diff --git a/src/main/java/MainClasses/Config.java b/src/main/java/MainClasses/Config.java
index 96f17dcfd9b8cb84480528d7c0ed6c403ae6e5cc..b5e374ab6610e75970212f39ae44e2fb0e6d84b5 100644
--- a/src/main/java/MainClasses/Config.java
+++ b/src/main/java/MainClasses/Config.java
@@ -47,6 +47,7 @@ public class Config {
private int imageFps;
private int imagesToFpsIncrease;
private int imageFpsMax;
+ private int imageInterval;
private boolean zoom;
// For images
@@ -188,6 +189,7 @@ public class Config {
imageFps = Integer.parseInt(this.properties.getProperty("imgFps"));
imagesToFpsIncrease = Integer.parseInt(this.properties.getProperty("imagesToFpsIncrease"));
imageFpsMax = Integer.parseInt(this.properties.getProperty("imgFpsMax"));
+ imageInterval = Integer.parseInt(this.properties.getProperty("imageInterval"));
zoom = this.properties.getProperty("zoom").equals("true");
}
@@ -295,6 +297,10 @@ public class Config {
return imageFpsMax;
}
+ public int getImageInterval() {
+ return imageInterval;
+ }
+
public boolean isZoom() {
return zoom;
}
diff --git a/src/main/java/MainClasses/GeneticAlgorithm.java b/src/main/java/MainClasses/GeneticAlgorithm.java
index 45ec810daf0c9ccfdd2fb2475e56e3a8bf725d72..5324cd8779ac6488f6254f541088269274c97fda 100644
--- a/src/main/java/MainClasses/GeneticAlgorithm.java
+++ b/src/main/java/MainClasses/GeneticAlgorithm.java
@@ -143,6 +143,7 @@ public class GeneticAlgorithm {
// mutateGeneration(Mutator e);
private void evaluateGeneration() {
for (int i = 0; i < population.length; i++) {
+
this.population[i] = this.evaluator.evaluateFitness(this.population[i]);
}
}
diff --git a/src/main/java/Visualizers/BestFoldingToImage.java b/src/main/java/Visualizers/BestFoldingToImage.java
index 1481b874b611fd36212303bb76ec4e031fe878f9..a271ce96d3330aaa5b56f3148271ee1d5e16b9a9 100644
--- a/src/main/java/Visualizers/BestFoldingToImage.java
+++ b/src/main/java/Visualizers/BestFoldingToImage.java
@@ -40,123 +40,133 @@ public class BestFoldingToImage implements Visualizer {
}
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;
+ if(geneticAlgorithm.generation% config.getImageInterval() == 0 || geneticAlgorithm.generation == config.getTotalGenerations()) {
+ 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();
+ ArrayList<Vertex> vertexList = bestCandidateOfGeneration.getVertices();
- Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, this.isHydrophobic);
+ Cell[][] cellArray = Visualizer.convertProteinTo2DArray(vertexList, this.isHydrophobic);
- int height = (cellArray.length * pixelsPerCell) + margin * 2;
- int width = (cellArray[0].length * pixelsPerCell) + margin * 2;
+ int height = (cellArray.length * pixelsPerCell) + margin * 2;
+ int width = (cellArray[0].length * pixelsPerCell) + margin * 2;
- if (height > maxHeight) {
- maxHeight = height;
- }
- if (width > maxWidth) {
- maxWidth = width;
- }
+ if (height > maxHeight) {
+ maxHeight = height;
+ }
+ if (width > maxWidth) {
+ maxWidth = width;
+ }
- BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
- Graphics2D g2 = image.createGraphics();
- g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
- g2.setFont(config.getFont());
- FontMetrics metrics = g2.getFontMetrics();
- int ascent = metrics.getAscent();
+ BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = image.createGraphics();
+ g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
+ RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+ g2.setFont(config.getFont());
+ FontMetrics metrics = g2.getFontMetrics();
+ int ascent = metrics.getAscent();
- // Background
- g2.setColor(config.getImageBackground());
- g2.fillRect(0, 0, width, height);
+ // Background
+ g2.setColor(config.getImageBackground());
