From 14aed039a5538f308b5ce8af6a68f25254a26e0a Mon Sep 17 00:00:00 2001
From: sherzinger <sascha.herzinger@uni.lu>
Date: Fri, 19 Oct 2018 11:27:23 +0200
Subject: [PATCH] removing all // that are not comments
---
.../cdplugin/copypaste/CopyPastePlugin.java | 12 +-
.../CopyPasteAbstractActionTest.java | 2 +-
.../annotation/AllAnnotationTests.java | 6 +-
.../annotation/AnnotationTestFunctions.java | 12 +-
.../annotation/cache/AllCacheTests.java | 16 +-
.../annotation/data/AllDataTests.java | 26 +-
.../annotation/services/AllServicesTests.java | 38 +-
.../annotators/AllAnnotatorTests.java | 38 +-
.../services/annotators/PdbAnnotatorTest.java | 14 +-
.../common/HttpConnectionMethodType.java | 2 +-
.../java/lcsb/mapviewer/common/MimeType.java | 10 +-
.../common/geometry/ColorParser.java | 4 +-
.../lcsb/mapviewer/common/AllCommonTests.java | 24 +-
.../mapviewer/common/TextFileUtilsTest.java | 8 +-
.../common/comparator/AllComparatorTests.java | 20 +-
.../common/geometry/AllGeometryTests.java | 12 +-
.../java/lcsb/mapviewer/run/Statistics.java | 12 +-
.../celldesigner/annotation/NoteField.java | 44 +-
.../AbstractCellDesignerAliasConverter.java | 4 +-
.../geometry/helper/CellDesignerAnchor.java | 32 +-
.../reaction/ReactionLineData.java | 2 +-
.../celldesigner/species/SpeciesMapping.java | 20 +-
.../structure/fields/ModificationType.java | 16 +-
.../celldesigner/AllCellDesignerTests.java | 40 +-
.../celldesigner/alias/AllAliasTests.java | 8 +-
.../annotation/AllAnnotationTests.java | 4 +-
.../compartment/AllCompartmentTests.java | 6 +-
.../geometry/AllGeometryTests.java | 26 +-
.../geometry/helper/AllHelperTests.java | 14 +-
.../reaction/AllReactionTests.java | 18 +-
.../celldesigner/species/AllSpeciesTests.java | 22 +-
.../structure/AllStructureTests.java | 50 +-
.../structure/fields/AllFieldsTests.java | 2 +-
.../celldesigner/types/AllTypesTests.java | 8 +-
.../model/sbgnml/AllSbgnmlTests.java | 12 +-
.../model/sbgnml/DbSerializationTest.java | 6 +-
.../graphics/AbstractImageGenerator.java | 20 +-
.../converter/graphics/ConverterParams.java | 8 +-
.../converter/graphics/ImageGenerators.java | 6 +-
.../geometry/ArrowTransformation.java | 2 +-
.../converter/graphics/AllGraphicsTests.java | 20 +-
.../converter/graphics/ConverterTest.java | 4 +-
.../graphics/bioEntity/AllBioEntityTests.java | 10 +-
.../species/AllSpeciesConverterTests.java | 2 +-
.../reaction/ReactionConverterTest.java | 6 +-
.../geometry/ArrowTransformationTest.java | 2 +-
.../graphics/geometry/FontFinderTest.java | 4 +-
.../sbml/reaction/SBOTermModifierType.java | 14 +-
.../sbml/reaction/SBOTermReactionType.java | 38 +-
.../model/sbml/species/ElementColorEnum.java | 34 +-
.../sbml/species/SBOTermSpeciesType.java | 28 +-
.../model/sbml/AllSbmlConverterTests.java | 16 +-
.../reaction/AllSbmlReactionParserTests.java | 4 +-
.../lcsb/mapviewer/converter/AllTests.java | 10 +-
.../converter/OverviewParserTest.java | 6 +-
.../main/js/gui/admin/CommentsAdminPanel.js | 20 +-
.../src/main/js/gui/admin/LogListDialog.js | 6 +-
.../js/gui/leftPanel/PublicationListDialog.js | 16 +-
.../src/main/js/map/AbstractCustomMap.js | 2 +-
frontend-js/src/main/js/map/CustomMap.js | 22 +-
frontend-js/src/main/js/map/canvas/Bounds.js | 6 +-
.../src/main/js/map/data/IdentifiedElement.js | 4 +-
.../main/js/map/window/AbstractInfoWindow.js | 12 +-
.../src/main/js/map/window/AliasInfoWindow.js | 14 +-
.../mapviewer/commands/AllCommandsTests.java | 14 +-
.../properties/AllPropertyCommandTests.java | 22 +-
.../mapviewer/model/graphics/ArrowType.java | 16 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 464 +++++++++---------
.../map/species/field/ModificationState.java | 26 +-
.../model/user/ConfigurationElementType.java | 44 +-
.../user/ConfigurationElementTypeGroup.java | 16 +-
.../test/java/lcsb/mapviewer/AllTests.java | 4 +-
.../lcsb/mapviewer/model/AllModelTests.java | 14 +-
.../mapviewer/model/cache/AllCacheTests.java | 8 +-
.../model/graphics/AllGraphicsTests.java | 12 +-
.../lcsb/mapviewer/model/log/AllLogTests.java | 6 +-
.../lcsb/mapviewer/model/map/AllMapTests.java | 54 +-
.../map/compartment/AllCompartmentTests.java | 18 +-
.../model/map/kinetics/AllKineticsTests.java | 20 +-
.../model/map/layout/AllLayoutTests.java | 24 +-
.../map/layout/graphics/AllGraphicsTests.java | 16 +-
.../model/map/model/AllModelTests.java | 20 +-
.../model/map/modifier/AllModifierTests.java | 14 +-
.../model/map/reaction/AllReactionTests.java | 36 +-
.../reaction/type/AllReactionTypeTests.java | 42 +-
.../model/map/species/AllSpeciesTests.java | 72 +--
.../map/species/field/AllFieldTests.java | 14 +-
.../map/statistics/AllStatisticsTests.java | 4 +-
.../mapviewer/model/user/AllUserTests.java | 22 +-
.../modelutils/map/AllMapUtilTests.java | 6 +-
.../mapviewer/wikipathway/XML/GpmlParser.java | 4 +-
.../wikipathway/model/Direction.java | 6 +-
.../model/GpmlInteractionType.java | 30 +-
.../model/GpmlLineConnectorType.java | 6 +-
.../wikipathway/model/GpmlLineType.java | 2 +-
.../model/GpmlModificationType.java | 22 +-
.../wikipathway/model/GpmlStateType.java | 2 +-
.../wikipathway/model/InteractionMapping.java | 266 +++++-----
.../wikipathway/model/MergeMapping.java | 14 +-
.../wikipathway/model/ReferenceMapping.java | 70 +--
.../wikipathway/AllWikipathwaysTests.java | 16 +-
.../wikipathway/XML/AllXmlTests.java | 22 +-
.../wikipathway/model/AllModelTests.java | 18 +-
.../lcsb/mapviewer/persist/AllDbTests.java | 10 +-
.../persist/PersistTestFunctions.java | 6 +-
.../mapviewer/persist/dao/AllDaoTests.java | 18 +-
.../persist/dao/cache/AllCacheDbTests.java | 8 +-
.../persist/dao/log/AllLogTests.java | 2 +-
.../persist/dao/map/AllMapDaoTests.java | 12 +-
.../dao/map/layout/AllLayoutTests.java | 6 +-
.../dao/map/layout/alias/AllAliasTests.java | 8 +-
.../persist/dao/plugin/AllPluginTests.java | 2 +-
.../persist/dao/user/AllUserTests.java | 2 +-
.../quadtree/quadtrees/PointQuadTree.java | 8 +-
.../mapviewer/utils/quadtree/SuitedTests.java | 18 +-
.../reactome/utils/ReactomeConnector.java | 4 +-
.../mapviewer/reactome/AllReactomeTests.java | 4 +-
.../reactome/ReactomeTestFunctions.java | 10 +-
.../reactome/utils/AllReactomeUtilsTests.java | 8 +-
.../reactome/xml/AllReactomeXmlTests.java | 66 +--
.../ConfigurationController.java | 8 +-
.../api/convert/ConvertController.java | 28 +-
.../api/convert/ConvertRestImpl.java | 8 +-
.../mapviewer/api/files/FileController.java | 20 +-
.../genomics/ReferenceGenomeController.java | 70 +--
.../mapviewer/api/mesh/MeshController.java | 6 +-
.../api/plugins/PluginController.java | 72 +--
.../api/projects/ProjectController.java | 68 +--
.../api/projects/ProjectRestImpl.java | 4 +-
.../chemicals/ChemicalController.java | 18 +-
.../projects/comments/CommentController.java | 114 ++---
.../api/projects/drugs/DrugController.java | 18 +-
.../api/projects/mirnas/MiRnaController.java | 18 +-
.../api/projects/models/ModelController.java | 64 +--
.../api/projects/models/ModelRestImpl.java | 18 +-
.../bioEntities/BioEntitiesController.java | 24 +-
.../elements/ElementsController.java | 18 +-
.../reactions/ReactionsController.java | 14 +-
.../models/functions/FunctionsController.java | 18 +-
.../parameters/ParametersController.java | 18 +-
.../publications/PublicationsController.java | 18 +-
.../publications/PublicationsRestImpl.java | 8 +-
.../models/units/UnitsController.java | 18 +-
.../projects/overlays/OverlayController.java | 98 ++--
.../mapviewer/api/users/UserController.java | 66 +--
.../java/lcsb/mapviewer/api/AllRestTests.java | 16 +-
.../lcsb/mapviewer/api/RestTestFunctions.java | 12 +-
.../api/projects/AllProjectTests.java | 10 +-
.../api/projects/models/AllModelsTests.java | 10 +-
.../bioEntities/AllBioeEntitiesTests.java | 6 +-
.../mapviewer/services/utils/EmailSender.java | 10 +-
.../services/utils/data/BuildInLayout.java | 14 +-
.../utils/data/ColorSchemaColumn.java | 48 +-
.../services/utils/data/ExportColumn.java | 22 +-
.../mapviewer/services/AllServicesTests.java | 8 +-
.../services/ServiceTestFunctions.java | 10 +-
.../services/impl/AllImplServiceTests.java | 18 +-
.../services/impl/LayoutServiceTest.java | 70 +--
.../services/impl/LayoutServiceTest2.java | 8 +-
.../services/impl/ProjectServiceTest.java | 132 ++---
.../services/overlay/AllOverlayTests.java | 6 +-
.../services/search/AllSearchTests.java | 10 +-
.../search/drug/AllSearchDrugTests.java | 2 +-
.../services/utils/AllUtilsTests.java | 8 +-
.../services/utils/ColorSchemaReaderTest.java | 6 +-
165 files changed, 1932 insertions(+), 1932 deletions(-)
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
index 8e2d09a645..17bdd87eeb 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
@@ -66,15 +66,15 @@ public class CopyPastePlugin extends CellDesignerPlugin {
public boolean dispatchKeyEvent(KeyEvent e) {
switch (e.getID()) {
case KeyEvent.KEY_PRESSED:
- if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V//
- && e.isControlDown()//
- && e.isAltDown()//
+ if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
+ && e.isControlDown()
+ && e.isAltDown()
) {
ppa.myActionPerformed(null);
return true;
- } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C//
- && e.isControlDown()//
- && e.isAltDown()//
+ } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
+ && e.isControlDown()
+ && e.isAltDown()
) {
cpa.myActionPerformed(null);
return true;
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
index 19366d3934..dc9a41e160 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
@@ -52,7 +52,7 @@ public class CopyPasteAbstractActionTest {
CopyPasteAbstractAction pa = new PasteAction();
String annString = "<rdf:RDF xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
+ "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\" "
- + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"//
+ + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"
+ "<rdf:Description rdf:about=\"#s1\">" + "<bqmodel:is>" + "<rdf:Bag>" + "<rdf:li rdf:resource=\"urn:miriam:hgnc:SNCA\"/>" + "</rdf:Bag>"
+ "</bqmodel:is>" + "</rdf:Description>" + "</rdf:RDF>";
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
index 4a05c389f6..90e78c71dd 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
@@ -9,9 +9,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllDataTests.class, //
- AllServicesTests.class, //
+@SuiteClasses({ AllCacheTests.class,
+ AllDataTests.class,
+ AllServicesTests.class,
})
public class AllAnnotationTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index 8d1e262d9a..ceb0595b15 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -54,12 +54,12 @@ import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
@Transactional(value = "txManager")
-@ContextConfiguration(locations = { //
- "/applicationContext-annotation.xml", //
- "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+@ContextConfiguration(locations = {
+ "/applicationContext-annotation.xml",
+ "/applicationContext-persist.xml",
+ "/test-applicationContext.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml",
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
index 6d7c27f99a..99707b056d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
@@ -5,14 +5,14 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ApplicationLevelCacheTest.class, //
- BigFileCacheTest.class, //
- CachableInterfaceTest.class, //
- GeneralCacheTest.class, //
- GeneralCacheWithExclusionTest.class, //
- PermanentDatabaseLevelCacheTest.class, //
- SourceNotAvailableTest.class, //
- WebPageDownloaderTest.class, //
+@SuiteClasses({ ApplicationLevelCacheTest.class,
+ BigFileCacheTest.class,
+ CachableInterfaceTest.class,
+ GeneralCacheTest.class,
+ GeneralCacheWithExclusionTest.class,
+ PermanentDatabaseLevelCacheTest.class,
+ SourceNotAvailableTest.class,
+ WebPageDownloaderTest.class,
})
public class AllCacheTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
index 88f7f1479b..b4a981f759 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
@@ -5,19 +5,19 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ArticleCitationComparatorTest.class, //
- ArticleTest.class, //
- ChebiRelationTest.class, //
- ChebiTest.class, //
- ChemicalTest.class, //
- ChemicalDirectEvidenceTest.class, //
- DrugTest.class, //
- EntrezDataTest.class, //
- GoTest.class, //
- MeSHTest.class, //
- MiRNATest.class, //
- TargetTest.class, //
- TargetTypeTest.class,//
+@SuiteClasses({ ArticleCitationComparatorTest.class,
+ ArticleTest.class,
+ ChebiRelationTest.class,
+ ChebiTest.class,
+ ChemicalTest.class,
+ ChemicalDirectEvidenceTest.class,
+ DrugTest.class,
+ EntrezDataTest.class,
+ GoTest.class,
+ MeSHTest.class,
+ MiRNATest.class,
+ TargetTest.class,
+ TargetTypeTest.class,
})
public class AllDataTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
index 9402bd6e15..228a4b67c7 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
@@ -8,25 +8,25 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllAnnotatorTests.class, //
- AllGenomeTests.class, //
- ChEMBLParserTest.class, //
- ChemicalParserTest.class, //
- ChemicalSearchExceptionTest.class, //
- DrugAnnotationTest.class, //
- DrugbankHTMLParserTest.class, //
- ExternalServiceStatusTest.class, //
- ExternalServiceStatusTypeTest.class, //
- ImproperAnnotationsTest.class, //
- MeSHParserTest.class, //
- MiriamConnectorTest.class, //
- MiRNASearchExceptionTest.class, //
- MissingAnnotationTest.class, //
- MissingRequiredAnnotationsTest.class, //
- MiRNAParserTest.class, //
- ModelAnnotatorTest.class, //
- PubmedParserTest.class, //
- TaxonomyBackendTest.class,//
+@SuiteClasses({ AllAnnotatorTests.class,
+ AllGenomeTests.class,
+ ChEMBLParserTest.class,
+ ChemicalParserTest.class,
+ ChemicalSearchExceptionTest.class,
+ DrugAnnotationTest.class,
+ DrugbankHTMLParserTest.class,
+ ExternalServiceStatusTest.class,
+ ExternalServiceStatusTypeTest.class,
+ ImproperAnnotationsTest.class,
+ MeSHParserTest.class,
+ MiriamConnectorTest.class,
+ MiRNASearchExceptionTest.class,
+ MissingAnnotationTest.class,
+ MissingRequiredAnnotationsTest.class,
+ MiRNAParserTest.class,
+ ModelAnnotatorTest.class,
+ PubmedParserTest.class,
+ TaxonomyBackendTest.class,
})
public class AllServicesTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index 5db640c506..ad8a637314 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -5,25 +5,25 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AnnotatorExceptionTest.class, //
- AnnotatorParamDefTest.class, //
- BrendaAnnotatorTest.class, //
- BiocompendiumAnnotatorTest.class, //
- CazyAnnotatorTest.class, //
- ChebiAnnotatorTest.class, //
- ElementAnnotatorTest.class, //
- EnsemblAnnotatorTest.class, //
- EntrezAnnotatorTest.class, //
- GoAnnotatorTest.class, //
- HgncAnnotatorTest.class, //
- KeggAnnotatorTest.class, //
- MultipleAnnotatorsTest.class, //
- PdbAnnotatorTest.class, //
- ReconAnnotatorTest.class, //
- StitchAnnotatorTest.class, //
- StringAnnotatorTest.class, //
- TairAnnotatorTest.class, //
- UniprotAnnotatorTest.class, //
+@SuiteClasses({ AnnotatorExceptionTest.class,
+ AnnotatorParamDefTest.class,
+ BrendaAnnotatorTest.class,
+ BiocompendiumAnnotatorTest.class,
+ CazyAnnotatorTest.class,
+ ChebiAnnotatorTest.class,
+ ElementAnnotatorTest.class,
+ EnsemblAnnotatorTest.class,
+ EntrezAnnotatorTest.class,
+ GoAnnotatorTest.class,
+ HgncAnnotatorTest.class,
+ KeggAnnotatorTest.class,
+ MultipleAnnotatorsTest.class,
+ PdbAnnotatorTest.class,
+ ReconAnnotatorTest.class,
+ StitchAnnotatorTest.class,
+ StringAnnotatorTest.class,
+ TairAnnotatorTest.class,
+ UniprotAnnotatorTest.class,
})
public class AllAnnotatorTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
index 1ea18ba92e..1f5091d9ce 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
@@ -102,11 +102,11 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
// */
// pdbAnnotator.annotateElement(protein);
// int cntAnnotations = protein.getMiriamData().size();
-//
+
// assertTrue(cntAnnotations > 0);
-//
+
// boolean pdb = false;
-//
+
// for (MiriamData md : protein.getMiriamData()) {
// if (md.getDataType().equals(MiriamType.PDB)) {
// pdb = true;
@@ -114,7 +114,7 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
// }
// }
// assertTrue("No PDB annotation extracted from pdb annotator", pdb);
-//
+
// } catch (Exception e) {
// e.printStackTrace();
// throw e;
@@ -161,9 +161,9 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
// pdbAnnotator.annotateElement(protein);
//
// assertTrue("UniProt annotation in PDB annotator failed", protein.getMiriamData().size() > 0);
-//
+
// boolean pdb = false;
-//
+
// for (MiriamData md : protein.getMiriamData()) {
// if (md.getDataType().equals(MiriamType.PDB)) {
// pdb = true;
@@ -171,7 +171,7 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
// }
// }
// assertTrue("No PDB annotation extracted from PDB annotator", pdb);
-//
+
// } catch (Exception e) {
// e.printStackTrace();
// throw e;
diff --git a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
index 78ed3bbf2c..3a1b970a00 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
@@ -11,7 +11,7 @@ public enum HttpConnectionMethodType {
/**
* GET method.
