curly braces are required in for/if statements

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

@@ -158,7 +158,7 @@ public abstract class ElementAnnotator extends CachableInterface {
    */
   public List<Class<? extends BioEntity>> getValidClasses() {
     return validClasses;
-  };
+  }
 
   /**
    * Returns <code>true</code> if this annotator can annotate the object given in

annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java

@@ -203,8 +203,9 @@ public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit
   }
 
   protected String nodeToString(Node node, boolean includeHeadNode) {
-    if (node == null)
+    if (node == null) {
       return null;
+    }
     StringWriter sw = new StringWriter();
     try {
       Transformer t = TransformerFactory.newInstance().newTransformer();

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

@@ -96,8 +96,9 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
       boolean deprecated = false;
       try {
         Field f = MiriamType.class.getField(mt.name());
-        if (f.isAnnotationPresent(Deprecated.class))
+        if (f.isAnnotationPresent(Deprecated.class)) {
           deprecated = true;
+        }
       } catch (NoSuchFieldException | SecurityException e) {
       }
 

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

@@ -127,10 +127,11 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
     modelAnnotator.copyAnnotationFromOtherSpecies(model, updater);
 
     for (Species element : model.getSpeciesList()) {
-      if (element.getName().equals("s4"))
+      if (element.getName().equals("s4")) {
         assertEquals(0, element.getMiriamData().size());
-      else if (element.getName().equals("hello"))
+      } else if (element.getName().equals("hello")) {
         assertEquals(1, element.getMiriamData().size());
+      }
     }
   }
 

checkstyle.xml

@@ -70,7 +70,7 @@
             <property name="tokens"
                       value="LITERAL_TRY, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE, LITERAL_SWITCH"/>
         </module>
-<!--        <module name="NeedBraces">
+        <module name="NeedBraces">
             <property name="tokens"
                       value="LITERAL_DO, LITERAL_ELSE, LITERAL_FOR, LITERAL_IF, LITERAL_WHILE"/>
         </module>
@@ -95,7 +95,7 @@
                       value="CLASS_DEF, METHOD_DEF, CTOR_DEF, LITERAL_FOR, LITERAL_WHILE, STATIC_INIT,
                     INSTANCE_INIT, ANNOTATION_DEF, ENUM_DEF"/>
         </module>
-        <module name="WhitespaceAround">
+<!--        <module name="WhitespaceAround">
             <property name="allowEmptyConstructors" value="true"/>
             <property name="allowEmptyLambdas" value="true"/>
             <property name="allowEmptyMethods" value="true"/>

commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java

@@ -121,8 +121,9 @@ public class XmlParserTest extends CommonTestFunctions {
   @Test
   public void testConcurrencyParse() throws Exception {
     StringBuilder builder = new StringBuilder("<doc>");
-    for (int i = 0; i < 30000; i++)
+    for (int i = 0; i < 30000; i++) {
       builder.append("<test_node>test_x</test_node>");
+    }
     builder.append("</doc>");
     final String xml = builder.toString();
     threadSucceded = false;

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

@@ -921,8 +921,9 @@ public class RestAnnotationParser {
   boolean isFieldAnnotated(NoteField field, Class<? extends Annotation> annotationClass) {
     try {
       Field f = field.getClass().getField(field.name());
-      if (f.isAnnotationPresent(annotationClass))
+      if (f.isAnnotationPresent(annotationClass)) {
         return true;
+      }
     } catch (NoSuchFieldException | SecurityException e) {
     }
     return false;

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

@@ -111,8 +111,9 @@ public class ReactionCollectionXmlParser {
       for (Reaction reaction : collection) {
         boolean reactionToCompartment = false;
         for (ReactionNode node : reaction.getReactionNodes()) {
-          if (node.getElement() instanceof Compartment)
+          if (node.getElement() instanceof Compartment) {
             reactionToCompartment = true;
+          }
         }
         if (reactionToCompartment) {
           logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction),

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java

@@ -165,8 +165,9 @@ public abstract class CellDesignerTestFunctions {
   }
 
   protected String nodeToString(Node node, boolean includeHeadNode) {
-    if (node == null)
+    if (node == null) {
       return null;
+    }
     StringWriter sw = new StringWriter();
     try {
       Transformer t = TransformerFactory.newInstance().newTransformer();

