wildcard imports are prohibited now

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java

@@ -3,7 +3,11 @@ package lcsb.mapviewer.cdplugin.copypaste;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java

@@ -9,7 +9,9 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
 
 /**
  * This abstract class defines common function for {@link CopyAction} and

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java

 package lcsb.mapviewer.cdplugin.copypaste;
 
-import java.awt.*;
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
 import java.awt.event.KeyEvent;
 
 import org.apache.logging.log4j.LogManager;

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java

@@ -5,7 +5,11 @@ import java.util.Set;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java

 package lcsb.mapviewer.cdplugin.info;
 
-import java.awt.*;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java

 package lcsb.mapviewer.cdplugin.info;
 
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.Timer;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 
 /**
  * This class represent a plugin to CellDesigner that add info text box with

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java

@@ -3,10 +3,15 @@ package lcsb.mapviewer.cdplugin;
 import java.util.List;
 
 import org.apache.logging.log4j.core.LogEvent;
-import org.junit.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
 import org.mockito.Mockito;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
 import lcsb.mapviewer.common.UnitTestFailedWatcher;
 

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java

 package lcsb.mapviewer.cdplugin.copypaste;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 
 import java.util.Set;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.junit.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
 
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
 
 public class CopyPasteAbstractActionTest extends CdPluginFunctions {
   Logger logger = LogManager.getLogger();

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java

@@ -8,7 +8,10 @@ import static org.mockito.Mockito.times;
 import org.junit.Test;
 import org.mockito.Mockito;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 import lcsb.mapviewer.common.SystemClipboard;
 

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java

@@ -2,7 +2,9 @@ package lcsb.mapviewer.cdplugin.info;
 
 import static org.junit.Assert.assertEquals;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;

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

 package lcsb.mapviewer.annotation.cache;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.HttpURLConnection;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
 import java.util.Calendar;
 import java.util.List;
-import java.util.concurrent.*;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
+import java.util.concurrent.ThreadFactory;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.output.CountingOutputStream;
-import org.apache.commons.net.ftp.*;
+import org.apache.commons.net.ftp.FTP;
+import org.apache.commons.net.ftp.FTPClient;
+import org.apache.commons.net.ftp.FTPFile;
+import org.apache.commons.net.ftp.FTPReply;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;

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

 package lcsb.mapviewer.annotation.cache;
 
-import java.util.*;
-import java.util.concurrent.*;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
+import java.util.concurrent.ThreadFactory;
 
 import javax.annotation.PostConstruct;
 

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

 package lcsb.mapviewer.annotation.cache;
 
-import java.io.*;
-import java.net.*;
-import java.util.concurrent.*;
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.logging.log4j.LogManager;

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

@@ -2,7 +2,10 @@ package lcsb.mapviewer.annotation.cache;
 
 import java.io.StringWriter;
 
-import javax.xml.bind.*;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
 
 import org.apache.commons.lang3.SerializationException;
 import org.apache.logging.log4j.LogManager;

annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java

@@ -9,7 +9,9 @@ import javax.xml.bind.annotation.XmlRootElement;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import uk.ac.ebi.chebi.webapps.chebiWS.model.*;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
 
 /**
  * This class represents <a href="http://www.ebi.ac.uk/chebi/">chebi</a> object.

annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java

@@ -5,7 +5,6 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.List;
-import java.util.Set;
 
 import javax.xml.bind.annotation.XmlRootElement;
 

annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java

 package lcsb.mapviewer.annotation.data;
 
 import java.io.Serializable;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
 
 import javax.xml.bind.annotation.XmlRootElement;
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java

@@ -2,18 +2,31 @@ package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
 import java.net.URLEncoder;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import org.apache.commons.lang3.SerializationException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
-import org.w3c.dom.*;
-
-import lcsb.mapviewer.annotation.cache.*;
-import lcsb.mapviewer.annotation.data.*;
-import lcsb.mapviewer.annotation.services.annotators.*;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;

annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java

 package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
 import lcsb.mapviewer.annotation.data.Drug;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;

annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java

 package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.lang3.SerializationException;
 import org.apache.http.HttpStatus;
@@ -12,7 +17,11 @@ import org.w3c.dom.Node;
 
 import com.google.gson.Gson;
 
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
 import lcsb.mapviewer.annotation.data.MeSH;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;

annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java

 package lcsb.mapviewer.annotation.services;
 
-import java.io.*;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
 import java.net.URISyntaxException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.poi.poifs.filesystem.NotOLE2FileException;
 import org.apache.poi.poifs.filesystem.POIFSFileSystem;
-import org.apache.poi.ss.usermodel.*;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellType;
+import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.ss.usermodel.WorkbookFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.w3c.dom.Node;
 
-import lcsb.mapviewer.annotation.cache.*;
-import lcsb.mapviewer.annotation.data.*;
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;

annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java

 package lcsb.mapviewer.annotation.services;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 
 import org.apache.logging.log4j.Marker;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
 
 /**
  * Defines problem with element annotation when there are some required

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

 package lcsb.mapviewer.annotation.services;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
 
 import org.apache.commons.collections4.ListUtils;
 import org.apache.logging.log4j.LogManager;
@@ -13,7 +21,9 @@ import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.LogMarker;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;

annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java

 package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
-import javax.xml.xpath.*;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
 
 import org.apache.commons.lang3.SerializationException;
 import org.apache.logging.log4j.LogManager;
@@ -13,7 +18,11 @@ import org.springframework.stereotype.Service;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
 
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.model.Article;

annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java

@@ -9,7 +9,10 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.stereotype.Service;
 
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;

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

 package lcsb.mapviewer.annotation.services.annotators;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -9,13 +12,19 @@ import org.springframework.stereotype.Service;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.*;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;