project/definition/DefineSearchController.java | 14 ++++++++------
 .../project/search/StartSearchController.java      |  2 +-
 .../search/config/CgpConfigurationModel.java       |  2 +-
 .../search/config/GepConfigurationModel.java       |  2 +-
 5 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java b/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
index 749da56..a4a9875 100644
--- a/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
+++ b/api/src/main/java/org/iconic/ea/operator/primitive/Constant.java
@@ -1,12 +1,12 @@
 /**
  * Copyright 2018 Iconic
- * <p>
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * <p>
- * http://www.apache.org/licenses/LICENSE-2.0
- * <p>
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
diff --git a/client/src/main/java/org/iconic/project/definition/DefineSearchController.java b/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
index 7eb411b..a742cad 100644
--- a/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
+++ b/client/src/main/java/org/iconic/project/definition/DefineSearchController.java
@@ -1,12 +1,12 @@
 /**
  * Copyright 2018 Iconic
- * <p>
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * <p>
- * http://www.apache.org/licenses/LICENSE-2.0
- * <p>
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -55,6 +55,7 @@
 import org.iconic.workspace.WorkspaceService;
 
 import java.io.IOException;
+import java.util.stream.Collectors;
 
 /**
  * Controller for the define search tab
@@ -136,10 +137,11 @@ public void initialize(URL location, ResourceBundle resources) {
 
         enableAll.setOnAction(event -> {
             boolean setBoolean = enableAll.getText().compareTo("Enable All") == 0;
-            for (Map.Entry<FunctionalPrimitive<Double, Double>, SimpleBooleanProperty> item :
+            for (Map.Entry<FunctionalPrimitive<Double, Double>, SimpleBooleanProperty> primitive :
                     blockDisplayTableView.getItems()) {
-                item.getValue().set(setBoolean);
+                primitive.getValue().set(setBoolean);
             }
+
             enableAll.setText(setBoolean?"Disable All":"Enable All");
         });
 
diff --git a/client/src/main/java/org/iconic/project/search/StartSearchController.java b/client/src/main/java/org/iconic/project/search/StartSearchController.java
index 828a775..42ed026 100644
--- a/client/src/main/java/org/iconic/project/search/StartSearchController.java
+++ b/client/src/main/java/org/iconic/project/search/StartSearchController.java
@@ -294,7 +294,7 @@ private void validateConfiguration(SearchConfigurationModel search) {
             return;
         }
 
-        if(search.getEnabledPrimitives().size() < 1){
+        if (search.getEnabledPrimitives().size() < 1){
             Alert alert = new Alert(Alert.AlertType.INFORMATION);
             alert.setTitle("Search Invalid");
             alert.setHeaderText("Missing Primitives");
diff --git a/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java b/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
index c6ed7d2..cb8170b 100644
--- a/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
+++ b/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
@@ -139,7 +139,7 @@ public int getNumLevelsBack() {
      */
     @Override
     protected boolean isValid() {
-        return getDatasetModel().isPresent();
+        return getEnabledPrimitives().size() > 0 && getDatasetModel().isPresent();
     }
 
     /**
diff --git a/client/src/main/java/org/iconic/project/search/config/GepConfigurationModel.java b/client/src/main/java/org/iconic/project/search/config/GepConfigurationModel.java
index 2e84eb2..2e49375 100644
--- a/client/src/main/java/org/iconic/project/search/config/GepConfigurationModel.java
+++ b/client/src/main/java/org/iconic/project/search/config/GepConfigurationModel.java
@@ -104,7 +104,7 @@ protected SearchExecutor<?> buildSearchExecutor() {
      */
     @Override
     protected boolean isValid() {
-        return getDatasetModel().isPresent();
+        return getEnabledPrimitives().size() > 0 && getDatasetModel().isPresent();
     }
 
     /**

From 5ad8d7f3269cc7a2a02573079ccdef2d7088959a Mon Sep 17 00:00:00 2001
From: Jasbir Shah <JasbirShah@outlook.com>
Date: Thu, 1 Nov 2018 17:35:04 +1100
Subject: [PATCH 04/11] Fix incorrect values being plotted in the solution fit
 plot

Bugfix: fixes the solution fit plot that was using only part of the evaluated results when plotting a solution. This only affected multi-output chromosomes.
---
 .../org/iconic/ea/chromosome/Chromosome.java  | 186 ++++++++----------
 .../project/results/ResultsController.java    |  11 +-
 .../search/config/CgpConfigurationModel.java  |  16 ++
 3 files changed, 108 insertions(+), 105 deletions(-)

diff --git a/api/src/main/java/org/iconic/ea/chromosome/Chromosome.java b/api/src/main/java/org/iconic/ea/chromosome/Chromosome.java
index 49fedb7..fda0a68 100644
--- a/api/src/main/java/org/iconic/ea/chromosome/Chromosome.java
+++ b/api/src/main/java/org/iconic/ea/chromosome/Chromosome.java
@@ -18,6 +18,7 @@
 import lombok.extern.log4j.Log4j2;
 import org.iconic.ea.chromosome.cartesian.CartesianChromosome;
 import org.iconic.ea.data.DataManager;
+import org.iconic.ea.operator.primitive.Constant;
 import org.iconic.ea.operator.primitive.FunctionalPrimitive;
 
 import java.util.HashMap;
@@ -116,18 +117,18 @@ public int getInputs() {
      * @return the processed expression string
      */
 
-    public String getExpression(String preorderExpression, List<FunctionalPrimitive<?, ?>> primitives, boolean topLevelFlag){
+    public String getExpression(String preorderExpression, List<FunctionalPrimitive<?, ?>> primitives, boolean topLevelFlag) {
         HashMap<String, String> symbolMap = getSymbolMap();
         /* if the input is only one term, return it */
-        if(preorderExpression.split(" ").length==1){
+        if (preorderExpression.split(" ").length == 1) {
             return preorderExpression;
         }
 
         String[] expressionSplit = preorderExpression.split("\n");
-        if(expressionSplit.length >= 2){
+        if (expressionSplit.length >= 2) {
             String output = "";
-            for(int i = 1; i < expressionSplit.length; i++){
-                if(i == expressionSplit.length-1)
+            for (int i = 1; i < expressionSplit.length; i++) {
+                if (i == expressionSplit.length - 1)
                     output += getExpression(expressionSplit[i], primitives, true);
                 else
                     output += getExpression(expressionSplit[i], primitives, true) + "\n";
@@ -136,8 +137,8 @@ public String getExpression(String preorderExpression, List<FunctionalPrimitive<
         }
 
