From a87b25b20d4084f6ed6bd052f1b5c0bab28ed924 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Jun 2017 18:41:33 +0200
Subject: [PATCH] organizing imports
---
.../lcsb/mapviewer/run/LegendGenerator.java | 51 ++++++++++---------
.../converter/graphics/MapGenerator.java | 16 +++---
.../model/map/reaction/ReactionTest.java | 3 +-
.../projects/chemicals/ChemicalRestImpl.java | 6 ++-
.../ReferenceGenomeControllerTest.java | 2 -
.../api/projects/models/AllModelsTests.java | 1 -
.../services/interfaces/ISearchService.java | 2 +-
.../lcsb/mapviewer/bean/ChemicalBeanTest.java | 11 ++--
8 files changed, 42 insertions(+), 50 deletions(-)
diff --git a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
index 4f989ff231..bccf00ae75 100644
--- a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
+++ b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
@@ -7,7 +7,6 @@ import java.io.IOException;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
@@ -31,18 +30,21 @@ public class LegendGenerator {
*
*/
private enum LegendObject {
-// /**
-// * First legend element.
-// */
-// LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600, 480),
-// /**
-// * Second legend element.
-// */
-// LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600, 480),
-// /**
-// * Third legend element.
-// */
-// LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600, 480),
+ // /**
+ // * First legend element.
+ // */
+ // LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600,
+ // 480),
+ // /**
+ // * Second legend element.
+ // */
+ // LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600,
+ // 480),
+ // /**
+ // * Third legend element.
+ // */
+ // LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600,
+ // 480),
/**
* Fourth legend element.
*/
@@ -51,27 +53,27 @@ public class LegendGenerator {
/**
* File with the legend data in CellDEsigner format.
*/
- private String inputFile = null;
+ private String inputFile = null;
/**
* Where the legend should be saved.
*/
- private String outputFile = null;
+ private String outputFile = null;
/**
* X coordinate where the image in input file starts.
*/
- private int startX = 0;
+ private int startX = 0;
/**
* Y coordinate where the image in input file starts.
*/
- private int startY = 0;
+ private int startY = 0;
/**
* Width of the legend image.
*/
- private Integer width = null;
+ private Integer width = null;
/**
* Height of the legend image.
*/
- private Integer height = null;
+ private Integer height = null;
/**
* Default constructor.
@@ -130,9 +132,9 @@ public class LegendGenerator {
*
* @throws IOException
* thrown when there are some general problems with files
- * @throws DrawingException
+ * @throws DrawingException
* thrown when there was a problem with drawing one of the maps
- * @throws InvalidInputDataExecption
+ * @throws InvalidInputDataExecption
*/
public void run() throws Exception {
for (LegendObject lo : LegendObject.values()) {
@@ -148,7 +150,7 @@ public class LegendGenerator {
* @throws IOException
* thrown when there are some general problems with input/output
* file
- * @throws DrawingException
+ * @throws DrawingException
* thrown when there was a problem with drawing a legend
* @throws InvalidInputDataExecption
* thrown when xml file is invalid
@@ -159,10 +161,9 @@ public class LegendGenerator {
// and save it to leged.png
String fileName = lo.outputFile;
- new CreateHierarchyCommand(model,5,20).execute();
Model copy = new CopyCommand(model).execute();
- PngImageGenerator generator = new PngImageGenerator(new Params()
- .scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(4).nested(true));
+ PngImageGenerator generator = new PngImageGenerator(
+ new Params().scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(2).nested(true));
generator.saveToFile(fileName);
Desktop.getDesktop().open(new File(fileName));
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index d2953a6deb..4500e81c15 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -6,8 +6,6 @@ import java.io.IOException;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
@@ -57,21 +55,21 @@ public class MapGenerator {
* Do we want to generate images in hierarchical view or normal.
*
*/
- private boolean nested = false;
+ private boolean nested = false;
/**
* Should we remove empty elements in nested view.
*
*/
- private boolean removeEmpty = false;
+ private boolean removeEmpty = false;
/**
* Callback function that update progress information.
*
*/
- private IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
+ private IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
/**
* Zoom factor on the lowest level.
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index 36bbc7596e..e8501dddfd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -31,7 +31,6 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
@@ -230,7 +229,7 @@ public class ReactionTest extends ModelTestFunctions {
try {
Reaction reaction1 = new Reaction();
assertEquals(null, reaction1.getVisibilityLevel());
-
+
reaction1.setVisibilityLevel(1);
assertEquals("1", reaction1.getVisibilityLevel());
} catch (Exception e) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index fdf54a0e32..fe8f909dd4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -70,7 +70,8 @@ public class ChemicalRestImpl {
if (organism == null) {
organism = TaxonomyBackend.HUMAN_TAXONOMY;
}
- ChemicalView chemical = chemicalService.getByName(query, new DbSearchCriteria().model(model).organisms(organism).colorSet(0).disease(project.getDisease()));
+ ChemicalView chemical = chemicalService
+ .getByName(query, new DbSearchCriteria().model(model).organisms(organism).colorSet(0).disease(project.getDisease()));
if (chemical != null) {
List<Model> models = getModels(model);
result.add(prepareChemical(chemical, columnSet, models));
@@ -271,7 +272,8 @@ public class ChemicalRestImpl {
Set<String> columnSet = createChemicalColumnSet(columns);
- List<ChemicalView> chemicals = chemicalService.getForTargets(targets, new DbSearchCriteria().model(model).organisms(organism).disease(project.getDisease()));
+ List<ChemicalView> chemicals = chemicalService
+ .getForTargets(targets, new DbSearchCriteria().model(model).organisms(organism).disease(project.getDisease()));
List<Map<String, Object>> result = new ArrayList<>();
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index b529a284f1..b1a2c84e9b 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.api.genomics;
-import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -13,7 +12,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
public class ReferenceGenomeControllerTest extends RestTestFunctions {
Logger logger = Logger.getLogger(ReferenceGenomeControllerTest.class);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
index f89ba7fa4d..58bce555cf 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
@@ -5,7 +5,6 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.projects.models.bioEntities.AllBioeEntitiesTests;
-import lcsb.mapviewer.api.projects.models.bioEntities.elements.AllElementsTests;
import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
@RunWith(Suite.class)
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 c32dee9143..1229bba669 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -320,6 +320,6 @@ public interface ISearchService {
*/
void assignIcons(SearchElementResult results, int iconSet);
- public String[] getSuggestedQueryList(Model model);
+ String[] getSuggestedQueryList(Model model);
}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ChemicalBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ChemicalBeanTest.java
index ab2b195432..17b67300d3 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/ChemicalBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/ChemicalBeanTest.java
@@ -7,21 +7,16 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
public class ChemicalBeanTest extends WebTestFunctions {
- Logger logger = Logger.getLogger(ChemicalBeanTest.class);
+ Logger logger = Logger.getLogger(ChemicalBeanTest.class);
+ ChemicalBean chemicalBean;
- ChemicalBean chemicalBean;
-
- String projectId = "Some_id";
+ String projectId = "Some_id";
@Before
public void setUp() throws Exception {
--
GitLab