operators should not be the last token in line

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java

@@ -21,15 +21,14 @@ public class CdPluginFunctions {
   public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
 
   String rdfString = "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
-      +
-      "<rdf:Description rdf:about=\"#s3\">\n" +
-      "<bqmodel:is>\n" +
-      "<rdf:Bag>\n" +
-      "<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n" +
-      "</rdf:Bag>\n" +
-      "</bqmodel:is>\n" +
-      "</rdf:Description>\n" +
-      "</rdf:RDF>\n";
+      + "<rdf:Description rdf:about=\"#s3\">\n"
+      + "<bqmodel:is>\n"
+      + "<rdf:Bag>\n"
+      + "<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n"
+      + "</rdf:Bag>\n"
+      + "</bqmodel:is>\n"
+      + "</rdf:Description>\n"
+      + "</rdf:RDF>\n";
 
   private MinervaLoggerAppender appender;
 

annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/ChemicalSerializer.java

@@ -93,8 +93,8 @@ public class ChemicalSerializer extends JsonSerializer<Chemical> {
   }
 
   private void writeField(final JsonGenerator gen, final String field, final Object value, final PropertyFilter filter) throws IOException {
-    if (filter == null ||
-        (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
+    if (filter == null
+        || (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
       gen.writeObjectField(field, value);
     }
   }

annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/DrugSerializer.java

@@ -56,8 +56,8 @@ public class DrugSerializer extends JsonSerializer<Drug> {
   }
 
   private void writeField(final JsonGenerator gen, final String field, final Object value, final PropertyFilter filter) throws IOException {
-    if (filter == null ||
-        (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
+    if (filter == null
+        || (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
       gen.writeObjectField(field, value);
     }
   }

annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/MiRNASerializer.java

@@ -50,8 +50,8 @@ public class MiRNASerializer extends JsonSerializer<MiRNA> {
   }
 
   private void writeField(final JsonGenerator gen, final String field, final Object value, final PropertyFilter filter) throws IOException {
-    if (filter == null ||
-        (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
+    if (filter == null
+        || (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
       gen.writeObjectField(field, value);
     }
   }

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

@@ -478,8 +478,8 @@ public abstract class ElementAnnotator extends CachableInterface {
       if (oldValue == null || oldValue.trim().equals("") || oldValue.equals(newValue)) {
         return true;
       } else {
-        logger.warn(getLogMarker(ProjectLogEntryType.ANNOTATION_CONFLICT), field.getCommonName() +
-            " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
+        logger.warn(getLogMarker(ProjectLogEntryType.ANNOTATION_CONFLICT), field.getCommonName()
+            + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
         return false;
       }
     }

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParser.java

@@ -143,8 +143,8 @@ public class ChemicalParser {
         String content = dapiConnector
             .getAuthenticatedContent(
                 url + "/drugs/?size=1000&columns=sourceIdentifier&target_identifier="
-                    + URLEncoder.encode(t.getPrefixedIdentifier(), "UTF-8") +
-                    "&target_disease_identifier=" + URLEncoder.encode(disease.getPrefixedIdentifier(), "UTF-8"));
+                    + URLEncoder.encode(t.getPrefixedIdentifier(), "UTF-8")
+                    + "&target_disease_identifier=" + URLEncoder.encode(disease.getPrefixedIdentifier(), "UTF-8"));
 
         ListChemicalEntityDto dto = objectMapper.readValue(content, ListChemicalEntityDto.class);
 

checkstyle.xml

@@ -234,7 +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,
@@ -247,7 +247,7 @@
                       value="BAND, BOR, BSR, BXOR, DIV, EQUAL, GE, GT, LAND, LE, LITERAL_INSTANCEOF, LOR,
                     LT, MINUS, MOD, NOT_EQUAL, PLUS, QUESTION, SL, SR, STAR, METHOD_REF "/>
         </module>
-        <module name="AnnotationLocation">
+<!--        <module name="AnnotationLocation">
             <property name="id" value="AnnotationLocationMostCases"/>
             <property name="tokens"
                       value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF"/>

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

@@ -28,11 +28,11 @@ public class TextFileUtilsTest extends CommonTestFunctions {
 
   @Test
   public void testGetHeaderParametersFromFile() throws Exception {
-    String fileContent = "#header\n" +
-        "#param1=value1\n" +
-        "#\n" +
-        "no header\n" +
-        "#param2=value\n";
+    String fileContent = "#header\n"
+        + "#param1=value1\n"
+        + "#\n"
+        + "no header\n"
+        + "#param2=value\n";
 