*/
- GET, //
+ GET,
/**
* POST method.
diff --git a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
index e63d118d52..3f4ca11a4e 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
@@ -14,12 +14,12 @@ public enum MimeType {
/**
* SBML type of file.
*/
- SBML("application/sbml+xml"), //
+ SBML("application/sbml+xml"),
/**
* Standard text file.
*/
- TEXT("text/plain"), //
+ TEXT("text/plain"),
/**
* Standard XML file.
@@ -45,12 +45,12 @@ public enum MimeType {
* PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC 3778,
* The application/pdf Media Type</a>).
*/
- PDF("application/pdf"), //
+ PDF("application/pdf"),
/**
* CSS files.
*/
- CSS("text/css"), //
+ CSS("text/css"),
/**
* JavaScript files.
@@ -60,7 +60,7 @@ public enum MimeType {
/**
* Zip files.
*/
- ZIP("application/zip"); //
+ ZIP("application/zip");
/**
* String representation of the MIME content.
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
index 18d218fd7a..2af7761b62 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -55,8 +55,8 @@ public class ColorParser {
"Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
} else {
return new Color(
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE),
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE),
Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
}
}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
index 8c28d00230..ddbabc8f96 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -9,18 +9,18 @@ import lcsb.mapviewer.common.exception.AllExceptionTests;
import lcsb.mapviewer.common.geometry.AllGeometryTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllComparatorTests.class, //
- AllExceptionTests.class, //
- AllGeometryTests.class, //
- ConfigurationTest.class, //
- EventStorageLoggerAppenderTest.class, //
- HttpConnectionMethodTypeTest.class, //
- MimeTypeTest.class, //
- ObjectUtilsTest.class, //
- PairTest.class, //
- SystemClipboardTest.class, //
- TextFileUtilsTest.class, //
- XmlParserTest.class, //
+@SuiteClasses({ AllComparatorTests.class,
+ AllExceptionTests.class,
+ AllGeometryTests.class,
+ ConfigurationTest.class,
+ EventStorageLoggerAppenderTest.class,
+ HttpConnectionMethodTypeTest.class,
+ MimeTypeTest.class,
+ ObjectUtilsTest.class,
+ PairTest.class,
+ SystemClipboardTest.class,
+ TextFileUtilsTest.class,
+ XmlParserTest.class,
})
public class AllCommonTests {
diff --git a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
index f7e8851f8c..635e492efe 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
@@ -29,10 +29,10 @@ public class TextFileUtilsTest {
@Test
public void testGetHeaderParametersFromFile() throws Exception {
try {
- String fileContent = "#header\n" + //
- "#param1=value1\n" + //
- "#\n" + //
- "no header\n" + //
+ String fileContent = "#header\n" +
+ "#param1=value1\n" +
+ "#\n" +
+ "no header\n" +
"#param2=value\n";
Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
index 3922a2b20b..16d18b9814 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
@@ -5,16 +5,16 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BooleanComparatorTest.class, //
- ColorComparatorTest.class, //
- DoubleComparatorTest.class, //
- EnumComparatorTest.class, //
- IntegerComparatorTest.class, //
- PointComparatorTest.class, //
- StringComparatorTest.class, //
- StringListComparatorTest.class, //
- StringSetComparatorTest.class, //
- SetComparatorTest.class,//
+@SuiteClasses({ BooleanComparatorTest.class,
+ ColorComparatorTest.class,
+ DoubleComparatorTest.class,
+ EnumComparatorTest.class,
+ IntegerComparatorTest.class,
+ PointComparatorTest.class,
+ StringComparatorTest.class,
+ StringListComparatorTest.class,
+ StringSetComparatorTest.class,
+ SetComparatorTest.class,
})
public class AllComparatorTests {
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
index 2ea3ba8a69..acf62ccd69 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
@@ -5,12 +5,12 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ColorParserTest.class, //
- CompositeStrokeTest.class, //
- EllipseTransformationTest.class, //
- LineTransformationTest.class, //
- PointTransformationTest.class, //
- TextAlignmentTest.class,//
+@SuiteClasses({ ColorParserTest.class,
+ CompositeStrokeTest.class,
+ EllipseTransformationTest.class,
+ LineTransformationTest.class,
+ PointTransformationTest.class,
+ TextAlignmentTest.class,
})
public class AllGeometryTests {
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index d812241e9e..0c6a655a54 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -76,10 +76,10 @@ public class Statistics {
*/
public static void main(String[] args) {
try {
- String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml", //
+ String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml",
+ "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml",
+ "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml",
+ "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml",
};
long startTime = System.nanoTime();
@@ -131,7 +131,7 @@ public class Statistics {
printStatistics(models);
// printAnnotationInformation(model);
- //
+
// PrintWriter writer = new PrintWriter("tmp.html", "UTF-8");
// writer.println(createPubmedExportString(model));
// writer.close();
@@ -266,7 +266,7 @@ public class Statistics {
// Collection<? extends ProblematicAnnotation> pubmes =
// modelAnnotator.findPubmedAnnotatedElements(model);
// for (ProblematicAnnotation improperAnnotation : pubmes) {
- //
+
// if (improperAnnotation.getObject() != null) {
// AnnotatedObject element = improperAnnotation.getObject();
// String ids = "";
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index 0476cd9706..dbccf07f6b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -18,107 +18,107 @@ public enum NoteField {
/**
* List of {@link MiriamType#HGNC} identifiers.
*/
- HGNC("HGNC_ID", BioEntity.class, MiriamType.HGNC), //
+ HGNC("HGNC_ID", BioEntity.class, MiriamType.HGNC),
/**
* List of {@link MiriamType#REFSEQ} identifiers.
*/
- REFSEQ("RefSeq_ID", BioEntity.class, MiriamType.REFSEQ), //
+ REFSEQ("RefSeq_ID", BioEntity.class, MiriamType.REFSEQ),
/**
* List of {@link MiriamType#ENTREZ} identifiers.
*/
- ENTREZ("EntrezGene_ID", BioEntity.class, MiriamType.ENTREZ), //
+ ENTREZ("EntrezGene_ID", BioEntity.class, MiriamType.ENTREZ),
/**
* List of {@link MiriamType#REACTOME} identifiers.
*/
- REACTOME("Reactome_ID", BioEntity.class, MiriamType.REACTOME), //
+ REACTOME("Reactome_ID", BioEntity.class, MiriamType.REACTOME),
/**
* List of {@link MiriamType#PUBMED} identifiers.
*/
- PUBMED("Pubmed_ID", BioEntity.class, MiriamType.PUBMED), //
+ PUBMED("Pubmed_ID", BioEntity.class, MiriamType.PUBMED),
/**
* List of {@link MiriamType#KEGG_GENES} identifiers.
*/
- KEGG_GENES("KEGG_ID", BioEntity.class, MiriamType.KEGG_GENES), //
+ KEGG_GENES("KEGG_ID", BioEntity.class, MiriamType.KEGG_GENES),
/**
* List of {@link MiriamType#PANTHER} identifiers.
*/
- PANTHER("PANTHER", BioEntity.class, MiriamType.PANTHER), //
+ PANTHER("PANTHER", BioEntity.class, MiriamType.PANTHER),
/**
* {@link Element#symbol}.
*/
- SYMBOL("Symbol", CellDesignerElement.class, null), //
+ SYMBOL("Symbol", CellDesignerElement.class, null),
/**
* {@link Element#fullName}.
*/
- NAME("Name", CellDesignerElement.class, null), //
+ NAME("Name", CellDesignerElement.class, null),
/**
* {@link Element#notes} or {@link Reaction#notes} .
*/
- DESCRIPTION("Description", BioEntity.class, null), //
+ DESCRIPTION("Description", BioEntity.class, null),
/**
* {@link Element#formerSymbols}.
*/
- PREVIOUS_SYMBOLS("Previous Symbols", CellDesignerElement.class, null), //
+ PREVIOUS_SYMBOLS("Previous Symbols", CellDesignerElement.class, null),
/**
* {@link Element#synonyms} or {@link Reaction#synonyms}.
*/
- SYNONYMS("Synonyms", BioEntity.class, null), //
+ SYNONYMS("Synonyms", BioEntity.class, null),
/**
* {@link Element#abbreviation} or {@link Reaction#abbreviation}.
*/
- ABBREVIATION("Abbreviation", BioEntity.class, null), //
+ ABBREVIATION("Abbreviation", BioEntity.class, null),
/**
* {@link Reaction#formula}.
*/
- FORMULA("Formula", Reaction.class, null), //
+ FORMULA("Formula", Reaction.class, null),
/**
* {@link Reaction#mechanicalConfidenceScore}.
*/
- MECHANICAL_CONFIDENCE_SCORE("MechanicalConfidenceScore", Reaction.class, null), //
+ MECHANICAL_CONFIDENCE_SCORE("MechanicalConfidenceScore", Reaction.class, null),
/**
* {@link Reaction#lowerBound}.
*/
- LOWER_BOUND("LowerBound", Reaction.class, null), //
+ LOWER_BOUND("LowerBound", Reaction.class, null),
/**
* {@link Reaction#upperBound}.
*/
- UPPER_BOUND("UpperBound", Reaction.class, null), //
+ UPPER_BOUND("UpperBound", Reaction.class, null),
/**
* {@link Reaction#subsystem}.
*/
- SUBSYSTEM("Subsystem", Reaction.class, null), //
+ SUBSYSTEM("Subsystem", Reaction.class, null),
/**
* {@link Reaction#geneProteinReaction}.
*/
- GENE_PROTEIN_REACTION("GeneProteinReaction", Reaction.class, null), //
+ GENE_PROTEIN_REACTION("GeneProteinReaction", Reaction.class, null),
/**
* {@link Element#formula}.
*/
- CHARGED_FORMULA("ChargedFormula", CellDesignerElement.class, null), //
+ CHARGED_FORMULA("ChargedFormula", CellDesignerElement.class, null),
/**
* {@link Species#charge}.
*/
- CHARGE("Charge", CellDesignerSpecies.class, null), //
+ CHARGE("Charge", CellDesignerSpecies.class, null),
/**
* {@link Element#getSemanticZoomLevelVisibility()}.
@@ -129,7 +129,7 @@ public enum NoteField {
* {@link Element#getSemanticZoomLevelVisibility()}.