         /* I don't remember adding this if block */
-        if(topLevelFlag){
-            if(preorderExpression.contains("Output")){
+        if (topLevelFlag) {
+            if (preorderExpression.contains("Output")) {
                 preorderExpression = preorderExpression.substring(10);
                 return getExpression(preorderExpression, primitives, true);
             }
@@ -147,30 +148,29 @@ public String getExpression(String preorderExpression, List<FunctionalPrimitive<
         FunctionalPrimitive<?, ?> leadingPrimitive;
 
         /* getting the string of the leading primitive by cutting the front off the input and trimming it */
-        if(!preorderExpression.contains("(")){
+        if (!preorderExpression.contains("(")) {
             return "";
         }
         String firstFunction = preorderExpression.substring(0, preorderExpression.indexOf("(")).trim();
 
         /* match the firstFunction string to a functional primitive */
-        leadingPrimitive = matchPrimitive(firstFunction, primitives);
-
-        if(leadingPrimitive==null){
-            log.warn("Unrecognised function in expression");
+        try {
+            leadingPrimitive = matchPrimitive(firstFunction, primitives);
+        } catch (RuntimeException ex) {
+            log.warn("{}: {}", ex::getMessage, ex::getCause);
             return "Unrecognised function in expression";
         }
 
-        /* this flag to determine whether or not this is the first time this method has been called, if it is, the
+        /* this flag to det ermine whether or not this is the first time this method has been called, if it is, the
          * substring is slightly different. In both cases it cuts the function and its front and back parentheses off
          */
 
-        if(topLevelFlag){
-            if(preorderExpression.endsWith("  ) "))
+        if (topLevelFlag) {
+            if (preorderExpression.endsWith("  ) "))
                 preorderExpression = preorderExpression.substring(leadingPrimitive.getSymbol().length() + 3, preorderExpression.length() - 4);
             else
                 preorderExpression = preorderExpression.substring(leadingPrimitive.getSymbol().length() + 3, preorderExpression.length() - 3);
-        }
-        else{
+        } else {
             preorderExpression = preorderExpression.substring(leadingPrimitive.getSymbol().length() + 3, preorderExpression.length() - 2);
         }
 
@@ -179,16 +179,16 @@ public String getExpression(String preorderExpression, List<FunctionalPrimitive<
         /* if it's a unary operator, return a string that has the operator at the front and this method recursively
          * called on the rest of the expression
          */
-        if(leadingPrimitive.getArity()==1){
+        if (leadingPrimitive.getArity() == 1) {
             return symbolMap.containsKey(leadingPrimitive.getSymbol()) ? symbolMap.get(leadingPrimitive.getSymbol()) +
-                    "(" + getExpression(preorderExpression,primitives,false) + ")" : leadingPrimitive.getSymbol() +
-                    "(" + getExpression(preorderExpression,primitives,false) + ")";
+                    "(" + getExpression(preorderExpression, primitives, false) + ")" : leadingPrimitive.getSymbol() +
+                    "(" + getExpression(preorderExpression, primitives, false) + ")";
         }
 
         /* if it's a binary operator we need to find its two inputs in the expression string
          * this is achieved by checking if the current number of open parentheses is equal to 0 and then finding the comma
          */
-        else if(leadingPrimitive.getArity()==2){
+        else if (leadingPrimitive.getArity() == 2) {
 
             /* to keep track of the number of open parentheses */
             int parenCount = 0;
@@ -197,15 +197,14 @@ else if(leadingPrimitive.getArity()==2){
              * if it is zero it means we aren't inside any of the functions that comes after the open paren
              * of this function - it makes sense, trust me
              */
-            for(int i = 0; i < preorderExpression.length(); i++){
-                if(preorderExpression.charAt(i) == ',' && parenCount == 0){
+            for (int i = 0; i < preorderExpression.length(); i++) {
+                if (preorderExpression.charAt(i) == ',' && parenCount == 0) {
 
                     /* this value is used to store the number of leading spaces in front of the comma */
                     int subValue = 0;
-                    if((i > 1) && (preorderExpression.charAt(i - 2) == ' ') && (preorderExpression.charAt(i - 1) == ' ')){
+                    if ((i > 1) && (preorderExpression.charAt(i - 2) == ' ') && (preorderExpression.charAt(i - 1) == ' ')) {
                         subValue = 2;
-                    }
-                    else if(preorderExpression.charAt(i-1) == ' '){
+                    } else if (preorderExpression.charAt(i - 1) == ' ') {
                         subValue = 1;
                     }
 
@@ -215,29 +214,26 @@ else if(preorderExpression.charAt(i-1) == ' '){
                      *
                      * If it's either max or min it has to be displayed in a different order
                      * */
-                    if(!leadingPrimitive.getSymbol().equals("MAX") && !leadingPrimitive.getSymbol().equals("MIN")){
+                    if (!leadingPrimitive.getSymbol().equals("MAX") && !leadingPrimitive.getSymbol().equals("MIN")) {
                         return "(" + getExpression(preorderExpression.substring(0, i - subValue), primitives, false) + ")"
                                 + (symbolMap.containsKey(leadingPrimitive.getSymbol()) ? symbolMap.get(leadingPrimitive.getSymbol()) : leadingPrimitive.getSymbol())
                                 + "(" + getExpression(preorderExpression.substring(i + 2, preorderExpression.length()), primitives, false) + ")";
-                    }
-                    else{
+                    } else {
                         return (symbolMap.containsKey(leadingPrimitive.getSymbol()) ? symbolMap.get(leadingPrimitive.
                                 getSymbol()) : leadingPrimitive.getSymbol()) + "((" + getExpression(preorderExpression.
                                 substring(0, i - subValue), primitives, false) + "),(" +
-                                getExpression(preorderExpression.substring(i + 2, preorderExpression.length()), primitives,false) + "))";
+                                getExpression(preorderExpression.substring(i + 2, preorderExpression.length()), primitives, false) + "))";
                     }
                 }
 
