epsilon in comparison wasn't used everywhere...

model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java

@@ -29,7 +29,7 @@ public class ModelComparator extends Comparator<Model> {
   /**
    * Default class logger.
    */
-  private static Logger logger = LogManager.getLogger(ModelComparator.class);
+  private static Logger logger = LogManager.getLogger();
 
   /**
    * Epsilon value used for comparison of doubles.
@@ -38,7 +38,7 @@ public class ModelComparator extends Comparator<Model> {
 
   private SetComparator<SbmlUnit> unitSetComparator = new SetComparator<>(new SbmlUnitComparator());
 
-  private SetComparator<Reaction> reactionSetComparator = new SetComparator<>(new ReactionComparator(epsilon));
+  private SetComparator<Reaction> reactionSetComparator;
 
   private ElementUtils eu = new ElementUtils();
 
@@ -51,6 +51,7 @@ public class ModelComparator extends Comparator<Model> {
   public ModelComparator(double epsilon) {
     super(Model.class);
     this.epsilon = epsilon;
+    reactionSetComparator = new SetComparator<>(new ReactionComparator(epsilon));
   }
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java

@@ -88,7 +88,7 @@ public class ComplexComparator extends Comparator<Complex> {
       }
     }
 
-    StructuralStateComparator structuralStateComparator = new StructuralStateComparator();
+    StructuralStateComparator structuralStateComparator = new StructuralStateComparator(epsilon);
 
     if (structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
       logger

model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java

@@ -59,7 +59,7 @@ public class ProteinComparator extends Comparator<Protein> {
 
   @Override
   protected int internalCompare(Protein arg0, Protein arg1) {
-    StructuralStateComparator structuralStateComparator = new StructuralStateComparator();
+    StructuralStateComparator structuralStateComparator = new StructuralStateComparator(epsilon);
     StringSetComparator stringSetComparator = new StringSetComparator();
 
     if (structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {

model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralStateComparator.java

@@ -4,6 +4,7 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.*;
 import lcsb.mapviewer.model.map.MiriamData;
 
@@ -15,13 +16,23 @@ import lcsb.mapviewer.model.map.MiriamData;
  */
 public class StructuralStateComparator extends Comparator<StructuralState> {
 
+  /**
+   * Epsilon value used for comparison of doubles.
+   */
+  private double epsilon;
+
   private static Logger logger = LogManager.getLogger();
 
   /**
    * Default constructor.
    */
   public StructuralStateComparator() {
+    this(Configuration.EPSILON);
+  }
+
+  public StructuralStateComparator(double epsilon) {
     super(StructuralState.class);
+    this.epsilon=epsilon;
   }
 
   @Override
@@ -30,7 +41,7 @@ public class StructuralStateComparator extends Comparator<StructuralState> {
     if (stringComparator.compare(arg0.getValue(), arg1.getValue()) != 0) {
       return stringComparator.compare(arg0.getValue(), arg1.getValue());
     }
-    PointComparator pointComparator = new PointComparator();
+    PointComparator pointComparator = new PointComparator(epsilon);
     if (pointComparator.compare(arg0.getPosition(), arg1.getPosition()) != 0) {
       logger.debug("position different: " + arg0.getPosition() + ", " + arg1.getPosition());
       return pointComparator.compare(arg0.getPosition(), arg1.getPosition());