*/
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY("TransparencyZoomLevelVisibility", Element.class, null),
- ; //
+ ;
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
index 308bef366a..cbe4ebb4e5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
@@ -365,7 +365,7 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
double minDist = Math.min(Math.min(distanceLeft, distanceRight), Math.min(distanceTop, distanceBottom));
- if (distanceRight == minDist && //
+ if (distanceRight == minDist &&
pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < epsilon) {
double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
result = (ratio - 0.5) * (PI / 2);
@@ -378,7 +378,7 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
} else if (distanceBottom == minDist) {
double ratio = (pointOnBorder.getX() - element.getX()) / element.getWidth();
result = ratio * (PI / 2) + LEFT_RESIDUE_MAX_ANGLE;
- } else if (distanceRight == minDist && //
+ } else if (distanceRight == minDist &&
pointOnBorder.getY() - element.getY() - element.getHeight() < epsilon) {
double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
result = ratio * (PI / 2) + BOTTOM_RESIDUE_MAX_ANGLE;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
index 6e84905d3d..00ac746770 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
@@ -13,82 +13,82 @@ public enum CellDesignerAnchor {
/**
* East direction.
*/
- E("E", 0.0), //
+ E("E", 0.0),
/**
* East southeast direction.
*/
- ESE("ESE", 22.5), //
+ ESE("ESE", 22.5),
/**
* Southeast direction.
*/
- SE("SE", 45.0), //
+ SE("SE", 45.0),
/**
* South southeast direction.
*/
- SSE("SSE", 67.5), //
+ SSE("SSE", 67.5),
/**
* South direction.
*/
- S("S", 90.0), //
+ S("S", 90.0),
/**
* South southwest direction.
*/
- SSW("SSW", 112.5), //
+ SSW("SSW", 112.5),
/**
* Southwest direction.
*/
- SW("SW", 135.0), //
+ SW("SW", 135.0),
/**
* West southwest direction.
*/
- WSW("WSW", 157.5), //
+ WSW("WSW", 157.5),
/**
* West direction.
*/
- W("W", 180.0), //
+ W("W", 180.0),
/**
* West northwest direction.
*/
- WNW("WNW", 202.5), //
+ WNW("WNW", 202.5),
/**
* Northwest direction.
*/
- NW("NW", 225.0), //
+ NW("NW", 225.0),
/**
* North northwest direction.
*/
- NNW("NNW", 247.5), //
+ NNW("NNW", 247.5),
/**
* North direction.
*/
- N("N", 270.0), //
+ N("N", 270.0),
/**
* North northeast direction.
*/
- NNE("NNE", 292.5), //
+ NNE("NNE", 292.5),
/**
* Northeast direction.
*/
- NE("NE", 315.0), //
+ NE("NE", 315.0),
/**
* East northeast direction.
*/
- ENE("ENE", 337.5), //
+ ENE("ENE", 337.5),
/**
* Unknown direction.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
index 7c37fcba83..2cf69ef22b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
@@ -178,7 +178,7 @@ public enum ReactionLineData {
* {@link UnknownReducedPhysicalStimulationReaction} class.
*/
UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class,
- "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED, //
+ "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED,
ArrowType.BLANK),
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
index 20a0223130..c086811d0c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
@@ -37,52 +37,52 @@ public enum SpeciesMapping {
/**
* {@link Protein}.
*/
- PROTEIN(CellDesignerProtein.class, Protein.class, "PROTEIN"), //
+ PROTEIN(CellDesignerProtein.class, Protein.class, "PROTEIN"),
/**
* {@link Gene}.
*/
- GENE(CellDesignerGene.class, Gene.class, "GENE"), //
+ GENE(CellDesignerGene.class, Gene.class, "GENE"),
/**
* {@link ComplexSpecies}.
*/
- COMPLEX(CellDesignerComplexSpecies.class, Complex.class, "COMPLEX"), //
+ COMPLEX(CellDesignerComplexSpecies.class, Complex.class, "COMPLEX"),
/**
* {@link SimpleMolecule}.
*/
- SIMPLE_MOLECULE(CellDesignerSimpleMolecule.class, SimpleMolecule.class, "SIMPLE_MOLECULE"), //
+ SIMPLE_MOLECULE(CellDesignerSimpleMolecule.class, SimpleMolecule.class, "SIMPLE_MOLECULE"),
/**
* {@link Ion}.
*/
- ION(CellDesignerIon.class, Ion.class, "ION"), //
+ ION(CellDesignerIon.class, Ion.class, "ION"),
/**
* {@link Phenotype}.
*/
- PHENOTYPE(CellDesignerPhenotype.class, Phenotype.class, "PHENOTYPE"), //
+ PHENOTYPE(CellDesignerPhenotype.class, Phenotype.class, "PHENOTYPE"),
/**
* {@link Drug}.
*/
- DRUG(CellDesignerDrug.class, Drug.class, "DRUG"), //
+ DRUG(CellDesignerDrug.class, Drug.class, "DRUG"),
/**
* {@link Rna}.
*/
- RNA(CellDesignerRna.class, Rna.class, "RNA"), //
+ RNA(CellDesignerRna.class, Rna.class, "RNA"),
/**
* {@link AntisenseRna}.
*/
- ANTISENSE_RNA(CellDesignerAntisenseRna.class, AntisenseRna.class, "ANTISENSE_RNA"), //
+ ANTISENSE_RNA(CellDesignerAntisenseRna.class, AntisenseRna.class, "ANTISENSE_RNA"),
/**
* {@link Unknown}.
*/
- UNKNOWN(CellDesignerUnknown.class, Unknown.class, "UNKNOWN"), //
+ UNKNOWN(CellDesignerUnknown.class, Unknown.class, "UNKNOWN"),
/**
* {@link Degraded}.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
index ca6bad57fe..db5a5e258b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
@@ -3,14 +3,14 @@ package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
public enum ModificationType {
- BINDING_REGION(null), //
- CODING_REGION("CodingRegion"), //
- PROTEIN_BINDING_DOMAIN("proteinBindingDomain"), //
- RESIDUE(null), //
- REGULATORY_REGION("RegulatoryRegion"), //
- TRANSCRIPTION_SITE_RIGHT("transcriptionStartingSiteR"), //
- TRANSCRIPTION_SITE_LEFT("transcriptionStartingSiteL"), //
- MODIFICATION_SITE("Modification Site");//
+ BINDING_REGION(null),
+ CODING_REGION("CodingRegion"),
+ PROTEIN_BINDING_DOMAIN("proteinBindingDomain"),
+ RESIDUE(null),
+ REGULATORY_REGION("RegulatoryRegion"),
+ TRANSCRIPTION_SITE_RIGHT("transcriptionStartingSiteR"),
+ TRANSCRIPTION_SITE_LEFT("transcriptionStartingSiteL"),
+ MODIFICATION_SITE("Modification Site");
private String cellDesignerName;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
index f40328f788..58cbcc4494 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
@@ -17,26 +17,26 @@ import lcsb.mapviewer.converter.model.celldesigner.types.AllTypesTests;
import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
@RunWith(Suite.class)
-@SuiteClasses({ //
- AllAnnotationTests.class, //
- AllAliasTests.class, //
- AllCompartmentTests.class, //
- AllFunctionTests.class, //
- AllGeometryTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStructureTests.class, //
- AllTypesTests.class, //
- CellDesignerElementCollectionTest.class, //
- CellDesignerXmlParserTest.class, //
- ComplexParserTests.class, //
- InvalidGroupExceptionTest.class, //
- LayerXmlParserTest.class, //
- NestedComplexParsingTests.class, //
- ModificationTest.class, //
- ParameterXmlParserTest.class, //
- ReconDataInCellDesignerXmlParserTest.class, //
- UnitXmlParserTest.class,//
+@SuiteClasses({
+ AllAnnotationTests.class,
+ AllAliasTests.class,
+ AllCompartmentTests.class,
+ AllFunctionTests.class,
+ AllGeometryTests.class,
+ AllReactionTests.class,
+ AllSpeciesTests.class,
+ AllStructureTests.class,
+ AllTypesTests.class,
+ CellDesignerElementCollectionTest.class,
+ CellDesignerXmlParserTest.class,
+ ComplexParserTests.class,
+ InvalidGroupExceptionTest.class,
+ LayerXmlParserTest.class,
+ NestedComplexParsingTests.class,
+ ModificationTest.class,
+ ParameterXmlParserTest.class,
+ ReconDataInCellDesignerXmlParserTest.class,
+ UnitXmlParserTest.class,
})
public class AllCellDesignerTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
index 82cf2ae958..0e90824423 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
@@ -4,10 +4,10 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ AliasCollectionXmlParserTest.class,//
- ComplexAliasXmlParserTest.class,//
- CompartmentAliasXmlParserTest.class,//
- SpeciesAliasXmlParserTest.class, //
+@Suite.SuiteClasses({ AliasCollectionXmlParserTest.class,
+ ComplexAliasXmlParserTest.class,
+ CompartmentAliasXmlParserTest.class,
+ SpeciesAliasXmlParserTest.class,
})
public class AllAliasTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
index 38b590fa33..d28cfc3739 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
@@ -5,8 +5,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ NoteFieldTest.class, //
- RestAnnotationParserTest.class, //
+@SuiteClasses({ NoteFieldTest.class,
+ RestAnnotationParserTest.class,
})
public class AllAnnotationTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
index 800262bfab..b8476cc09e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
@@ -5,9 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CompartmentCollectionXmlParserTest.class,//
- CompartmentParserTests.class,//
- CompartmentXmlParserTest.class,//
+@SuiteClasses({ CompartmentCollectionXmlParserTest.class,
+ CompartmentParserTests.class,
+ CompartmentXmlParserTest.class,
})
public class AllCompartmentTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
index 514045015c..596be399a0 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
@@ -7,19 +7,19 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AbstractCellDesignerAliasConverterTest.class, //
- AllHelperTests.class, //
- AntisenseRnaCellDesignerAliasConverterTest.class, //
- CellDesignerAliasConverterTest.class, //
- DegradedCellDesignerAliasConverterTest.class, //
- GeneCellDesignerAliasConverterTest.class, //
- IonCellDesignerAliasConverterTest.class, //
- ProteinConverterTest.class, //
- ProteinCellDesignerAliasConverterTest.class, //
- ReactionCellDesignerConverterTest.class, //
- RnaCellDesignerAliasConverterTest.class, //
- SimpleMoleculeCellDesignerAliasConverterTest.class, //
- UnknownCellDesignerAliasConverterTest.class, //
+@SuiteClasses({ AbstractCellDesignerAliasConverterTest.class,
+ AllHelperTests.class,
+ AntisenseRnaCellDesignerAliasConverterTest.class,
+ CellDesignerAliasConverterTest.class,
+ DegradedCellDesignerAliasConverterTest.class,
+ GeneCellDesignerAliasConverterTest.class,
+ IonCellDesignerAliasConverterTest.class,
+ ProteinConverterTest.class,
+ ProteinCellDesignerAliasConverterTest.class,
+ ReactionCellDesignerConverterTest.class,
+ RnaCellDesignerAliasConverterTest.class,
+ SimpleMoleculeCellDesignerAliasConverterTest.class,
+ UnknownCellDesignerAliasConverterTest.class,
})
public class AllGeometryTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
index f4b30b1fa2..364015e077 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
@@ -5,13 +5,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CellDesignerAnchorTest.class, //
- CellDesignerEllipseTransformationTest.class, //
- CellDesignerLineTransformationTest.class, //
- CellDesignerPointTransformationTest.class, //
- CellDesignerPolygonTransformationTest.class, //
- CellDesignerRectangleTransformationTest.class, //
- PolylineDataFactoryTest.class,//
+@SuiteClasses({ CellDesignerAnchorTest.class,
+ CellDesignerEllipseTransformationTest.class,
+ CellDesignerLineTransformationTest.class,
+ CellDesignerPointTransformationTest.class,
+ CellDesignerPolygonTransformationTest.class,
+ CellDesignerRectangleTransformationTest.class,
+ PolylineDataFactoryTest.class,
})
public class AllHelperTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
index 3b095692f5..79c6f49476 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
@@ -5,15 +5,15 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ KineticsXmlParserTest.class, //
- ModificationReactionTest.class, //
- ReactionCollectionXmlParserTest.class, //
- ReactionFromXmlTest.class, //
- ReactionLineDataTest.class, //
- ReactionParserExceptionTest.class, //
- ReactionParserTests.class, //
- ReactionToXmlTest.class, //
- UnknownModifierClassExceptionTest.class, //
+@SuiteClasses({ KineticsXmlParserTest.class,
+ ModificationReactionTest.class,
+ ReactionCollectionXmlParserTest.class,
+ ReactionFromXmlTest.class,
+ ReactionLineDataTest.class,
+ ReactionParserExceptionTest.class,
+ ReactionParserTests.class,
+ ReactionToXmlTest.class,
+ UnknownModifierClassExceptionTest.class,
})
public class AllReactionTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
index f6b46cd415..e55c6c43f1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
@@ -4,17 +4,17 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class, //
- ComplexParserTest.class, //
- GeneXmlParserTest.class, //
- InternalModelSpeciesDataTest.class, //
- ProteinMappingTest.class, //
- ProteinXmlParserTest.class, //
- RnaXmlParserTest.class, //
- SpeciesCollectionTest.class, //
- SpeciesCollectionXmlParserTest.class, //
- SpeciesMappingTest.class, //
- SpeciesSbmlParserTest.class,//
+@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class,
+ ComplexParserTest.class,
+ GeneXmlParserTest.class,
+ InternalModelSpeciesDataTest.class,
+ ProteinMappingTest.class,
+ ProteinXmlParserTest.class,
+ RnaXmlParserTest.class,
+ SpeciesCollectionTest.class,
+ SpeciesCollectionXmlParserTest.class,
+ SpeciesMappingTest.class,
+ SpeciesSbmlParserTest.class,
})
public class AllSpeciesTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
index 2cf4d96ad2..e9194757a1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
@@ -7,31 +7,31 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllFieldsTests.class, //
- AntisenseRnaTest.class, //
- CellDesignerChemicalTest.class, //
- CompartmentTest.class, //
- ComplexSpeciesTest.class, //
- ConnectSchemeTest.class, //
- DegradedTest.class, //
- DrugTest.class, //
- ElementTest.class, //
- GenericProteinTest.class, //
- GeneTest.class, //
- IonChannelProteinTest.class, //
- IonTest.class, //
- LinePropertiesTest.class, //
- ModificationResidueTest.class, //
- PhenotypeTest.class, //
- ProteinTest.class, //
- ReceptorProteinTest.class, //
- RnaTest.class, //
- SimpleMoleculeTest.class, //
- SpeciesStateTest.class, //
- SpeciesTest.class, //
- TruncatedProteinTest.class, //
- UnknownTest.class, //
- ViewTest.class, //
+@SuiteClasses({ AllFieldsTests.class,
+ AntisenseRnaTest.class,
+ CellDesignerChemicalTest.class,
+ CompartmentTest.class,
+ ComplexSpeciesTest.class,
+ ConnectSchemeTest.class,
+ DegradedTest.class,
+ DrugTest.class,
+ ElementTest.class,
+ GenericProteinTest.class,
+ GeneTest.class,
+ IonChannelProteinTest.class,
+ IonTest.class,
+ LinePropertiesTest.class,
+ ModificationResidueTest.class,
+ PhenotypeTest.class,
+ ProteinTest.class,
+ ReceptorProteinTest.class,
+ RnaTest.class,
+ SimpleMoleculeTest.class,
+ SpeciesStateTest.class,
+ SpeciesTest.class,
+ TruncatedProteinTest.class,
+ UnknownTest.class,
+ ViewTest.class,
})
public class AllStructureTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
index bc93824a6c..5d9a178c9c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CellDesignerModificationResidueTest.class, //
+@SuiteClasses({ CellDesignerModificationResidueTest.class,
})
public class AllFieldsTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
index dd93d8d0e7..d76440b14f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
@@ -5,10 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ModifierTypeTest.class, //
- ModifierTypeUtilsTest.class, //
- OperatorTypeTest.class, //
- OperatorTypeUtilsTest.class, //
+@SuiteClasses({ ModifierTypeTest.class,
+ ModifierTypeUtilsTest.class,
+ OperatorTypeTest.class,
+ OperatorTypeUtilsTest.class,
})
public class AllTypesTests {
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
index dd9c78c762..1c40a8d7eb 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
@@ -5,12 +5,12 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CellDesigner2SbgnmlConversionTest.class, //
- CellDesignerToSbgnTest.class, //
- DbSerializationTest.class, //
- SbgnmlXmlExporterTest.class, //
- SbgnmlXmlParserTest.class, //
- SbgnmlXmlParserTest2.class, //
+@SuiteClasses({ CellDesigner2SbgnmlConversionTest.class,
+ CellDesignerToSbgnTest.class,
+ DbSerializationTest.class,
+ SbgnmlXmlExporterTest.class,
+ SbgnmlXmlParserTest.class,
+ SbgnmlXmlParserTest2.class,
})
public class AllSbgnmlTests {
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index e201a30589..ef96828ab1 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -20,9 +20,9 @@ import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.ModelDao;
@Transactional(value = "txManager")
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+@ContextConfiguration(locations = { "/applicationContext-persist.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml",
})
@RunWith(SpringJUnit4ClassRunner.class)
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index d3ae21c24b..8ac01b5315 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -471,14 +471,14 @@ public abstract class AbstractImageGenerator {
@Override
public String toString() {
- String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," + //
- "scale:" + scale + "," + //
- "x:" + x + "," + //
- "y:" + y + "," + //
- "width:" + width + "," + //
- "height:" + height + "," + //
- "background:" + background + "," + //
- "level:" + level + "," + //
+ String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," +
+ "scale:" + scale + "," +
+ "x:" + x + "," +
+ "y:" + y + "," +
+ "width:" + width + "," +
+ "height:" + height + "," +
+ "background:" + background + "," +
+ "level:" + level + "," +
"nested:" + nested + ",";
return result;
}
@@ -603,8 +603,8 @@ public abstract class AbstractImageGenerator {
}
public Params colorExtractor(ColorExtractor colorExtractor) {
- return minColor(colorExtractor.getMinColor()).//
- maxColor(colorExtractor.getMaxColor()).//
+ return minColor(colorExtractor.getMinColor()).
