From 7fb2e47c13f798511b0fa6b47c34f53d42c00f34 Mon Sep 17 00:00:00 2001
From: OszkarSemerath <semerath@mit.bme.hu>
Date: Tue, 8 Aug 2023 19:37:54 +0200
Subject: ObjectCodeImpl.effectiveSize introduced to correctly handle models
 with different indices.

---
 .../neighbourhood/NeighbourhoodCalculator.java     |  2 +-
 .../statecoding/neighbourhood/ObjectCodeImpl.java  | 29 ++++++++++++++--------
 2 files changed, 20 insertions(+), 11 deletions(-)

(limited to 'subprojects/store/src/main/java/tools')

diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java
index d3b3ccae..5b3e5ea3 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/NeighbourhoodCalculator.java
@@ -34,7 +34,7 @@ public class NeighbourhoodCalculator extends AbstractNeighbourhoodCalculator imp
 			constructNextObjectCodes(previousObjectCode, nextObjectCode);
 			previousObjectCode = nextObjectCode;
 			rounds++;
-		} while (rounds <= 7 && rounds <= previousObjectCode.getSize());
+		} while (rounds <= 7 && rounds <= previousObjectCode.getEffectiveSize());
 
 		long result = calculateLastSum(previousObjectCode);
 		return new StateCoderResult((int) result, previousObjectCode);
diff --git a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java
index 0d629176..0cd7ff58 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/statecoding/neighbourhood/ObjectCodeImpl.java
@@ -12,31 +12,35 @@ import java.util.Arrays;
 public class ObjectCodeImpl implements ObjectCode {
 	private long[] vector;
 	private int size;
+	private int effectiveSize;
 
 	public ObjectCodeImpl() {
 		vector = new long[10];
 		size = 0;
+		effectiveSize = 0;
 	}
 
 	public ObjectCodeImpl(int size) {
 		this.vector = new long[size];
 		this.size = size;
+		effectiveSize = 0;
 	}
 
 	public ObjectCodeImpl(ObjectCodeImpl copy) {
-		this.vector = Arrays.copyOf(copy.vector,copy.size);
+		this.vector = Arrays.copyOf(copy.vector, copy.size);
 		this.size = copy.size;
+		effectiveSize = copy.effectiveSize;
 	}
 
 	public void ensureSize(int object) {
-		if(object >= size) {
-			size = object+1;
+		if (object >= size) {
+			size = object + 1;
 		}
 
-		if(object >= vector.length) {
-			int newLength = vector.length*2;
-			while(object >= newLength) {
-				newLength*=2;
+		if (object >= vector.length) {
+			int newLength = vector.length * 2;
+			while (object >= newLength) {
+				newLength *= 2;
 			}
 
 			long[] newVector = new long[newLength];
@@ -46,7 +50,7 @@ public class ObjectCodeImpl implements ObjectCode {
 	}
 
 	public long get(int object) {
-		if(object < vector.length) {
+		if (object < vector.length) {
 			return vector[object];
 		} else {
 			return 0;
@@ -56,17 +60,22 @@ public class ObjectCodeImpl implements ObjectCode {
 	public void set(int object, long value) {
 		ensureSize(object);
 		final long valueToPut = value == 0 ? 1 : value;
-		vector[object]=valueToPut;
+		if (vector[object] == 0) effectiveSize++;
+		vector[object] = valueToPut;
 	}
 
 	public int getSize() {
 		return this.size;
 	}
 
+	public int getEffectiveSize() {
+		return this.effectiveSize;
+	}
+
 	@Override
 	public String toString() {
 		return "ObjectCodeImpl{" +
-				"vector=" + Arrays.toString(Arrays.copyOf(vector,this.size)) +
+				"vector=" + Arrays.toString(Arrays.copyOf(vector, this.size)) +
 				'}';
 	}
 }
-- 
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