     Map<String, String> params = TextFileUtils
         .getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));

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

@@ -130,8 +130,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
   }
 
   /**
-   * This method computes coordinates that should be associated with the angle on
-   * the border of the alias.
+   * This method computes coordinates that should be associated with the angle
+   * on the border of the alias.
    *
    * @param alias
    *          alias to be investigated
@@ -230,8 +230,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
 
     double minDist = Math.min(Math.min(distanceLeft, distanceRight), Math.min(distanceTop, distanceBottom));
 
-    if (distanceRight == minDist &&
-        pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < epsilon) {
+    if (distanceRight == minDist
+        && pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < epsilon) {
       double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
       result = (ratio - 0.5) * (PI / 2);
     } else if (distanceTop == minDist) {
@@ -243,8 +243,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
     } else if (distanceBottom == minDist) {
       double ratio = (pointOnBorder.getX() - element.getX()) / element.getWidth();
       result = ratio * (PI / 2) + LEFT_RESIDUE_MAX_ANGLE;
-    } else if (distanceRight == minDist &&
-        pointOnBorder.getY() - element.getY() - element.getHeight() < epsilon) {
+    } else if (distanceRight == minDist
+        && pointOnBorder.getY() - element.getY() - element.getHeight() < epsilon) {
       double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
       result = ratio * (PI / 2) + BOTTOM_RESIDUE_MAX_ANGLE;
     } else {
@@ -280,7 +280,6 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
     throw new NotImplementedException("Not implemented for: " + this.getClass());
   }
 
-
   /**
    * This method returns border of the alias as a PathIterator.
    *
@@ -385,8 +384,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
    * @param elemnt
    *          {@link Element} on border which the point is looked for
    * @param angle
-   *          angle between X axis center point of {@link Species} and point that
-   *          we are looking for
+   *          angle between X axis center point of {@link Species} and point
+   *          that we are looking for
    * @return coordinates on the {@link Species} border that correspond to the
    *         angle
    */

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

@@ -67,7 +67,7 @@ public abstract class CellDesignerTestFunctions {
   private static int BLOCK_SIZE = 65536;
 
   protected static double EPSILON = Configuration.EPSILON;
-  
+
   @Rule
   public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
   private Logger logger = LogManager.getLogger();
@@ -261,10 +261,10 @@ public abstract class CellDesignerTestFunctions {
 
     // import of unbounded compartments is problematic
     for (final Compartment compartment : model.getCompartments()) {
-      if (compartment instanceof BottomSquareCompartment ||
-          compartment instanceof TopSquareCompartment ||
-          compartment instanceof LeftSquareCompartment ||
-          compartment instanceof RightSquareCompartment) {
+      if (compartment instanceof BottomSquareCompartment
+          || compartment instanceof TopSquareCompartment
+          || compartment instanceof LeftSquareCompartment
+          || compartment instanceof RightSquareCompartment) {
         model2.getElementByElementId(compartment.getElementId()).setWidth(compartment.getWidth());
         model2.getElementByElementId(compartment.getElementId()).setHeight(compartment.getHeight());
       }

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

@@ -283,13 +283,13 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
   public void testGetNotesWithMissingBody() throws Exception {
     RestAnnotationParser rap = new RestAnnotationParser();
 
-    Node node = super.getNodeFromXmlString("<celldesigner:notes>\n" +
-        "              <html xmlns=\"http://www.w3.org/1999/xhtml\">\n" +
-        "                <head>\n" +
-        "                  <title/>\n" +
-        "                </head>\n" +
-        "              </html>\n" +
-        "            </celldesigner:notes>");
+    Node node = super.getNodeFromXmlString("<celldesigner:notes>\n"
+        + "              <html xmlns=\"http://www.w3.org/1999/xhtml\">\n"
+        + "                <head>\n"
+        + "                  <title/>\n"
+        + "                </head>\n"
+        + "              </html>\n"
+        + "            </celldesigner:notes>");
     String notes = rap.getNotes(node);
     assertNotNull(notes);
   }
@@ -298,18 +298,18 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
   public void testGetNotesWithLinkInside() throws Exception {
     RestAnnotationParser rap = new RestAnnotationParser();
 