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java

@@ -66,14 +66,18 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
     Species aliasSa10 = null;
     Species aliasSa11 = null;
     for (Species alias : list) {
-      if (alias.getElementId().equals("sa8"))
+      if (alias.getElementId().equals("sa8")) {
         aliasSa8 = alias;
-      if (alias.getElementId().equals("sa9"))
+      }
+      if (alias.getElementId().equals("sa9")) {
         aliasSa9 = alias;
-      if (alias.getElementId().equals("sa10"))
+      }
+      if (alias.getElementId().equals("sa10")) {
         aliasSa10 = alias;
-      if (alias.getElementId().equals("sa11"))
+      }
+      if (alias.getElementId().equals("sa11")) {
         aliasSa11 = alias;
+      }
     }
     assertNotNull(aliasSa8);
     assertNotNull(aliasSa9);
@@ -165,12 +169,15 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
     Complex aliasSa2 = null;
     Complex aliasSa3 = null;
     for (Complex alias : list) {
-      if (alias.getElementId().equals("csa1"))
+      if (alias.getElementId().equals("csa1")) {
         aliasSa1 = alias;
-      if (alias.getElementId().equals("csa2"))
+      }
+      if (alias.getElementId().equals("csa2")) {
         aliasSa2 = alias;
-      if (alias.getElementId().equals("csa3"))
+      }
+      if (alias.getElementId().equals("csa3")) {
         aliasSa3 = alias;
+      }
     }
     assertNotNull(aliasSa1);
     assertNotNull(aliasSa2);
@@ -196,12 +203,15 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
     Complex aliasSa2 = null;
     Complex aliasSa3 = null;
     for (Complex alias : list) {
-      if (alias.getElementId().equals("csa1"))
+      if (alias.getElementId().equals("csa1")) {
         aliasSa1 = alias;
-      if (alias.getElementId().equals("csa2"))
+      }
+      if (alias.getElementId().equals("csa2")) {
         aliasSa2 = alias;
-      if (alias.getElementId().equals("csa3"))
+      }
+      if (alias.getElementId().equals("csa3")) {
         aliasSa3 = alias;
+      }
     }
     assertNotNull(aliasSa1);
     assertNotNull(aliasSa2);
@@ -243,12 +253,15 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
     Compartment aliasCa2 = null;
     Compartment aliasCa3 = null;
     for (Compartment alias : list) {
-      if (alias.getElementId().equals("ca1"))
+      if (alias.getElementId().equals("ca1")) {
         aliasCa1 = alias;
-      if (alias.getElementId().equals("ca2"))
+      }
+      if (alias.getElementId().equals("ca2")) {
         aliasCa2 = alias;
-      if (alias.getElementId().equals("ca3"))
+      }
+      if (alias.getElementId().equals("ca3")) {
         aliasCa3 = alias;
+      }
     }
     assertNotNull(aliasCa1);
     assertNotNull(aliasCa2);

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java

@@ -239,8 +239,9 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     assertEquals(1, reactant.getLine().getLines().size());
     NodeOperator operator = null;
     for (NodeOperator operator2 : reaction.getOperators()) {
-      if (operator2 instanceof SplitOperator)
+      if (operator2 instanceof SplitOperator) {
         operator = operator2;
+      }
     }
     assertEquals(LineType.DASH_DOT_DOT, operator.getLine().getType());
 
@@ -361,8 +362,9 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     assertEquals(2, model.getReactions().size());
     Reaction reaction = null;
     for (Reaction reaction2 : model.getReactions()) {
-      if (reaction2.getIdReaction().equals("re1"))
+      if (reaction2.getIdReaction().equals("re1")) {
         reaction = reaction2;
+      }
     }
     assertTrue(reaction instanceof DissociationReaction);
     assertEquals(1, reaction.getReactants().size());
@@ -396,8 +398,9 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     assertEquals(2, model.getReactions().size());
     Reaction reaction = null;
     for (Reaction reaction2 : model.getReactions()) {
-      if (reaction2.getIdReaction().equals("re1"))
+      if (reaction2.getIdReaction().equals("re1")) {
         reaction = reaction2;
+      }
     }
     assertTrue(reaction instanceof DissociationReaction);
     assertEquals(2, reaction.getReactants().size());
@@ -548,10 +551,12 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     Reaction reaction1 = null;
     Reaction reaction2 = null;
     for (Reaction reaction : model.getReactions()) {
-      if (reaction.getIdReaction().equals("re2"))
+      if (reaction.getIdReaction().equals("re2")) {
         reaction1 = reaction;
-      if (reaction.getIdReaction().equals("re3"))
+      }
+      if (reaction.getIdReaction().equals("re3")) {
         reaction2 = reaction;
+      }
     }
     Reactant reactant = reaction1.getReactants().get(0);
     Element alias1 = reaction1.getReactants().get(0).getElement();
@@ -577,8 +582,9 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     Model model = getModelForFile("testFiles/reactions/problemWithAnchors3.xml");
     Reaction reaction = null;
     for (Reaction reaction2 : model.getReactions()) {
-      if (reaction2.getIdReaction().equals("re3"))
+      if (reaction2.getIdReaction().equals("re3")) {
         reaction = reaction2;
+      }
     }
     Point2D point = new Point2D.Double(164.85583789974368, 86.060142902597);
     Point2D point2 = new Point2D.Double(397.06477630152193, 284.99999999999994);

