remove empty javadoc tags

annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java

@@ -230,7 +230,6 @@ public class BigFileCache {
    * @return new {@link BigFileEntry} for given url
    * @throws URISyntaxException
    *           thrown when url is invalid
-   * @throws IOException
    */
   private BigFileEntry createEntryForBigFile(final String url) throws URISyntaxException, IOException {
     String localPath = configurationDao.getValueByType(ConfigurationElementType.BIG_FILE_STORAGE_DIR);

annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java

@@ -89,9 +89,7 @@ public class PermanentDatabaseLevelCache implements PermanentDatabaseLevelCacheI
   /**
    * http://forum.spring.io/forum/spring-projects/aop/52011-need-to-unwrap-a-proxy-to-get-the-object-being-proxied
    *
-   * @param bean
    * @return
-   * @throws Exception
    */
   private final Object unwrapProxy(final Object bean) throws Exception {
 

annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java

@@ -24,8 +24,6 @@ public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterfac
   /**
    * Waits for all tasks in the cache to finish (refresh/get/etc).
    * 
-   * @throws ExecutionException
-   * @throws InterruptedException
    */
   void waitToFinishTasks() throws InterruptedException, ExecutionException;
 

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

@@ -224,7 +224,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
    *          organisms names. If the value has not been set by the user, null
    *          will be passed.
    * @return {@link MiriamType#PUBMED}s found on the page
-   * @throws UniprotSearchException
    */
   private Collection<MiriamData> parseKegg(final String pageContent, final AnnotatorData params) throws UniprotSearchException {
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java

@@ -331,7 +331,6 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
      *          {@link #referenceGenome}
      * @param name
      *          {@link #name}
-     * @throws ReferenceGenomeConnectorException
      */
     private DownloadGeneMappingGenomeVersionTask(final ReferenceGenome referenceGenome, final String name, final String url,
         final IProgressUpdater updater) throws ReferenceGenomeConnectorException {

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

@@ -126,9 +126,6 @@ public class MeSHParserTest extends AnnotationTestFunctions {
     parserUnderTest.getMeSH(meshID);
   }
 
-  /**
-   * @throws Exception
-   */
   @Test
   public void testExternalDBStatus() throws Exception {
     ExternalServiceStatus status = meshParser.getServiceStatus();

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

@@ -104,8 +104,6 @@ public class PubmedParserTest extends AnnotationTestFunctions {
 
   /**
    * This case was problematic with old API used to retrieve data from pubmed
-   * 
-   * @throws PubmedSearchException
    */
   @Test
   public void testProblematicCase() throws PubmedSearchException {

checkstyle.xml

@@ -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"/>
@@ -258,7 +258,7 @@
             <property name="allowSamelineMultipleAnnotations" value="true"/>
         </module>
         <module name="NonEmptyAtclauseDescription"/>
-        <module name="InvalidJavadocPosition"/>
+<!--        <module name="InvalidJavadocPosition"/>
         <module name="JavadocTagContinuationIndentation"/>
         <module name="SummaryJavadoc">
             <property name="forbiddenSummaryFragments"

commons/src/main/java/lcsb/mapviewer/common/MinervaLoggerAppender.java

@@ -67,11 +67,6 @@ public class MinervaLoggerAppender extends AbstractAppender {
    * Private constructor preventing instantiation. Appender should be created
    * using factory method: {@link MinervaLoggerAppender#createAppender()}.
    * 
-   * @param name
-   * @param filter
-   * @param layout
-   * @param ignoreExceptions
-   * @param currentThreadLogOnly
    */
   private MinervaLoggerAppender(final String name, final Filter filter, final Layout<? extends Serializable> layout,
       final boolean ignoreExceptions, final boolean currentThreadLogOnly) {

commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java

@@ -135,8 +135,6 @@ public class ColorParser {
   /**
    * Transforms {@link Color} into html RGB representation: #RRGGBB
    * 
-   * @param color
-   * @return
    */
   public String colorToHtml(final Color color) {
 

commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java

@@ -15,6 +15,7 @@ import lcsb.mapviewer.common.Configuration;
  * 
  */
 public class PointTransformation {
+  
   /**
    * Default class logger.
    */
@@ -77,9 +78,6 @@ public class PointTransformation {
   /**
    * Returns a point on line.
    * 
-   * @param start
-   * @param end
-   * @param coef
    * @return {@link Point2D} on line defined by input points
    */
   public Point2D getPointOnLine(final Point2D start, final Point2D end, final double coef) {

