Refactored Visualizer interface

src/main/java/Interfaces/Visualizer.java

 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();
 }

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;
     }
 }

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();
 

src/main/java/Visualization/Visualizers/PrintFoldingToConsole.java → 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;
-    }
 }

src/main/java/Visualization/Visualizers/PrintFoldingToFile.java → src/main/java/Visualization/Visualizers/BestFoldingToImage.java

 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;
     }