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();