+ maxColor(colorExtractor.getMaxColor()).
simpleColor(colorExtractor.getSimpleColor());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
index 9e07193401..5e09864ab1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
@@ -107,10 +107,10 @@ public class ConverterParams {
@Override
public String toString() {
- String result = "[" + this.getClass().getSimpleName() + "] " + //
- "level:" + level + "," + //
- "scale:" + scale + "," + //
- "nested:" + nested + "," + //
+ String result = "[" + this.getClass().getSimpleName() + "] " +
+ "level:" + level + "," +
+ "scale:" + scale + "," +
+ "nested:" + nested + "," +
"sbgnFormat:" + sbgnFormat;
return result;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
index 7436591a33..64d7b409b1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
@@ -47,9 +47,9 @@ public class ImageGenerators {
try {
availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
Model model = new ModelFullIndexed(null);
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().//
- model(model).//
- width(1).//
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().
+ model(model).
+ width(1).
minColor(Color.WHITE).maxColor(Color.WHITE).height(1);
generatorInstances = new ArrayList<>();
generatorInstances.add(new PngImageGenerator(params));
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
index 97f403563d..979a7987ea 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
@@ -446,7 +446,7 @@ public class ArrowTransformation {
} else if (arrowType.getArrowType() == ArrowType.CIRCLE) {
drawCircleEnd(line, graphics, arrowType.getLen());
} else if (arrowType.getArrowType() == ArrowType.NONE) {
- //
+
return;
} else if (arrowType.getArrowType() == ArrowType.BLANK) {
drawBlankEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
index b6eeeff919..b0a0d88529 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
@@ -9,16 +9,16 @@ import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
@RunWith(Suite.class)
-@SuiteClasses({ //
- AbstractImageGeneratorTest.class, //
- AllBioEntityTests.class, //
- AllGeometryTests.class, //
- AllPlaceFinderTest.class, //
- ConverterTest.class, //
- ImageGeneratorsTest.class, //
- MapGeneratorTest.class, //
- NormalImageGeneratorTest.class, //
- PdfImageGeneratorTest.class,//
+@SuiteClasses({
+ AbstractImageGeneratorTest.class,
+ AllBioEntityTests.class,
+ AllGeometryTests.class,
+ AllPlaceFinderTest.class,
+ ConverterTest.class,
+ ImageGeneratorsTest.class,
+ MapGeneratorTest.class,
+ NormalImageGeneratorTest.class,
+ PdfImageGeneratorTest.class,
})
public class AllGraphicsTests {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index c4f3038875..aafdac3836 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -78,8 +78,8 @@ public class ConverterTest {
private Color getColor(double d, Color startColor, Color endColor) {
- return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())), //
- (int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())), //
+ return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())),
+ (int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())),
(int) (startColor.getBlue() + d * (endColor.getBlue() - startColor.getBlue())));
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
index 93148f166b..ba27b1c2f4 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
@@ -9,11 +9,11 @@ import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AllSpeciesCon
import lcsb.mapviewer.converter.graphics.bioEntity.reaction.AllReactionTests;
@RunWith(Suite.class)
-@SuiteClasses({ //
- AllSpeciesConverterTests.class, //
- AllReactionTests.class, //
- BioEntityConverterImplTest.class, //
- PathwayCompartmentConverterTest.class,//
+@SuiteClasses({
+ AllSpeciesConverterTests.class,
+ AllReactionTests.class,
+ BioEntityConverterImplTest.class,
+ PathwayCompartmentConverterTest.class,
})
public class AllBioEntityTests {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
index eeda18cf8c..3cd2dfc629 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ComplexConverterTest.class, //
+@SuiteClasses({ ComplexConverterTest.class,
SpeciesConverterTest.class })
public class AllSpeciesConverterTests {
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 8828a574ff..896796030f 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
@@ -85,7 +85,7 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
// FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
// FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
+
// Desktop.getDesktop().open(new File("tmp.png"));
// Desktop.getDesktop().open(new File("tmp2.png"));
@@ -132,7 +132,7 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
// FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
// FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
+
// Desktop.getDesktop().open(new File("tmp.png"));
// Desktop.getDesktop().open(new File("tmp2.png"));
@@ -177,7 +177,7 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
// FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
// FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
+
// Desktop.getDesktop().open(new File("tmp.png"));
// Desktop.getDesktop().open(new File("tmp2.png"));
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
index 31286aff38..628b799f8c 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
@@ -53,7 +53,7 @@ public class ArrowTransformationTest {
// FileOutputStream fos = new FileOutputStream(new File(type.name() + ".png"));
// ImageIO.write(bi, "PNG", fos);
// fos.close();
- //
+
// Desktop.getDesktop().open(new File(type.name() + ".png"));
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
index 9d77bdff06..634f24d841 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
@@ -69,11 +69,11 @@ public class FontFinderTest {
FontFinder.drawText((int) size, Font.SANS_SERIF, graphics, border, text);
// graphics.drawString(text, coordX, coordY + height);
- //
+
// FileOutputStream fos = new FileOutputStream(new File("tmp.png"));
// ImageIO.write(bi, "PNG", fos);
// fos.close();
- //
+
// Desktop.getDesktop().open(new File("tmp.png"));
//different os compute it differnetly ...
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
index 8d89fc76ef..a11b9e26e5 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
@@ -15,13 +15,13 @@ import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
import lcsb.mapviewer.model.map.reaction.Modifier;
public enum SBOTermModifierType {
- CATALYSIS(Catalysis.class, new String[] { "SBO:0000013" }), //
- INHIBITION(Inhibition.class, new String[] { "SBO:0000537" }), //
- MODULATION(Modulation.class, new String[] { "SBO:0000594" }), //
- PHYSICAL_STIMULATION(PhysicalStimulation.class, new String[] { "SBO:0000459" }), //
- TRIGGER(Trigger.class, new String[] { "SBO:0000461" }), //
- UNKNOWN_CATALYSIS(UnknownCatalysis.class, new String[] { "SBO:0000462" }), //
- UNKNOWN_INHIBITION(UnknownInhibition.class, new String[] { "SBO:0000536" }), //
+ CATALYSIS(Catalysis.class, new String[] { "SBO:0000013" }),
+ INHIBITION(Inhibition.class, new String[] { "SBO:0000537" }),
+ MODULATION(Modulation.class, new String[] { "SBO:0000594" }),
+ PHYSICAL_STIMULATION(PhysicalStimulation.class, new String[] { "SBO:0000459" }),
+ TRIGGER(Trigger.class, new String[] { "SBO:0000461" }),
+ UNKNOWN_CATALYSIS(UnknownCatalysis.class, new String[] { "SBO:0000462" }),
+ UNKNOWN_INHIBITION(UnknownInhibition.class, new String[] { "SBO:0000536" }),
;
private static Logger logger = Logger.getLogger(SBOTermModifierType.class);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
index db9adef5f5..1461e078d0 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
@@ -27,25 +27,25 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
public enum SBOTermReactionType {
- DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
- HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
- KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
- NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
- POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
- REDUCED_MODULATION(ReducedModulationReaction.class, new String[] { "SBO:0000632" }), //
- REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000411" }), //
- REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000461" }), //
- STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }), //
- TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }), //
- TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }), //
- TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }), //
- TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }), //
- UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }), //
- UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000172" }), //
- UNKNOWN_REDUCED_MODULATION(UnknownReducedModulationReaction.class, new String[] { "SBO:0000631" }), //
- UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000170" }), //
- UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000533" }), //
- UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
+ DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }),
+ HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }),
+ KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }),
+ NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }),
+ POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }),
+ REDUCED_MODULATION(ReducedModulationReaction.class, new String[] { "SBO:0000632" }),
+ REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000411" }),
+ REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000461" }),
+ STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }),
+ TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }),
+ TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }),
+ TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }),
+ TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }),
+ UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }),
+ UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000172" }),
+ UNKNOWN_REDUCED_MODULATION(UnknownReducedModulationReaction.class, new String[] { "SBO:0000631" }),
+ UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000170" }),
+ UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000533" }),
+ UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }),
;
private static Logger logger = Logger.getLogger(SBOTermReactionType.class);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
index 7dd12ee398..60d94fd7ff 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
@@ -22,23 +22,23 @@ import lcsb.mapviewer.model.map.species.TruncatedProtein;
import lcsb.mapviewer.model.map.species.Unknown;
public enum ElementColorEnum {
- ANTISENSE_RNA(AntisenseRna.class, "#ff6666"), //
- COMPLEX(Complex.class, "#f7f7f7"), //
- DEGRADED(Degraded.class, "#ffcccc"), //
- DRUG(Drug.class, "#ff00ff"), //
- ELEMENT(Element.class, "#000000"), //
- GENE(Gene.class, "#ffff66"), //
- GENERIC_PROTEIN(GenericProtein.class, "ccffcc"), //
- TRUNCATED_PROTEIN(TruncatedProtein.class, "#ffcccc"), //
- ION(Ion.class, "#9999ff"), //
- ION_CHANNEL(IonChannelProtein.class, "#ccffff"), //
- OVAL_COMPARTMENT(OvalCompartment.class, "#cccc00"), //
- PHENOTYPE(Phenotype.class, "#cc99ff"), //
- RECEPTOR(ReceptorProtein.class, "#ffffcc"), //
- RNA(Rna.class, "#66ff66"), //
- SIMPLE_MOLECULE(SimpleMolecule.class, "#ccff66"), //
- SQUARE_COMPARTMENT(SquareCompartment.class, "#cccc00"), //
- UNKNOWN(Unknown.class, "#cccccc"), //
+ ANTISENSE_RNA(AntisenseRna.class, "#ff6666"),
+ COMPLEX(Complex.class, "#f7f7f7"),
+ DEGRADED(Degraded.class, "#ffcccc"),
+ DRUG(Drug.class, "#ff00ff"),
+ ELEMENT(Element.class, "#000000"),
+ GENE(Gene.class, "#ffff66"),
+ GENERIC_PROTEIN(GenericProtein.class, "ccffcc"),
+ TRUNCATED_PROTEIN(TruncatedProtein.class, "#ffcccc"),
+ ION(Ion.class, "#9999ff"),
+ ION_CHANNEL(IonChannelProtein.class, "#ccffff"),
+ OVAL_COMPARTMENT(OvalCompartment.class, "#cccc00"),
+ PHENOTYPE(Phenotype.class, "#cc99ff"),
+ RECEPTOR(ReceptorProtein.class, "#ffffcc"),
+ RNA(Rna.class, "#66ff66"),
+ SIMPLE_MOLECULE(SimpleMolecule.class, "#ccff66"),
+ SQUARE_COMPARTMENT(SquareCompartment.class, "#cccc00"),
+ UNKNOWN(Unknown.class, "#cccccc"),
;
private Class<? extends Element> clazz;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
index b73d4fa9e9..a425255a1a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java
@@ -22,20 +22,20 @@ import lcsb.mapviewer.model.map.species.TruncatedProtein;
import lcsb.mapviewer.model.map.species.Unknown;
public enum SBOTermSpeciesType {
- ANTISENSE_RNA(AntisenseRna.class, new String[] { "SBO:0000334" }), //
- COMPLEX(Complex.class, new String[] { "SBO:0000297" }), //
- DEGRADED(Degraded.class, new String[] { "SBO:0000291" }), //
- DRUG(Drug.class, new String[] { "SBO:0000298" }), //
- GENE(Gene.class, new String[] { "SBO:0000243" }), //
- GENERIC_PROTEIN(GenericProtein.class, new String[] { "SBO:0000252" }), //
- TRUNCATED_PROTEIN(TruncatedProtein.class, new String[] {}, new String[] { "SBO:0000252" }), //
- ION(Ion.class, new String[] { "SBO:0000327" }), //
- ION_CHANNEL(IonChannelProtein.class, new String[] { "SBO:0000284" }), //
- PHENOTYPE(Phenotype.class, new String[] { "SBO:0000358" }), //
- RECEPTOR(ReceptorProtein.class, new String[] { "SBO:0000244" }), //
- RNA(Rna.class, new String[] { "SBO:0000278" }), //
- SIMPLE_MOLECULE(SimpleMolecule.class, new String[] { "SBO:0000247", "SBO:0000299" }), //
- UNKNOWN(Unknown.class, new String[] { "SBO:0000285" }), //
+ ANTISENSE_RNA(AntisenseRna.class, new String[] { "SBO:0000334" }),
+ COMPLEX(Complex.class, new String[] { "SBO:0000297" }),
+ DEGRADED(Degraded.class, new String[] { "SBO:0000291" }),
+ DRUG(Drug.class, new String[] { "SBO:0000298" }),
+ GENE(Gene.class, new String[] { "SBO:0000243" }),
+ GENERIC_PROTEIN(GenericProtein.class, new String[] { "SBO:0000252" }),
+ TRUNCATED_PROTEIN(TruncatedProtein.class, new String[] {}, new String[] { "SBO:0000252" }),
+ ION(Ion.class, new String[] { "SBO:0000327" }),
+ ION_CHANNEL(IonChannelProtein.class, new String[] { "SBO:0000284" }),
+ PHENOTYPE(Phenotype.class, new String[] { "SBO:0000358" }),
+ RECEPTOR(ReceptorProtein.class, new String[] { "SBO:0000244" }),
+ RNA(Rna.class, new String[] { "SBO:0000278" }),
+ SIMPLE_MOLECULE(SimpleMolecule.class, new String[] { "SBO:0000247", "SBO:0000299" }),
+ UNKNOWN(Unknown.class, new String[] { "SBO:0000285" }),
;
private static Logger logger = Logger.getLogger(SBOTermSpeciesType.class);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index 2e9a90faca..faddef001b 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -8,14 +8,14 @@ import lcsb.mapviewer.converter.model.sbml.reaction.AllSbmlReactionParserTests;
import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllSbmlReactionParserTests.class, //
- AllSbmlSpeciesTests.class, //
- GenericSbmlParserTest.class, //
- GenericSbmlToXmlParserTest.class, //
- SbmlBioEntityExporterTest.class, //
- SbmlExporterTest.class, //
- SbmlPareserForInvalidReactionTest.class, //
- SbmlParserTest.class, //
+@SuiteClasses({ AllSbmlReactionParserTests.class,
+ AllSbmlSpeciesTests.class,
+ GenericSbmlParserTest.class,
+ GenericSbmlToXmlParserTest.class,