-    Node node = super.getNodeFromXmlString("<notes>\n" +
-        "Name: L-cystine\n" +
-        "Synonyms: (R,R)-3,3&apos;-dithiobis(2-aminopropanoic acid), "
+    Node node = super.getNodeFromXmlString("<notes>\n"
+        + "Name: L-cystine\n"
+        + "Synonyms: (R,R)-3,3&apos;-dithiobis(2-aminopropanoic acid), "
         + "(R-(R*,R*))-3,3&apos;-Dithiobis(2-aminopropanoic acid), "
         + "3,3&apos;-Dithiobis-L-alanine, beta,beta&apos;-diamino-beta,beta&apos;-dicarboxydiethyl disulfide, "
         + "beta,beta&apos;-dithiodialanine, bis(beta-amino-beta-carboxyethyl) disulfide, E921, "
         + "L-alpha-Diamino-beta-dithiolactic acid, L-Cystine, L-Dicysteine, oxidized L-cysteine, final Recon metabolite: mma\n"
         + "Description: VMH database: <a xmlns=\"http://www.w3.org/1999/xhtml\" href=\"http://vmh.uni.lu/#metabolite/mma\">mma</a>\n"
-        + "SemanticZoomLevelVisibility: 5\n" +
-        "Charge: 0\n" +
-        "</notes>\n" +
-        "");
+        + "SemanticZoomLevelVisibility: 5\n"
+        + "Charge: 0\n"
+        + "</notes>\n"
+        + "");
     String notes = rap.getNotes(node);
     assertFalse(notes.contains("http://www.w3.org/1999/xhtml"));
   }

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -1003,8 +1003,8 @@ public class SbgnmlXmlExporter {
         arcList.add(getArcFromNode(node, glyphList));
       } catch (final InvalidArgumentException ex) {
         logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, node),
-            new ElementUtils().getElementTag(node.getElement()) +
-                "Node skipped in export process, since it is not compliant with SBGN-ML format.");
+            new ElementUtils().getElementTag(node.getElement())
+                + "Node skipped in export process, since it is not compliant with SBGN-ML format.");
         continue;
       }
     }

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -1722,8 +1722,8 @@ public class SbgnmlXmlParser {
     Product firstProduct = reaction.getProducts().get(0);
     boolean shouldReverse = reaction.getProducts().size() > 1;
     for (final Product product : reaction.getProducts()) {
-      if (product.getLine().getStartPoint().distance(firstProduct.getLine().getStartPoint()) < Configuration.EPSILON &&
-          product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
+      if (product.getLine().getStartPoint().distance(firstProduct.getLine().getStartPoint()) < Configuration.EPSILON
+          && product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
         shouldReverse = false;
       }
     }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java

@@ -107,11 +107,11 @@ public class ConverterParams {
 
   @Override
   public String toString() {
-    String result = "[" + this.getClass().getSimpleName() + "] " +
-        "level:" + level + "," +
-        "scale:" + scale + "," +
-        "nested:" + nested + "," +
-        "sbgnFormat:" + sbgnFormat;
+    String result = "[" + this.getClass().getSimpleName() + "] "
+        + "level:" + level + ","
+        + "scale:" + scale + ","
+        + "nested:" + nested + ","
+        + "sbgnFormat:" + sbgnFormat;
     return result;
   }
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java

@@ -95,8 +95,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
         }
         sbmlElementByElementId.put(getElementId(bioEntity), sbmlElement);
       } catch (final Exception e) {
-        throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity) +
-            "Problem with exporting bioEntity", e);
+        throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity)
+            + "Problem with exporting bioEntity", e);
       }
     }
     if (isExtensionEnabled(SbmlExtension.LAYOUT)) {
@@ -106,8 +106,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
             AbstractReferenceGlyph elementGlyph = createGlyph(bioEntity);
             sbmlGlyphByElementId.put(getElementId(bioEntity), elementGlyph);
           } catch (final Exception e) {
-            throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity) +
-                "Problem with exporting bioEntity", e);
+            throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity)
+                + "Problem with exporting bioEntity", e);
           }
         }
       }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java