                 /* just counting and un-counting parens */
-                if(preorderExpression.charAt(i) == '('){
+                if (preorderExpression.charAt(i) == '(') {
                     parenCount++;
-                }
-                else if(preorderExpression.charAt(i) == ')'){
+                } else if (preorderExpression.charAt(i) == ')') {
                     parenCount--;
                 }
             }
-        }
-        else if(leadingPrimitive.getSymbol().equals("IF")){
+        } else if (leadingPrimitive.getSymbol().equals("IF")) {
             /* to keep track of the number of open parentheses */
             int parenCount = 0;
             /* loops through the expression string until it finds a comma when open parentheses is 0
@@ -245,36 +241,32 @@ else if(leadingPrimitive.getSymbol().equals("IF")){
              * of this function - it makes sense, trust me
              */
             int firstCommaPosition = 0, secondCommaPosition = 0;
-            for(int i = 0; i < preorderExpression.length(); i++){
-                if(preorderExpression.charAt(i) == ',' && parenCount == 0){
-                    if(firstCommaPosition == 0){
+            for (int i = 0; i < preorderExpression.length(); i++) {
+                if (preorderExpression.charAt(i) == ',' && parenCount == 0) {
+                    if (firstCommaPosition == 0) {
                         firstCommaPosition = i;
-                    }
-                    else{
+                    } else {
                         secondCommaPosition = i;
                     }
                 }
                 /* just counting and un-counting parens */
-                if(preorderExpression.charAt(i) == '('){
+                if (preorderExpression.charAt(i) == '(') {
                     parenCount++;
-                }
-                else if(preorderExpression.charAt(i) == ')'){
+                } else if (preorderExpression.charAt(i) == ')') {
                     parenCount--;
                 }
             }
 
             /* this value is used to store the number of leading spaces in front of the comma */
             int subValueOne = 0, subValueTwo = 0;
-            if((firstCommaPosition > 1) && (preorderExpression.charAt(firstCommaPosition - 2) == ' ') && (preorderExpression.charAt(firstCommaPosition - 1) == ' ')){
+            if ((firstCommaPosition > 1) && (preorderExpression.charAt(firstCommaPosition - 2) == ' ') && (preorderExpression.charAt(firstCommaPosition - 1) == ' ')) {
                 subValueOne = 2;
-            }
-            else if(preorderExpression.charAt(firstCommaPosition-1) == ' '){
+            } else if (preorderExpression.charAt(firstCommaPosition - 1) == ' ') {
                 subValueOne = 1;
             }
-            if((secondCommaPosition > 1) && (preorderExpression.charAt(secondCommaPosition - 2) == ' ') && (preorderExpression.charAt(secondCommaPosition - 1) == ' ')){
+            if ((secondCommaPosition > 1) && (preorderExpression.charAt(secondCommaPosition - 2) == ' ') && (preorderExpression.charAt(secondCommaPosition - 1) == ' ')) {
                 subValueTwo = 2;
-            }
-            else if(preorderExpression.charAt(secondCommaPosition-1) == ' '){
+            } else if (preorderExpression.charAt(secondCommaPosition - 1) == ' ') {
                 subValueTwo = 1;
             }
 
@@ -284,8 +276,8 @@ else if(preorderExpression.charAt(secondCommaPosition-1) == ' '){
              * + this method called on the right input to the function*/
 
             return "IF((" + getExpression(preorderExpression.substring(0, firstCommaPosition - subValueOne), primitives, false) + ") < 0) : "
-                + "(" + getExpression(preorderExpression.substring(firstCommaPosition + 2, secondCommaPosition - subValueTwo), primitives, false) + ") ELSE : ("
-                + "(" + getExpression(preorderExpression.substring(secondCommaPosition + 2, preorderExpression.length()), primitives, false) + "))";
+                    + "(" + getExpression(preorderExpression.substring(firstCommaPosition + 2, secondCommaPosition - subValueTwo), primitives, false) + ") ELSE : ("
+                    + "(" + getExpression(preorderExpression.substring(secondCommaPosition + 2, preorderExpression.length()), primitives, false) + "))";
         }
 
         /* this should only output on invalid expressions */
@@ -294,7 +286,7 @@ else if(preorderExpression.charAt(secondCommaPosition-1) == ' '){
     }
 
     /* this is just used to map some pre-order symbols to maths symbols */
-    private HashMap<String, String> getSymbolMap(){
+    private HashMap<String, String> getSymbolMap() {
         HashMap<String, String> output = new HashMap<>();
 
         output.put("ADD", "+");
@@ -317,16 +309,22 @@ private HashMap<String, String> getSymbolMap(){
     /* this loops through all of the primitives in the input primitive list to match the text of the input primitive
      * string and return the matched primitive
      */
-    private FunctionalPrimitive<?, ?> matchPrimitive(String primString, List<FunctionalPrimitive<?, ?>> primitives){
+    private FunctionalPrimitive<?, ?> matchPrimitive(String primString, List<FunctionalPrimitive<?, ?>> primitives)
+            throws RuntimeException {
 
         FunctionalPrimitive<?, ?> tempPrim = null;
-        for(FunctionalPrimitive f :
-                primitives){
-            if(f.getSymbol().toLowerCase().equals(primString.toLowerCase())){
+        for (FunctionalPrimitive f :
+                primitives) {
+            if (f.getSymbol().toLowerCase().equals(primString.toLowerCase())) {
                 tempPrim = f;
                 break;
             }
         }
+
+        if (tempPrim == null) {
+            throw new RuntimeException("Unrecognised function in expression");
+        }
+
         return tempPrim;
     }
 
@@ -336,7 +334,7 @@ private HashMap<String, String> getSymbolMap(){
      * @param expression - the expression to be simplified
      * @return
      */
-    public String simplifyExpression(String expression){
+    public String simplifyExpression(String expression) {
 
         /* these are the regexes used to find common patterns that can be simplified */
         String coXPlusCoXPattern = "\\(([-?0-9]+)?\\*?([A-Za-z0-9_]+)\\)\\+\\(([-?0-9]+)?\\*?\\2\\)";
@@ -360,104 +358,92 @@ public String simplifyExpression(String expression){
         Pattern pattern = Pattern.compile(xTimesRootPattern);
         Matcher matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             expression = expression.replaceFirst("\\(" + matcher.group(1) + "\\)ROOT", matcher.group(1) + "*ROOT");
         }
 
         pattern = Pattern.compile(coXPlusCoXPattern);
         matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             int a = 1, b = 1;
-            if(matcher.group(1) != null){
+            if (matcher.group(1) != null) {
                 a = Integer.parseInt(matcher.group(1));
             }
-            if(matcher.group(3) != null){
+            if (matcher.group(3) != null) {
                 b = Integer.parseInt(matcher.group(3));
             }
-            if(a+b == 0){
+            if (a + b == 0) {
                 expression = expression.replaceAll(coXPlusCoXPattern, "(0)");
-            }
-            else if(a+b == 1){
+            } else if (a + b == 1) {
                 expression = expression.replaceAll(coXPlusCoXPattern, "($2)");
-            }
-            else if(a+b == -1){
+            } else if (a + b == -1) {
                 expression = expression.replaceAll(coXPlusCoXPattern, "(-$2)");
-            }
-            else{
-                expression = expression.replaceAll(coXPlusCoXPattern, "(" + (a+b) + "*$2)");
+            } else {
+                expression = expression.replaceAll(coXPlusCoXPattern, "(" + (a + b) + "*$2)");
             }
 