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java

@@ -257,10 +257,12 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
     int complexes = 0;
     int proteins = 0;
     for (Pair<String, ? extends CellDesignerSpecies<?>> species : list) {
-      if (species.getRight() instanceof CellDesignerComplexSpecies)
+      if (species.getRight() instanceof CellDesignerComplexSpecies) {
         complexes++;
-      if (species.getRight() instanceof CellDesignerProtein)
+      }
+      if (species.getRight() instanceof CellDesignerProtein) {
         proteins++;
+      }
     }
     assertEquals(1, complexes);
     assertEquals(2, proteins);

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java

@@ -82,7 +82,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
    */
   protected CompartmentConverter(ColorExtractor colorExtractor) {
     super(colorExtractor);
-  };
+  }
 
   /**
    * @return the alphaLevel

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -123,7 +123,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
    */
   protected SpeciesConverter(ColorExtractor colorExtractor) {
     super(colorExtractor);
-  };
+  }
 
   /**
    * Returns default shape of the {@link Species}.

converter/src/test/java/lcsb/mapviewer/converter/ConverterTestFunctions.java

@@ -142,8 +142,9 @@ public abstract class ConverterTestFunctions {
   }
 
   protected String nodeToString(Node node, boolean includeHeadNode) {
-    if (node == null)
+    if (node == null) {
       return null;
+    }
     StringWriter sw = new StringWriter();
     try {
       Transformer t = TransformerFactory.newInstance().newTransformer();

model/src/main/java/lcsb/mapviewer/model/security/Privilege.java

@@ -62,10 +62,12 @@ public class Privilege implements Serializable {
 
   @Override
   public boolean equals(Object o) {
-    if (this == o)
+    if (this == o) {
       return true;
-    if (!(o instanceof Privilege))
+    }
+    if (!(o instanceof Privilege)) {
       return false;
+    }
     Privilege that = (Privilege) o;
     return type == that.type
         && Objects.equals(objectId, that.objectId);

model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeGenericTest.java

@@ -53,8 +53,9 @@ public class MiriamTypeGenericTest extends ModelTestFunctions {
     boolean deprecated = false;
     try {
       Field f = MiriamType.class.getField(mt.name());
-      if (f.isAnnotationPresent(clazz))
+      if (f.isAnnotationPresent(clazz)) {
         deprecated = true;
+      }
     } catch (NoSuchFieldException | SecurityException e) {
     }
     return deprecated;

model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java

@@ -86,8 +86,9 @@ public class ElementUtilsTest extends ModelTestFunctions {
       throw new InvalidArgumentException();
     }
     String tmp = "";
-    for (int i = 0; i < indent; i++)
+    for (int i = 0; i < indent; i++) {
       tmp += "  ";
+    }
     logger.debug(tmp + top.getCommonName());
     for (ClassTreeNode node : top.getChildren()) {
       print(node, indent + 1);

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java

@@ -1129,8 +1129,9 @@ public class ModelContructor {
     Integer result = null;
     for (Species species : allChildren) {
       if (species.getZ() != null) {
-        if (result == null)
+        if (result == null) {
           result = species.getZ();
+        }
         result = Math.min(result, species.getZ());
       }
     }

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinder.java

@@ -333,8 +333,9 @@ class ReactionLayoutFinder {
   private boolean pointOnPolyline(PolylineData line, Point2D point) {
     // point cannot be on the edge
     if (line.getStartPoint().distance(point) <= Configuration.EPSILON ||
-        line.getEndPoint().distance(point) <= Configuration.EPSILON)
+        line.getEndPoint().distance(point) <= Configuration.EPSILON) {
       return false;
+    }
 
     for (Line2D l : line.getLines()) {
       if (lt.distBetweenPointAndLineSegment(l, point) <= Configuration.EPSILON) {

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java

@@ -163,8 +163,9 @@ public abstract class WikipathwaysTestFunctions {
   }
 
   protected String nodeToString(Node node, boolean includeHeadNode) {
-    if (node == null)
+    if (node == null) {
       return null;
+    }
     StringWriter sw = new StringWriter();
     try {
       Transformer t = TransformerFactory.newInstance().newTransformer();

rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java

@@ -232,8 +232,9 @@ public abstract class RestTestFunctions {
   }
 
   protected String nodeToString(Node node, boolean includeHeadNode) {
-    if (node == null)
+    if (node == null) {
       return null;
+    }
     StringWriter sw = new StringWriter();
     try {
       Transformer t = TransformerFactory.newInstance().newTransformer();

service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java

@@ -33,5 +33,5 @@ public class MiriamService implements IMiriamService {
   @Override
   public Article getArticle(MiriamData miriamData) throws PubmedSearchException {
     return pubmedParser.getPubmedArticleById(miriamData.getResource());
-  };
+  }
 }

service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java

@@ -106,7 +106,7 @@ public class SearchService implements ISearchService {
    */
   private void addSearchPrefix(String prefix, List<Class<? extends BioEntity>> clazz) {
     speciesSearchReversePrefix.put(prefix, clazz);
-  };
+  }
 