@@ -288,8 +288,8 @@ public class SbmlParser extends Converter {
   private void checkAvailableExtensions(final org.sbml.jsbml.Model sbmlModel) {
     if (sbmlModel.getExtensionCount() > 0) {
       for (final SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
-        if (!plugin.getClass().equals(LayoutModelPlugin.class) &&
-            !plugin.getClass().equals(MultiModelPlugin.class)) {
+        if (!plugin.getClass().equals(LayoutModelPlugin.class)
+            && !plugin.getClass().equals(MultiModelPlugin.class)) {
           logger.warn("Unknown sbml plugin: " + plugin);
         }
       }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -126,7 +126,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
       try {
         Map<ReactionNode, SpeciesReferenceGlyph> glyphByNode = new HashMap<>();
         Reaction reactionWithLayout = source.copy();
-        // getId doesn't have to be unique, therefore we concatenate with reaction
+        // getId doesn't have to be unique, therefore we concatenate with
+        // reaction
         reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
 
         // z index
@@ -280,7 +281,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
     for (final Reaction reaction : reactions) {
       if (!used.contains(reaction)) {
         for (final ReactionNode node : reaction.getReactionNodes()) {
-          // we might have different elements here, the reason is that single SBML species
+          // we might have different elements here, the reason is that single
+          // SBML species
           // can be split into two or more (due to layout)
           node.setElement(speciesParser.getAnyElementBySbmlElementId(node.getElement().getElementId()));
         }
@@ -330,8 +332,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
       PolylineData line = new PolylineData();
       reaction.setLine(line);
       // if there is no layout don't create center line
-      if (startNode.getLine() != null && startNode.getLine().length() > Configuration.EPSILON &&
-          endNode.getLine() != null && endNode.getLine().length() > Configuration.EPSILON) {
+      if (startNode.getLine() != null && startNode.getLine().length() > Configuration.EPSILON
+          && endNode.getLine() != null && endNode.getLine().length() > Configuration.EPSILON) {
         startNode.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE);
         endNode.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE);
 
@@ -409,9 +411,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
   }
 
   /**
-   * Extracts {@link Curve} associated to {@link ReactionGlyph}. If curve doesn't
-   * exist then method will try to create it from {@link BoundingBox} (due to SBML
-   * specification). This {@link Curve} is split into parts belonging to:
+   * Extracts {@link Curve} associated to {@link ReactionGlyph}. If curve
+   * doesn't exist then method will try to create it from {@link BoundingBox}
+   * (due to SBML specification). This {@link Curve} is split into parts
+   * belonging to:
    * <ul>
    * <li>input operator</li>
    * <li>center line</li>
@@ -421,9 +424,9 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
    * 
    * @param reactionGlyph
    * @param operator
-   *          class of {@link NodeOperator} that requires the line (this line can
-   *          be separated into 3 different segments - reactant, center, product
-   *          parts)
+   *          class of {@link NodeOperator} that requires the line (this line
+   *          can be separated into 3 different segments - reactant, center,
+   *          product parts)
    * @return
    */
   PolylineData extractCurve(final ReactionGlyph reactionGlyph, final Reaction reaction,
@@ -517,20 +520,20 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
     }
 
     PolylineData result = new PolylineData();
-    if (operator == TruncationOperator.class ||
-        operator == DissociationOperator.class ||
-        operator == SplitOperator.class) {
+    if (operator == TruncationOperator.class
+        || operator == DissociationOperator.class
+        || operator == SplitOperator.class) {
       // Product operator
 
       for (int i = productLineStarts; i < curve.getCurveSegmentCount(); i++) {
-        CurveSegment   segment = curve.getCurveSegment(i);
+        CurveSegment segment = curve.getCurveSegment(i);
         result.addLine(segment.getStart().getX(), segment.getStart().getY(),
             segment.getEnd().getX(), segment.getEnd().getY());
       }
     } else if (operator == AssociationOperator.class || operator == AndOperator.class) {
       // Reactant operator
       for (int i = 0; i < reactantLineEnds; i++) {
-        CurveSegment   segment = curve.getCurveSegment(i);
+        CurveSegment segment = curve.getCurveSegment(i);
         result.addLine(segment.getStart().getX(), segment.getStart().getY(), segment.getEnd().getX(), segment.getEnd().getY());
       }
     } else if (operator == null) {

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

@@ -205,9 +205,9 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
     Map<String, String> params = new HashMap<>();
     params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
 
