From cf408e0e4647057ac1b9ab4ca296ba8df040ed70 Mon Sep 17 00:00:00 2001
From: Lennart Eichhorn <lennart@madmanfred.com>
Date: Fri, 29 May 2020 20:19:38 +0200
Subject: [PATCH] Removed protein information from Candidate.
---
src/main/java/Evaluators/EvaluatorNESW.java | 8 ++++---
.../java/InitialGenerationCreators/Curl.java | 9 ++++----
.../RandomDirection.java | 9 ++++----
.../StraightLine.java | 9 ++++----
src/main/java/Interfaces/Evaluator.java | 4 ----
.../Interfaces/InitialGenerationCreator.java | 2 +-
src/main/java/Interfaces/Visualizer.java | 6 ++---
src/main/java/MainClasses/Candidate.java | 9 +++-----
.../java/MainClasses/GeneticAlgorithm.java | 22 +++++++++----------
src/main/java/MainClasses/Vertex.java | 4 +---
.../java/Selectors/FitnessProportional.java | 2 +-
src/main/java/Selectors/OnlyBest.java | 2 +-
src/main/java/Selectors/Tournament.java | 2 +-
.../Visualizers/VisualizerNESWtoConsole.java | 6 +++--
.../Visualizers/VisualizerNESWtoFile.java | 6 +++--
15 files changed, 47 insertions(+), 53 deletions(-)
diff --git a/src/main/java/Evaluators/EvaluatorNESW.java b/src/main/java/Evaluators/EvaluatorNESW.java
index 35d5763..dd4d9e6 100644
--- a/src/main/java/Evaluators/EvaluatorNESW.java
+++ b/src/main/java/Evaluators/EvaluatorNESW.java
@@ -8,9 +8,11 @@ import MainClasses.Vertex;
public class EvaluatorNESW implements Evaluator {
final int POINTS_PER_BOND;
+ final int[] isHydrophobic;
- public EvaluatorNESW(int pointsPerBond) {
+ public EvaluatorNESW(int pointsPerBond, int[] isHydrophobic) {
this.POINTS_PER_BOND = pointsPerBond;
+ this.isHydrophobic = isHydrophobic;
}
@Override
@@ -36,10 +38,10 @@ public class EvaluatorNESW implements Evaluator {
for (int i = 0; i < candidate.vertexList.size() - 2; i++) {
Vertex toCompare = candidate.vertexList.get(i);
- if (toCompare.isHydrophobic) {
+ if (isHydrophobic[i]==1) {
for (int j = i + 2; j < candidate.vertexList.size(); j++) {
Vertex vertex = candidate.vertexList.get(j);
- if (vertex.isHydrophobic) {
+ if (isHydrophobic[j]==1) {
if (toCompare.neighbouringPosition(vertex)) {
bonds++;
}
diff --git a/src/main/java/InitialGenerationCreators/Curl.java b/src/main/java/InitialGenerationCreators/Curl.java
index 798da72..56fd59a 100644
--- a/src/main/java/InitialGenerationCreators/Curl.java
+++ b/src/main/java/InitialGenerationCreators/Curl.java
@@ -14,19 +14,18 @@ public class Curl<T extends Enum<?>> implements InitialGenerationCreator {
}
@Override
- public Candidate[] initializeDirections(int populationSize, int[] isHydrophobic) {
+ public Candidate[] initializeDirections(int populationSize, int sequenceLength) {
Candidate[] population = new Candidate[populationSize];
- int proteinLength = isHydrophobic.length;
int[] candidateDirections;
if (isFRLEncoding(possibleDirections) && populationSize > 0) {
- candidateDirections = curlFRL(proteinLength);
+ candidateDirections = curlFRL(sequenceLength);
} else {
- candidateDirections = curlNESW(proteinLength);
+ candidateDirections = curlNESW(sequenceLength);
}
for (int i = 0; i < populationSize; i++) {
- population[i] = new Candidate(isHydrophobic, candidateDirections);
+ population[i] = new Candidate(candidateDirections);
}
return population;
