StringListComparator removed

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

-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-import java.util.List;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-/**
- * Comparator used for list of strings.
- * 
- * @author Piotr Gawron
- * 
- */
-public class StringListComparator implements Comparator<List<String>> {
-  /**
-   * Default class logger.
-   */
-  private static Logger logger = LogManager.getLogger();
-
-  /**
-   * String comparator used for comparing strings.
-   */
-  private StringComparator stringComparator = new StringComparator();
-  /**
-   * Integer comparator used for comparing integers.
-   */
-  private IntegerComparator integerComparator = new IntegerComparator();
-
-  @Override
-  public int compare(final List<String> arg0, final List<String> arg1) {
-    if (arg0 == null) {
-      if (arg1 == null) {
-        return 0;
-      } else {
-        return 1;
-      }
-    } else if (arg1 == null) {
-      return -1;
-    }
-
-    if (arg0.size() != arg1.size()) {
-      logger.debug("String lists have different size: " + arg0.size() + ", " + arg1.size());
-      return integerComparator.compare(arg0.size(), arg1.size());
-    }
-
-    for (int i = 0; i < arg0.size(); i++) {
-      if (stringComparator.compare(arg0.get(i), arg1.get(i)) != 0) {
-        logger.debug("Strings in list different: \"" + arg0.get(i) + "\", \"" + arg1.get(i) + "\"");
-        return stringComparator.compare(arg0.get(i), arg1.get(i));
-      }
-    }
-
-    return 0;
-  }
-
-}

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

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

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

@@ -20,6 +20,7 @@ import org.xml.sax.SAXParseException;
 
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.geometry.DoubleDimension;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
 import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -32,31 +33,8 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
  */
 public class CommonXmlParser {
 
-  private static class DimensionDouble extends Dimension2D {
-
-    private double width;
-    private double height;
-
-    @Override
-    public double getWidth() {
-      return width;
-    }
-
-    @Override
-    public double getHeight() {
-      return height;
-    }
-
-    @Override
-    public void setSize(final double width, final double height) {
-      this.width = width;
-      this.height = height;
-    }
-
-  }
-
   public static final Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = new HashSet<>();
-  
+
   {
     RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.addAll(Arrays.asList(MiriamRelationType.values()));
     RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
@@ -120,8 +98,7 @@ public class CommonXmlParser {
   public Dimension2D getDimension(final Node node) {
     double width = Double.parseDouble(XmlParser.getNodeAttr("width", node));
     double height = Double.parseDouble(XmlParser.getNodeAttr("height", node));
-    DimensionDouble result = new DimensionDouble();
-    result.setSize(width, height);
+    DoubleDimension result = new DoubleDimension(width, height);
     return result;
   }
 
@@ -147,7 +124,8 @@ public class CommonXmlParser {
    */
   public Color getColor(final Node node) {
     String color = XmlParser.getNodeAttr("color", node);
-    // cellDesigner has a bug that removes info about alpha when alpha is 0 (#1103)
+    // cellDesigner has a bug that removes info about alpha when alpha is 0
+    // (#1103)
     color = StringUtils.leftPad(color, 8, "0");
 
     return XmlParser.stringToColor(color);

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

@@ -19,8 +19,8 @@ import org.w3c.dom.Node;
 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.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
 import lcsb.mapviewer.common.comparator.StringSetComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -506,7 +506,7 @@ public class RestAnnotationParser {
     if (element.getFormerSymbols() == null || element.getFormerSymbols().size() == 0) {
       element.setFormerSymbols(formerSymbols);
     } else {
-      StringListComparator stringListComparator = new StringListComparator();
+      ListComparator<String> stringListComparator = new ListComparator<>(new StringComparator());
       if (stringListComparator.compare(element.getFormerSymbols(), formerSymbols) != 0) {
         logger.warn(elementUtils.getElementTag(element) + " Former symbols list different than default ["
             + formerSymbols + "][" + element.getFormerSymbols() + "]. Ignoring.");

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java

@@ -4,8 +4,8 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.ListComparator;
 import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
 
 public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
   private static Logger logger = LogManager.getLogger();
@@ -17,7 +17,7 @@ public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
   @Override
   protected int internalCompare(final SbmlFunction arg0, final SbmlFunction arg1) {
     StringComparator stringComparator = new StringComparator();
-    StringListComparator stringListComparator = new StringListComparator();
+    ListComparator<String> stringListComparator = new ListComparator<>(stringComparator);
     if (stringComparator.compare(arg0.getFunctionId(), arg1.getFunctionId()) != 0) {
       logger.debug("functionId different");
       return stringComparator.compare(arg0.getFunctionId(), arg1.getFunctionId());

model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java

@@ -8,10 +8,10 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.BooleanComparator;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.ListComparator;
 import lcsb.mapviewer.common.comparator.PointComparator;
 import lcsb.mapviewer.common.comparator.SetComparator;
 import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
 import lcsb.mapviewer.model.graphics.PolylineDataComparator;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamDataComparator;
@@ -130,7 +130,7 @@ public class ReactionComparator extends Comparator<Reaction> {
       return doubleComparator.compare(arg0.getUpperBound(), arg1.getUpperBound());
     }
 
-    StringListComparator stringListComparator = new StringListComparator();
+    ListComparator<String> stringListComparator = new ListComparator<>(stringComparator);
 
     if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
       logger.debug("Synonyms dataset different");

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

@@ -9,9 +9,9 @@ import lcsb.mapviewer.common.comparator.ColorComparator;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.comparator.EnumComparator;
 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.StringListComparator;
 import lcsb.mapviewer.model.graphics.HorizontalAlign;
 import lcsb.mapviewer.model.graphics.VerticalAlign;
 import lcsb.mapviewer.model.map.MiriamData;
@@ -168,7 +168,7 @@ public class ElementComparator extends Comparator<Element> {
       return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
     }
 
-    StringListComparator stringListComparator = new StringListComparator();
+    ListComparator<String> stringListComparator = new ListComparator<>(stringComparator);
 
     if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
       logger.debug("List of synonyms different");