+ g2.fillRect(0, 0, width, height);
- for (int yIndex = cellArray.length-1; yIndex >= 0; yIndex--) {
- int yIndexPosition = cellArray.length-1 - yIndex;
+ for (int yIndex = cellArray.length - 1; yIndex >= 0; yIndex--) {
+ int yIndexPosition = cellArray.length - 1 - yIndex;
- for (int xIndex = 0; xIndex < cellArray[0].length; xIndex++) {
- Color aminoColor = null;
+ for (int xIndex = 0; xIndex < cellArray[0].length; xIndex++) {
+ Color aminoColor = null;
- State cellState = cellArray[yIndex][xIndex].getRelevantDrawState();
+ State cellState = cellArray[yIndex][xIndex].getRelevantDrawState();
- switch (cellState) {
- case Empty:
- break;
+ switch (cellState) {
+ case Empty:
+ break;
- case Hydrophobic:
- case HydrophobicMulti:
- aminoColor = config.getImageHydrophobic();
- break;
+ case Hydrophobic:
+ case HydrophobicMulti:
+ aminoColor = config.getImageHydrophobic();
+ break;
- case Hydrophilic:
- case HydrophilicMulti:
- aminoColor = config.getImageHydrophilic();
- break;
+ case Hydrophilic:
+ case HydrophilicMulti:
+ aminoColor = config.getImageHydrophilic();
+ break;
- case Mixed:
- aminoColor = config.getImageMixed();
- break;
+ case Mixed:
+ aminoColor = config.getImageMixed();
+ break;
- case ConnectionVertical:
- g2.setColor(config.getImageConnection());
- g2.fillRect((xIndex * pixelsPerCell) + margin + (pixelsPerCell/2)-outline,
+ case ConnectionVertical:
+ g2.setColor(config.getImageConnection());
+ g2.fillRect(
+ (xIndex * pixelsPerCell) + margin + (pixelsPerCell / 2) - outline,
(yIndexPosition * pixelsPerCell) + margin,
outline * 2, pixelsPerCell);
- break;
+ break;
- case ConnectionHorizontal:
- g2.setColor(config.getImageConnection());
- g2.fillRect((xIndex * pixelsPerCell) + margin,
- (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell/2)-outline,
+ case ConnectionHorizontal:
+ g2.setColor(config.getImageConnection());
+ g2.fillRect((xIndex * pixelsPerCell) + margin,
+ (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell / 2)
+ - outline,
pixelsPerCell, outline * 2);
- break;
- }
+ break;
+ }
- if (aminoColor != null) {
- g2.setColor(config.getImageOutline());
- g2.fillRect((xIndex * pixelsPerCell) + margin, (yIndexPosition * pixelsPerCell) + margin,
+ if (aminoColor != null) {
+ g2.setColor(config.getImageOutline());
+ g2.fillRect((xIndex * pixelsPerCell) + margin,
+ (yIndexPosition * pixelsPerCell) + margin,
pixelsPerCell, pixelsPerCell);
- g2.setColor(aminoColor);
- g2.fillRect((xIndex * pixelsPerCell) + outline + margin, (yIndexPosition * pixelsPerCell) + outline + margin,
+ g2.setColor(aminoColor);
+ g2.fillRect((xIndex * pixelsPerCell) + outline + margin,
+ (yIndexPosition * pixelsPerCell) + outline + margin,
pixelsPerCell - (outline * 2), pixelsPerCell - (outline * 2));
- g2.setColor(config.getImageAminoText());
- String label = "";
- for (int aminoIndex : cellArray[yIndex][xIndex].aminoIndexes) {
- label += aminoIndex + " ";
+ g2.setColor(config.getImageAminoText());
+ String label = "";
+ for (int aminoIndex : cellArray[yIndex][xIndex].aminoIndexes) {
+ label += aminoIndex + " ";
+ }
+ int labelWidth = metrics.stringWidth(label);
+ int x =
+ (xIndex * pixelsPerCell) + margin + (pixelsPerCell / 2) - (labelWidth
+ / 2) + outline;
+ int y = (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell / 2) + (
+ ascent / 2) - outline;
+ g2.drawString(label, x, y);
}
- int labelWidth = metrics.stringWidth(label);
- int x = (xIndex * pixelsPerCell) + margin + (pixelsPerCell/2) - (labelWidth/2) + outline;
- int y = (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell/2) + (ascent/2) - outline;
- g2.drawString(label, x, y);
}
}
- }
- g2.setColor(config.getImageText());
- //TODO Get the labels from the new Generation class?
