formatting issues

checkstyle.xml

@@ -224,13 +224,6 @@
         </module>
     
         <module name="OverloadMethodsDeclarationOrder"/>
-<!--        <module name="VariableDeclarationUsageDistance"/>
-        <module name="CustomImportOrder">
-            <property name="sortImportsInGroupAlphabetically" value="true"/>
-            <property name="separateLineBetweenGroups" value="true"/>
-            <property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
-            <property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
-        </module>
         <module name="MethodParamPad">
             <property name="tokens"
                       value="CTOR_DEF, LITERAL_NEW, METHOD_CALL, METHOD_DEF,
@@ -241,7 +234,7 @@
                       value="COMMA, SEMI, POST_INC, POST_DEC, DOT, ELLIPSIS, METHOD_REF"/>
             <property name="allowLineBreaks" value="true"/>
         </module>
-        <module name="ParenPad">
+<!--        <module name="ParenPad">
             <property name="tokens"
                       value="ANNOTATION, ANNOTATION_FIELD_DEF, CTOR_CALL, CTOR_DEF, DOT, ENUM_CONSTANT_DEF,
                     EXPR, LITERAL_CATCH, LITERAL_DO, LITERAL_FOR, LITERAL_IF, LITERAL_NEW,
@@ -308,6 +301,13 @@
             <property name="tokens"
                       value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF, ANNOTATION_FIELD_DEF,
                     PARAMETER_DEF, VARIABLE_DEF, METHOD_DEF"/>
+        </module>
+        <module name="VariableDeclarationUsageDistance"/>
+        <module name="CustomImportOrder">
+            <property name="sortImportsInGroupAlphabetically" value="true"/>
+            <property name="separateLineBetweenGroups" value="true"/>
+            <property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
+            <property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
         </module>
          -->
     </module> 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexSbgnConverter.java

@@ -32,8 +32,8 @@ public class ComplexSbgnConverter extends ComplexConverter {
    * Default constructor.
    * 
    * @param colorExtractor
-   *          Object that helps to convert {@link DataOverlayEntry} values into colors
-   *          when drawing {@link Species}
+   *          Object that helps to convert {@link DataOverlayEntry} values into
+   *          colors when drawing {@link Species}
    */
   public ComplexSbgnConverter(final ColorExtractor colorExtractor) {
     super(colorExtractor);
@@ -73,7 +73,7 @@ public class ComplexSbgnConverter extends ComplexConverter {
 
   @Override
   Shape getStructuralStateShape(final StructuralState state) {
-    double arcSize = Math.min(state.getWidth(), state.getHeight()) ;
+    double arcSize = Math.min(state.getWidth(), state.getHeight());
     return new RoundRectangle2D.Double(state.getPosition().getX(), state.getPosition().getY(), state.getWidth(),
         state.getHeight(), arcSize, arcSize);
   }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParserTest.java

@@ -16,8 +16,8 @@ import lcsb.mapviewer.model.map.species.Protein;
 
 public class SbmlElementParserTest extends SbmlTestFunctions {
 
-  SbmlElementParser<?> parser ;
-  
+  SbmlElementParser<?> parser;
+
   @Before
   public void setUp() {
     Model sbmlModel = new Model();
@@ -27,9 +27,9 @@ public class SbmlElementParserTest extends SbmlTestFunctions {
     layoutPlugin.add(layout);
     sbmlModel.addExtension("layout", layoutPlugin);
 
-    parser = new SbmlSpeciesParser(sbmlModel,null);
+    parser = new SbmlSpeciesParser(sbmlModel, null);
   }
-  
+
   @Test
   public void testCreateElementWithLayoutWithoutBox() throws Exception {
     Protein protein = super.createProtein();
@@ -37,7 +37,7 @@ public class SbmlElementParserTest extends SbmlTestFunctions {
     Element result = parser.createElementWithLayout(protein, glyph);
     assertNotNull(result);
   }
-  
+
   @Test
   public void testCreateElementWithLayoutWithoutPosition() throws Exception {
     Protein protein = super.createProtein();

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

@@ -54,7 +54,7 @@ public class ModelComparator extends Comparator<Model> {
 
   private SetComparator<Reaction> reactionSetComparator;
 
-  private ElementComparator elementComparator ;
+  private ElementComparator elementComparator;
 
   private ElementUtils eu = new ElementUtils();
 
@@ -205,8 +205,8 @@ public class ModelComparator extends Comparator<Model> {
    *          first set of layers
    * @param layers2
    *          second set of layers
-   * @return if sets are equal then returns 0. If they are different then -1/1 is
-   *         returned.
+   * @return if sets are equal then returns 0. If they are different then -1/1
+   *         is returned.
    */
   private int compareLayers(final Set<Layer> layers, final Set<Layer> layers2) {
     LayerComparator layerComparator = new LayerComparator(epsilon);
@@ -242,8 +242,8 @@ public class ModelComparator extends Comparator<Model> {
    *          first set of elements
    * @param elements2
    *          second set of elements
-   * @return if sets are equal then returns 0. If they are different then -1/1 is
-   *         returned.
+   * @return if sets are equal then returns 0. If they are different then -1/1
+   *         is returned.
    */
   private int compareElements(final Set<Element> elements, final Set<Element> elements2) {
 

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/BiopaxParserTest.java

@@ -16,7 +16,7 @@ import lcsb.mapviewer.wikipathway.xml.BiopaxParser;
 
 public class BiopaxParserTest extends WikipathwaysTestFunctions {
 
-  BiopaxParser parser ;
+  BiopaxParser parser;
 
   @Before
   public void setUp() throws Exception {

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/EdgeParserTest.java

@@ -22,13 +22,13 @@ public class EdgeParserTest {
 
   Logger logger = LogManager.getLogger();
 
-  EdgeParser parser ;
+  EdgeParser parser;
 
   @Before
   public void setUp() {
     parser = new EdgeParser("mapName");
   }
-  
+
   @Test
   public void testGetPointsWithoutTargetDirection() throws Exception {
     List<PointData> gpmlPoints = new ArrayList<>();

service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java

@@ -100,9 +100,9 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
   public void testCacheDataForModelWithAnyIdentifierType() throws Exception {
     Model model = new ModelFullIndexed(null);
     model.setProject(new Project());
-    model.getProject().setDisease(new MiriamData( MiriamType.MESH_2012, "X111111"));
+    model.getProject().setDisease(new MiriamData(MiriamType.MESH_2012, "X111111"));
     GenericProtein protein = new GenericProtein("x");
-    for (final MiriamType type: MiriamType.values()) {
+    for (final MiriamType type : MiriamType.values()) {
       protein.addMiriamData(new MiriamData(type, type.getExampleIdentifier()));
     }
     model.addElement(protein);
@@ -110,7 +110,7 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
     chemicalService.cacheDataForModel(model, new IProgressUpdater() {
       @Override
       public void setProgress(final double progress) {
-        called .setValue(true);;
+        called.setValue(true);
       }
     });
     assertTrue(called.booleanValue());