diff --git a/src/main/java/InitialGenerationCreators/RandomDirection.java b/src/main/java/InitialGenerationCreators/RandomDirection.java
index 63bd16d..ecdc775 100644
--- a/src/main/java/InitialGenerationCreators/RandomDirection.java
+++ b/src/main/java/InitialGenerationCreators/RandomDirection.java
@@ -17,16 +17,15 @@ public class RandomDirection<T extends Enum<?>> implements InitialGenerationCre
}
@Override
- public Candidate[] initializeDirections(int populationSize, int[] isHydrophobic) {
+ public Candidate[] initializeDirections(int populationSize, int sequenceLength) {
Candidate[] population = new Candidate[populationSize];
- int proteinLength = isHydrophobic.length;
for (int i = 0; i < populationSize; i++) {
- int[] candidateDirections = new int[proteinLength];
- for (int j = 0; j < proteinLength; j++) {
+ int[] candidateDirections = new int[sequenceLength];
+ for (int j = 0; j < sequenceLength; j++) {
candidateDirections[j] = this.randomDirection(this.possibleDirections);
}
- population[i] = new Candidate(isHydrophobic, candidateDirections);
+ population[i] = new Candidate(candidateDirections);
}
return population;
diff --git a/src/main/java/InitialGenerationCreators/StraightLine.java b/src/main/java/InitialGenerationCreators/StraightLine.java
index abdde5c..63bd1e7 100644
--- a/src/main/java/InitialGenerationCreators/StraightLine.java
+++ b/src/main/java/InitialGenerationCreators/StraightLine.java
@@ -12,17 +12,16 @@ public class StraightLine implements InitialGenerationCreator {
}
@Override
- public Candidate[] initializeDirections(int populationSize, int[] isHydrophobic) {
+ public Candidate[] initializeDirections(int populationSize, int sequenceLength) {
Candidate[] population = new Candidate[populationSize];
- int proteinLength = isHydrophobic.length;
- int[] candidateDirections = new int[proteinLength];
- for (int j = 0; j < proteinLength; j++) {
+ int[] candidateDirections = new int[sequenceLength];
+ for (int j = 0; j < sequenceLength; j++) {
candidateDirections[j] = 0; // Default starting direction is set by Enum
}
for (int i = 0; i < populationSize; i++) {
- population[i] = new Candidate(isHydrophobic, candidateDirections);
+ population[i] = new Candidate(candidateDirections);
}
return population;
diff --git a/src/main/java/Interfaces/Evaluator.java b/src/main/java/Interfaces/Evaluator.java
index c386943..1e9ccb4 100644
--- a/src/main/java/Interfaces/Evaluator.java
+++ b/src/main/java/Interfaces/Evaluator.java
@@ -5,8 +5,4 @@ import MainClasses.Candidate;
public interface Evaluator {
double evaluateFitness(Candidate candidate);
-
- int evaluateBonds(Candidate candidate);
-
- int evaluateOverlaps(Candidate candidate);
}
diff --git a/src/main/java/Interfaces/InitialGenerationCreator.java b/src/main/java/Interfaces/InitialGenerationCreator.java
index 182069c..c905701 100644
--- a/src/main/java/Interfaces/InitialGenerationCreator.java
+++ b/src/main/java/Interfaces/InitialGenerationCreator.java
@@ -4,5 +4,5 @@ import MainClasses.Candidate;
public interface InitialGenerationCreator {
- Candidate[] initializeDirections(int populationSize, int[] isHydrophobic);
+ Candidate[] initializeDirections(int populationSize, int sequenceLength);
}
diff --git a/src/main/java/Interfaces/Visualizer.java b/src/main/java/Interfaces/Visualizer.java