         }
         pattern = Pattern.compile(coXMinusCoXPattern);
         matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             int a = 1, b = 1;
-            if(matcher.group(1) != null){
+            if (matcher.group(1) != null) {
                 a = Integer.parseInt(matcher.group(1));
             }
-            if(matcher.group(3) != null){
+            if (matcher.group(3) != null) {
                 b = Integer.parseInt(matcher.group(3));
             }
-            if(a-b == 0){
+            if (a - b == 0) {
                 expression = expression.replaceAll(coXMinusCoXPattern, "(0)");
-            }
-            else if(a-b == 1){
+            } else if (a - b == 1) {
                 expression = expression.replaceAll(coXMinusCoXPattern, "($2)");
-            }
-            else if(a-b == -1){
+            } else if (a - b == -1) {
                 expression = expression.replaceAll(coXMinusCoXPattern, "(-$2)");
-            }
-            else{
+            } else {
                 expression = expression.replaceAll(coXMinusCoXPattern, "(" + (a - b) + "*$2)");
             }
         }
         pattern = Pattern.compile(coXTimesCoXPattern);
         matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             int a = 1, b = 1;
-            if(matcher.group(1) != null){
+            if (matcher.group(1) != null) {
                 a = Integer.parseInt(matcher.group(1));
             }
-            if(matcher.group(3) != null){
+            if (matcher.group(3) != null) {
                 b = Integer.parseInt(matcher.group(3));
             }
-            if(a*b == 1){
+            if (a * b == 1) {
                 expression = expression.replaceAll(coXTimesCoXPattern, "($2^2)");
-            }
-            else if(a*b == -1){
+            } else if (a * b == -1) {
                 expression = expression.replaceAll(coXTimesCoXPattern, "(-$2^2)");
-            }
-            else{
+            } else {
                 expression = expression.replaceAll(coXTimesCoXPattern, "(" + (a * b) + "$2^2)");
             }
         }
         pattern = Pattern.compile(coXDividesCoXPattern);
         matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             int a = 1, b = 1;
-            if(matcher.group(1) != null){
+            if (matcher.group(1) != null) {
                 a = Integer.parseInt(matcher.group(1));
             }
-            if(matcher.group(3) != null){
+            if (matcher.group(3) != null) {
                 b = Integer.parseInt(matcher.group(3));
             }
-            if(a/b == 1){
+            if (a / b == 1) {
                 expression = expression.replaceAll(coXDividesCoXPattern, "(1)");
-            }
-            else if(a/b == -1){
+            } else if (a / b == -1) {
                 expression = expression.replaceAll(coXDividesCoXPattern, "(-1)");
-            }
-            else if((float)a/(float)b < 0){
+            } else if ((float) a / (float) b < 0) {
                 expression = expression.replaceAll(coXDividesCoXPattern, "(-(" + Math.abs(a) + "/" + Math.abs(b) + "))");
-            }
-            else if(a < 0 && b < 0){
+            } else if (a < 0 && b < 0) {
                 expression = expression.replaceAll(coXDividesCoXPattern, "(" + Math.abs(a) + "/" + Math.abs(b) + ")");
-            }
-            else{
+            } else {
                 expression = expression.replaceAll(coXDividesCoXPattern, "(" + a + "/" + b + ")");
             }
         }
@@ -465,7 +451,7 @@ else if(a < 0 && b < 0){
         pattern = Pattern.compile(anythingOpAnythingPattern);
         matcher = pattern.matcher(expression);
 
-        while(matcher.find()){
+        while (matcher.find()) {
             expression = expression.replaceFirst("\\(" + matcher.group(1) + "\\)", matcher.group(1));
             expression = expression.replaceFirst("\\(" + matcher.group(3) + "\\)", matcher.group(3));
         }
diff --git a/client/src/main/java/org/iconic/project/results/ResultsController.java b/client/src/main/java/org/iconic/project/results/ResultsController.java
index 88be284..76e4051 100644
--- a/client/src/main/java/org/iconic/project/results/ResultsController.java
+++ b/client/src/main/java/org/iconic/project/results/ResultsController.java
@@ -202,7 +202,7 @@ private void graphExpectedValues() {
         // This will be the referenced chromosome that was selected if it finds a match
         Chromosome<?> selectedChromosome = solutions.get(size);
 
-        // If no chromosome was found (aka the block is missing and the strings dont match)
+        // If no chromosome was found (aka the block is missing and the strings don't match)
         if (selectedChromosome == null) {
             log.info("There was no chromosome found in the storage");
             solutionsPlot.getData().clear();
@@ -216,16 +216,17 @@ private void graphExpectedValues() {
             return;
         }
 
-        // Go through all the results, There are multiple outputs
+        // Go through each sample
         for (int i = 0; i < results.size(); i++) {
-            // This is the list of results for all the different outputs
+            // A map of outputs and their results
             Map<Integer, Number> rowOfResults = results.get(i);
 
             // Keys (They are random numbers, i think it might be the node id's of the output nodes in cgp
-            Integer[] keys = rowOfResults.keySet().toArray(new Integer[0]);
+            Number netResults = rowOfResults.values().stream().mapToDouble(Number::doubleValue)
+                    .sum();
 
             // My shit attempt to only display the "first" element in the list
-            seriesActual.getData().add(new XYChart.Data<>(i, rowOfResults.get(keys[0])));
+            seriesActual.getData().add(new XYChart.Data<>(i, netResults));
         }
 