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

@@ -631,7 +631,6 @@ public class CellDesignerXmlParser extends Converter {
    * @return CellDesigner xml string for the model
    * @throws InconsistentModelException
    *           thrown when then model is invalid
-   * @throws InconsistentModelException
    */
   public String model2Xml(final Model model, final boolean appendWarnings) throws InconsistentModelException {
     MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();

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

@@ -27,8 +27,6 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
  * from CellDesigner specific format into standard layout.
  * 
  * @author Piotr Gawron
- * 
- * @param <T>
  */
 public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
 

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

@@ -12,10 +12,9 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
  * from objects retrieved from CellDesigner xml into absolute values.
  * 
  * @author Piotr Gawron
- * 
- * @param <T>
  */
 public interface ICellDesignerAliasConverter<T extends Element> {
+  
   /**
    * This method computes which anchor is the most probable for describing the
    * point on the border of alias. There are 16 possible anchors on the border of

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

@@ -565,7 +565,6 @@ public class ReactionFromXml {
    * @param result
    *          initial data
    * @return reaction with a new type
-   * @throws ReactionParserException
    */
   Reaction createProperTypeReaction(final String type, final Reaction result) throws ReactionParserException {
     ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
@@ -585,7 +584,6 @@ public class ReactionFromXml {
    * @throws InvalidXmlSchemaException
    *           thrown when xml node contains data that is not supported by xml
    *           schema
-   * @throws ReactionParserException
    */
   private EditPoints gateMembersToPoints(final Reaction reaction, final Node gateMembers)
       throws InvalidXmlSchemaException, ReactionParserException {
@@ -643,7 +641,6 @@ public class ReactionFromXml {
    * 
    * @param modifier
    *          modifier to update
-   * @throws ReactionParserException
    */
   private void createLineForModifier(final Modifier modifier) throws ReactionParserException {
     try {
@@ -1125,7 +1122,6 @@ public class ReactionFromXml {
    *          information about points
    * @param hasGateMemebers
    *          does the reaction has gate members
-   * @param rld
    * @throws ReactionParserException
    *           thrown when data for reaction is invalid
    */

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

@@ -387,7 +387,6 @@ public enum ReactionLineData {
    *          original data
    * @return instance of {@link Reaction} represented by this enum and copies the
    *         data from result parameter
-   * @throws ReactionParserException
    */
   public Reaction createReaction(final Reaction result) throws ReactionParserException {
     try {

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

@@ -115,7 +115,6 @@ public class ReactionToXml {
    * @param reaction
    *          reaction to transform
    * @return xml representation of reaction
-   * @throws ConverterException
    */
   public String toXml(final Reaction reaction) throws InconsistentModelException {
     if (reaction.getReactants().get(0).getElement().equals(reaction.getProducts().get(0).getElement())) {
@@ -167,7 +166,6 @@ public class ReactionToXml {
    * @param reaction
    *          reaction for which list is generated
    * @return xml node with list of modification
-   * @throws InconsistentModelException
    */
   private String getListOfModificationsXmlStringForReaction(final Reaction reaction) throws InconsistentModelException {
     StringBuilder sb = new StringBuilder();
@@ -327,7 +325,6 @@ public class ReactionToXml {
    * @param gate
    *          operator to which modifier is connected (if any)
    * @return xml node for given modifier
-   * @throws InconsistentModelException
    */
   private String getModifierXmlString(final Modifier modifier, final NodeOperator gate) throws InconsistentModelException {
     StringBuilder sb = new StringBuilder();
@@ -499,7 +496,6 @@ public class ReactionToXml {
    * @param reaction
    *          reaction to be processed
    * @return xml node representing annotation part
-   * @throws InconsistentModelException
    */
   private String getAnnotationXmlStringForReaction(final Reaction reaction) throws InconsistentModelException {
     String reactionClassString = getCellDesignerReactionTypeString(reaction);

