StringSetComparator removed

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java

@@ -11,7 +11,8 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
@@ -437,7 +438,7 @@ public abstract class ElementAnnotator extends CachableInterface {
       } else if (newCollection == null || newCollection.size() == 0) {
         return false;
       } else {
-        StringSetComparator stringSetComparator = new StringSetComparator();
+        SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
         Set<String> set1 = new HashSet<>();
         Set<String> set2 = new HashSet<>();
 

commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java

-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-/**
- * Comparator used for comparing sets of strings.
- * 
- * @author Piotr Gawron
- * 
- */
-public class StringSetComparator implements Comparator<Set<String>> {
-  /**
-   * Default class logger.
-   */
-  private Logger logger = LogManager.getLogger();
-
-  @Override
-  public int compare(final Set<String> arg0, final Set<String> arg1) {
-    if (arg0 == null) {
-      if (arg1 == null) {
-        return 0;
-      } else {
-        return 1;
-      }
-    } else if (arg1 == null) {
-      return -1;
-    }
-
-    for (final String string : arg1) {
-      if (!arg0.contains(string)) {
-        logger.debug(string + " couldn't be found in " + arg0);
-        return 1;
-      }
-    }
-
-    for (final String string : arg0) {
-      if (!arg1.contains(string)) {
-        logger.debug(string + " couldn't be found in " + arg1);
-        return -1;
-      }
-    }
-    return 0;
-  }
-
-}

commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java

@@ -14,8 +14,6 @@ import org.junit.runners.Suite.SuiteClasses;
     ListComparatorTest.class,
     PointComparatorTest.class,
     StringComparatorTest.class,
-    StringListComparatorTest.class,
-    StringSetComparatorTest.class,
     SetComparatorTest.class,
 })
 public class AllComparatorTests {

commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java

-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class StringSetComparatorTest {
-
-  @Before
-  public void setUp() throws Exception {
-  }
-
-  @After
-  public void tearDown() throws Exception {
-  }
-
-  @Test
-  public void testNotNullComparisonEqualLength() {
-    Set<String> list1 = new HashSet<>();
-    Set<String> list2 = new HashSet<>();
-    Set<String> list3 = new HashSet<>();
-    list1.add("str1");
-    list1.add("x");
-    list2.add("str2");
-    list2.add("x");
-    list3.add("x");
-    list3.add("str1");
-    StringSetComparator comp = new StringSetComparator();
-    assertTrue(comp.compare(list1, list3) == 0);
-    assertFalse(comp.compare(list1, list2) == 0);
-    assertFalse(comp.compare(list2, list3) == 0);
-  }
-
-  @Test
-  public void testNotNullComparisonDiffLength() {
-    Set<String> list1 = new HashSet<>();
-    Set<String> list2 = new HashSet<>();
-    list1.add("str1");
-    list2.add("str2");
-    list2.add("str1");
-    StringSetComparator comp = new StringSetComparator();
-    assertFalse(comp.compare(list1, list2) == 0);
-    assertFalse(comp.compare(list2, list1) == 0);
-  }
-
-  @Test
-  public void testNullComparison() {
-    StringSetComparator comp = new StringSetComparator();
-    assertTrue(comp.compare(null, null) == 0);
-    assertFalse(comp.compare(new HashSet<>(), null) == 0);
-    assertFalse(comp.compare(null, new HashSet<>()) == 0);
-  }
-
-}

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -20,8 +20,8 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.comparator.IntegerComparator;
 import lcsb.mapviewer.common.comparator.ListComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
 import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -478,7 +478,7 @@ public class RestAnnotationParser {
     if (element.getSynonyms() == null || element.getSynonyms().size() == 0) {
       element.setSynonyms(synonyms);
     } else {
-      StringSetComparator stringSetComparator = new StringSetComparator();
+      SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
       Set<String> set1 = new HashSet<String>();
       Set<String> set2 = new HashSet<String>();
       set1.addAll(element.getSynonyms());

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

@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 
 /**
@@ -54,7 +55,7 @@ public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
 
   @Override
   protected int internalCompare(final AntisenseRna arg0, final AntisenseRna arg1) {
-    StringSetComparator stringSetComparator = new StringSetComparator();
+    SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
 
     Set<String> set1 = new HashSet<>();
     Set<String> set2 = new HashSet<>();

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

@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
@@ -55,7 +56,7 @@ public class GeneComparator extends Comparator<Gene> {
 
   @Override
   protected int internalCompare(final Gene arg0, final Gene arg1) {
-    StringSetComparator stringSetComparator = new StringSetComparator();
+    SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
 
     Set<String> set1 = new HashSet<>();
     Set<String> set2 = new HashSet<>();

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

@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
 
@@ -60,7 +61,7 @@ public class ProteinComparator extends Comparator<Protein> {
   @Override
   protected int internalCompare(final Protein arg0, final Protein arg1) {
     StructuralStateComparator structuralStateComparator = new StructuralStateComparator(epsilon);
-    StringSetComparator stringSetComparator = new StringSetComparator();
+    SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
 
     if (structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
       logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());

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

@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 
 /**
@@ -54,7 +55,7 @@ public class RnaComparator extends Comparator<Rna> {
 
   @Override
   protected int internalCompare(final Rna arg0, final Rna arg1) {
-    StringSetComparator stringSetComparator = new StringSetComparator();
+    SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
 
     Set<String> set1 = new HashSet<>();
     Set<String> set2 = new HashSet<>();