         // Update the graph
diff --git a/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java b/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
index cb8170b..03a945b 100644
--- a/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
+++ b/client/src/main/java/org/iconic/project/search/config/CgpConfigurationModel.java
@@ -17,6 +17,8 @@
 
 import javafx.beans.property.SimpleIntegerProperty;
 import lombok.NonNull;
+import org.iconic.ea.operator.primitive.Constant;
+import org.iconic.ea.operator.primitive.FunctionalPrimitive;
 import org.iconic.ea.strategies.EvolutionaryAlgorithm;
 import org.iconic.ea.chromosome.cartesian.CartesianChromosome;
 import org.iconic.ea.chromosome.cartesian.CartesianChromosomeFactory;
@@ -29,6 +31,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.ThreadLocalRandom;
 
 /**
  * {@inheritDoc}
@@ -85,6 +88,19 @@ protected SearchExecutor<?> buildSearchExecutor() {
                 );
         supplier.addFunction(new ArrayList<>(getEnabledPrimitives()));
 
+        final int numConstants = 100;
+        final int min = -100;
+        final int max = 100;
+//        final List<FunctionalPrimitive<Double, Double>> constants = new ArrayList<>(numConstants);
+//
+//        while (constants.size() < numConstants) {
+//            constants.add(new Constant<>(ThreadLocalRandom.current().nextDouble(
+//                    min, max
+//            )));
+//        }
+//        FIXME: Expression parser doesn't handle constants in CGP function nodes
+//        supplier.addFunction(constants);
+
         EvolutionaryAlgorithm<CartesianChromosome<Double>, Double> ea =
                 new CartesianGeneticProgramming<>(supplier);
         ea.addMutator(new CartesianSingleActiveMutator<>());

From f4df7a655b98f714c36e2d359347f9fe55bacb37 Mon Sep 17 00:00:00 2001
From: Jasbir Shah <JasbirShah@outlook.com>
Date: Thu, 1 Nov 2018 17:38:14 +1100
Subject: [PATCH 05/11] Change graph export format from PDF to PNG and remove
 axis scaling

Refactor: graphs are exported as PNGs instead of PDFs vastly reducing export times.
Refactor: stops logarithmically scaling the axes of the solution fit plot.
---
 .../org/iconic/ea/strategies/gsemo/GSEMO.java |  6 ++---
 cli/src/main/java/org/iconic/Client.java      | 25 ++++++++++++++++---
 .../java/org/iconic/utils/GraphWriter.java    | 20 +++++++++++++--
 .../java/org/iconic/utils/XYGraphWriter.java  |  5 +++-
 4 files changed, 47 insertions(+), 9 deletions(-)

diff --git a/api/src/main/java/org/iconic/ea/strategies/gsemo/GSEMO.java b/api/src/main/java/org/iconic/ea/strategies/gsemo/GSEMO.java
index cff8ffa..9705636 100644
--- a/api/src/main/java/org/iconic/ea/strategies/gsemo/GSEMO.java
+++ b/api/src/main/java/org/iconic/ea/strategies/gsemo/GSEMO.java
@@ -70,11 +70,11 @@ public List<R> evolve(List<R> population) {
         // Exactly one parent is required
         final R parent = getSelector(0).apply(newPopulation);
 
-        // Create a single offspring by performing mutation on the parent
+        // Create a single offspring by performing crossover and mutation on the parent
         R offspring = mutate((R) parent.clone());
 
-        // Continue mutating the offspring based on its parent's length
-        // reducing the probability of mutation with each attempt
+        // Continue evolving the offspring based on its parent's length
+        // reducing the probability of evolution with each attempt
         for (int j = 2; j <= parent.getSize(); ++j) {
             if ((1. / (double) j) >= ThreadLocalRandom.current().nextDouble()) {
                 offspring = mutate(offspring);
diff --git a/cli/src/main/java/org/iconic/Client.java b/cli/src/main/java/org/iconic/Client.java
index c9c0797..456adad 100644
--- a/cli/src/main/java/org/iconic/Client.java
+++ b/cli/src/main/java/org/iconic/Client.java
@@ -19,10 +19,10 @@
 import lombok.extern.log4j.Log4j2;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVPrinter;
+import org.iconic.ea.chromosome.cartesian.CartesianChromosome;
 import org.iconic.ea.strategies.EvolutionaryAlgorithm;
 import org.iconic.ea.chromosome.Chromosome;
 import org.iconic.ea.chromosome.ChromosomeFactory;
-import org.iconic.ea.chromosome.cartesian.CartesianChromosome;
 import org.iconic.ea.chromosome.cartesian.CartesianChromosomeFactory;
 import org.iconic.ea.data.DataManager;
 import org.iconic.ea.data.FeatureClass;
@@ -51,6 +51,7 @@
 import java.time.Instant;
 import java.util.*;
 import java.util.List;
+import java.util.concurrent.ThreadLocalRandom;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
@@ -96,7 +97,7 @@ public static void main(String[] args) {
             log.info("Feature Size: {}", () -> featureSize - 1);
             log.info("Sample Size: {}", () -> sampleSize);
 
-            // Create a supplier for Gene Expression Programming chromosomes
+            // Create a supplier for Gene Cartesian Programming chromosomes
             List<String> inputs = new ArrayList<>(featureSize - 1);
             for (int i = 0; i < featureSize - 1; ++i) {
                 inputs.add(String.valueOf(i));
@@ -116,6 +117,19 @@ public static void main(String[] args) {
                     new Division(), new Power(), new Exponential(), new Sin(), new Cos()
             ));
 
+            final int numConstants = 100;
+            final int min = -100;
+            final int max = 100;
+            final List<FunctionalPrimitive<Double, Double>> constants = new ArrayList<>(numConstants);
+
+            while (constants.size() < numConstants) {
+                constants.add(new Constant<>(ThreadLocalRandom.current().nextDouble(
+                        min, max
+                )));
+            }
+
+            supplier.addFunction(constants);
+
             final int generations = client.getArgs().getGenerations();
             final Set<Chromosome<Double>> nonDominatedFinal = new LinkedHashSet<>();
             final List<Set<Chromosome<Double>>> nonDominatedAll = new ArrayList<>(generations);
@@ -181,6 +195,7 @@ public static void main(String[] args) {
                         graphWriter.write(series.draw());
                     }
 
+                    graphWriter.setAxesLogarithmic(true);
                     graphWriter.export("All Generations - Non-Dominated", directory, "results-all");
                     graphWriter.clear();
 