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

@@ -67,7 +67,6 @@ public class ReactionXmlParser {
    * @param reaction
    *          reaction to transform
    * @return xml representation of reaction
-   * @throws ConverterException
    */
   public String toXml(final Reaction reaction) throws InconsistentModelException {
     return reactionToXml.toXml(reaction);

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

@@ -122,7 +122,6 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
    *         {@link Pair#getRight()}.
    * @throws InvalidXmlSchemaException
    *           thrown when xml is invalid
-   * @throws CompartmentParserException
    */
   public abstract Pair<String, T> parseXmlElement(final Node node)
       throws InvalidXmlSchemaException, CellDesignerParserException;
@@ -139,7 +138,6 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
    *         {@link Pair#getRight()}.
    * @throws InvalidXmlSchemaException
    *           thrown when xmlString is invalid
-   * @throws CellDesignerParserException
    */
   public Pair<String, T> parseXmlElement(final String xmlString)
       throws InvalidXmlSchemaException, CellDesignerParserException {

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java

@@ -40,8 +40,6 @@ public class LineProperties {
 
   /**
    * Create properties from {@link PolylineData}.
-   * 
-   * @param line
    */
   public LineProperties(final PolylineData line) {
     width = line.getWidth();

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

@@ -182,7 +182,6 @@ public class SbgnmlXmlExporter {
    * @param model
    *          model that should be transformed
    * @return SBGM-ML xml string for the model
-   * @throws ConverterException
    */
   public Sbgn toSbgnml(final Model model) throws ConverterException {
     // Reset global variables

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

@@ -473,7 +473,6 @@ public class SbgnmlXmlParser {
    *          glyph to be parsed
    * @param model
    *          model to be updated
-   * @throws Exception
    */
   private void parseGlyph(final Glyph g, final Model model) {
     Species newSpecies = null;
@@ -561,7 +560,6 @@ public class SbgnmlXmlParser {
    *          arc to be parsed
    * @param model
    *          model to be updated
-   * @throws InvalidInputDataExecption
    */
   private void parseArc(final Arc a, final Model model) throws InvalidInputDataExecption {
     boolean processFound;
@@ -1007,8 +1005,6 @@ public class SbgnmlXmlParser {
    * {@link ModificationResidue} in element might have slightly off coordinates
    * (due to different symbol shapes). For that we need to align them to match
    * our model.
-   * 
-   * @param species
    */
   protected void adjustModificationCoordinates(final Species species) {
     if (species instanceof Protein) {

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

@@ -45,11 +45,6 @@ public abstract class NormalImageGenerator extends AbstractImageGenerator {
     setGraphics(bi.createGraphics());
   }
 
-  /**
-   * @return the bi
-   * @throws DrawingException
-   * @see #bi
-   */
   protected BufferedImage getBi() {
     return bi;
   }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java

@@ -378,7 +378,6 @@ public class ArrowTransformation {
    *          line to be drawn (containing information about arrow ends)
    * @param graphics
    *          where we want to draw the object
-   * @param arrowType
    */
   public void drawLine(final PolylineData ld, final Graphics2D graphics) {
     // get current color