+ SbmlBioEntityExporterTest.class,
+ SbmlExporterTest.class,
+ SbmlPareserForInvalidReactionTest.class,
+ SbmlParserTest.class,
})
public class AllSbmlConverterTests {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
index 50a0ba00c3..d6e54657fa 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
@@ -5,8 +5,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ SbmlReactionExporterTest.class, //
- SbmlReactionParserTest.class //
+@SuiteClasses({ SbmlReactionExporterTest.class,
+ SbmlReactionParserTest.class
})
public class AllSbmlReactionParserTests {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
index 845e755bc4..551c10dd3b 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
@@ -7,11 +7,11 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParserTest;
@RunWith(Suite.class)
-@SuiteClasses({ ComplexZipConverterParamsTest.class, //
- ComplexZipConverterTest.class, //
- OverviewParserTest.class, //
- ProjectFactoryTest.class, //
- XmlAnnotationParserTest.class,//
+@SuiteClasses({ ComplexZipConverterParamsTest.class,
+ ComplexZipConverterTest.class,
+ OverviewParserTest.class,
+ ProjectFactoryTest.class,
+ XmlAnnotationParserTest.class,
})
public class AllTests {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
index 48f89eac4c..bf5bf8d780 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
@@ -227,7 +227,7 @@ public class OverviewParserTest {
@Test
public void testParseInvalidCoordinates() throws Exception {
try {
- String invalidCoordinates = "test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3\n" + //
+ String invalidCoordinates = "test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3\n" +
"test.png 10,10 10,400 400,400 400,10 main.xml 10,10 4";
Set<Model> models = createValidTestMapModel();
@@ -251,8 +251,8 @@ public class OverviewParserTest {
@Test
public void testParseValidCoordinates() throws Exception {
try {
- String invalidCoordinates = "FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE\n" + //
- "test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3 MODEL\n" + //
+ String invalidCoordinates = "FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE\n" +
+ "test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3 MODEL\n" +
"test.png 200,200 200,400 400,400 400,200 main.xml 10,10 4 MODEL";
Set<Model> models = createValidTestMapModel();
diff --git a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
index 5d42c41079..432cd9ad99 100644
--- a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
@@ -131,10 +131,10 @@ CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
};
var title = null;
if (!comment.isRemoved()) {
- var commentLink = "index.xhtml?id=" + projectId + //
- "&x=" + comment.getCoordinates().x + //
- "&y=" + comment.getCoordinates().y + //
- "&zoom=12" + //
+ var commentLink = "index.xhtml?id=" + projectId +
+ "&x=" + comment.getCoordinates().x +
+ "&y=" + comment.getCoordinates().y +
+ "&zoom=12" +
"&comments=on";
title = "<a href='" + commentLink + "' target='" + projectId + "'>" + comment.getTitle() + "</a>";
} else {
@@ -158,12 +158,12 @@ CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
email = "N/A";
}
- return [comment.getId(), //
- xss(title), //
- xss(author), //
- xss(email), //
- xss(comment.getContent()), //
- remove, //
+ return [comment.getId(),
+ xss(title),
+ xss(author),
+ xss(email),
+ xss(comment.getContent()),
+ remove,
toYesNo(comment.isPinned())];
};
diff --git a/frontend-js/src/main/js/gui/admin/LogListDialog.js b/frontend-js/src/main/js/gui/admin/LogListDialog.js
index 6bc07a0f0b..3c4bb3e607 100644
--- a/frontend-js/src/main/js/gui/admin/LogListDialog.js
+++ b/frontend-js/src/main/js/gui/admin/LogListDialog.js
@@ -40,9 +40,9 @@ LogListDialog.prototype.createLogListDialogGui = function () {
var self = this;
var head = Functions.createElement({
type: "thead",
- content: "<tr>" + "<th>ID</th>" + //
- "<th>Content</th>" + //
- "</tr>"//
+ content: "<tr>" + "<th>ID</th>" +
+ "<th>Content</th>" +
+ "</tr>"
});
var body = Functions.createElement({
type: "tbody"
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 9735174270..23a09b5aef 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -40,14 +40,14 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function () {
var self = this;
var head = Functions.createElement({
type: "thead",
- content: "<tr>" + "<th>Pubmed ID</th>" + //
- "<th>Title</th>" + //
- "<th>Authors</th>" + //
- "<th>Journal</th>" + //
- "<th>Year</th>" + //
- "<th>Elements on map</th>" + //
- "<th>Submaps</th>" + //
- "</tr>"//
+ content: "<tr>" + "<th>Pubmed ID</th>" +
+ "<th>Title</th>" +
+ "<th>Authors</th>" +
+ "<th>Journal</th>" +
+ "<th>Year</th>" +
+ "<th>Elements on map</th>" +
+ "<th>Submaps</th>" +
+ "</tr>"
});
var body = Functions.createElement({
type: "tbody"
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 5df5c1d721..94c0b54406 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -144,7 +144,7 @@ AbstractCustomMap.prototype.createMapOptions = function () {
AbstractCustomMap.prototype.registerMapClickEvents = function () {
// find top map (CustomMap)
- //
+
var customMap = this.getTopMap();
var self = this;
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index e7550fa091..4209da61ba 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -1218,26 +1218,26 @@ CustomMap.prototype.getDistance = function (params) {
if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
return 0;
} else {
- return Math.min( //
- Math.abs(element.getY() - y), //
- Math.abs(element.getY() + element.getHeight() - y) //
+ return Math.min(
+ Math.abs(element.getY() - y),
+ Math.abs(element.getY() + element.getHeight() - y)
);
}
} else if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
- return Math.min( //
- Math.abs(element.getX() - x), //
- Math.abs(element.getX() + element.getWidth() - x) //
+ return Math.min(
+ Math.abs(element.getX() - x),
+ Math.abs(element.getX() + element.getWidth() - x)
);
} else {
var elementX = element.getX();
var elementY = element.getY();
var elementWidth = element.getWidth();
var elementHeight = element.getHeight();
- return Math.min( //
- Functions.distance(p1, new Point(elementX, y)), //
- Functions.distance(p1, new Point(elementX + elementWidth, elementY)), //
- Functions.distance(p1, new Point(elementX, elementY + elementHeight)), //
- Functions.distance(p1, new Point(elementX + elementWidth, elementY + elementHeight)) //
+ return Math.min(
+ Functions.distance(p1, new Point(elementX, y)),
+ Functions.distance(p1, new Point(elementX + elementWidth, elementY)),
+ Functions.distance(p1, new Point(elementX, elementY + elementHeight)),
+ Functions.distance(p1, new Point(elementX + elementWidth, elementY + elementHeight))
);
}
} else if (element instanceof Reaction) {
diff --git a/frontend-js/src/main/js/map/canvas/Bounds.js b/frontend-js/src/main/js/map/canvas/Bounds.js
index 0cbc6b1f2c..5795e7fd3f 100644
--- a/frontend-js/src/main/js/map/canvas/Bounds.js
+++ b/frontend-js/src/main/js/map/canvas/Bounds.js
@@ -66,9 +66,9 @@ Bounds.prototype.getRightBottom = function () {
* @returns {boolean}
*/
Bounds.prototype.contains = function (point) {
- return this._topLeft.x <= point.x && //
- this._topLeft.y <= point.y && //
- this._rightBottom.x >= point.x && //
+ return this._topLeft.x <= point.x &&
+ this._topLeft.y <= point.y &&
+ this._rightBottom.x >= point.x &&
this._rightBottom.y >= point.y;
};
diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index 5b2e69861f..d659e27a7b 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -272,8 +272,8 @@ IdentifiedElement.prototype.setLineColor = function (lineColor) {
*/
IdentifiedElement.prototype.equals = function (argument) {
if (argument instanceof IdentifiedElement) {
- return (this.getType() === argument.getType() && //
- this.getId() === argument.getId() && //
+ return (this.getType() === argument.getType() &&
+ this.getId() === argument.getId() &&
this.getModelId() === argument.getModelId());
} else {
return false;
diff --git a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
index 63a91ad290..8c9c543cdc 100644
--- a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
@@ -174,24 +174,24 @@ AbstractInfoWindow.prototype.createOverlayInfoDiv = function (overlay, data) {
if (alias !== undefined) {
if (alias.getType() !== undefined) {
if (overlay.name === "drug") {
- if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
+ if (alias.getType().toUpperCase() === "RNA" ||
+ alias.getType().toUpperCase() === "PROTEIN" ||
alias.getType().toUpperCase() === "GENE") {
return this._createDrugInfoDiv(overlay, data);
} else {
return null;
}
} else if (overlay.name === "chemical") {
- if (this.alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
+ if (this.alias.getType().toUpperCase() === "RNA" ||
+ alias.getType().toUpperCase() === "PROTEIN" ||
alias.getType().toUpperCase() === "GENE") {
return this._createChemicalInfoDiv(overlay, data);
} else {
return null;
}
} else if (overlay.name === "mirna") {
- if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
+ if (alias.getType().toUpperCase() === "RNA" ||
+ alias.getType().toUpperCase() === "PROTEIN" ||
alias.getType().toUpperCase() === "GENE") {
return this._createMiRnaInfoDiv(overlay, data);
} else {
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index 49c1729989..f57b704bed 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -525,13 +525,13 @@ AliasInfoWindow.prototype.createVcfString = function (geneVariants) {
if (variant.getVariantIdentifier() !== undefined) {
variantId = variant.getVariantIdentifier();
}
- result += variant.getContig() + "\t" + //
- variant.getPosition() + "\t" + //
- variantId + "\t" + //
- variant.getOriginalDna() + "\t" + //
- variant.getModifiedDna() + "\t" + //
- "100.0\t" + //
- "PASS\t" + //
+ result += variant.getContig() + "\t" +
+ variant.getPosition() + "\t" +
+ variantId + "\t" +
+ variant.getOriginalDna() + "\t" +
+ variant.getModifiedDna() + "\t" +
+ "100.0\t" +
+ "PASS\t" +
additionalInfo + "\n";
}
return result;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
index d391ec54da..1357d8589e 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
@@ -8,13 +8,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllLayoutTests.class, //
- AllPropertyCommandTests.class, //
- ColorModelCommandTest.class, //
- CopyCommandTest.class, //
- CreateHierarchyCommandTest.class, //
- MoveElementsCommandTest.class, //
- SubModelCommandTest.class,//
+@SuiteClasses({ AllLayoutTests.class,
+ AllPropertyCommandTests.class,
+ ColorModelCommandTest.class,
+ CopyCommandTest.class,
+ CreateHierarchyCommandTest.class,
+ MoveElementsCommandTest.class,
+ SubModelCommandTest.class,
})
public class AllCommandsTests {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
index 3253f2fbbd..d0b9fc798b 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
@@ -5,17 +5,17 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ChangeElementAbbreviationCommandTest.class,//
- ChangeElementColorCommandTest.class,//
- ChangeElementFontSizeCommandTest.class,//
- ChangeElementFormerSymbolCommandTest.class,//
- ChangeElementFormulaCommandTest.class,//
- ChangeElementFullNameCommandTest.class,//
- ChangeElementMiriamDataCommandTest.class,//
- ChangeElementNameCommandTest.class,//
- ChangeElementNotesCommandTest.class,//
- ChangeElementSymbolCommandTest.class,//
- ChangeElementSynonymCommandTest.class,//
+@SuiteClasses({ ChangeElementAbbreviationCommandTest.class,
+ ChangeElementColorCommandTest.class,
+ ChangeElementFontSizeCommandTest.class,
+ ChangeElementFormerSymbolCommandTest.class,
+ ChangeElementFormulaCommandTest.class,
+ ChangeElementFullNameCommandTest.class,
+ ChangeElementMiriamDataCommandTest.class,
+ ChangeElementNameCommandTest.class,
+ ChangeElementNotesCommandTest.class,
+ ChangeElementSymbolCommandTest.class,
+ ChangeElementSynonymCommandTest.class,
})
public class AllPropertyCommandTests {
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
index 509d773625..57c2ebebe5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
@@ -26,7 +26,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAVElEQVR42u3WsQoAIAhFUf//p21qM0miQd890NISXKQyA4B+/HJPMoIrxQgjbCox0ghBDJeNMD1IOcIhSHpAy1XVfTK+TwJ3Aq8D/wR+jFPDAHizAFMtRsiqJUUMAAAAAElFTkSuQmCC"
* />
*/
- BLANK_CROSSBAR, //
+ BLANK_CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -35,7 +35,7 @@ public enum ArrowType {
* />
*
*/
- FULL_CROSSBAR, //
+ FULL_CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -44,7 +44,7 @@ public enum ArrowType {
* />
*
*/
- DIAMOND, //
+ DIAMOND,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -52,7 +52,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAATElEQVR42u3XMQ4AEBAFUfe/9ChEo5DVSPjzEgcwEVZrkvQHTDAikB6DKTkGq8TTwU5KEKoqMXh1nfrxZERv3jvB18E5wYnRv4N0RwevuDvTQl9v5wAAAABJRU5ErkJggg=="
* />
*/
- BLANK, //
+ BLANK,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -61,7 +61,7 @@ public enum ArrowType {
* />
*
*/
- CROSSBAR, //
+ CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -69,7 +69,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3XgQkAIAzEwO6/9DtCVUQw5qALhIK2ShJMmuEH6NBDZBY1RFYRQ3wfIbtIIY5HyIvjJhjBCL4ORvDH6O3gFalLBns+vGCSjHRAAAAAAElFTkSuQmCC"
* /> *
*/
- CIRCLE, //
+ CIRCLE,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -77,7 +77,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAANklEQVR42u3UMQ4AQAQEQP//tGuUCrmSmcQDbJYIAFbJGoTRhyEQgXyeSx4cTfATLK7ulgeYehEYVKxEPu3IAAAAAElFTkSuQmCC"
* />
*/
- OPEN, //
+ OPEN,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
@@ -85,7 +85,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAO0lEQVR42u3WsQ0AIAwDwey/tCloKF2TOykLvCLIDABfiQQ3wjsibI2RYkRoY2Th2ARvgt/BneBiBGgdPHh6hnF4gJ8AAAAASUVORK5CYII="
* />
*/
- FULL, //
+ FULL,
/**
* The arrow end that should look as an image bellow. <br/>
* <br/>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 5cdce9d91e..3b18a9638a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -23,386 +23,386 @@ import lcsb.mapviewer.model.map.species.Rna;
@SuppressWarnings("unchecked")
public enum MiriamType {
- BiGG_COMPARTMENT("BiGG Compartment", //
- "http://bigg.ucsd.edu/compartments/", //
- new String[] { "urn:miriam:bigg.compartment" }, //
- new Class<?>[] {}, "MIR:00000555"), //
+ BiGG_COMPARTMENT("BiGG Compartment",
+ "http://bigg.ucsd.edu/compartments/",
+ new String[] { "urn:miriam:bigg.compartment" },
+ new Class<?>[] {}, "MIR:00000555"),
- BiGG_METABOLITE("BiGG Metabolite", //
- "http://bigg.ucsd.edu/universal/metabolites", //
- new String[] { "urn:miriam:bigg.metabolite" }, //
- new Class<?>[] {}, "MIR:00000556"), //
+ BiGG_METABOLITE("BiGG Metabolite",
+ "http://bigg.ucsd.edu/universal/metabolites",
+ new String[] { "urn:miriam:bigg.metabolite" },
+ new Class<?>[] {}, "MIR:00000556"),
- BiGG_REACTIONS("BiGG Reaction", //
- "http://bigg.ucsd.edu/universal/reactions", //
- new String[] { "urn:miriam:bigg.reaction" }, //
- new Class<?>[] {}, "MIR:00000557"), //
+ BiGG_REACTIONS("BiGG Reaction",
+ "http://bigg.ucsd.edu/universal/reactions",
+ new String[] { "urn:miriam:bigg.reaction" },
+ new Class<?>[] {}, "MIR:00000557"),
/**
* Brenda enzyme database: http://www.brenda-enzymes.org.
