diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
index 9a7e8d6fe33c600b4c321c5af9e2ed88da9654b8..80d2c2f7a7d76259ebfd9e032514fb1d70abf7be 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -4,7 +4,6 @@ import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.net.ConnectException;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
@@ -85,8 +84,8 @@ public class WebPageDownloader {
urlConn.setRequestMethod("GET");
urlConn.addRequestProperty("User-Agent", "minerva-framework");
try {
- urlConn.connect();
- code = urlConn.getResponseCode();
+ urlConn.connect();
+ code = urlConn.getResponseCode();
} catch (FileNotFoundException e) {
code = HttpURLConnection.HTTP_NOT_FOUND;
} catch (IOException e) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index b8a32ba7767c231bda64d3693e75733a51df6187..6f9714b2cf08d8227619a279e7295e7f55a69fe3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -19,7 +19,6 @@ import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This interface defines what operations should be possible to convert
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index 6d2fe4eb5e8eb990290aede6ee4cfcb8cc431d42..4623a640195498ae168413bdec83498a2e4ebc6b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -7,21 +7,18 @@ import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import java.awt.Color;
-import java.awt.Desktop;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.geom.GeneralPath;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
-import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import javax.imageio.ImageIO;
-import org.apache.commons.io.FileUtils;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.junit.After;
import org.junit.Before;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 80530dda25a2054e2047923bb3ac015d3baf9052..b9b09c03c2d22c6e56b6c3710c166f57079f9319 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -1096,8 +1096,8 @@ public abstract class Element implements AnnotatedObject, Serializable {
this.zoomLevelVisibility = zoomLevelVisibility;
}
- public String getSemanticZoomLevelVisibility(){
- return this.zoomLevelVisibility;
+ public String getSemanticZoomLevelVisibility() {
+ return this.zoomLevelVisibility;
}
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
index 95cdfe87f7512719d1860a4c7bda61f9cb2dc170..427b20fb2a8c6fc641c77a781ff8c19080ee73a8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.api.projects.chemicals;
-import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index f7ec8bcfb8c201cc49df0a229cd872e8491b07b8..75f01d1125cadac9bd7edb37bcf0020f62d3f3d4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -21,8 +21,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
index 9f8bd3fe86291062473e0240e67a49eef7a7cfa1..2c96827f476b4a9a847018358401e3b5b0995976 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
@@ -68,7 +68,7 @@ public class BioEntitiesController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public String[] getSuggestedQueryList( //
+ public String[] getSuggestedQueryList(//
@PathVariable(value = "projectId") String projectId, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index c1305c14372b227c0cbbe080b7237a8ffc2152d3..3529d79e687dcd402cc7727327db39c31385ba4c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
-import java.awt.geom.PathIterator;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index a17deb36691a28a079d48478b158aaa848a707cc..50f9b691892db89ac0941f0c54abe744bf448191 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -16,27 +16,21 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
-public class PublicationsRestImpl extends BaseRestImpl{
+public class PublicationsRestImpl extends BaseRestImpl {
Logger logger = Logger.getLogger(PublicationsRestImpl.class);
@@ -158,7 +152,8 @@ public class PublicationsRestImpl extends BaseRestImpl{
this.factory = factory;
}
- public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString, Integer length) throws SecurityException, QueryException {
+ public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString, Integer length)
+ throws SecurityException, QueryException {
List<Model> models = getModels(projectId, modelId, token);
Integer start = Math.max(0, Integer.valueOf(startString));
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index 45a4ada00d1e377fb5074471b13441b6bf8ae353..815d1b9aff25e37ad4bc32f9c02f300313ac4f16 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -90,7 +90,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public LayoutView addOverlay( //
+ public LayoutView addOverlay(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@RequestParam(value = "name") String name, //
@@ -103,7 +103,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeOverlay( //
+ public Map<String, Object> removeOverlay(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId //
@@ -112,7 +112,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public LayoutView updateOverlay( //
+ public LayoutView updateOverlay(//
@RequestBody String body, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId, //
@@ -125,7 +125,7 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}:downloadSource", method = { RequestMethod.GET },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getOverlaySource( //
+ public ResponseEntity<byte[]> getOverlaySource(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId //
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 9544bbeb5b86719879c212700278259070095e89..ed690aaad7e343d312adb59129a0ee2b7889f400 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -38,8 +38,6 @@ import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightReactionView;
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index 67952223b4b70e21706c1bfe295064caf50a8c1e..43cc0ff508433a0296c7596093d257bcbe3460a1 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -7,7 +7,6 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.search.data.FullAliasView;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightReactionView;
import lcsb.mapviewer.services.view.AuthenticationToken;
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index 704b6abb7a4b58ec875a78a72196aa057df606db..bc59fb9104b9321272dececad18ec75e053a8afc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -4,7 +4,6 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.user.BasicPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index e1a59f32d37cb373563a3aa7e40ed93aa5860aa1..ee446efa7ec86b8158848196155c4a4fb1941df7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -1,26 +1,16 @@
package lcsb.mapviewer.services.search;
import java.util.Collection;
-import java.util.HashSet;
import java.util.List;
-import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.GeneRow;
@@ -62,10 +52,10 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
* {@link lcsb.mapviewer.services.view.AnnotationView} elements.
*/
@Autowired
- private AnnotationViewFactory annotationViewFactory;
+ private AnnotationViewFactory annotationViewFactory;
@Autowired
- private ElementMatcher elementMatcher;
+ private ElementMatcher elementMatcher;
/**
* Returns detailed information about element respective to the set of targets
@@ -114,12 +104,10 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return null;
}
-
protected boolean elementMatch(TargetView target, Element element) {
return elementMatcher.elementMatch(target, element);
}
-
/**
* @return the annotationViewFactory
* @see #annotationViewFactory
@@ -137,7 +125,6 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
this.annotationViewFactory = annotationViewFactory;
}
-
/**
* @return the elementMatcher
* @see #elementMatcher
@@ -146,9 +133,9 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return elementMatcher;
}
-
/**
- * @param elementMatcher the elementMatcher to set
+ * @param elementMatcher
+ * the elementMatcher to set
* @see #elementMatcher
*/
public void setElementMatcher(ElementMatcher elementMatcher) {