Commit 859dcef4 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

remove empty javadoc tags

parent 09221ef7
......@@ -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);
......
......@@ -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 {
......
......@@ -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;
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -126,9 +126,6 @@ public class MeSHParserTest extends AnnotationTestFunctions {
parserUnderTest.getMeSH(meshID);
}
/**
* @throws Exception
*/
@Test
public void testExternalDBStatus() throws Exception {
ExternalServiceStatus status = meshParser.getServiceStatus();
......
......@@ -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 {
......
......@@ -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"
......
......@@ -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) {
......
......@@ -135,8 +135,6 @@ public class ColorParser {
/**
* Transforms {@link Color} into html RGB representation: #RRGGBB
*
* @param color
* @return
*/
public String colorToHtml(final Color color) {
......
......@@ -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) {
......
......@@ -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();
......
......@@ -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> {
......
......@@ -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
......
......@@ -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
*/
......
......@@ -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 {
......
......@@ -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);
......
......@@ -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);
......
......@@ -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 {
......
......@@ -40,8 +40,6 @@ public class LineProperties {
/**
* Create properties from {@link PolylineData}.
*
* @param line
*/
public LineProperties(final PolylineData line) {
width = line.getWidth();
......
......@@ -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
......
......@@ -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) {
......
......@@ -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;
}
......
......@@ -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
......
......@@ -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,
......
......@@ -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 {
......
......@@ -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);
......
......@@ -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<>();
......
......@@ -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 {
......
......@@ -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;
......
......@@ -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;
}
......
......@@ -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:
......
......@@ -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 {
......
......@@ -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> {
......
......@@ -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) {
......
......@@ -58,11 +58,6 @@ public class DbUtils extends Observable {
*/
private SessionFactory sessionFactory;
/**
* Constructor
*
* @param sessionFactory
*/
@Autowired
public DbUtils(final SessionFactory sessionFactory) {
this.sessionFactory = sessionFactory;
......
......@@ -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");
......
......@@ -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();
......
......@@ -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 {
......
......@@ -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);
......
......@@ -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,
......
......@@ -6,8 +6,6 @@ import java.io.Serializable;
* Abstract class that handles {@link Event events}.
*
* @author Piotr Gawron
*
* @param <T>
*/
public abstract