@@ -192,6 +207,7 @@ public static void main(String[] args) {
 
                     nonDominatedFinal.forEach(seriesWriter::write);
                     graphWriter.write(seriesWriter.draw());
+                    graphWriter.setAxesLogarithmic(true);
                     graphWriter.export("Last Generation - Non-Dominated", directory, "results-last");
 
                     // Create a map of global best values so we can graph just their solution-fit plots
@@ -327,6 +343,9 @@ private static void exportCsv(
                 new FileWriter(new File(directory + "//" + fileName + ".csv")),
                 CSVFormat.EXCEL
         )) {
+            printer.printRecord(
+                    "Mean Squared Error", "Size", "Model"
+            );
             for (final Chromosome<?> chromosome : population) {
                 printer.printRecord(
                         chromosome.getFitness(), chromosome.getSize(), chromosome.toString()
@@ -349,7 +368,7 @@ private static EvolutionaryAlgorithm<CartesianChromosome<Double>, Double> getEvo
         // Create the evolutionary algorithm
         EvolutionaryAlgorithm<CartesianChromosome<Double>, Double> ea =
                 // TODO: generify with a factory so it isn't always GSEMO
-                new GSEMO<>(supplier, 1);
+                new GSEMO<>(supplier, 4);
         ea.setCrossoverProbability(args.getCrossoverProbability());
         ea.setMutationProbability(args.getMutationProbability());
 
diff --git a/cli/src/main/java/org/iconic/utils/GraphWriter.java b/cli/src/main/java/org/iconic/utils/GraphWriter.java
index 68c590d..3b9f546 100644
--- a/cli/src/main/java/org/iconic/utils/GraphWriter.java
+++ b/cli/src/main/java/org/iconic/utils/GraphWriter.java
@@ -16,6 +16,7 @@
 package org.iconic.utils;
 
 import org.iconic.ea.chromosome.Chromosome;
+import org.knowm.xchart.BitmapEncoder;
 import org.knowm.xchart.VectorGraphicsEncoder;
 import org.knowm.xchart.internal.chartpart.Chart;
 import org.knowm.xchart.internal.series.Series;
@@ -25,6 +26,7 @@
 
 public abstract class GraphWriter<T extends Series> {
     private boolean axesTruncated;
+    private boolean axesLogarithmic;
 
     /**
      * Constructs a new GraphWriter that will truncate outliers from its axes by default.
@@ -48,9 +50,9 @@ public abstract class GraphWriter<T extends Series> {
     public void export(final String chartTitle, final String directory, final String fileName) throws IOException {
         Chart<?, ?> chart = draw();
         chart.setTitle(chartTitle);
-        VectorGraphicsEncoder.saveVectorGraphic(
+        BitmapEncoder.saveBitmap(
                 chart, directory + "//" + fileName,
-                VectorGraphicsEncoder.VectorGraphicsFormat.PDF
+                BitmapEncoder.BitmapFormat.PNG
         );
     }
 
@@ -71,10 +73,24 @@ public boolean isAxesTruncated() {
         return axesTruncated;
     }
 
+    /**
+     * @return True if axes of  the graph written by the GraphWriter will use logarithmic scaling.
+     */
+    public boolean isAxesLogarithmic() {
+        return axesLogarithmic;
+    }
+
     /**
      * @param truncate True if the axes of the graph being written should remove outliers.
      */
     public void setAxesTruncated(boolean truncate) {
         this.axesTruncated = truncate;
     }
+
+    /**
+     * @param logarithmic True if the axes of the graph being written should use logarithmic scaling.
+     */
+    public void setAxesLogarithmic(boolean logarithmic) {
+        this.axesLogarithmic = logarithmic;
+    }
 }
diff --git a/cli/src/main/java/org/iconic/utils/XYGraphWriter.java b/cli/src/main/java/org/iconic/utils/XYGraphWriter.java
index 3bf6e54..c4f6aca 100644
--- a/cli/src/main/java/org/iconic/utils/XYGraphWriter.java
+++ b/cli/src/main/java/org/iconic/utils/XYGraphWriter.java
@@ -179,7 +179,10 @@ private XYChart getChart() {
                     .theme(Styler.ChartTheme.Matlab).build();
             chart.getStyler().setChartTitleVisible(true);
             chart.getStyler().setMarkerSize(12);
-            chart.getStyler().setXAxisLogarithmic(true);
+
+            if (isAxesLogarithmic()) {
+                chart.getStyler().setXAxisLogarithmic(true);
+            }
         }
 
         return chart;

From 8bc673ee804b10582a27cffebeb30bc1e58e9288 Mon Sep 17 00:00:00 2001
From: Jack Ratcliffe <jack-rat@hotmail.com>
Date: Thu, 1 Nov 2018 19:54:33 +1100
Subject: [PATCH 06/11] data removal fixed

---
 .../project/input/InputDataController.java    | 24 ++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/client/src/main/java/org/iconic/project/input/InputDataController.java b/client/src/main/java/org/iconic/project/input/InputDataController.java
index 5ee3bff..bade1dc 100644
--- a/client/src/main/java/org/iconic/project/input/InputDataController.java
+++ b/client/src/main/java/org/iconic/project/input/InputDataController.java
@@ -162,7 +162,13 @@ private void setupContextMenu(){
             extendWithClipboard();
             pasteFromClipboard();
         });
-        contextMenu.getItems().addAll(copy,paste);
+        MenuItem delete = new MenuItem("Delete");
+        delete.setAccelerator(KeyCombination.keyCombination("Delete"));
+        delete.setOnAction(actionEvent -> {
+            deleteSelection();
+
+        });
+        contextMenu.getItems().addAll(copy,paste,delete);
         spreadsheet.setContextMenu(contextMenu);
     }
 
@@ -270,6 +276,22 @@ private void pasteFromClipboard() {
 
     }
 
+    /**
+     * Finds the selected cells and deletes the values within them
+     */
+    private void deleteSelection() {
+        ObservableList<TablePosition> positionList = spreadsheet.getSelectionModel().getSelectedCells();
+
+        for (TablePosition position : positionList) {
+            int row = position.getRow();
+            int col = position.getColumn();
+
+            spreadsheet.getGrid().getRows().get(row).get(col).setItem(null);
+
+            updateProjectDataset(row-2,col,null);
+        }
+    }
+
     /**
      * Calculates the size of the extended spreadsheet after the clipboard will be pasted
      */

