Commit 9b9c33ed authored by Piotr Gawron's avatar Piotr Gawron
Browse files

wildcard imports are prohibited now

parent 21fa9bed
......@@ -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;
......
......@@ -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
......
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;
......
......@@ -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;
......
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;
......
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
......
......@@ -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;
......
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();
......
......@@ -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;
......
......@@ -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;
......
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;
......
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;
......
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;
......
......@@ -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;
......
......@@ -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.
......
......@@ -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;
......
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;
......
......@@ -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;
......
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;
......
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;
......
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;
......
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
......
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;
......
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;
......
......@@ -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;
......
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;