From 5cc7ecf113c40017b03aec2aa058388043654def Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 10 May 2019 19:00:16 +0200
Subject: [PATCH] unused code removed
---
.../services/impl/SearchService.java | 116 +-----------
.../services/interfaces/ISearchService.java | 168 ------------------
.../services/impl/SearchServiceTest.java | 89 +++-------
3 files changed, 24 insertions(+), 349 deletions(-)
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 a536521da9..9bda1fdbdf 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -15,7 +15,6 @@ import org.apache.log4j.Logger;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
@@ -58,8 +57,6 @@ import lcsb.mapviewer.services.utils.SearchIndexer;
@Service
public class SearchService implements ISearchService {
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
/**
* Prefix used in search by name interface to limit results only to species.
*/
@@ -221,13 +218,13 @@ public class SearchService implements ISearchService {
* @return list of object found for the query string sorted by the score value
*/
protected List<BioEntity> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch,
- Class<? extends Element> type) {
+ Class<? extends Element> type) {
List<BioEntity> result = new ArrayList<>();
if (query.startsWith(REACTION_SEARCH_PREFIX)) {
return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
Element element = model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""));
- if (element !=null) {
+ if (element != null) {
result.add(element);
}
} else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
@@ -358,114 +355,9 @@ public class SearchService implements ISearchService {
return result;
}
- @Override
- public List<BioEntity> searchByCoordinates(CoordinatesSearchParams params) {
- List<Object> results = new ArrayList<Object>();
-
- Set<Element> aliases = params.getModel().getElements();
- Point2D point = new Point2D.Double(params.getX(), params.getY());
- for (Element alias : aliases) {
- if (alias instanceof Species) {
- if (alias.contains(point)) {
- if (isVisible(alias, params)) {
- results.add(alias);
- }
- }
- }
- }
- List<BioEntity> result = new ArrayList<>();
- double dist = params.getDistance();
- if (results.size() == 0) {
- Reaction r = null;
- Set<Reaction> reactions = params.getModel().getReactions();
- for (Reaction reaction : reactions) {
- double newDist = reaction.getDistanceFromPoint(point);
- if (newDist < dist) {
- if (isVisible(reaction, params)) {
- r = reaction;
- dist = reaction.getDistanceFromPoint(point);
- }
- }
- }
- if (r != null) {
- result.addAll(reactionToResultList(r));
- return result;
- }
- }
-
- if (results.size() > 1) {
- Element alias = (Element) results.get(0);
- for (Object obj : results) {
- if (((Element) (obj)).getSize() < alias.getSize()) {
- alias = (Element) obj;
- }
- }
- results.clear();
- results.add(alias);
- }
- if (results.size() == 0) {
- return result;
- } else {
- Object obj = results.get(0);
- if (obj instanceof Element) {
- result.add((BioEntity) obj);
- return result;
- } else if (obj instanceof Reaction) {
- result.addAll(reactionToResultList((Reaction) obj));
- return result;
- } else {
- throw new InvalidStateException("Unknown class type: " + obj.getClass());
- }
- }
- }
-
- /**
- * Check if reaction is visible for the user. Reaction is visible when at least
- * one node of the reaction is visible.
- *
- * @param reaction
- * which reaction is tested
- * @param params
- * params that determines the client search environment (zoom level,
- * type of the layout)
- * @return <code>true</code> if reaction is visible for the user,
- * <code>false</code> otherwise
- */
- private boolean isVisible(Reaction reaction, CoordinatesSearchParams params) {
- if (params.getLevel() == null) {
- return true;
- }
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (isVisible(node.getElement(), params)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Checks if alias is visible for the user. Alias is invisible when the search
- * is performed on the hierarchical layout and the alias is hidden by the
- * complex or compartment.
- *
- * @param alias
- * alias to be checked for visibility
- * @param params
- * that determines the client search environment (zoom level, type of
- * the layout)
- * @return <code>true</code> if alias is visible for the user,
- * <code>false</code> otherwise
- */
- private boolean isVisible(Element alias, CoordinatesSearchParams params) {
- if (params.getLevel() == null) {
- return true;
- }
- return zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
- }
-
@Override
public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch,
- String ipAddress) {
+ String ipAddress) {
query = query.toLowerCase();
if (query == null) {
throw new InvalidArgumentException("Invalid query: null");
@@ -552,7 +444,7 @@ public class SearchService implements ISearchService {
@Override
public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit,
- Collection<String> types) {
+ Collection<String> types) {
List<BioEntity> result = new ArrayList<>();
// probably this could be improved algorithmitically, right now all objects
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 11cff639a7..fb76a0602a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -4,8 +4,6 @@ import java.awt.geom.Point2D;
import java.util.Collection;
import java.util.List;
-import org.apache.log4j.Logger;
-
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
@@ -16,172 +14,6 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
public interface ISearchService {
- /**
- * Parameters of search objects on the map using coordinates. It's possible to
- * add also information about nested model and level at which searching is
- * performed in the hierarchical view. More information about hierarchical view
- * can be found in the definition of
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
- * AbstractImageGenerator}.
