diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index a82e66e114699e9ec8a1ca8a64c3323036b37bf2..599e6256c9b24ea6b8d26662db1a7b60bdcf5043 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -10,18 +10,22 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
@Transactional(value = "txManager")
public class BioEntitiesRestImpl extends BaseRestImpl {
- Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
@Autowired
private IUserService userService;
@@ -32,9 +36,6 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
@Autowired
private ISearchService searchService;
- @Autowired
- AnnotationViewFactory annotationViewFactory;
-
/**
* @return the userService
* @see #userService
@@ -60,7 +61,7 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
Model submodel = model.getSubmodelById(modelId);
- List<Object> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
+ List<AnnotatedObject> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
for (Object object : elements) {
Map<String, Object> result = createMinifiedSearchResult(object);
resultMap.add(result);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 947a3d32991a6e0c51c83535987c72923b18b4da..c99199d01ec1d90b8a2dab61a7a043c89c63cc04 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -527,8 +527,8 @@ public class SearchService implements ISearchService {
}
@Override
- public List<Object> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
- List<Object> result = new ArrayList<>();
+ public List<AnnotatedObject> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
+ List<AnnotatedObject> result = new ArrayList<>();
// probably this could be improved algorithmitically, right now all objects
// are sorted by distance, and numberOfElements closest are chosen as a list
@@ -566,12 +566,18 @@ public class SearchService implements ISearchService {
/**
* Reference to the object.
*/
- private Object reference;
+ private AnnotatedObject reference;
+
/**
* Distance between the object and some point.
*/
private double distance;
+ /**
+ * Size of the object.
+ */
+ private double size;
+
/**
* Constructor for reaction objects.
*
@@ -583,6 +589,7 @@ public class SearchService implements ISearchService {
DistanceToObject(Reaction reaction, Point2D point) {
reference = reaction;
distance = reaction.getDistanceFromPoint(point);
+ size = 0;
}
/**
@@ -596,6 +603,7 @@ public class SearchService implements ISearchService {
DistanceToObject(Element alias, Point2D point) {
reference = alias;
distance = alias.getDistanceFromPoint(point);
+ size = alias.getSize();
}
@@ -606,7 +614,13 @@ public class SearchService implements ISearchService {
} else if (arg0.getDistance() > getDistance()) {
return -1;
} else {
- return 0;
+ if (arg0.getSize() < getSize()) {
+ return 1;
+ } else if (arg0.getSize() > getSize()) {
+ return -1;
+ } else {
+ return 0;
+ }
}
}
@@ -614,7 +628,7 @@ public class SearchService implements ISearchService {
* @return the reference
* @see #reference
*/
- public Object getReference() {
+ public AnnotatedObject getReference() {
return reference;
}
@@ -626,6 +640,13 @@ public class SearchService implements ISearchService {
return distance;
}
+ /**
+ * @return the size
+ * @see #size
+ */
+ public double getSize() {
+ return size;
+ }
}
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
index c7f51a65f43b178ba00c4eed1258cdaf3938bc4f..ba82510d70903606ce9591c699d1ca28d2ccb9a4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -5,6 +5,7 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -295,7 +296,7 @@ public interface ISearchService {
* how many closest elements should be returned
* @return list of the closest elements
*/
- List<Object> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
+ List<AnnotatedObject> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
/**
* Returns list of autocomplete strings for the partial query.
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 571ef6105b32936e8d38fdcabce39d4d96cfe470..64ff5dc2de7f86973ef15604b34035dd5a409e9c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -18,6 +18,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -45,7 +46,7 @@ import lcsb.mapviewer.services.search.data.SearchElementResult;
import lcsb.mapviewer.services.utils.SearchIndexer;
public class SearchServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(SearchService.class);
+ static Logger logger = Logger.getLogger(SearchServiceTest.class);
private Model model = null;
SearchIndexer indexer = new SearchIndexer();
@@ -231,7 +232,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosest() throws Exception {
try {
model = getModelForFile("testFiles/graph_path_example3.xml", true);
- List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+ List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(5, elements.size());
assertTrue(elements.get(0) instanceof Species);
@@ -256,11 +257,50 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testSearchClosest2() throws Exception {
+ try {
+ model = new ModelFullIndexed(null);
+ GenericProtein protein1 = new GenericProtein("s1");
+ protein1.setWidth(20);
+ protein1.setHeight(20);
+ protein1.setX(5);
+ protein1.setY(5);
+ model.addElement(protein1);
+ GenericProtein protein2 = new GenericProtein("s2");
+ protein2.setWidth(10);
+ protein2.setHeight(10);
+ protein2.setX(5);
+ protein2.setY(5);
+ model.addElement(protein2);
+ GenericProtein protein3 = new GenericProtein("s3");
+ protein3.setWidth(30);
+ protein3.setHeight(30);
+ protein3.setX(0);
+ protein3.setY(0);
+ model.addElement(protein3);
+
+ List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
+ assertNotNull(elements);
+ assertEquals(3, elements.size());
+ AnnotatedObject sAlias = elements.get(0);
+ assertEquals("s2", sAlias.getName());
+ AnnotatedObject reaction = elements.get(1);
+ assertEquals("s1", reaction.getName());
+ sAlias = elements.get(2);
+ assertEquals("s3", sAlias.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testSearchClosestWithEmptyModel() throws Exception {
try {
model = new ModelFullIndexed(null);
- List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+ List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(0, elements.size());