From 61f550b0f4bc23a579766064d84407b10987dc23 Mon Sep 17 00:00:00 2001
From: Jack Ratcliffe <jack-rat@hotmail.com>
Date: Thu, 1 Nov 2018 20:38:21 +1100
Subject: [PATCH 07/11] fixed copy/paste of missing values

---
 .../project/input/InputDataController.java    | 28 ++++++++-----------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/client/src/main/java/org/iconic/project/input/InputDataController.java b/client/src/main/java/org/iconic/project/input/InputDataController.java
index bade1dc..f6d3fb8 100644
--- a/client/src/main/java/org/iconic/project/input/InputDataController.java
+++ b/client/src/main/java/org/iconic/project/input/InputDataController.java
@@ -198,8 +198,10 @@ else if (prevRow != -1) {
 
             Object observableValue = spreadsheet.getGrid().getRows().get(row).get(col).getItem();
 
-            // add new item to clipboard
-            clipboardString.append(String.valueOf(observableValue));
+            if(observableValue != null){
+                // add new item to clipboard
+                clipboardString.append(String.valueOf(observableValue));
+            }
 
             // remember previous
             prevRow = row;
@@ -229,24 +231,16 @@ private void pasteFromClipboard() {
 
         int rowClipboard = -1;
 
-        StringTokenizer rowTokenizer = new StringTokenizer( pasteString, "\n");
-        while(rowTokenizer.hasMoreTokens()) {
 
+        Scanner s = new Scanner(pasteString);
+        while (s.hasNextLine()) {
             rowClipboard++;
-
-            String rowString = rowTokenizer.nextToken();
-
-            StringTokenizer columnTokenizer = new StringTokenizer(rowString, "\t");
-
+            String line = s.nextLine();
+            String[] items= line.split("\t", -1);
             int colClipboard = -1;
-
-            while(columnTokenizer.hasMoreTokens()) {
-
+            for(int i = 0; i < items.length; i++){
                 colClipboard++;
-
-                // get next cell data from clipboard
-                String clipboardCellContent = columnTokenizer.nextToken();
-
+                String clipboardCellContent = items[i];
                 // calculate the position in the table cell
                 int rowTable = pasteCellPosition.getRow() + rowClipboard;
                 int colTable = pasteCellPosition.getColumn() + colClipboard;
@@ -270,8 +264,8 @@ private void pasteFromClipboard() {
                     } catch (Exception ignored) {
                     }
                 }
-            }
 
+            }
         }
 
     }

From a8033cce6a290df39cd1f7b726d9d928160e5f74 Mon Sep 17 00:00:00 2001
From: Jack Ratcliffe <jack-rat@hotmail.com>
Date: Thu, 1 Nov 2018 22:20:45 +1100
Subject: [PATCH 08/11] Pasting missing values from excel into ICONIC now
 overwrites nonnull values

---
 .../main/java/org/iconic/project/input/InputDataController.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/src/main/java/org/iconic/project/input/InputDataController.java b/client/src/main/java/org/iconic/project/input/InputDataController.java
index f6d3fb8..7e28aa6 100644
--- a/client/src/main/java/org/iconic/project/input/InputDataController.java
+++ b/client/src/main/java/org/iconic/project/input/InputDataController.java
@@ -262,6 +262,8 @@ private void pasteFromClipboard() {
                         double content = Double.parseDouble(clipboardCellContent);
                         spreadsheet.getGrid().getRows().get(rowTable).get(colTable).setItem(String.valueOf(content));
                     } catch (Exception ignored) {
+                        spreadsheet.getGrid().getRows().get(rowTable).get(colTable).setItem(null);
+                        updateProjectDataset(rowTable-2,colTable,null);
                     }
                 }
 

From d8b6e906980f39c92fe2fbce93810404842e41df Mon Sep 17 00:00:00 2001
From: Jack Ratcliffe <jack-rat@hotmail.com>
Date: Thu, 1 Nov 2018 22:29:43 +1100
Subject: [PATCH 09/11] Updated help dialogue

---
 client/src/main/java/org/iconic/menu/MenuController.java | 2 +-
 client/src/main/resources/views/menu/MenuView.fxml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/main/java/org/iconic/menu/MenuController.java b/client/src/main/java/org/iconic/menu/MenuController.java
index ce25beb..6c56988 100644
--- a/client/src/main/java/org/iconic/menu/MenuController.java
+++ b/client/src/main/java/org/iconic/menu/MenuController.java
@@ -104,7 +104,7 @@ public void showAbout(ActionEvent actionEvent) {
         );
 
         alert.setTitle("About");
-        alert.setHeaderText("Version:    1.0\n\nIcons made by Smashicons, Roundicons, Freepik and DinosoftLabs from www.flaticon.com");
+        alert.setHeaderText("Version: 0.7.0\n\nhttps://github.com/koosvary/Iconic\n\nIcons made by Smashicons, Roundicons, Freepik and DinosoftLabs from www.flaticon.com");
 
         alert.showAndWait()
                 .filter(response -> response == ButtonType.OK)
diff --git a/client/src/main/resources/views/menu/MenuView.fxml b/client/src/main/resources/views/menu/MenuView.fxml
index 50b87b8..282d032 100644
--- a/client/src/main/resources/views/menu/MenuView.fxml
+++ b/client/src/main/resources/views/menu/MenuView.fxml
@@ -62,7 +62,7 @@
 
         <Menu text="%menu.help">
             <items>
-                <MenuItem text="About Ionic Workbench" onAction="#showAbout"/>
+                <MenuItem text="About Iconic Workbench" onAction="#showAbout"/>
             </items>
         </Menu>
     </MenuBar>

From 9e30dff421bf8ec15e2f382d532ce5eebdba6306 Mon Sep 17 00:00:00 2001
From: Jack Ratcliffe <jack-rat@hotmail.com>
Date: Thu, 1 Nov 2018 23:10:56 +1100
Subject: [PATCH 10/11] Added top menu edit functionality

---
 .../java/org/iconic/menu/MenuController.java  | 119 +++++++++++++++++-
 .../main/resources/views/menu/MenuView.fxml   |  15 ++-
 2 files changed, 125 insertions(+), 9 deletions(-)

diff --git a/client/src/main/java/org/iconic/menu/MenuController.java b/client/src/main/java/org/iconic/menu/MenuController.java
index 6c56988..1ce0ed0 100644
--- a/client/src/main/java/org/iconic/menu/MenuController.java
+++ b/client/src/main/java/org/iconic/menu/MenuController.java
@@ -29,6 +29,8 @@
 import org.iconic.project.ProjectModel;
 import org.iconic.project.ProjectService;
 
