diff --git a/src/main/java/Enums/VisualizerMethods.java b/src/main/java/Enums/VisualizerMethods.java
index 30b14737a58affa1559912bf83de6ebcc29de16e..9bb67731d50c36d5fa8b88f9af46f6cebc33b00b 100644
--- a/src/main/java/Enums/VisualizerMethods.java
+++ b/src/main/java/Enums/VisualizerMethods.java
@@ -3,5 +3,6 @@ package Enums;
public enum VisualizerMethods {
Console,
Image,
- Video
+ Video,
+ Log
}
diff --git a/src/main/java/MainClasses/Config.java b/src/main/java/MainClasses/Config.java
index 7cbaee3f9c8c23d7eba9229fadb66105b36c20b7..adebb9c55d3020977199ece05247c60b1b597c46 100644
--- a/src/main/java/MainClasses/Config.java
+++ b/src/main/java/MainClasses/Config.java
@@ -173,6 +173,9 @@ public class Config {
case "video":
visualizers[i] = VisualizerMethods.Video;
break;
+ case "log":
+ visualizers[i] = VisualizerMethods.Log;
+ break;
}
}
diff --git a/src/main/java/MainClasses/GeneticAlgorithm.java b/src/main/java/MainClasses/GeneticAlgorithm.java
index 13be23837ba320743ff1163238862d57ef5ec387..b483b43a141f25d17dbe1632178c87e08c8e813d 100644
--- a/src/main/java/MainClasses/GeneticAlgorithm.java
+++ b/src/main/java/MainClasses/GeneticAlgorithm.java
@@ -14,6 +14,7 @@ import Selectors.Tournament;
import Visualization.Visualizers.BestFoldingToConsole;
import Visualization.Visualizers.BestFoldingToImage;
+import Visualization.Visualizers.GenerationProgressToLog;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
@@ -50,7 +51,6 @@ public class GeneticAlgorithm {
this.config = config;
this.initializeSettings();
- this.clearLog();
this.population = this.initialGenCreator.initializeDirections(config.getPopulationSize(), this.isHydrophobic.length);
this.totalFitness = 0;
@@ -70,12 +70,12 @@ public class GeneticAlgorithm {
// Settings that are dependant on encoding
if (config.getEncodingVariant().equals("NESW")) {
int nullCount = 0;
- for (int i = 0; i < config.getVisualizers().length; i++) {
+ /*for (int i = 0; i < config.getVisualizers().length; i++) {
if (!config.getVisualizers()[i].equals(VisualizerMethods.Console)
&& !config.getVisualizers()[i].equals(VisualizerMethods.Image)) {
nullCount++;
}
- }
+ }*/
this.visualizers = new Visualizer[config.getVisualizers().length - nullCount];
int j = 0;
for (VisualizerMethods vm : config.getVisualizers()) {
@@ -85,6 +85,9 @@ public class GeneticAlgorithm {
} else if (vm.equals(VisualizerMethods.Image)) {
this.visualizers[j] = new BestFoldingToImage(isHydrophobic, config);
j++;
+ }else if (vm.equals(VisualizerMethods.Log)) {
+ this.visualizers[j] = new GenerationProgressToLog(isHydrophobic, config);
+ j++;
}
}
@@ -123,19 +126,6 @@ public class GeneticAlgorithm {
}
}
- private void clearLog() {
- String content = "Generation\tAverage Fitness\tBest Fitness\tOverall Best Fitness\tBonds\tOverlaps\n";
- try {
- //TODO This does not belong here
- Files.createDirectories(Paths.get(config.getLogfileDirectory()));
- String logfilePath = config.getLogfileDirectory() + "/" + config.getJobName() + ".txt";
- Files.write(Paths.get(logfilePath), content.getBytes());
-
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
public void simulateGenerations() {
for (int gen = 0; gen < config.getTotalGenerations()-1; gen++) {
//TODO Remove with the new Generation class
@@ -186,19 +176,6 @@ public class GeneticAlgorithm {
}
double averageFitness = this.totalFitness / config.getPopulationSize();
- String log = String.format("%d\t%.4f\t%.4f\t%.4f\t %d\t%d\n",
- gen, averageFitness, bestFitness,
- this.overallBest.getFitness(),
- -1,
- -1);
-
- try {
- String logfilePath = config.getLogfileDirectory() + "/" + config.getJobName() + ".txt";