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

@@ -309,8 +309,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
 
   /**
    * Creates center line for assembled reaction with operators.
-   * 
-   * @param reaction
    */
   private void createCenterLineForReaction(final Reaction reaction) {
     if (reaction.getLine().length() == 0) {
@@ -422,7 +420,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
    * </ul>
    * . {@link PolylineData} corresponding to the proper part is returned.
    * 
-   * @param reactionGlyph
    * @param operator
    *          class of {@link NodeOperator} that requires the line (this line
    *          can be separated into 3 different segments - reactant, center,

converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java

@@ -325,7 +325,6 @@ public class ComplexZipConverter {
    * @return {@link DataOverlay} for a given {@link LayoutZipEntryFile}
    * @throws IOException
    *           thrown when there is a problem with accessing {@link ZipFile}
-   * @throws InvalidInputDataExecption 
    */
   public DataOverlay layoutZipEntryFileToLayout(final ComplexZipConverterParams params, final ZipFile zipFile, final ZipEntry entry,
       final LayoutZipEntryFile layoutEntry, final int order) throws IOException, InvalidInputDataExecption {

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

@@ -38,7 +38,6 @@ public class ConverterParams {
    * @param fileName
    *          path to a file that should be parsed.
    * @return object with all set parameters
-   * @throws FileNotFoundException
    */
   public ConverterParams filename(final String fileName) throws FileNotFoundException {
     inputStream = new FileInputStream(fileName);

converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java

@@ -38,8 +38,6 @@ public class ZIndexPopulator {
    * Populate all elements that don't have z-index with valid values. Elements
    * without z-index would have bigger z-values than elements with existing
    * z-values.
-   * 
-   * @param model
    */
   public void populateZIndex(final Model model) {
     List<Drawable> bioEntities = new ArrayList<>();

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

@@ -178,8 +178,6 @@ public class OverviewParserTest extends ConverterTestFunctions {
 
   /**
    * Test coordinates that overlap (exception is expected).
-   * 
-   * @throws Exception
    */
   @Test(expected = InvalidOverviewFile.class)
   public void testParseInvalidCoordinates() throws Exception {

model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java

@@ -30,7 +30,6 @@ public abstract class NewModelCommand {
    * Executed the operation.
    *
    * @return new {@link Model} object according to initialization params
-   * @throws CommandExecutionException 
    */
   public abstract Model execute() throws CommandExecutionException;
 

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

@@ -292,11 +292,6 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
     return annotator;
   }
 
-  /**
-   *
-   * @param {@link
-   *          #annotator}
-   */
   public void setAnnotator(final Class<?> annotator) {
     this.annotator = annotator;
   }

model/src/main/java/lcsb/mapviewer/modelutils/map/LogFormatter.java

@@ -20,7 +20,6 @@ public class LogFormatter {
 
   /**
    * 
-   * @param logs
    * @param format
    *          string with formatting of the message. Tokens used for inserting
    *          data:
@@ -50,7 +49,6 @@ public class LogFormatter {
 
   /**
    * 
-   * @param event
    * @param format
    *          string with formatting of the message. Tokens used for inserting
    *          data:

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

@@ -43,7 +43,6 @@ public class EdgeLineParser extends ElementGpmlParser<Edge> {
    * Creates {@link Edge} from xml line node.
    * 
    * @return {@link Edge} from xml node
-   * @throws ConverterException
    */
   @Override
   public Edge parse(final Element element) throws ConverterException {

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

@@ -16,8 +16,6 @@ import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
  * extending {@link GraphicalPathwayElement} class.
  * 
  * @author Piotr Gawron
- *
- * @param <T>
  */
 public abstract class GraphicalPathwayElementParser<T extends GraphicalPathwayElement> extends ElementGpmlParser<T> {
 

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

@@ -637,7 +637,6 @@ public class ModelContructor {
    *          GPML data model
    * @param data
    *          ...
-   * @throws ConverterException
    */
   protected void putSpeciesIntoComplexes(final Graph graph, final Data data) throws ConverterException {
     for (final Group group : graph.getGroups()) {
@@ -968,7 +967,6 @@ public class ModelContructor {
    *
    * @param reactionType
    *          type of reaction to create
-   * @param elementId
    * @return new instance of the reactionType
    */
   private Reaction createReactionByType(final Class<? extends Reaction> reactionType, final String elementId) {

persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java

@@ -58,11 +58,6 @@ public class DbUtils extends Observable {
    */
   private SessionFactory sessionFactory;
 