*/
- BRENDA("BRENDA", //
- "http://www.brenda-enzymes.org", //
- new String[] { "urn:miriam:brenda" }, //
- new Class<?>[] {}, "MIR:00100101"), //
+ BRENDA("BRENDA",
+ "http://www.brenda-enzymes.org",
+ new String[] { "urn:miriam:brenda" },
+ new Class<?>[] {}, "MIR:00100101"),
/**
* Chemical Abstracts Service database: http://commonchemistry.org.
*/
- CAS("Chemical Abstracts Service", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cas" }, //
- new Class<?>[] {}, "MIR:00000237"), //
+ CAS("Chemical Abstracts Service",
+ "http://commonchemistry.org",
+ new String[] { "urn:miriam:cas" },
+ new Class<?>[] {}, "MIR:00000237"),
/**
* The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
*/
- CAZY("CAZy", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cazy" }, //
- new Class<?>[] {}, "MIR:00000195"), //
+ CAZY("CAZy",
+ "http://commonchemistry.org",
+ new String[] { "urn:miriam:cazy" },
+ new Class<?>[] {}, "MIR:00000195"),
/**
* Consensus CDS: http://identifiers.org/ccds/.
*/
- CCDS("Consensus CDS", //
- "http://www.ncbi.nlm.nih.gov/CCDS/", //
- new String[] { "urn:miriam:ccds" }, //
- new Class<?>[] {}, "MIR:00000375"), //
+ CCDS("Consensus CDS",
+ "http://www.ncbi.nlm.nih.gov/CCDS/",
+ new String[] { "urn:miriam:ccds" },
+ new Class<?>[] {}, "MIR:00000375"),
/**
* Chebi database:
* <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
*/
- CHEBI("Chebi", //
- "http://www.ebi.ac.uk/chebi/", //
- new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
- new Class<?>[] { Chemical.class }), //
+ CHEBI("Chebi",
+ "http://www.ebi.ac.uk/chebi/",
+ new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" },
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002",
+ new Class<?>[] { Chemical.class }),
/**
* ChemSpider database:
* <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
*/
- CHEMSPIDER("ChemSpider", //
- "http://www.chemspider.com//", //
- new String[] { "urn:miriam:chemspider" }, //
- new Class<?>[] {}, "MIR:00000138"), //
+ CHEMSPIDER("ChemSpider",
+ "http://www.chemspider.com//",
+ new String[] { "urn:miriam:chemspider" },
+ new Class<?>[] {}, "MIR:00000138"),
/**
* Chembl database: https://www.ebi.ac.uk/chembldb/.
*/
- CHEMBL_COMPOUND("ChEMBL", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { Drug.class }, "MIR:00000084"), //
+ CHEMBL_COMPOUND("ChEMBL",
+ "https://www.ebi.ac.uk/chembldb/",
+ new String[] { "urn:miriam:chembl.compound" },
+ new Class<?>[] { Drug.class }, "MIR:00000084"),
/**
* Target in chembl database: https://www.ebi.ac.uk/chembldb/.
*/
- CHEMBL_TARGET("ChEMBL target", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
+ CHEMBL_TARGET("ChEMBL target",
+ "https://www.ebi.ac.uk/chembldb/",
+ new String[] { "urn:miriam:chembl.target" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"),
/**
* Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
*/
- COG("Clusters of Orthologous Groups", //
- "https://www.ncbi.nlm.nih.gov/COG/", //
- new String[] { "urn:miriam:cogs" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000296"), //
+ COG("Clusters of Orthologous Groups",
+ "https://www.ncbi.nlm.nih.gov/COG/",
+ new String[] { "urn:miriam:cogs" },
+ new Class<?>[] { Reaction.class }, "MIR:00000296"),
/**
* Digital Object Identifier: http://www.doi.org/.
*/
- DOI("Digital Object Identifier", //
- "http://www.doi.org/", //
- new String[] { "urn:miriam:doi" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000019"), //
+ DOI("Digital Object Identifier",
+ "http://www.doi.org/",
+ new String[] { "urn:miriam:doi" },
+ new Class<?>[] { Reaction.class }, "MIR:00000019"),
/**
* Drugbank database: http://www.drugbank.ca/.
*/
- DRUGBANK("DrugBank", //
- "http://www.drugbank.ca/", //
- new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { Drug.class }, "MIR:00000102"), //
+ DRUGBANK("DrugBank",
+ "http://www.drugbank.ca/",
+ new String[] { "urn:miriam:drugbank" },
+ new Class<?>[] { Drug.class }, "MIR:00000102"),
/**
* Drugbank targets: http://www.drugbank.ca/targets.
*/
- DRUGBANK_TARGET_V4("DrugBank Target v4", //
- "http://www.drugbank.ca/targets", //
- new String[] { "urn:miriam:drugbankv4.target" }, //
- new Class<?>[] {}, "MIR:00000528"), //
+ DRUGBANK_TARGET_V4("DrugBank Target v4",
+ "http://www.drugbank.ca/targets",
+ new String[] { "urn:miriam:drugbankv4.target" },
+ new Class<?>[] {}, "MIR:00000528"),
/**
* Enzyme Nomenclature: http://www.enzyme-database.org/.
*/
- EC("Enzyme Nomenclature", //
- "http://www.enzyme-database.org/", //
- new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
+ EC("Enzyme Nomenclature",
+ "http://www.enzyme-database.org/",
+ new String[] { "urn:miriam:ec-code" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"),
/**
* Ensembl: www.ensembl.org.
*/
- ENSEMBL("Ensembl", //
- "www.ensembl.org", //
- new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
+ ENSEMBL("Ensembl",
+ "www.ensembl.org",
+ new String[] { "urn:miriam:ensembl" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"),
/**
* Ensembl Plants: http://plants.ensembl.org/.
*/
- ENSEMBL_PLANTS("Ensembl Plants", //
- "http://plants.ensembl.org/", //
- new String[] { "urn:miriam:ensembl.plant" }, //
- new Class<?>[] {}, "MIR:00000205"), //
+ ENSEMBL_PLANTS("Ensembl Plants",
+ "http://plants.ensembl.org/",
+ new String[] { "urn:miriam:ensembl.plant" },
+ new Class<?>[] {}, "MIR:00000205"),
/**
* Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
*/
- ENTREZ("Entrez Gene", //
- "http://www.ncbi.nlm.nih.gov/gene", //
- new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
+ ENTREZ("Entrez Gene",
+ "http://www.ncbi.nlm.nih.gov/gene",
+ new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"),
/**
* Gene Ontology: http://amigo.geneontology.org/amigo.
*/
- GO("Gene Ontology", //
- "http://amigo.geneontology.org/amigo", //
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
+ GO("Gene Ontology",
+ "http://amigo.geneontology.org/amigo",
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go" },
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"),
/**
* HGNC: http://www.genenames.org.
*/
- HGNC("HGNC", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+ HGNC("HGNC",
+ "http://www.genenames.org",
+ new String[] { "urn:miriam:hgnc" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080",
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }),
/**
* HGNC symbol: http://www.genenames.org.
*/
- HGNC_SYMBOL("HGNC Symbol", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc.symbol" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+ HGNC_SYMBOL("HGNC Symbol",
+ "http://www.genenames.org",
+ new String[] { "urn:miriam:hgnc.symbol" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362",
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }),
/**
* HMDB: http://www.hmdb.ca/.
*/
- HMDB("HMDB", //
- "http://www.hmdb.ca/", //
- "urn:miriam:hmdb", //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
+ HMDB("HMDB",
+ "http://www.hmdb.ca/",
+ "urn:miriam:hmdb",
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"),
/**
* InterPro: http://www.ebi.ac.uk/interpro/.
*/
- INTERPRO("InterPro", //
- "http://www.ebi.ac.uk/interpro/", //
- new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
+ INTERPRO("InterPro",
+ "http://www.ebi.ac.uk/interpro/",
+ new String[] { "urn:miriam:interpro" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"),
/**
* KEGG Compound: http://www.genome.jp/kegg/ligand.html.
*/
- KEGG_COMPOUND("Kegg Compound", //
- "http://www.genome.jp/kegg/ligand.html", //
- "urn:miriam:kegg.compound", //
- new Class<?>[] { Chemical.class }, "MIR:00000013"), //
+ KEGG_COMPOUND("Kegg Compound",
+ "http://www.genome.jp/kegg/ligand.html",
+ "urn:miriam:kegg.compound",
+ new Class<?>[] { Chemical.class }, "MIR:00000013"),
/**
* KEGG Genes: http://www.genome.jp/kegg/genes.html.
*/
- KEGG_GENES("Kegg Genes", //
- "http://www.genome.jp/kegg/genes.html", //
- new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
+ KEGG_GENES("Kegg Genes",
+ "http://www.genome.jp/kegg/genes.html",
+ new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"),
/**
* KEGG Orthology: http://www.genome.jp/kegg/ko.html.
*/
- KEGG_ORTHOLOGY("KEGG Orthology", //
- "http://www.genome.jp/kegg/ko.html", //
- new String[] { "urn:miriam:kegg.orthology" }, //
- new Class<?>[] {}, "MIR:00000116"), //
+ KEGG_ORTHOLOGY("KEGG Orthology",
+ "http://www.genome.jp/kegg/ko.html",
+ new String[] { "urn:miriam:kegg.orthology" },
+ new Class<?>[] {}, "MIR:00000116"),
/**
* KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
*/
- KEGG_PATHWAY("Kegg Pathway", //
- "http://www.genome.jp/kegg/pathway.html", //
- "urn:miriam:kegg.pathway", //
- new Class<?>[] { Reaction.class }, "MIR:00000012"), //
+ KEGG_PATHWAY("Kegg Pathway",
+ "http://www.genome.jp/kegg/pathway.html",
+ "urn:miriam:kegg.pathway",
+ new Class<?>[] { Reaction.class }, "MIR:00000012"),
/**
* KEGG Reaction: http://www.genome.jp/kegg/reaction/.
*/
- KEGG_REACTION("Kegg Reaction", //
- "http://www.genome.jp/kegg/reaction/", //
- "urn:miriam:kegg.reaction", //
- new Class<?>[] { Reaction.class }, "MIR:00000014"), //
+ KEGG_REACTION("Kegg Reaction",
+ "http://www.genome.jp/kegg/reaction/",
+ "urn:miriam:kegg.reaction",
+ new Class<?>[] { Reaction.class }, "MIR:00000014"),
/**
* MeSH 2012: http://www.nlm.nih.gov/mesh/.
*/
- MESH_2012("MeSH", //
- "http://www.nlm.nih.gov/mesh/", //
- new String[] { "urn:miriam:mesh" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
+ MESH_2012("MeSH",
+ "http://www.nlm.nih.gov/mesh/",
+ new String[] { "urn:miriam:mesh" },
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"),
/**
* miRBase Sequence: http://www.mirbase.org/.
*/
- MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase" }, //
- new Class<?>[] {}, "MIR:00000078"), //
+ MI_R_BASE_SEQUENCE("miRBase Sequence Database",
+ "http://www.mirbase.org/",
+ new String[] { "urn:miriam:mirbase" },
+ new Class<?>[] {}, "MIR:00000078"),
/**
* miRBase Mature Sequence: http://www.mirbase.org/.
*/
- MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase.mature" }, //
- new Class<?>[] {}, "MIR:00000235"), //
+ MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database",
+ "http://www.mirbase.org/",
+ new String[] { "urn:miriam:mirbase.mature" },
+ new Class<?>[] {}, "MIR:00000235"),
/**
* miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
*/
- MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
- "http://mirtarbase.mbc.nctu.edu.tw/", //
- new String[] { "urn:miriam:mirtarbase" }, //
- new Class<?>[] {}, "MIR:00100739"), //
+ MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database",
+ "http://mirtarbase.mbc.nctu.edu.tw/",
+ new String[] { "urn:miriam:mirtarbase" },
+ new Class<?>[] {}, "MIR:00100739"),
/**
* Mouse Genome Database: http://www.informatics.jax.org/.
