warnings removal

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

@@ -17,7 +17,6 @@ import org.apache.log4j.Logger;
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
 import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
 import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
 import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
 import lcsb.mapviewer.model.map.compartment.Compartment;

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

@@ -3,7 +3,11 @@ package lcsb.mapviewer.commands;
 import org.apache.log4j.Logger;
 
 public class SemanticZoomLevelMatcher {
-	Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
 
 	/**
 	 * Checks if level belongs to the range defined in

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -33,7 +33,11 @@ import lcsb.mapviewer.services.view.AnnotationView;
 
 @Transactional(value = "txManager")
 public abstract class BaseRestImpl {
-	Logger									logger = Logger.getLogger(BaseRestImpl.class);
+	
+	/**
+	 * Default class logger.
+	 */
+	private Logger					logger = Logger.getLogger(BaseRestImpl.class);
 
 	@Autowired
 	private IModelService		modelService;

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java

@@ -6,7 +6,6 @@ import java.util.Map;
 
 import org.apache.log4j.Logger;
 
-import lcsb.mapviewer.services.view.AnnotationView;
 import lcsb.mapviewer.services.view.OverviewImageView;
 
 public class ProjectMetaData implements Serializable {

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

@@ -62,7 +62,6 @@ import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.utils.ColorSchemaReader;
 import lcsb.mapviewer.services.utils.data.BuildInLayout;
 import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
 import lcsb.mapviewer.services.view.AuthenticationToken;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java

@@ -36,7 +36,6 @@ public class ChemicalRestImpl extends BaseRestImpl {
 	/**
 	 * Default class logger.
 	 */
-	@SuppressWarnings("unused")
 	private Logger					 logger	= Logger.getLogger(ChemicalRestImpl.class);
 
 	@Autowired

rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java

@@ -22,7 +22,6 @@ import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementMatcher;
 import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
 import lcsb.mapviewer.services.search.db.DbSearchCriteria;
 import lcsb.mapviewer.services.search.db.drug.IDrugService;
@@ -35,16 +34,16 @@ public class DrugRestImpl extends BaseRestImpl {
 	 * Default class logger.
 	 */
 	@SuppressWarnings("unused")
-	private Logger				 logger	= Logger.getLogger(DrugRestImpl.class);
+	private Logger				logger = Logger.getLogger(DrugRestImpl.class);
 
 	@Autowired
-	private IDrugService	 drugService;
+	private IDrugService	drugService;
 
 	@Autowired
-	private IModelService	 modelService;
+	private IModelService	modelService;
 
 	@Autowired
-	private IUserService	 userService;
+	private IUserService	userService;
 
 	public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
 		AuthenticationToken authenticationToken = userService.getToken(token);

rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java

@@ -20,7 +20,6 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.search.ElementMatcher;
 import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
 import lcsb.mapviewer.services.search.db.DbSearchCriteria;
 import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
@@ -33,13 +32,10 @@ public class MiRnaRestImpl extends BaseRestImpl {
 	 * Default class logger.
 	 */
 	@SuppressWarnings("unused")
-	private Logger				 logger	= Logger.getLogger(MiRnaRestImpl.class);
+	private Logger				logger = Logger.getLogger(MiRnaRestImpl.class);
 
 	@Autowired
-	private IMiRNAService	 miRnaService;
-
-	@Autowired
-	private ElementMatcher elementMatcher;
+	private IMiRNAService	miRnaService;
 
 	public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
 		AuthenticationToken authenticationToken = getUserService().getToken(token);

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java

@@ -19,8 +19,6 @@ import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.Rna;
 import lcsb.mapviewer.model.map.species.Species;
 import lcsb.mapviewer.model.map.species.field.ElementModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.UserAccessException;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java

 package lcsb.mapviewer.api.projects.models.publications;
 
 import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -33,7 +31,6 @@ import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.ISearchService;
 import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;
 
 @Transactional(value = "txManager")

rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java

@@ -16,8 +16,6 @@ import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidenceTest;
 import lcsb.mapviewer.api.RestTestFunctions;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;

service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java

@@ -28,6 +28,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
 	/**
 	 * Default class logger.
 	 */
+	@SuppressWarnings("unused")
 	private final Logger logger = Logger.getLogger(SearchResultFactory.class);
 
 	/**

web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java

 package lcsb.mapviewer.bean;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.view.ConfigurationView;
-import lcsb.mapviewer.services.view.ConfigurationViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
 
 import org.apache.commons.lang3.SerializationUtils;
 import org.junit.After;
@@ -21,15 +8,21 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.view.ConfigurationViewFactory;
+
 public class ConfigurationBeanTest extends WebTestFunctions {
 
-	ConfigurationBean					cBean;
-	UserBean									uBean;
-	String										oldValue;
-	User											user2;
+	ConfigurationBean				 cBean;
+	UserBean								 uBean;
+	String									 oldValue;
+	User										 user2;
 
 	@Autowired
-	ConfigurationViewFactory	configurationViewFactory;
+	ConfigurationViewFactory configurationViewFactory;
 
 	@Before
 	public void setUp() throws Exception {