   /**
    * Transform {@link Reaction} into set of result entries.

service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java

@@ -17,4 +17,4 @@ import lcsb.mapviewer.services.utils.AllUtilsTests;
 })
 public class AllServicesTests {
 
-};
\ No newline at end of file
+}
\ No newline at end of file

web/src/main/java/lcsb/mapviewer/web/bean/utils/CustomHttpServletResponseWrapper.java

@@ -45,7 +45,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public void addCookie(Cookie cookie) {
     logger.debug("addCookie");
     this.addCookie(cookie);
-  }  @Override
+  }
+
+  @Override
   public PrintWriter getWriter() throws IOException {
     logger.debug("getWriter");
     return this.getWriter();
@@ -55,7 +57,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public boolean containsHeader(String name) {
     logger.debug("containsHeader");
     return this.containsHeader(name);
-  }  @Override
+  }
+
+  @Override
   public ServletOutputStream getOutputStream() throws IOException {
     logger.debug("getOutputStream");
     logger.debug(new Exception(), new Exception());
@@ -66,7 +70,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public String encodeURL(String url) {
     logger.debug("encodeURL");
     return this.encodeURL(url);
-  }  @Override
+  }
+
+  @Override
   public String getCharacterEncoding() {
     logger.debug("getCharacterEncoding");
     return this.getCharacterEncoding();
@@ -76,7 +82,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public String encodeRedirectURL(String url) {
     logger.debug("encodeRedirectURL");
     return this.encodeRedirectURL(url);
-  }  @Override
+  }
+
+  @Override
   public String getContentType() {
     logger.debug("getContentType");
     return this.getContentType();
@@ -86,7 +94,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public String encodeUrl(String url) {
     logger.debug("encodeUrl");
     return this.encodeUrl(url);
-  }  @Override
+  }
+
+  @Override
   public void setCharacterEncoding(String charset) {
     logger.debug("setCharacterEncoding");
     this.setCharacterEncoding(charset);
@@ -96,7 +106,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
   public String encodeRedirectUrl(String url) {
     logger.debug("encodeRedirectUrl");
     return this.encodeRedirectUrl(url);
-  }  @Override
+  }
+
+  @Override
   public void setContentLength(int len) {
     logger.debug("setContentLength");
     this.setContentLength(len);
@@ -107,7 +119,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("sendError");
     this.sendError(sc);
 
-  }  @Override
+  }
+
+  @Override
   public void setContentType(String type) {
     logger.debug("setContentType: " + type);
     logger.debug(new Exception(), new Exception());
@@ -119,7 +133,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("sendError");
     this.sendError(sc);
 
-  }  @Override
+  }
+
+  @Override
   public void setBufferSize(int size) {
     logger.debug("setBufferSize");
     this.setBufferSize(size);
@@ -130,7 +146,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("sendRedirect");
     this.sendRedirect(location);
 
-  }  @Override
+  }
+
+  @Override
   public int getBufferSize() {
     logger.debug("getBufferSize");
     return this.getBufferSize();
@@ -141,7 +159,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("setDateHeader");
     this.setDateHeader(name, date);
 
-  }  @Override
+  }
+
+  @Override
   public void flushBuffer() throws IOException {
     logger.debug("flushBuffer");
     this.flushBuffer();
@@ -152,7 +172,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("addDateHeader");
     this.addDateHeader(name, date);
 
-  }  @Override
+  }
+
+  @Override
   public void resetBuffer() {
     logger.debug("resetBuffer");
     this.resetBuffer();
@@ -163,7 +185,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("setHeader");
     this.setHeader(name, value);
 
-  }  @Override
+  }
+
+  @Override
   public boolean isCommitted() {
     logger.debug("isCommitted");
     return this.isCommitted();
@@ -174,7 +198,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("addHeader: " + name + " - " + value);
     this.addHeader(name, value);
 
-  }  @Override
+  }
+
+  @Override
   public void reset() {
     logger.debug("reset");
     this.reset();
@@ -185,7 +211,9 @@ public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper
     logger.debug("setIntHeader");
     this.setIntHeader(name, value);
 
-  }  @Override
+  }
+
+  @Override