diff --git a/src/main/java/Interfaces/Visualizer.java b/src/main/java/Interfaces/Visualizer.java
index f1440a5b2f56545599f8749308e593b746914d3f..1b6c6469d26ab638e7da50c435a5c72dc67587c4 100644
--- a/src/main/java/Interfaces/Visualizer.java
+++ b/src/main/java/Interfaces/Visualizer.java
@@ -1,6 +1,8 @@
package Interfaces;
import Enums.State;
+import MainClasses.Candidate;
+import MainClasses.GeneticAlgorithm;
import MainClasses.Vertex;
import Visualization.Cell;
@@ -9,7 +11,8 @@ import java.util.List;
public interface Visualizer {
- void drawProtein(ArrayList<Vertex> vertexListOriginal, double fit, int bond, int over, int gen);
+ //TODO There should probably be a seperate datastructure for generation information/ga information
+ void drawProtein(Candidate[] generation, GeneticAlgorithm geneticAlgorithm);
static ArrayList<Vertex> deepCopyVertexList (List<Vertex> vertexListOriginal) {
ArrayList<Vertex> vertexList = new ArrayList<>();
@@ -84,8 +87,4 @@ public interface Visualizer {
return cellArray;
}
-
- void setFilename(String filename);
- int getMaxH();
- int getMaxW();
}
diff --git a/src/main/java/MainClasses/GeneticAlgorithm.java b/src/main/java/MainClasses/GeneticAlgorithm.java
index 4a3a987d9700e7d20ac76f7dc4b0cc5c776b34b5..13be23837ba320743ff1163238862d57ef5ec387 100644
--- a/src/main/java/MainClasses/GeneticAlgorithm.java
+++ b/src/main/java/MainClasses/GeneticAlgorithm.java
@@ -11,8 +11,8 @@ import Mutators.SinglePoint;
import Selectors.FitnessProportional;
import Selectors.OnlyBest;
import Selectors.Tournament;
-import Visualization.Visualizers.PrintFoldingToConsole;
-import Visualization.Visualizers.PrintFoldingToFile;
+import Visualization.Visualizers.BestFoldingToConsole;
+import Visualization.Visualizers.BestFoldingToImage;
import java.io.IOException;
import java.nio.file.Files;
@@ -25,20 +25,24 @@ public class GeneticAlgorithm {
Config config;
- int[] isHydrophobic;
- Candidate[] population;
+ //TODO Make private again when the Generation class is created
+ public int[] isHydrophobic;
+ public Candidate[] population;
- double totalFitness;
- double[] fitness;
+ public double totalFitness;
+ public double[] fitness;
- double overallBestFitness;
- Candidate overallBest;
+ public double overallBestFitness;
+ public Candidate overallBest;
- InitialGenerationCreator initialGenCreator;
- Mutator[] mutators;
- Selector selector;
- Evaluator evaluator;
- Visualizer[] visualizers;
+ public InitialGenerationCreator initialGenCreator;
+ public Mutator[] mutators;
+ public Selector selector;
+ public Evaluator evaluator;
+ public Visualizer[] visualizers;
+
+ //TODO Remove again with the new Generation class
+ public int generation;
// Initialize with protein
public GeneticAlgorithm (int[] protein, Config config) {
@@ -52,6 +56,7 @@ public class GeneticAlgorithm {
this.totalFitness = 0;
this.fitness = new double[config.getPopulationSize()];
this.overallBestFitness = 0;
+ this.generation = 0;
}
@@ -75,10 +80,10 @@ public class GeneticAlgorithm {
int j = 0;
for (VisualizerMethods vm : config.getVisualizers()) {
if (vm.equals(VisualizerMethods.Console)) {
- this.visualizers[j] = new PrintFoldingToConsole(isHydrophobic, config);
+ this.visualizers[j] = new BestFoldingToConsole(isHydrophobic, config);
j++;
} else if (vm.equals(VisualizerMethods.Image)) {
- this.visualizers[j] = new PrintFoldingToFile(isHydrophobic, config);
+ this.visualizers[j] = new BestFoldingToImage(isHydrophobic, config);
j++;
}
}
@@ -133,6 +138,8 @@ public class GeneticAlgorithm {
public void simulateGenerations() {
for (int gen = 0; gen < config.getTotalGenerations()-1; gen++) {
+ //TODO Remove with the new Generation class
+ generation = gen;
this.evaluateGeneration(gen);
this.population = this.selector.selectNewPopulation(this.population, this.fitness, this.totalFitness);
@@ -164,10 +171,8 @@ public class GeneticAlgorithm {
}
for (Visualizer v : this.visualizers) {
