ObjectCodeImpl.effectiveSize introduced to correctly handle models with different indices.

2 files changed, 20 insertions, 11 deletions

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)) +
                                 '}';
         }
 }