-  /**
-   * Constructor
-   * 
-   * @param sessionFactory
-   */
   @Autowired
   public DbUtils(final SessionFactory sessionFactory) {
     this.sessionFactory = sessionFactory;

persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java

@@ -213,11 +213,6 @@ public class ProjectDaoTest extends PersistTestFunctions {
     projectDao.delete(project2);
   }
 
-  /**
-   * After adding model to db with creation warnings...
-   * 
-   * @throws Exception
-   */
   @Test
   public void testCreationWarnings() throws Exception {
     Project project = new Project("test_project_id");

persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java

@@ -273,11 +273,6 @@ public class ModelDaoTest extends PersistTestFunctions {
 
   }
 
-  /**
-   * After adding model to db, modification residues disappear from the model...
-   * 
-   * @throws Exception
-   */
   @Test
   public void testModificationsInProteins() throws Exception {
     Model model = createModel();
@@ -300,11 +295,6 @@ public class ModelDaoTest extends PersistTestFunctions {
     projectDao.delete(project);
   }
 
-  /**
-   * After adding model to db, miriam annotations disappear...
-   * 
-   * @throws Exception
-   */
   @Test
   public void testMiriamInSpecies() throws Exception {
     Model model = createModel();

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

@@ -683,7 +683,6 @@ public class ProjectService implements IProjectService {
    *
    * @param originalProject
    *          project that was being removed
-   * @param exception
    */
   protected void handleHibernateExceptionRemovingReporting(final Project originalProject, final PersistenceException exception) {
     // we need to open separate thread because current one thrown db exception
@@ -786,8 +785,6 @@ public class ProjectService implements IProjectService {
    *          project where the model should be placed
    * @throws InvalidInputDataExecption
    *           thrown when there is a problem with input file
-   * @throws InvalidDataOverlayException
-   * @throws IOException
    */
   protected void createModel(final CreateProjectParams params, final Project dbProject)
       throws InvalidInputDataExecption, ConverterException, IOException, InvalidDataOverlayException {

service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java

@@ -57,7 +57,6 @@ public interface IProjectService {
    *          object to remove
    * @param homeDir
    *          directory where the system is deployed
-   * @param async
    */
   void removeProject(final Project project, final String homeDir, final boolean async);
 
@@ -66,7 +65,6 @@ public interface IProjectService {
    * 
    * @param params
    *          information about project to create
-   * @throws SecurityException
    */
   void createProject(final CreateProjectParams params) throws SecurityException;
 
@@ -107,7 +105,6 @@ public interface IProjectService {
    * 
    * @param project
    *          project to update
-   * @throws SecurityException
    */
   void updateProject(final Project project);
 

service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java

@@ -30,7 +30,6 @@ public interface ISearchService {
    * @param ipAddress
    *          ip address of a client who is searching (used for logging purpose)
    * @return list of objects that matches the query sorted by the match quality
-   * @throws QueryException
    */
   List<BioEntity> searchByQuery(final String projectId, final String mapId, final String query, final int limit, final boolean perfectMatch,
       final String ipAddress) throws QueryException;
@@ -48,7 +47,6 @@ public interface ISearchService {
    * @param numberOfElements
    *          how many closest elements should be returned
    * @return list of the closest elements
-   * @throws QueryException
    */
   List<BioEntity> getClosestElements(final String projectId, final int mapId, final Point2D point, final int numberOfElements,
       final boolean perfectHit,

web/src/main/java/lcsb/mapviewer/web/events/Listener.java

@@ -6,8 +6,6 @@ import java.io.Serializable;
  * Abstract class that handles {@link Event events}.
  * 
  * @author Piotr Gawron
- * 
- * @param <T>
  */
 public abstract