- String imagePath = config.getImageSequenceDirectory() + "/" + config.getJobName() + "_" + gen + ".png";
- v.setFilename(imagePath);
//TODO Print real bond and overlap amount
- v.drawProtein(this.population[bestIndex].getVertices(), bestFitness, -1, -1, gen);
+ v.drawProtein(this.population, this);
}
//TODO Print real bond and overlap amount
@@ -199,22 +204,20 @@ public class GeneticAlgorithm {
}
public int getMaxH() {
- int maxHAcrossVisualiszators = 0;
for (Visualizer v : visualizers) {
- if (maxHAcrossVisualiszators < v.getMaxH()) {
- maxHAcrossVisualiszators = v.getMaxH();
+ if(v instanceof BestFoldingToImage){
+ return ((BestFoldingToImage)v).getMaxH();
}
}
- return maxHAcrossVisualiszators;
+ return 0;
}
public int getMaxW() {
- int maxWAcrossVisualiszators = 0;
for (Visualizer v : visualizers) {
- if (maxWAcrossVisualiszators < v.getMaxW()) {
- maxWAcrossVisualiszators = v.getMaxW();
+ if(v instanceof BestFoldingToImage){
+ return ((BestFoldingToImage)v).getMaxW();
}
}
- return maxWAcrossVisualiszators;
+ return 0;
}
}
diff --git a/src/main/java/MainClasses/Main.java b/src/main/java/MainClasses/Main.java
index e9f8f7e751016716d39c302683414f912aea4f73..d063f4800f8a5fc83cf476c2ceef0329dfe593f8 100644
--- a/src/main/java/MainClasses/Main.java
+++ b/src/main/java/MainClasses/Main.java
@@ -12,7 +12,7 @@ public class Main {
String propertyPath = "./src/main/resources/genetic.properties";
Config config = new Config(propertyPath);
- int[] protein = Examples.convertStringToIntArray(Examples.SEQ36);
+ int[] protein = Examples.convertStringToIntArray(Examples.SEQ50);
GeneticAlgorithm ga = new GeneticAlgorithm(protein, config);
ga.simulateGenerations();
diff --git a/src/main/java/Visualization/Visualizers/PrintFoldingToConsole.java b/src/main/java/Visualization/Visualizers/BestFoldingToConsole.java
similarity index 70%
rename from src/main/java/Visualization/Visualizers/PrintFoldingToConsole.java
rename to src/main/java/Visualization/Visualizers/BestFoldingToConsole.java
index 3a9b4da3d17ce694c279703e7b4ce2144b7ad48d..d5eb289c7f405d65e4fc5d0eedd982418ab32509 100644
--- a/src/main/java/Visualization/Visualizers/PrintFoldingToConsole.java
+++ b/src/main/java/Visualization/Visualizers/BestFoldingToConsole.java
@@ -2,7 +2,9 @@ package Visualization.Visualizers;
import Enums.State;
import Interfaces.Visualizer;
+import MainClasses.Candidate;
import MainClasses.Config;
+import MainClasses.GeneticAlgorithm;
import MainClasses.Vertex;
import Visualization.Cell;
@@ -13,23 +15,25 @@ import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
-public class PrintFoldingToConsole implements Visualizer {
+public class BestFoldingToConsole implements Visualizer {
- int maxHeight;
- int maxWidth;
final int[] isHydrophobic;
Config config;
- public PrintFoldingToConsole(int[] isHydrophobic, Config config) {
- this.maxHeight = 0;
- this.maxWidth = 0;
+ public BestFoldingToConsole(int[] isHydrophobic, Config config) {
this.isHydrophobic = isHydrophobic;
this.config = config;
}
- 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);
+ public void drawProtein(Candidate[] generation, GeneticAlgorithm geneticAlgorithm) {
+ Candidate bestCandidateOfGeneration = generation[0];
+ for (Candidate evaluatedCandidate : generation) {
+ if(bestCandidateOfGeneration.getFitness() < evaluatedCandidate.getFitness()){
+ bestCandidateOfGeneration=evaluatedCandidate;
+ }
+ }
+
+ ArrayList<Vertex> vertexList = bestCandidateOfGeneration.getVertices();
Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, isHydrophobic);
@@ -75,20 +79,4 @@ public class PrintFoldingToConsole implements Visualizer {
// Fallback
return config.getConsoleEmpty();
}
-
-
- @Override
- public void setFilename(String format) {
- // Only here so file based visualizers work
- }
-
- @Override
- public int getMaxH() {
- return this.maxHeight;
- }
-
- @Override
- public int getMaxW() {
- return this.maxWidth;
- }
}