+import java.awt.*;
+import java.awt.event.KeyEvent;
 import java.net.URL;
 import java.util.ResourceBundle;
 
@@ -69,6 +71,122 @@ public void initialize(URL arg1, ResourceBundle arg2) {
         // Do nothing
     }
 
+    /**
+     * <p>
+     *Simulates ctrl + z to undo
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void undo(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_Z;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+        r.keyRelease(keyCode2);
+    }
+
+    /**
+     * <p>
+     *Simulates ctrl + y to redo
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void redo(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_Y;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+        r.keyRelease(keyCode2);
+    }
+
+    /**
+     * <p>
+     *Simulates ctrl + x to cut
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void cut(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_X;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+        r.keyRelease(keyCode2);
+    }
+
+    /**
+     * <p>
+     *Simulates ctrl + c to copy
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void copy(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_C;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+        r.keyRelease(keyCode2);
+    }
+
+    /**
+     * <p>
+     *Simulates ctrl + v to copy
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void paste(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_V;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+        r.keyRelease(keyCode2);
+    }
+
+    /**
+     * <p>
+     *Simulates delete to delete
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void delete(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_DELETE;
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode);
+    }
+
+    /**
+     * <p>
+     *Simulates ctrl + a to select all
+     *
+     *
+     * @param actionEvent The action that triggered this event
+     */
+    public void selectAll(ActionEvent actionEvent) throws AWTException {
+        Robot r = new Robot();
+        int keyCode = KeyEvent.VK_A;
+        int keyCode2 = KeyEvent.VK_CONTROL;
+        r.keyPress(keyCode2);
+        r.keyPress(keyCode);
+        r.keyRelease(keyCode2);
+        r.keyRelease(keyCode);
+    }
+
     /**
      * <p>
      * Closes all stages and exits the application.
@@ -79,7 +197,6 @@ public void initialize(URL arg1, ResourceBundle arg2) {
     public void exit(ActionEvent actionEvent) {
         Platform.exit();
     }
-
     /**
      * <p>
      * Returns the root StackPane associated with this view.
diff --git a/client/src/main/resources/views/menu/MenuView.fxml b/client/src/main/resources/views/menu/MenuView.fxml
index 282d032..5ca0bd0 100644
--- a/client/src/main/resources/views/menu/MenuView.fxml
+++ b/client/src/main/resources/views/menu/MenuView.fxml
@@ -40,16 +40,15 @@
         </Menu>
 
         <Menu text="%menu.edit">
-            <MenuItem text="%menu.undo" />
-            <MenuItem text="%menu.redo" />
+            <MenuItem text="%menu.undo" onAction="#undo"/>
+            <MenuItem text="%menu.redo" onAction="#redo"/>
             <SeparatorMenuItem/>
-            <MenuItem text="%menu.cut" />
-            <MenuItem text="%menu.copy" />
-            <MenuItem text="%menu.paste" />
-            <MenuItem text="%menu.delete" />
+            <MenuItem text="%menu.cut" onAction="#cut"/>
+            <MenuItem text="%menu.copy" onAction="#copy"/>
+            <MenuItem text="%menu.paste" onAction="#paste"/>
+            <MenuItem text="%menu.delete" onAction="#delete"/>
             <SeparatorMenuItem/>
-            <MenuItem text="%menu.selectAll" />
-            <MenuItem text="%menu.deselectAll" />
+            <MenuItem text="%menu.selectAll" onAction="#selectAll"/>
         </Menu>
 
         <Menu text="%menu.view">

From b4728aab19943174770160557e45846502e7daac Mon Sep 17 00:00:00 2001
From: Jayden626 <jayden_626@hotmail.com>
Date: Fri, 2 Nov 2018 13:20:50 +1100
Subject: [PATCH 11/11] Updated version numbers and Readme for v 0.7.0

---
 README.md           | 23 +++++++++++++++++++++++
 api/build.gradle    |  2 +-
 cli/build.gradle    |  2 +-
 client/build.gradle |  2 +-
 4 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 6ceff03..4155fd0 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,29 @@
 
 ## What's New
 
+### Release Notes - 0.7.0 - November 2nd, 2018
+
+#### CLI
+* Graph output changed from PDF to PNG, bringing speed improvements
+* Logarithmic scaling of axes in the solution fit plot has been disabled
+
+#### General
+* Added link to repository to the “About Iconic Workbench” dialog in the Help section of the menu bar
+* Updated range of constants in GEP search from 0 – 100 to -100 – 100.
+
+#### Input Data
+* Bugs around copying from Iconic into Excel and vice versa have been fixed
+* Deleting values from cells now working correctly
+* Can copy, paste and delete using the Edit section of the menu bar
+
+#### Define Search
+* Implemented Enable All / Disable All button for building blocks
+* Added additional checks and a warning dialog to starting a search with no primitives
+* Changed default complexities back to 1
+
+#### Results
+* Fixed a bug where results from a CGP search would not plot correctly
+
 ### Release Notes - 0.6.0 - October 25th, 2018
 
 #### General
diff --git a/api/build.gradle b/api/build.gradle
index f354bbe..119eaf5 100644
--- a/api/build.gradle
+++ b/api/build.gradle
@@ -19,7 +19,7 @@ dependencies {
     testRuntimeOnly group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.1.0'
 }
 
-version = '0.6.0'
+version = '0.7.0'
 
 jar {
     baseName = 'iconic-api'
diff --git a/cli/build.gradle b/cli/build.gradle
index 9a6c51e..6b64a72 100644
--- a/cli/build.gradle
+++ b/cli/build.gradle
@@ -18,7 +18,7 @@ dependencies {
 
 jar {
   baseName = 'iconic-cli'
-  version = '0.6.0'
+  version = '0.7.0'
 
   // The Java plugin doesn't specify any of the 
   // manifest attributes, so we need at least
diff --git a/client/build.gradle b/client/build.gradle
index 5152304..634d74c 100644
--- a/client/build.gradle
+++ b/client/build.gradle
@@ -13,7 +13,7 @@ buildscript {
     }
 }
 
-version = '0.6.0'
+version = '0.7.0'
 
 dependencies {
     compile 'org.controlsfx:controlsfx:8.40.14'