index 50dbf16..f1440a5 100644
--- a/src/main/java/Interfaces/Visualizer.java
+++ b/src/main/java/Interfaces/Visualizer.java
@@ -14,13 +14,13 @@ public interface Visualizer {
static ArrayList<Vertex> deepCopyVertexList (List<Vertex> vertexListOriginal) {
ArrayList<Vertex> vertexList = new ArrayList<>();
for (Vertex v : vertexListOriginal) {
- Vertex vNew = new Vertex(v.x, v.y, v.isHydrophobic, v.outgoingDirection);
+ Vertex vNew = new Vertex(v.x, v.y, v.outgoingDirection);
vertexList.add(vNew);
}
return vertexList;
}
- static Cell[][] convertProteinTo2DArray(ArrayList<Vertex> vertexList) {
+ static Cell[][] convertProteinTo2DArray(ArrayList<Vertex> vertexList, int[] isHydrophobic) {
// Determine size
int minX = 0;
int maxX = 0;
@@ -61,7 +61,7 @@ public interface Visualizer {
for (int i = 0; i < vertexList.size(); i++) {
Vertex vertex = vertexList.get(i);
- if (vertex.isHydrophobic) {
+ if (isHydrophobic[i]==1) {
cellArray[vertex.y][vertex.x].addState(State.Hydrophobic);
} else {
cellArray[vertex.y][vertex.x].addState(State.Hydrophilic);
diff --git a/src/main/java/MainClasses/Candidate.java b/src/main/java/MainClasses/Candidate.java
index 985f542..10683bb 100644
--- a/src/main/java/MainClasses/Candidate.java
+++ b/src/main/java/MainClasses/Candidate.java
@@ -5,13 +5,11 @@ import java.util.Arrays;
public class Candidate {
- int[] isHydrophobic; // 0 = no | 1 = yes
public int[] outgoingDirection; // 0 = North | 1 = East | 2 = South | 3 = West
public ArrayList<Vertex> vertexList;
public double fitness;
- public Candidate(int[] isH, int[] oD) {
- this.isHydrophobic = isH;
+ public Candidate(int[] oD) {
this.outgoingDirection = oD;
this.vertexList = constructVertexes();
@@ -23,9 +21,8 @@ public class Candidate {
int currentX = 0;
int currentY = 0;
- for (int currentVertex = 0; currentVertex < isHydrophobic.length; currentVertex++) {
- vertexList.add(new Vertex(currentX, currentY,
- isHydrophobic[currentVertex] == 1, outgoingDirection[currentVertex]));
+ for (int currentVertex = 0; currentVertex < outgoingDirection.length; currentVertex++) {
+ vertexList.add(new Vertex(currentX, currentY, outgoingDirection[currentVertex]));
// Update position
if (outgoingDirection[currentVertex] == 0) {
diff --git a/src/main/java/MainClasses/GeneticAlgorithm.java b/src/main/java/MainClasses/GeneticAlgorithm.java
index e6dd179..654517b 100644
--- a/src/main/java/MainClasses/GeneticAlgorithm.java
+++ b/src/main/java/MainClasses/GeneticAlgorithm.java
@@ -45,7 +45,7 @@ public class GeneticAlgorithm {
this.initializeSettings();
this.clearLog();
- this.population = this.initialGenCreator.initializeDirections(Config.POPULATION_SIZE, this.isHydrophobic);
+ this.population = this.initialGenCreator.initializeDirections(Config.POPULATION_SIZE, this.isHydrophobic.length);
this.totalFitness = 0;
this.fitness = new double[Config.POPULATION_SIZE];
this.overallBestFitness = 0;
@@ -71,10 +71,10 @@ public class GeneticAlgorithm {
int j = 0;
for (VisualizerMethods vm : Config.VISUALIZERS) {
if (vm.equals(VisualizerMethods.Console)) {
- this.visualizers[j] = new VisualizerNESWtoConsole();
+ this.visualizers[j] = new VisualizerNESWtoConsole(isHydrophobic);
j++;
} else if (vm.equals(VisualizerMethods.Image)) {