*/
- MGD("Mouse Genome Database", //
- "http://www.informatics.jax.org/", //
- new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
+ MGD("Mouse Genome Database",
+ "http://www.informatics.jax.org/",
+ new String[] { "urn:miriam:mgd" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"),
/**
* Online Mendelian Inheritance in Man: http://omim.org/.
*/
- OMIM("Online Mendelian Inheritance in Man", //
- "http://omim.org/", //
- new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
+ OMIM("Online Mendelian Inheritance in Man",
+ "http://omim.org/",
+ new String[] { "urn:miriam:omim" },
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"),
/**
* PANTHER Family: http://www.pantherdb.org/.
*/
- PANTHER("PANTHER Family", //
- "http://www.pantherdb.org/", //
- new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
+ PANTHER("PANTHER Family",
+ "http://www.pantherdb.org/",
+ new String[] { "urn:miriam:panther.family", "urn:miriam:panther" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"),
/**
* PDB: http://www.pdbe.org/.
*/
- PDB("Protein Data Bank", //
- "http://www.pdbe.org/", //
- "urn:miriam:pdb", //
+ PDB("Protein Data Bank",
+ "http://www.pdbe.org/",
+ "urn:miriam:pdb",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
/**
* Protein Family Database: http://pfam.xfam.org/.
*/
- PFAM("Protein Family Database", //
- "http://pfam.xfam.org//", //
- "urn:miriam:pfam", //
- new Class<?>[] {}, "MIR:00000028"), //
+ PFAM("Protein Family Database",
+ "http://pfam.xfam.org//",
+ "urn:miriam:pfam",
+ new Class<?>[] {}, "MIR:00000028"),
/**
* PharmGKB Pathways: http://www.pharmgkb.org/.
*/
- PHARM("PharmGKB Pathways", //
- "http://www.pharmgkb.org/", //
- "urn:miriam:pharmgkb.pathways", //
- new Class<?>[] {}, "MIR:00000089"), //
+ PHARM("PharmGKB Pathways",
+ "http://www.pharmgkb.org/",
+ "urn:miriam:pharmgkb.pathways",
+ new Class<?>[] {}, "MIR:00000089"),
/**
* PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
*/
- PUBCHEM("PubChem-compound", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000034", //
- new Class<?>[] { Chemical.class }), //
+ PUBCHEM("PubChem-compound",
+ "http://pubchem.ncbi.nlm.nih.gov/",
+ new String[] { "urn:miriam:pubchem.compound" },
+ new Class<?>[] { Chemical.class }, "MIR:00000034",
+ new Class<?>[] { Chemical.class }),
/**
* PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
*/
- PUBCHEM_SUBSTANCE("PubChem-substance", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000033", //
- new Class<?>[] { Chemical.class }), //
+ PUBCHEM_SUBSTANCE("PubChem-substance",
+ "http://pubchem.ncbi.nlm.nih.gov/",
+ new String[] { "urn:miriam:pubchem.substance" },
+ new Class<?>[] { Chemical.class }, "MIR:00000033",
+ new Class<?>[] { Chemical.class }),
/**
* PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
*/
- PUBMED("PubMed", //
- "http://www.ncbi.nlm.nih.gov/PubMed/", //
- new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { BioEntity.class }, "MIR:00000015", //
- new Class<?>[] { Reaction.class }), //
+ PUBMED("PubMed",
+ "http://www.ncbi.nlm.nih.gov/PubMed/",
+ new String[] { "urn:miriam:pubmed" },
+ new Class<?>[] { BioEntity.class }, "MIR:00000015",
+ new Class<?>[] { Reaction.class }),
/**
* Reactome: http://www.reactome.org/.
*/
- REACTOME("Reactome", //
- "http://www.reactome.org/", //
- "urn:miriam:reactome", //
- new Class<?>[] { Reaction.class }, "MIR:00000018"), //
+ REACTOME("Reactome",
+ "http://www.reactome.org/",
+ "urn:miriam:reactome",
+ new Class<?>[] { Reaction.class }, "MIR:00000018"),
/**
* RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
*/
- REFSEQ("RefSeq", //
- "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
- "urn:miriam:refseq", //
+ REFSEQ("RefSeq",
+ "http://www.ncbi.nlm.nih.gov/projects/RefSeq/",
+ "urn:miriam:refseq",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
/**
* Rhea: http://www.rhea-db.org/.
*/
- RHEA("Rhea", //
- "http://www.rhea-db.org/", //
- "urn:miriam:rhea", //
+ RHEA("Rhea",
+ "http://www.rhea-db.org/",
+ "urn:miriam:rhea",
new Class<?>[] { Reaction.class }, "MIR:00000082"),
/**
* SGD: http://www.yeastgenome.org/.
*/
- SGD("Saccharomyces Genome Database", //
- "http://www.yeastgenome.org/", //
- "urn:miriam:sgd", //
+ SGD("Saccharomyces Genome Database",
+ "http://www.yeastgenome.org/",
+ "urn:miriam:sgd",
new Class<?>[] {}, "MIR:00000023"),
/**
* STITCH: http://stitch.embl.de/.
*/
- STITCH("STITCH", //
- "http://stitch.embl.de/", //
- "urn:miriam:stitch", //
+ STITCH("STITCH",
+ "http://stitch.embl.de/",
+ "urn:miriam:stitch",
new Class<?>[] {}, "MIR:00100343"),
/**
* STRING: http://string-db.org/.
*/
- STRING("STRING", //
- "http://string-db.org/", //
- "urn:miriam:string", //
+ STRING("STRING",
+ "http://string-db.org/",
+ "urn:miriam:string",
new Class<?>[] {}, "MIR:00000265"),
/**
@@ -411,105 +411,105 @@ public enum MiriamType {
* The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
* http://arabidopsis.org/index.jsp.
*/
- TAIR_LOCUS("TAIR Locus", //
- "http://arabidopsis.org/index.jsp", //
- "urn:miriam:tair.locus", //
+ TAIR_LOCUS("TAIR Locus",
+ "http://arabidopsis.org/index.jsp",
+ "urn:miriam:tair.locus",
new Class<?>[] {}, "MIR:00000050"),
/**
* Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
*/
- TAXONOMY("Taxonomy", //
- "http://www.ncbi.nlm.nih.gov/taxonomy/", //
- "urn:miriam:taxonomy", //
+ TAXONOMY("Taxonomy",
+ "http://www.ncbi.nlm.nih.gov/taxonomy/",
+ "urn:miriam:taxonomy",
new Class<?>[] {}, "MIR:00000006"),
/**
* Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
* http://ctdbase.org/detail.go
*/
- TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
- "http://ctdbase.org/", //
- "urn:miriam:ctd.chemical", //
- new Class<?>[] {}, "MIR:00000098"), //
+ TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical",
+ "http://ctdbase.org/",
+ "urn:miriam:ctd.chemical",
+ new Class<?>[] {}, "MIR:00000098"),
/**
* UniGene: http://www.ncbi.nlm.nih.gov/unigene.
*/
- UNIGENE("UniGene", //
- "http://www.ncbi.nlm.nih.gov/unigene", //
- "urn:miriam:unigene", //
+ UNIGENE("UniGene",
+ "http://www.ncbi.nlm.nih.gov/unigene",
+ "urn:miriam:unigene",
new Class<?>[] {}, "MIR:00000346"),
/**
* Uniprot: http://www.uniprot.org/.
*/
- UNIPROT("Uniprot", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot", //
+ UNIPROT("Uniprot",
+ "http://www.uniprot.org/",
+ "urn:miriam:uniprot",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
/**
* UniProt Isoform: http://www.uniprot.org/.
*/
- UNIPROT_ISOFORM("UniProt Isoform", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot.isoform", //
+ UNIPROT_ISOFORM("UniProt Isoform",
+ "http://www.uniprot.org/",
+ "urn:miriam:uniprot.isoform",
new Class<?>[] { Protein.class }, "MIR:00000388"),
/**
* Unknown reference type...
*/
- UNKNOWN("Unknown", //
- null, //
- new String[] {}, //
+ UNKNOWN("Unknown",
+ null,
+ new String[] {},
new Class<?>[] {}, null),
/**
* VMH reaction
*/
- VMH_REACTION("VMH reaction", //
- "http://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" }, //
+ VMH_REACTION("VMH reaction",
+ "http://vmh.uni.lu/",
+ new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" },
new Class<?>[] { Reaction.class }, "MIR:00000640"),
/**
* VMH reaction
*/
- VMH_METABOLITE("VMH metabolite", //
- "http://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" }, //
+ VMH_METABOLITE("VMH metabolite",
+ "http://vmh.uni.lu/",
+ new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" },
new Class<?>[] { Chemical.class }, "MIR:00000636"),
/**
* Wikidata: https://www.wikidata.org/.
*/
- WIKIDATA("Wikidata", //
- "https://www.wikidata.org/", //
- new String[] { "urn:miriam:wikidata" }, //
- new Class<?>[] {}, "MIR:00000549"), //
+ WIKIDATA("Wikidata",
+ "https://www.wikidata.org/",
+ new String[] { "urn:miriam:wikidata" },
+ new Class<?>[] {}, "MIR:00000549"),
/**
* WikiPathways: http://www.wikipathways.org/.
*/
- WIKIPATHWAYS("WikiPathways", //
- "http://www.wikipathways.org/", //
- new String[] { "urn:miriam:wikipathways" }, //
- new Class<?>[] {}, "MIR:00000076"), //
+ WIKIPATHWAYS("WikiPathways",
+ "http://www.wikipathways.org/",
+ new String[] { "urn:miriam:wikipathways" },
+ new Class<?>[] {}, "MIR:00000076"),
/**
* Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
*/
- WIKIPEDIA("Wikipedia (English)", //
+ WIKIPEDIA("Wikipedia (English)",
"http://en.wikipedia.org/wiki/Main_Page", // /
- new String[] { "urn:miriam:wikipedia.en" }, //
+ new String[] { "urn:miriam:wikipedia.en" },
new Class<?>[] {}, "MIR:00000384"),
/**
* WormBase: http://wormbase.bio2rdf.org/fct.
*/
- WORM_BASE("WormBase", //
+ WORM_BASE("WormBase",
"http://wormbase.bio2rdf.org/fct", // /
- new String[] { "urn:miriam:wormbase" }, //
+ new String[] { "urn:miriam:wormbase" },
new Class<?>[] {}, "MIR:00000027");
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
index 32184f55ee..2aaa570b36 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
@@ -27,67 +27,67 @@ public enum ModificationState {
/**
* Phosporylated state.
*/
- PHOSPHORYLATED("phosphorylated", "P"), //
+ PHOSPHORYLATED("phosphorylated", "P"),
/**
* Acetylated state.
*/
- ACETYLATED("acetylated", "Ac"), //
+ ACETYLATED("acetylated", "Ac"),
/**
* Ubiquitinated state.
*/
- UBIQUITINATED("ubiquitinated", "Ub"), //
+ UBIQUITINATED("ubiquitinated", "Ub"),
/**
* Methylated state.
*/
- METHYLATED("methylated", "Me"), //
+ METHYLATED("methylated", "Me"),
/**
* Hydroxylated state.
*/
- HYDROXYLATED("hydroxylated", "OH"), //
+ HYDROXYLATED("hydroxylated", "OH"),
/**
* Myristoylated state.
*/
- MYRISTOYLATED("myristoylated", "My"), //
+ MYRISTOYLATED("myristoylated", "My"),
/**
* Sulfated state.
*/
- SULFATED("sulfated", "S"), //
+ SULFATED("sulfated", "S"),
/**
* Prenylated state.
*/
- PRENYLATED("prenylated", "Pr"), //
+ PRENYLATED("prenylated", "Pr"),
/**
* Glycosylated state.
*/
- GLYCOSYLATED("glycosylated", "G"), //
+ GLYCOSYLATED("glycosylated", "G"),
/**
* Palmytoylated state.
*/
- PALMYTOYLATED("palmytoylated", "Pa"), //
+ PALMYTOYLATED("palmytoylated", "Pa"),
/**
* Unknown state.
*/
- UNKNOWN("unknown", "?"), //
+ UNKNOWN("unknown", "?"),
/**
* Empty state.
*/
- EMPTY("empty", ""), //
+ EMPTY("empty", ""),
/**
* Protonated state.
*/
- PROTONATED("protonated", "H"), //
+ PROTONATED("protonated", "H"),
/**
* We don't care in which state it is.
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index d22f4f940c..33111aa6bc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -13,55 +13,55 @@ public enum ConfigurationElementType {
* Email address used for sending email from the system.
*/
EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Login for the email account.
*/
EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Password for the email account.
*/
EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Address of the IMAP server.
*/
EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Address of the SMTP server.
*/
EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Port used for SMTP connection (sending e-mails).
*/
EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
/**
* Default map that should be presented if no map is selected by user side.
*/
DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING, false,
- ConfigurationElementTypeGroup.SERVER_CONFIGURATION), //
+ ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
/**
* Logo presented in the system.
*/
LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
/**
* Address connected to the logo.
