organizing imports

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

@@ -2,10 +2,8 @@ package lcsb.mapviewer.converter;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
@@ -18,8 +16,14 @@ import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.model.Model;
 
 public class ProjectFactory {
-	Logger logger = Logger.getLogger(ProjectFactory.class);
-	private ComplexZipConverter converter;
+	
+	/**
+	 * Deafult class clogger.
+	 */
+	@SuppressWarnings("unused")
+	private Logger							logger = Logger.getLogger(ProjectFactory.class);
+	
+	private ComplexZipConverter	converter;
 
 	public ProjectFactory(ComplexZipConverter converter) {
 		this.converter = converter;
@@ -31,16 +35,15 @@ public class ProjectFactory {
 
 	public Project create(ComplexZipConverterParams params, Project project) throws InvalidInputDataExecption {
 		Model model = converter.createModel(params);
-		
+
 		Set<Model> models = new HashSet<>();
 		models.add(model);
 		models.addAll(model.getSubmodels());
-		
+
 		project.addModel(model);
 		ZipFile zipFile = params.getZipFile();
 		Enumeration<? extends ZipEntry> entries;
 
-
 		entries = zipFile.entries();
 		List<ImageZipEntryFile> imageEntries = new ArrayList<>();
 		while (entries.hasMoreElements()) {

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

@@ -9,7 +9,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidClassException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.Layout;
@@ -23,8 +22,8 @@ import lcsb.mapviewer.model.map.reaction.AbstractNode;
 import lcsb.mapviewer.model.map.reaction.NodeOperator;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
 
 /**
@@ -194,9 +193,9 @@ public class CopyCommand extends NewModelCommand {
 					parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
 					copy.setCompartment(parentCompartment);
 				}
-				
+
 			} else if (alias instanceof Compartment) {
-				
+
 				Compartment parentCompartment = alias.getCompartment();
 
 				if (parentCompartment != null) {

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

@@ -19,8 +19,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewModelLink;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.layout.graphics.Layer;

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

@@ -13,8 +13,6 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.comparator.IntegerComparator;
 import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageComparator;
 import lcsb.mapviewer.model.map.graph.DataMiningSetComparator;
 import lcsb.mapviewer.model.map.layout.Layout;
 import lcsb.mapviewer.model.map.layout.LayoutComparator;

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

@@ -27,7 +27,6 @@ import org.hibernate.annotations.CascadeType;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.BlockDiagram;
 import lcsb.mapviewer.model.map.layout.ElementGroup;
@@ -138,7 +137,6 @@ public class ModelData implements Serializable {
 	 */
 	private String											 notifyEmail;
 
-
 	/**
 	 * How many hierarchical levels are in this map.
 	 */

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

@@ -16,9 +16,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -43,6 +40,7 @@ public class ModelFullIndexed implements Model {
 	/**
 	 * Default class logger.
 	 */
+	@SuppressWarnings("unused")
 	private static Logger					 logger								= Logger.getLogger(ModelFullIndexed.class);
 
 	/**
@@ -571,7 +569,6 @@ public class ModelFullIndexed implements Model {
 		return null;
 	}
 
-
 	@Override
 	public void addLayout(int index, Layout layout) {
 		this.modelData.getLayouts().add(index, layout);

model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java

@@ -15,7 +15,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;

model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java

@@ -239,7 +239,6 @@ public class ModelDataTest {
 			int tileSize = 512;
 			String modelId = "modId";
 			String email = "a@b.cc";
-			String mapVersion = "1.2.6";
 			String notes = "nOT";
 			String name = "n_ma";
 			Double heightDouble = 29.0;

model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java

@@ -25,8 +25,6 @@ import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
@@ -739,8 +737,6 @@ public class ModelFullIndexedTest {
 		try {
 			Model model = new ModelFullIndexed(null);
 
-			String mapVersion = "v12";
-
 			Double width = 12.0;
 			int widthInt = 12;
 			String widthStr = "12.0";

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

@@ -245,7 +245,6 @@ public class ProjectDaoTest extends PersistTestFunctions {
 			Project project2 = projectDao.getProjectByProjectId(projectId);
 			assertNotNull(project2);
 
-			Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
 			OverviewImage oi2 = project2.getOverviewImages().get(0);
 			OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);