- EvaluatorNESW evaluator = new EvaluatorNESW(1,isHydrophobic);
- int bonds = evaluator.evaluateBonds(bestCandidateOfGeneration);
- int overlaps = evaluator.evaluateOverlaps(bestCandidateOfGeneration);
- String label = "Gen: " + geneticAlgorithm.generation
+ g2.setColor(config.getImageText());
+ //TODO Get the labels from the new Generation class?
+ EvaluatorNESW evaluator = new EvaluatorNESW(1, isHydrophobic);
+ int bonds = evaluator.evaluateBonds(bestCandidateOfGeneration);
+ int overlaps = evaluator.evaluateOverlaps(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);
-
- try {
- //ImageIO.write(image, "png", new File(folder + File.separator + filename));
- ImageIO.write(image, "png", new File(filename));
- } catch (IOException e) {
- e.printStackTrace();
- System.exit(0);
+ int labelWidth = metrics.stringWidth(label);
+ int x = margin / 4;
+ int y = margin / 4;
+ g2.drawString(label, x, y);
+
+ try {
+ //ImageIO.write(image, "png", new File(folder + File.separator + filename));
+ ImageIO.write(image, "png", new File(filename));
+ } catch (IOException e) {
+ e.printStackTrace();
+ System.exit(0);
+ }
}
}
diff --git a/src/main/resources/genetic.properties b/src/main/resources/genetic.properties
index f5cc49353d68b8e68465837d2ff355f028e4d035..c92d9ca5add4438ec651bbc2b93cad69f60f750f 100644
--- a/src/main/resources/genetic.properties
+++ b/src/main/resources/genetic.properties
@@ -7,13 +7,13 @@
### Algorithm settings
# Size of the population in one generation
- populationSize = 100
+ populationSize = 1000
# Number of generations to run the algorithm for
- noGenerations = 20
+ noGenerations = 10000
# Type of population initialization [curl | straight | random]
initializationMethod = random
# Type of selection that should be used [proportional | tournament | onlybest]
- selectionMethod = proportional
+ selectionMethod = tournament
# Number of tournament participants, only relevant when selection is set to tournament
k = 5
# Type(s) of mutators to use in the algorithm, separated by comma [singlePoint / crossover / singlePointGlobal]
@@ -24,21 +24,21 @@
### Mutation settings
# How often a single point mutation should be attempted per candidate
- mutationAttemptsPerCandidate = 1
+ mutationAttemptsPerCandidate = 100
# Chance for a successful single point mutation [1.0 = 100%]
- mutationChance = 1.0
+ mutationChance = 0.011
# The mutation chance cannot drop below this value [1.0 = 100%]
- mutationMinimalChance = 0.001
+ mutationMinimalChance = 0.01
# Multiplicand for mutation probability with each generation -> ex with 0.05: 1st 1.0, 2nd 0.95, 3rd 0.9025, 4th 0.857
- mutationMultiplier = 0.001
+ mutationMultiplier = 0.0
# How often a crossover should be attempted per candidate
crossoverAttemptsPerCandidate = 1
# Chance for a successful crossover [1.0 = 100%]
- crossoverChance = 0.6
+ crossoverChance = 0.051
# The crossover chance cannot drop below this value [1.0 = 100%]
- crossoverMinimalChance = 0.001
+ crossoverMinimalChance = 0.05
# Multiplicand for mutation probability with each generation -> ex with -0.05: 1st 1.0, 2nd 1.05, 3rd 1,1025, 4th 1,157
- crossoverMultiplier = 0.005
+ crossoverMultiplier = 0.0
### Output settings
@@ -48,7 +48,7 @@
# video = Generate a video from the created images. Requires image
# log = Generate tab seperated file with a bit of information about each generation
# generation = print a short overview about each generation to stdout
- visualizerType = log,generation,image,video
+ visualizerType = generation,image
# Name of the job, filenames will be based on this name. If left empty a timestamp is used
jobName =
# Directory for the image sequence
@@ -57,6 +57,8 @@
videoDirectory = visualization
# Directory for the log file, always active
logfileDirectory = log
+ # Interval of generations between rendered images
+ imageInterval = 100
# Frames per second in the beginning of the video
imgFps = 10
# Number of images until fps increases by one