diff --git a/src/main/java/Visualization/Visualizers/PrintFoldingToFile.java b/src/main/java/Visualization/Visualizers/BestFoldingToImage.java
similarity index 74%
rename from src/main/java/Visualization/Visualizers/PrintFoldingToFile.java
rename to src/main/java/Visualization/Visualizers/BestFoldingToImage.java
index 787339be0ce04ed023824fc0911f4257ba840e23..32d4c55a9306a1087af48182dbdda589b5790c98 100644
--- a/src/main/java/Visualization/Visualizers/PrintFoldingToFile.java
+++ b/src/main/java/Visualization/Visualizers/BestFoldingToImage.java
@@ -1,11 +1,17 @@
package Visualization.Visualizers;
import Enums.State;
+import Evaluators.EvaluatorNESW;
+import Interfaces.Evaluator;
import Interfaces.Visualizer;
+import MainClasses.Candidate;
import MainClasses.Config;
+import MainClasses.GeneticAlgorithm;
import MainClasses.Vertex;
import Visualization.Cell;
+import java.nio.file.Files;
+import java.nio.file.Paths;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.BufferedImage;
@@ -13,10 +19,7 @@ import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
-public class PrintFoldingToFile implements Visualizer {
-
- String folder;
- String filename;
+public class BestFoldingToImage implements Visualizer {
int maxHeight;
int maxWidth;
@@ -28,21 +31,31 @@ public class PrintFoldingToFile implements Visualizer {
final int[] isHydrophobic;
Config config;
- public PrintFoldingToFile(int[] isHydrophobic, Config config) {
- //TODO This is not really needed
- //this.folder = config.getImageSequenceDirectory();
- this.folder = "";
- this.filename = "image.png"; // Default
-
+ public BestFoldingToImage(int[] isHydrophobic, Config config) {
this.maxHeight = 0;
this.maxWidth = 0;
this.isHydrophobic = isHydrophobic;
this.config = config;
+ try {
+ Files.createDirectories(Paths.get(config.getImageSequenceDirectory()));
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
}
- 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);
+ public void drawProtein(Candidate[] generation, GeneticAlgorithm geneticAlgorithm) {
+ String filename = config.getImageSequenceDirectory() + "/" + config.getJobName() + "_" + geneticAlgorithm.generation + ".png";
+
+ //TODO This should probably be in the new Generation Class
+ Candidate bestCandidateOfGeneration = generation[0];
+ for (Candidate evaluatedCandidate : generation) {
+ if(bestCandidateOfGeneration.getFitness() < evaluatedCandidate.getFitness()){
+ bestCandidateOfGeneration=evaluatedCandidate;
+ }
+ }
+
+ ArrayList<Vertex> vertexList = bestCandidateOfGeneration.getVertices();
Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, this.isHydrophobic);
@@ -130,17 +143,19 @@ public class PrintFoldingToFile implements Visualizer {
}
g2.setColor(config.getImageText());
- String label = "Gen: " + gen
- + " Fitness: " + String.format("%.4f", fit)
- + " H/H Bonds: " + bond
- + " Overlaps: " + over;
+ //TODO Get the labels from the new Generation class?
+ EvaluatorNESW evaluator = new EvaluatorNESW(1,isHydrophobic);
+ int bonds = evaluator.evaluateBonds(bestCandidateOfGeneration);
+ int overlaps = evaluator.evaluateBonds(bestCandidateOfGeneration);
+ String label = "Gen: " + geneticAlgorithm.generation
+ + " Fitness: " + String.format("%.4f", bestCandidateOfGeneration.getFitness())
+ + " H/H Bonds: " + bonds
+ + " Overlaps: " + overlaps;
int labelWidth = metrics.stringWidth(label);
int x = margin / 4;
int y = margin / 4;
g2.drawString(label, x, y);
- if (!new File(folder).exists()) new File(folder).mkdirs();
-
try {
//ImageIO.write(image, "png", new File(folder + File.separator + filename));
ImageIO.write(image, "png", new File(filename));
@@ -150,17 +165,10 @@ public class PrintFoldingToFile implements Visualizer {
}
}
- @Override
- public void setFilename(String filename) {
- this.filename = filename;
- }
-
- @Override
public int getMaxH() {
return this.maxHeight;
}
- @Override
public int getMaxW() {
return this.maxWidth;
}