- *
- * @author Piotr Gawron
- *
- */
- class CoordinatesSearchParams {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(CoordinatesSearchParams.class);
-
- /**
- * Model where we perform search.
- */
- private Model model = null;
-
- /**
- * X coordinate of the search event.
- */
- private double x = 0;
-
- /**
- * Y coordinate of the search event.
- */
- private double y = 0;
-
- /**
- * Maximum distance between object that could be found and point that is valid.
- */
- private double distance = 0;
-
- /**
- * Level at which the search is performed. It's used during determining if the
- * object is visible in hierarchical view.
- */
- private Integer level = null;
-
- /**
- * @return the model
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @return object with all parameters
- * @see #model
- */
- public CoordinatesSearchParams model(Model model) {
- this.model = model;
- return this;
- }
-
- /**
- * @param point
- * the coordinates to set
- * @return object with all parameters
- * @see #model
- */
- public CoordinatesSearchParams point(Point2D point) {
- this.x = point.getX();
- this.y = point.getY();
- return this;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @return object with all parameters
- * @see #x
- */
- public CoordinatesSearchParams x(double x) {
- this.x = x;
- return this;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @return object with all parameters
- * @see #y
- */
- public CoordinatesSearchParams y(double y) {
- this.y = y;
- return this;
- }
-
- /**
- * @return the distance
- * @see #distance
- */
- public double getDistance() {
- return distance;
- }
-
- /**
- * @param distance
- * the distance to set
- * @return object with all parameters
- * @see #distance
- */
- public CoordinatesSearchParams distance(double distance) {
- this.distance = distance;
- return this;
- }
-
- /**
- * @param level
- * the level to set
- * @return object with all parameters
- * @see #level
- */
- public CoordinatesSearchParams level(Integer level) {
- this.level = level;
- return this;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public Integer getLevel() {
- return level;
- }
-
- }
-
- /**
- * Search the element on the map using coordinates. It is also possible to
- * provide information about layout (if it's nested or not) and hierarchical
- * level.
- *
- * @param params
- * set of search params. More information can be found here:
- * {@link CoordinatesSearchParams}
- * @return object that match best the search criteria. If such object doesn't
- * exist then <code>null</code> is returned.
- */
- List<BioEntity> searchByCoordinates(CoordinatesSearchParams params);
/**
* Search for elements on the map by query. Returns many possibilities from best
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 3fd35f90e7..a5771d8953 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -42,7 +42,6 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
import lcsb.mapviewer.services.utils.SearchIndexer;
public class SearchServiceTest extends ServiceTestFunctions {
@@ -53,6 +52,8 @@ public class SearchServiceTest extends ServiceTestFunctions {
Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
Map<String, Class<?>> speciesSearchReversePrefix = new HashMap<String, Class<?>>();
+ int elementCounter = 0;
+
@Before
public void setUp() throws Exception {
addSearchPrefix("complex", Complex.class);
@@ -329,11 +330,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosest2() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- GenericProtein protein1 = new GenericProtein("s1");
- protein1.setWidth(20);
- protein1.setHeight(20);
- protein1.setX(5);
- protein1.setY(5);
+ GenericProtein protein1 = createProtein();
model.addElement(protein1);
GenericProtein protein2 = new GenericProtein("s2");
protein2.setWidth(10);
@@ -352,12 +349,14 @@ public class SearchServiceTest extends ServiceTestFunctions {
new ArrayList<>());
assertNotNull(elements);
assertEquals(3, elements.size());
- BioEntity sAlias = elements.get(0);
- assertEquals("s2", sAlias.getName());
- BioEntity reaction = elements.get(1);
- assertEquals("s1", reaction.getName());
- sAlias = elements.get(2);
- assertEquals("s3", sAlias.getName());
+ BioEntity element0 = elements.get(0);
+ assertEquals("s2", element0.getName());
+
+ BioEntity element1 = elements.get(1);
+ assertEquals(protein1.getName(), element1.getName());
+
+ BioEntity element2 = elements.get(2);
+ assertEquals("s3", element2.getName());
} catch (Exception e) {
e.printStackTrace();
@@ -365,6 +364,15 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ private GenericProtein createProtein() {
+ GenericProtein protein1 = new GenericProtein("s" + elementCounter++);
+ protein1.setWidth(20);
+ protein1.setHeight(20);
+ protein1.setX(5);
+ protein1.setY(5);
+ return protein1;
+ }
+
@Test
public void testSearchClosestWithEmptyModel() throws Exception {
try {
@@ -476,63 +484,6 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
- @Test
- public void testSearchByCoordCompartment() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- // we search in non-nested model
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50));
- assertNotNull(res);
- assertEquals(0, res.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- // find compartment
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model));
- // reaction is too far
- assertEquals(0, res.size());
-
- res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).distance(1000));
- assertEquals(3, res.size());
-
- assertTrue(res.get(0) instanceof Reaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordAlias() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(60).y(60));
- assertNotNull(res);
- assertTrue(res.size() > 0);
-
- assertTrue(res.get(0) instanceof Species);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
@Test
public void testGetMiriamTypeForQuery() throws Exception {
try {
--
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