From fe4f088a72d3ec9d9cc1b4c917f37ff6d48b9e54 Mon Sep 17 00:00:00 2001
From: istkabra <kyrill.abrams@stud.h-da.de>
Date: Tue, 2 Jun 2020 17:31:10 +0200
Subject: [PATCH] * Global bending of proteins is now working on singlePoint
mutations * Closes #9
---
src/main/java/Enums/MutatorMethods.java | 1 +
src/main/java/MainClasses/Config.java | 2 ++
.../java/MainClasses/GeneticAlgorithm.java | 11 +++++----
...ntBend.java => SinglePointGlobalBend.java} | 23 +++++++++++++++----
4 files changed, 27 insertions(+), 10 deletions(-)
rename src/main/java/Mutators/{SinglePointBend.java => SinglePointGlobalBend.java} (57%)
diff --git a/src/main/java/Enums/MutatorMethods.java b/src/main/java/Enums/MutatorMethods.java
index 3ec0bb1..fe3a5ef 100644
--- a/src/main/java/Enums/MutatorMethods.java
+++ b/src/main/java/Enums/MutatorMethods.java
@@ -2,5 +2,6 @@ package Enums;
public enum MutatorMethods {
SinglePoint,
+ SinglePointGlobal,
Crossover
}
diff --git a/src/main/java/MainClasses/Config.java b/src/main/java/MainClasses/Config.java
index 58f1b75..96f17dc 100644
--- a/src/main/java/MainClasses/Config.java
+++ b/src/main/java/MainClasses/Config.java
@@ -134,6 +134,8 @@ public class Config {
mutatorMethods[i] = MutatorMethods.SinglePoint;
} else if (mutatorsToUse[i].equals("crossover")) {
mutatorMethods[i] = MutatorMethods.Crossover;
+ } else if (mutatorsToUse[i].equals("singlePointGlobal")) {
+ mutatorMethods[i] = MutatorMethods.SinglePointGlobal;
}
}
diff --git a/src/main/java/MainClasses/GeneticAlgorithm.java b/src/main/java/MainClasses/GeneticAlgorithm.java
index 5951276..45ec810 100644
--- a/src/main/java/MainClasses/GeneticAlgorithm.java
+++ b/src/main/java/MainClasses/GeneticAlgorithm.java
@@ -8,15 +8,12 @@ import InitialGenerationCreators.StraightLine;
import Interfaces.*;
import Mutators.Crossover;
import Mutators.SinglePoint;
+import Mutators.SinglePointGlobalBend;
import Selectors.FitnessProportional;
import Selectors.OnlyBest;
import Selectors.Tournament;
-import Visualizers.BestFoldingToConsole;
-import Visualizers.BestFoldingToImage;
+import Visualizers.*;
-import Visualizers.BestFoldingsToVideo;
-import Visualizers.GenerationOverviewToConsole;
-import Visualizers.GenerationProgressToLog;
import java.util.Random;
public class GeneticAlgorithm {
@@ -105,6 +102,10 @@ public class GeneticAlgorithm {
} else if (config.getMutatorMethods()[i].equals(MutatorMethods.Crossover)) {
this.mutators[i] = new Crossover<>(DirectionNESW.class, this.rand,
config.getCrossoverAttemptsPerCandidate(), config.getCrossoverChance(), config.getCrossoverMinimalChance(), config.getCrossoverMultiplier());
+
+ } else if (config.getMutatorMethods()[i].equals(MutatorMethods.SinglePointGlobal)) {
+ this.mutators[i] = new SinglePointGlobalBend<>(DirectionNESW.class, this.rand,
+ config.getMutationAttemptsPerCandidate(), config.getMutationChance(), config.getMutationMinimalChance(), config.getMutationMultiplier());
}
}
diff --git a/src/main/java/Mutators/SinglePointBend.java b/src/main/java/Mutators/SinglePointGlobalBend.java
similarity index 57%
rename from src/main/java/Mutators/SinglePointBend.java
rename to src/main/java/Mutators/SinglePointGlobalBend.java
index 1fc4146..ab03523 100644
--- a/src/main/java/Mutators/SinglePointBend.java
+++ b/src/main/java/Mutators/SinglePointGlobalBend.java
@@ -2,9 +2,10 @@ package Mutators;
import Interfaces.Mutator;
import MainClasses.Candidate;
+
import java.util.Random;
-public class SinglePointBend<T extends Enum<?>> implements Mutator {
+public class SinglePointGlobalBend<T extends Enum<?>> implements Mutator { // TODO: Maybe this should just extend SinglePoint
boolean isFRL;
Class<T> possibleDirections;
@@ -14,8 +15,8 @@ public class SinglePointBend<T extends Enum<?>> implements Mutator {
double mutationMinimalChance;
double mutationMultiplier;
- public SinglePointBend(Class<T> possibleDirections, Random rand, int mutationAttemptsPerCandidate,
- double mutationChance, double mutationMinimalChance, double mutationMultiplier) {
+ public SinglePointGlobalBend(Class<T> possibleDirections, Random rand, int mutationAttemptsPerCandidate,
+ double mutationChance, double mutationMinimalChance, double mutationMultiplier) {
this.possibleDirections = possibleDirections;
this.isFRL = Mutator.isFRLEncoding(possibleDirections);
this.rand = rand;
@@ -38,11 +39,23 @@ public class SinglePointBend<T extends Enum<?>> implements Mutator {
for (int j = 0; j < this.mutationAttemptsPerCandidate; j++) {
if (this.mutationChance > this.rand.nextDouble()) {
int mutationPlace = this.rand.nextInt(proteinLength);
- // TODO Do complete bend instead of local bend
if (this.isFRL) {
mutatedFolding[mutationPlace] = this.rand.nextInt(3);
} else {
- mutatedFolding[mutationPlace] = this.rand.nextInt(4);
+ int oldDirection = mutatedFolding[mutationPlace];
+ if (mutationPlace == 0) {
+ // Allow any direction in the first position
+ mutatedFolding[mutationPlace] = this.rand.nextInt(4);
+ } else {
+ // Make sure there can never be a backtracking overlap while mutating
+ mutatedFolding[mutationPlace] =
+ ((mutatedFolding[mutationPlace-1] - 1 + this.rand.nextInt(3)) + 4 ) % 4;
+ }
+ // Also bend the following amino acids in the right way to achieve a "global" bend
+ int offset = (mutatedFolding[mutationPlace] - oldDirection + 4) % 4;
+ for (int r = mutationPlace + 1; r < mutatedFolding.length; r++) {
+ mutatedFolding[r] = (mutatedFolding[r] + offset) % 4;
+ }
}
}
}
--
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