-    String input = "name\tcolor\tvalue\n" +
-        "s1\t#ff0000\t\n" +
-        "s2\t\t1.0\n";
+    String input = "name\tcolor\tvalue\n"
+        + "s1\t#ff0000\t\n"
+        + "s2\t\t1.0\n";
     Collection<DataOverlayEntry> schemas = reader
         .readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params);
     assertEquals(2, schemas.size());
@@ -218,8 +218,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
     Map<String, String> params = new HashMap<>();
     params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
 
-    String input = "type\tname\tvalue\n" +
-        "protein\t\t1.0\n";
+    String input = "type\tname\tvalue\n"
+        + "protein\t\t1.0\n";
     Collection<DataOverlayEntry> schemas = reader
         .readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params);
     assertEquals(1, schemas.size());
@@ -320,8 +320,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
 
   @Test
   public void testColoringWithModelName() throws Exception {
-    String input = "name\tcolor\tmap_name\n" +
-        "s1\t#ff0000\txxx\n";
+    String input = "name\tcolor\tmap_name\n"
+        + "s1\t#ff0000\txxx\n";
     Map<String, String> params = new HashMap<>();
     params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
 
@@ -333,8 +333,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
 
   @Test
   public void testColoringWithMapName() throws Exception {
-    String input = "name\tcolor\tmap_name\n" +
-        "s1\t#ff0000\txxx\n";
+    String input = "name\tcolor\tmap_name\n"
+        + "s1\t#ff0000\txxx\n";
     Map<String, String> params = new HashMap<>();
     params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
 

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

@@ -183,8 +183,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
    */
   @Test(expected = InvalidOverviewFile.class)
   public void testParseInvalidCoordinates() throws Exception {
-    String invalidCoordinates = "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n" +
-        "test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4";
+    String invalidCoordinates = "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n"
+        + "test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4";
     Set<Model> models = createValidTestMapModel();
 
     List<OverviewImage> images = new ArrayList<OverviewImage>();
@@ -199,9 +199,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
 
   @Test
   public void testParseValidCoordinates() throws Exception {
-    String invalidCoordinates = "FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n" +
-        "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n" +
-        "test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL";
+    String invalidCoordinates = "FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n"
+        + "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n"
+        + "test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL";
     Set<Model> models = createValidTestMapModel();
 
     List<OverviewImage> images = new ArrayList<OverviewImage>();

model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java

@@ -365,11 +365,11 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
 
     Layer layer = new Layer();
     LayerText layerText = new LayerText();
-    layerText.setNotes("colors check\n" +
-        "SemanticZoomLevelVisibility: 3\n" +
-        "SemanticZoomLevelTransparency: 4\n" +
-        "BackgroundColor:#0000ee\n" +
-        "BorderColor:#00ee00");
+    layerText.setNotes("colors check\n"
+        + "SemanticZoomLevelVisibility: 3\n"
+        + "SemanticZoomLevelTransparency: 4\n"
+        + "BackgroundColor:#0000ee\n"
+        + "BorderColor:#00ee00");
     layer.addLayerText(layerText);
     model.addLayer(layer);
 

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/CommentSerializer.java

@@ -107,26 +107,26 @@ public class CommentSerializer extends JsonSerializer<Comment> {
   }
 
   private void writeField(final JsonGenerator gen, final String field, final Object value, final PropertyFilter filter) throws IOException {
-    if (filter == null ||
-        (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
+    if (filter == null
+        || (filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
       gen.writeObjectField(field, value);
     }
   }
 
   public static List<String> availableColumns() {
     return Arrays.asList(
-        "title", 
-        "icon", 
-        "type", 
-        "content", 
-        "removed", 
-        "coord", 
-        "modelId", 
-        "elementId", 
-        "id", 
-        "pinned", 
-        "email", 
-        "owner", 
+        "title",
+        "icon",
+        "type",
+        "content",
+        "removed",
+        "coord",
+        "modelId",
+        "elementId",
+        "id",
+        "pinned",
+        "email",
+        "owner",
         "removeReason");
   }
 

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/EdgeParser.java

@@ -232,10 +232,10 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
 
       edge.setType(pointData.getType());
     }
-    boolean reversible = (pointDataList.get(0).getType() != GpmlInteractionType.LINE) &&
-        (pointDataList.get(0).getType() != null) &&
-        (pointDataList.get(points.size() - 1).getType() != GpmlInteractionType.LINE) &&
-        (pointDataList.get(points.size() - 1).getType() != null);
+    boolean reversible = (pointDataList.get(0).getType() != GpmlInteractionType.LINE)