- this.visualizers[j] = new VisualizerNESWtoFile(Config.IMAGE_SEQUENCE_PATH);
+ this.visualizers[j] = new VisualizerNESWtoFile(Config.IMAGE_SEQUENCE_PATH,isHydrophobic);
j++;
}
}
@@ -99,7 +99,7 @@ public class GeneticAlgorithm {
}
}
- this.evaluator = new EvaluatorNESW(Config.POINTS_PER_BOND);
+ this.evaluator = new EvaluatorNESW(Config.POINTS_PER_BOND, isHydrophobic);
} else {
// TODO: initialization for FRL settings
@@ -154,29 +154,29 @@ public class GeneticAlgorithm {
bestIndex = i;
}
}
- int bonds = this.evaluator.evaluateBonds(this.population[bestIndex]);
- int overlaps = this.evaluator.evaluateOverlaps(this.population[bestIndex]);
for (Visualizer v : this.visualizers) {
v.setFilename(String.format("gen_%d.png", gen));
- v.drawProtein(this.population[bestIndex].getVertexList(), bestFitness, bonds, overlaps, gen);
+ //TODO Print real bond and overlap amount
+ v.drawProtein(this.population[bestIndex].getVertexList(), bestFitness, -1, -1, gen);
}
+ //TODO Print real bond and overlap amount
System.out.println("The fitness is: " + bestFitness
- + " [hydrophobicBonds = " + bonds + " | overlaps = " + overlaps + "]");
+ + " [hydrophobicBonds = " + -1 + " | overlaps = " + -1 + "]");
// Save the overall best
if (bestFitness >= this.overallBestFitness) {
this.overallBestFitness = bestFitness;
- this.overallBest = new Candidate(this.isHydrophobic, this.population[bestIndex].getOutgoing());
+ this.overallBest = new Candidate(this.population[bestIndex].getOutgoing());
}
double averageFitness = this.totalFitness / Config.POPULATION_SIZE;
String log = String.format("%d\t%.4f\t%.4f\t%.4f\t %d\t%d\n",
gen, averageFitness, bestFitness,
this.evaluator.evaluateFitness(overallBest),
- this.evaluator.evaluateBonds(overallBest),
- this.evaluator.evaluateOverlaps(overallBest));
+ -1,
+ -1);
try {
Files.write(Paths.get(Config.LOGFILE), log.getBytes(), StandardOpenOption.APPEND);
diff --git a/src/main/java/MainClasses/Vertex.java b/src/main/java/MainClasses/Vertex.java
index 7c90580..ee55b92 100644
--- a/src/main/java/MainClasses/Vertex.java
+++ b/src/main/java/MainClasses/Vertex.java
@@ -4,13 +4,11 @@ package MainClasses;
public class Vertex {
public int x;
public int y;
- public boolean isHydrophobic;
public int outgoingDirection;
- public Vertex(int x, int y, boolean isHydrophobic, int outgoingDirection) {
+ public Vertex(int x, int y, int outgoingDirection) {
this.x = x;
this.y = y;
- this.isHydrophobic = isHydrophobic;
this.outgoingDirection = outgoingDirection;
}
diff --git a/src/main/java/Selectors/FitnessProportional.java b/src/main/java/Selectors/FitnessProportional.java
index b5c0c08..68225ac 100644
--- a/src/main/java/Selectors/FitnessProportional.java
+++ b/src/main/java/Selectors/FitnessProportional.java
@@ -33,7 +33,7 @@ public class FitnessProportional implements Selector {
j++;
picked -= proportionalFitness[j];
}
- newPopulation[i] = new Candidate(this.isHydrophobic, population[j].getOutgoing());
+ newPopulation[i] = new Candidate(population[j].getOutgoing());
}
return newPopulation;
diff --git a/src/main/java/Selectors/OnlyBest.java b/src/main/java/Selectors/OnlyBest.java
index 6193a62..fff027f 100644
--- a/src/main/java/Selectors/OnlyBest.java
+++ b/src/main/java/Selectors/OnlyBest.java
@@ -31,7 +31,7 @@ public class OnlyBest implements Selector {
