var nams refactored

annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java

@@ -14,6 +14,8 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;
@@ -49,15 +51,15 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
 
     model.addReaction(new Reaction());
 
-    Species proteinAlias1 = new GenericProtein("a1");
-    proteinAlias1.setName("SNCA");
+    Species protein1 = new GenericProtein("a1");
+    protein1.setName("SNCA");
 
-    Species proteinAlias2 = new GenericProtein("a2");
-    proteinAlias2.setName("PDK1");
-    proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
+    Species protein2 = new GenericProtein("a2");
+    protein2.setName("PDK1");
+    protein2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
 
-    model.addElement(proteinAlias1);
-    model.addElement(proteinAlias2);
+    model.addElement(protein1);
+    model.addElement(protein2);
 
     modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());