- Files.write(Paths.get(logfilePath), log.getBytes(), StandardOpenOption.APPEND);
-
- } catch (IOException e) {
- e.printStackTrace();
- }
return bestIndex;
}
diff --git a/src/main/java/Visualization/Visualizers/GenerationProgressToLog.java b/src/main/java/Visualization/Visualizers/GenerationProgressToLog.java
new file mode 100644
index 0000000000000000000000000000000000000000..8feb05324f72f3212c68d9f4f0901c2ff7dfe760
--- /dev/null
+++ b/src/main/java/Visualization/Visualizers/GenerationProgressToLog.java
@@ -0,0 +1,83 @@
+package Visualization.Visualizers;
+
+import Evaluators.EvaluatorNESW;
+import Interfaces.Visualizer;
+import MainClasses.Candidate;
+import MainClasses.Config;
+import MainClasses.GeneticAlgorithm;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+
+public class GenerationProgressToLog implements Visualizer {
+ Path logfilePath;
+ final int[] isHydrophobic;
+ Config config;
+
+ //TODO Make sure this is initialized or prepare for bugs
+ Candidate overallBestCandidate;
+ EvaluatorNESW bondsOverlapsEvaluator;
+
+ public GenerationProgressToLog(int[] isHydrophobic, Config config) {
+ this.isHydrophobic = isHydrophobic;
+ this.config = config;
+ String filename = config.getLogfileDirectory() + "/" + config.getJobName() + ".txt";
+ logfilePath = Paths.get(filename);
+ bondsOverlapsEvaluator = new EvaluatorNESW(1,isHydrophobic);
+
+ //Initialize the logfile
+ initializeLogfile();
+ }
+
+ @Override
+ public void drawProtein(Candidate[] generation, GeneticAlgorithm geneticAlgorithm) {
+ //TODO This should be done in the new Generation class
+ double averageFitness = 0.0;
+ Candidate bestCandidateOfGeneration = generation[0];
+ for(Candidate candidate: generation){
+ averageFitness += candidate.getFitness();
+ if(candidate.getFitness() > bestCandidateOfGeneration.getFitness()){
+ bestCandidateOfGeneration = candidate;
+ }
+ }
+ averageFitness /= generation.length;
+
+ //Find overall best Candidate
+ if(geneticAlgorithm.generation == 0) {
+ overallBestCandidate = bestCandidateOfGeneration;
+ }else if(bestCandidateOfGeneration.getFitness() > overallBestCandidate.getFitness()){
+ overallBestCandidate = bestCandidateOfGeneration;
+ }
+
+ int bonds = bondsOverlapsEvaluator.evaluateBonds(bestCandidateOfGeneration);
+ int overlaps = bondsOverlapsEvaluator.evaluateBonds(bestCandidateOfGeneration);
+
+ String log = String.format("%d\t%.4f\t%.4f\t%.4f\t %d\t%d\n",
+ geneticAlgorithm.generation,
+ averageFitness,
+ bestCandidateOfGeneration.getFitness(),
+ overallBestCandidate.getFitness(),
+ bonds,
+ overlaps);
+
+ try {
+ String logfilePath = config.getLogfileDirectory() + "/" + config.getJobName() + ".txt";
+ Files.write(Paths.get(logfilePath), log.getBytes(), StandardOpenOption.APPEND);
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void initializeLogfile() {
+ String content = "Generation\tAverage Fitness\tBest Fitness\tOverall Best Fitness\tBonds\tOverlaps\n";
+ try {
+ Files.createDirectories(Paths.get(config.getLogfileDirectory()));
+ Files.write(logfilePath, content.getBytes());
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/main/resources/genetic.properties b/src/main/resources/genetic.properties
index 9044afaa3d4d2c9341cd18a97359fbb9f5c5565c..27f864e487ab1ff31515f4f3679c908063816eee 100644
--- a/src/main/resources/genetic.properties
+++ b/src/main/resources/genetic.properties
@@ -43,7 +43,7 @@
### Output settings
# Type(s) of visualization to enable, separated with comma [console / image / video]
- visualizerType = image,video
+ visualizerType = log
# Name of the job, filenames will be based on this name. If left empty a timestamp is used
jobName = example1
# Directory for the image sequence