int[] bestFolding = population[bestIndex].getOutgoing();
for (int i = 0; i < populationSize; i++) {
- newPopulation[i] = new Candidate(this.isHydrophobic, bestFolding);
+ newPopulation[i] = new Candidate(bestFolding);
}
return newPopulation;
diff --git a/src/main/java/Selectors/Tournament.java b/src/main/java/Selectors/Tournament.java
index e39e8fc..3cb928d 100644
--- a/src/main/java/Selectors/Tournament.java
+++ b/src/main/java/Selectors/Tournament.java
@@ -35,7 +35,7 @@ public class Tournament implements Selector {
tournamentChoosenIndex = nextIndex;
}
}
- newPopulation[i] = new Candidate(this.isHydrophobic, population[tournamentChoosenIndex].getOutgoing());
+ newPopulation[i] = new Candidate(population[tournamentChoosenIndex].getOutgoing());
}
return newPopulation;
diff --git a/src/main/java/Visualization/Visualizers/VisualizerNESWtoConsole.java b/src/main/java/Visualization/Visualizers/VisualizerNESWtoConsole.java
index 22af4d1..fa9de95 100644
--- a/src/main/java/Visualization/Visualizers/VisualizerNESWtoConsole.java
+++ b/src/main/java/Visualization/Visualizers/VisualizerNESWtoConsole.java
@@ -17,17 +17,19 @@ public class VisualizerNESWtoConsole implements Visualizer {
int maxHeight;
int maxWidth;
+ final int[] isHydrophobic;
- public VisualizerNESWtoConsole() {
+ public VisualizerNESWtoConsole(int[] isHydrophobic) {
this.maxHeight = 0;
this.maxWidth = 0;
+ this.isHydrophobic = isHydrophobic;
}
public void drawProtein(ArrayList<Vertex> vertexListOriginal, double fit, int bond, int over, int gen) {
// Copy VertexList to be able to manipulate it
ArrayList<Vertex> vertexList = Visualizer.deepCopyVertexList(vertexListOriginal);
- Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList);
+ Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, isHydrophobic);
for (int yIndex = cellArray.length-1; yIndex >= 0; yIndex--) {
for (int xIndex = 0; xIndex < cellArray[0].length; xIndex++) {
diff --git a/src/main/java/Visualization/Visualizers/VisualizerNESWtoFile.java b/src/main/java/Visualization/Visualizers/VisualizerNESWtoFile.java
index 78d8cfe..15ba9a6 100644
--- a/src/main/java/Visualization/Visualizers/VisualizerNESWtoFile.java
+++ b/src/main/java/Visualization/Visualizers/VisualizerNESWtoFile.java
@@ -25,20 +25,22 @@ public class VisualizerNESWtoFile implements Visualizer {
int pixelsPerCell = 40;
int margin = pixelsPerCell * 2;
int outline = 2;
+ final int[] isHydrophobic;
- public VisualizerNESWtoFile(String folder) {
+ public VisualizerNESWtoFile(String folder, int[] isHydrophobic) {
this.folder = folder;
this.filename = "image.png"; // Default
this.maxHeight = 0;
this.maxWidth = 0;
+ this.isHydrophobic = isHydrophobic;
}
public void drawProtein(ArrayList<Vertex> vertexListOriginal, double fit, int bond, int over, int gen) {
// Copy VertexList to be able to manipulate it
ArrayList<Vertex> vertexList = Visualizer.deepCopyVertexList(vertexListOriginal);
- Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList);
+ Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, this.isHydrophobic);
int height = (cellArray.length * pixelsPerCell) + margin * 2;
int width = (cellArray[0].length * pixelsPerCell) + margin * 2;
--
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