*/
LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
/**
* Maximum distance (in pixels) that is allowed during finding closest element
@@ -202,34 +202,34 @@ public enum ConfigurationElementType {
ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
LDAP_ADDRESS("LDAP address", "", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_PORT("LDAP port", "389", ConfigurationElementEditType.INTEGER, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_SSL("LDAP uses SSL", "false", ConfigurationElementEditType.BOOLEAN, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_BIND_DN("LDAP bind DN", "", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_PASSWORD("LDAP password", "", ConfigurationElementEditType.PASSWORD, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_BASE_DN("LDAP base DN", "", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_OBJECT_CLASS("LDAP filter objectClass", "*", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_FIRST_NAME_ATTRIBUTE("LDAP first name attribute", "givenName", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_LAST_NAME_ATTRIBUTE("LDAP last name attribute", "sn", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_EMAIL_ATTRIBUTE("LDAP email attribute", "mail", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
LDAP_FILTER("LDAP filter", "(memberof=cn=minerva,cn=groups,cn=accounts,dc=uni,dc=lu)",
- ConfigurationElementEditType.STRING, true, ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementEditType.STRING, true, ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
DEFAULT_CUSTOM_LAYOUTS("Default user privilege for: " + PrivilegeType.CUSTOM_LAYOUTS.getCommonName(), "0",
ConfigurationElementEditType.INTEGER, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
LDAP_UID("LDAP login (user id)", "uid", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
SHOW_REACTION_TITLE("Show reaction title", "true", ConfigurationElementEditType.BOOLEAN, false,
@@ -291,7 +291,7 @@ public enum ConfigurationElementType {
ConfigurationElementTypeGroup.SEARCH_VISIBLE_PARAMETERS),
SESSION_LENGTH("Max session inactivity time (in seconds)", "7200", ConfigurationElementEditType.INTEGER, false,
- ConfigurationElementTypeGroup.SERVER_CONFIGURATION), //
+ ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
index 3142624c33..55cc6ea9ed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
@@ -1,14 +1,14 @@
package lcsb.mapviewer.model.user;
public enum ConfigurationElementTypeGroup {
- EMAIL_NOTIFICATION("Email notification details"), //
- DEFAULT_USER_PRIVILEGES("Default user privileges"), //
- LEGEND_AND_LOGO("Legend and logo"), //
- OVERLAYS("Overlays"), //
- POINT_AND_CLICK("Point and click"), //
- SERVER_CONFIGURATION("Server configuration"),//
- LDAP_CONFIGURATION("LDAP configuration"),//
- SEARCH_VISIBLE_PARAMETERS("Search panel options"), //
+ EMAIL_NOTIFICATION("Email notification details"),
+ DEFAULT_USER_PRIVILEGES("Default user privileges"),
+ LEGEND_AND_LOGO("Legend and logo"),
+ OVERLAYS("Overlays"),
+ POINT_AND_CLICK("Point and click"),
+ SERVER_CONFIGURATION("Server configuration"),
+ LDAP_CONFIGURATION("LDAP configuration"),
+ SEARCH_VISIBLE_PARAMETERS("Search panel options"),
;
private String commonName;
diff --git a/model/src/test/java/lcsb/mapviewer/AllTests.java b/model/src/test/java/lcsb/mapviewer/AllTests.java
index 60ea0c795e..d7ed5099a5 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -8,8 +8,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class, //
- AllMapUtilTests.class,//
+@SuiteClasses({ AllModelTests.class,
+ AllMapUtilTests.class,
})
public class AllTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
index 9387ffa40a..0a4f42cfd0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
@@ -11,13 +11,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllGraphicsTests.class, //
- AllLogTests.class, //
- AllMapTests.class, //
- AllUserTests.class, //
- ProjectStatusTest.class, //
- ProjectTest.class,//
+@SuiteClasses({ AllCacheTests.class,
+ AllGraphicsTests.class,
+ AllLogTests.class,
+ AllMapTests.class,
+ AllUserTests.class,
+ ProjectStatusTest.class,
+ ProjectTest.class,
})
public class AllModelTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java b/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
index 063c947872..5eca526011 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
@@ -5,10 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BigFileEntryTest.class, //
- CacheQueryTest.class, //
- CacheTypeTest.class,//
- UploadedFileEntryTest.class,//
+@SuiteClasses({ BigFileEntryTest.class,
+ CacheQueryTest.class,
+ CacheTypeTest.class,
+ UploadedFileEntryTest.class,
})
public class AllCacheTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java b/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
index a17a49b09b..8f3f0f4e75 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
@@ -5,12 +5,12 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ArrowTypeDataComparatorTest.class, //
- ArrowTypeDataTest.class, //
- ArrowTypeTest.class, //
- LineTypeTest.class, //
- PolylineDataTest.class, //
- PolylineDataComparatorTest.class,//
+@SuiteClasses({ ArrowTypeDataComparatorTest.class,
+ ArrowTypeDataTest.class,
+ ArrowTypeTest.class,
+ LineTypeTest.class,
+ PolylineDataTest.class,
+ PolylineDataComparatorTest.class,
})
public class AllGraphicsTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java b/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
index 9c2ae5c6d3..bf80d2d2b9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
@@ -5,9 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ LogTypeTest.class, //
- ObjectLogTest.class, //
- SystemLogTest.class //
+@SuiteClasses({ LogTypeTest.class,
+ ObjectLogTest.class,
+ SystemLogTest.class
})
public class AllLogTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
index 5f78c6bd33..5bbd36f3b0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -15,33 +15,33 @@ import lcsb.mapviewer.model.map.species.AllSpeciesTests;
import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllCompartmentTests.class, //
- ElementInFewParentsExceptionTest.class, //
- AllGraphicsTests.class, //
- AllKineticsTests.class, //
- AllLayoutTests.class, //
- AllModelTests.class, //
- AllModifierTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStatisticsTests.class, //
- CommentTest.class, //
- InconsistentModelExceptionTest.class, //
- LayoutComparatorTest.class, //
- MiriamDataTest.class, //
- MiriamRelationTypeTest.class, //
- MiriamTypeTest.class, //
- MiriamTypeNameComparatorTest.class, //
- OverviewImageComparatorTest.class, //
- OverviewImageLinkComparatorTest.class, //
- OverviewImageLinkTest.class, //
- OverviewImageTest.class, //
- OverviewLinkComparatorTest.class, //
- OverviewLinkTest.class, //
- OverviewModelLinkComparatorTest.class, //
- OverviewModelLinkTest.class, //
- OverviewSearchLinkTest.class, //
- SearchIndexTest.class,//
+@SuiteClasses({ AllCompartmentTests.class,
+ ElementInFewParentsExceptionTest.class,
+ AllGraphicsTests.class,
+ AllKineticsTests.class,
+ AllLayoutTests.class,
+ AllModelTests.class,
+ AllModifierTests.class,
+ AllReactionTests.class,
+ AllSpeciesTests.class,
+ AllStatisticsTests.class,
+ CommentTest.class,
+ InconsistentModelExceptionTest.class,
+ LayoutComparatorTest.class,
+ MiriamDataTest.class,
+ MiriamRelationTypeTest.class,
+ MiriamTypeTest.class,
+ MiriamTypeNameComparatorTest.class,
+ OverviewImageComparatorTest.class,
+ OverviewImageLinkComparatorTest.class,
+ OverviewImageLinkTest.class,
+ OverviewImageTest.class,
+ OverviewLinkComparatorTest.class,
+ OverviewLinkTest.class,
+ OverviewModelLinkComparatorTest.class,
+ OverviewModelLinkTest.class,
+ OverviewSearchLinkTest.class,
+ SearchIndexTest.class,
})
public class AllMapTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
index abad8d91d0..8fab2b8b02 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
@@ -5,15 +5,15 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BottomSquareCompartmentTest.class, //
- CompartmentComparatorTest.class, //
- CompartmentTest.class, //
- LeftSquareCompartmentTest.class, //
- OvalCompartmentTest.class, //
- PathwayCompartmentTest.class, //
- RightSquareCompartmentTest.class, //
- SquareCompartmentTest.class, //
- TopSquareCompartmentTest.class, //
+@SuiteClasses({ BottomSquareCompartmentTest.class,
+ CompartmentComparatorTest.class,
+ CompartmentTest.class,
+ LeftSquareCompartmentTest.class,
+ OvalCompartmentTest.class,
+ PathwayCompartmentTest.class,
+ RightSquareCompartmentTest.class,
+ SquareCompartmentTest.class,
+ TopSquareCompartmentTest.class,
})
public class AllCompartmentTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
index 5509035aac..51d54bf708 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
@@ -5,16 +5,16 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ SbmlFunctionTest.class, //
- SbmlFunctionComparatorTest.class, //
- SbmlKineticsTest.class, //
- SbmlKineticsComparatorTest.class, //
- SbmlParameterTest.class, //
- SbmlParameterComparatorTest.class, //
- SbmlUnitTest.class, //
- SbmlUnitComparatorTest.class, //
- SbmlUnitTypeFactorTest.class,//
- SbmlUnitTypeFactorComparatorTest.class, //
+@SuiteClasses({ SbmlFunctionTest.class,
+ SbmlFunctionComparatorTest.class,
+ SbmlKineticsTest.class,
+ SbmlKineticsComparatorTest.class,
+ SbmlParameterTest.class,
+ SbmlParameterComparatorTest.class,
+ SbmlUnitTest.class,
+ SbmlUnitComparatorTest.class,
+ SbmlUnitTypeFactorTest.class,
+ SbmlUnitTypeFactorComparatorTest.class,
})
public class AllKineticsTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
index 0d89ca417c..a0c2e8cc67 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
@@ -7,18 +7,18 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllGraphicsTests.class, //
- ColorSchemaTest.class, //
- ElementGroupTest.class, //
- GenericColorSchemaTest.class, //
- GeneVariationTest.class, //
- GeneVariationColorSchemaTest.class, //
- InvalidColorSchemaExceptionTest.class, //
- LayoutStatusTest.class, //
- LayoutTest.class, //
- ReferenceGenomeGeneMappingTest.class, //
- ReferenceGenomeTest.class, //
- ReferenceGenomeTypeTest.class,//
+@SuiteClasses({ AllGraphicsTests.class,
+ ColorSchemaTest.class,
+ ElementGroupTest.class,
+ GenericColorSchemaTest.class,
+ GeneVariationTest.class,
+ GeneVariationColorSchemaTest.class,
+ InvalidColorSchemaExceptionTest.class,
+ LayoutStatusTest.class,
+ LayoutTest.class,
+ ReferenceGenomeGeneMappingTest.class,
+ ReferenceGenomeTest.class,
+ ReferenceGenomeTypeTest.class,
})
public class AllLayoutTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
index 7901cc401a..6c08e4c7f1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
@@ -5,14 +5,14 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ LayerComparatorTest.class,//
- LayerOvalComparatorTest.class,//
- LayerOvalTest.class,//
- LayerRectComparatorTest.class,//
- LayerRectTest.class,//
- LayerTest.class,//
- LayerTextComparatorTest.class,//
- LayerTextTest.class,//
+@SuiteClasses({ LayerComparatorTest.class,
+ LayerOvalComparatorTest.class,
+ LayerOvalTest.class,
+ LayerRectComparatorTest.class,
+ LayerRectTest.class,
+ LayerTest.class,
+ LayerTextComparatorTest.class,
+ LayerTextTest.class,
})
public class AllGraphicsTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
index 52fe9455b4..7251f41bdf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
@@ -5,16 +5,16 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ElementSubmodelConnectionComparatorTest.class, //
- ElementSubmodelConnectionTest.class, //
- ModelComparatorTest.class, //
- ModelDataTest.class, //
- ModelFullIndexedTest.class, //
- ModelSubmodelConnectionComparatorTest.class, //
- ModelSubmodelConnectionTest.class, //
- ModelTest.class, //
- SubmodelConnectionComparatorTest.class,//
- SubmodelTypeTest.class,//
+@SuiteClasses({ ElementSubmodelConnectionComparatorTest.class,
+ ElementSubmodelConnectionTest.class,
+ ModelComparatorTest.class,
+ ModelDataTest.class,
+ ModelFullIndexedTest.class,
+ ModelSubmodelConnectionComparatorTest.class,
+ ModelSubmodelConnectionTest.class,
+ ModelTest.class,
+ SubmodelConnectionComparatorTest.class,
+ SubmodelTypeTest.class,
})
public class AllModelTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
index f6ec478388..e2533ce33f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
@@ -5,13 +5,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CatalysisTest.class, //
- InhibitionTest.class, //
- ModulationTest.class, //
- PhysicalStimulationTest.class, //
- TriggerTest.class, //
- UnknownCatalysisTest.class,//
- UnknownInhibitionTest.class,//
+@SuiteClasses({ CatalysisTest.class,
+ InhibitionTest.class,
+ ModulationTest.class,
+ PhysicalStimulationTest.class,
+ TriggerTest.class,
+ UnknownCatalysisTest.class,
+ UnknownInhibitionTest.class,
})
public class AllModifierTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
index 99a848941d..4f7ccaa125 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
@@ -7,24 +7,24 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AbstractNodeComparatorTest.class, //
- AllReactionTypeTests.class,//
- AndOperatorTest.class, //
- AssociationOperatorTest.class, //
- DissociationOperatorTest.class, //
- ModifierTest.class,//
- NandOperatorTest.class, //
- NodeOperatorComparatorTest.class, //
- NodeOperatorTest.class, //
- OrOperatorTest.class, //
- ProductTest.class, //
- ReactantTest.class,//
- ReactionComparatorTest.class, //
- ReactionNodeComparatorTest.class, //
- ReactionTest.class, //
- SplitOperatorTest.class,//
- TruncationOperatorTest.class, //
- UnknownOperatorTest.class,//
+@SuiteClasses({ AbstractNodeComparatorTest.class,
+ AllReactionTypeTests.class,
+ AndOperatorTest.class,
+ AssociationOperatorTest.class,
+ DissociationOperatorTest.class,
+ ModifierTest.class,
+ NandOperatorTest.class,
+ NodeOperatorComparatorTest.class,
+ NodeOperatorTest.class,
+ OrOperatorTest.class,
+ ProductTest.class,
+ ReactantTest.class,
+ ReactionComparatorTest.class,
+ ReactionNodeComparatorTest.class,
+ ReactionTest.class,
+ SplitOperatorTest.class,
+ TruncationOperatorTest.class,
+ UnknownOperatorTest.class,
})
public class AllReactionTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
index f0a8d101d1..b13150f5c4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
@@ -5,27 +5,27 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BooleanLogicGateReactionTest.class, //
- DissociationReactionTest.class, //
- HeterodimerAssociationReactionTest.class, //
- KnownTransitionOmittedReactionTest.class, //
- NegativeInfluenceReactionTest.class, //
- PositiveInfluenceReactionTest.class, //
- ReactionRectTest.class, //
- ReducedModulationReactionTest.class, //
- ReducedPhysicalStimulationReactionTest.class, //
- ReducedTriggerReactionTest.class, //
- StateTransitionReactionTest.class, //
- TranscriptionReactionTest.class, //
- TranslationReactionTest.class, //
- TransportReactionTest.class, //
- TruncationReactionTest.class, //
- UnknownNegativeInfluenceReactionTest.class, //
- UnknownPositiveInfluenceReactionTest.class, //
- UnknownReducedModulationReactionTest.class, //
- UnknownReducedPhysicalStimulationReactionTest.class, //
- UnknownReducedTriggerReactionTest.class, //
- UnknownTransitionReactionTest.class, //
+@SuiteClasses({ BooleanLogicGateReactionTest.class,
+ DissociationReactionTest.class,
+ HeterodimerAssociationReactionTest.class,
+ KnownTransitionOmittedReactionTest.class,
+ NegativeInfluenceReactionTest.class,
+ PositiveInfluenceReactionTest.class,
+ ReactionRectTest.class,
+ ReducedModulationReactionTest.class,
+ ReducedPhysicalStimulationReactionTest.class,
+ ReducedTriggerReactionTest.class,
+ StateTransitionReactionTest.class,
+ TranscriptionReactionTest.class,
+ TranslationReactionTest.class,
+ TransportReactionTest.class,
+ TruncationReactionTest.class,
+ UnknownNegativeInfluenceReactionTest.class,
+ UnknownPositiveInfluenceReactionTest.class,
+ UnknownReducedModulationReactionTest.class,
+ UnknownReducedPhysicalStimulationReactionTest.class,
+ UnknownReducedTriggerReactionTest.class,
+ UnknownTransitionReactionTest.class,
})
public class AllReactionTypeTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
index 6bdf056efd..41464b30cc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
@@ -7,42 +7,42 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.model.map.species.field.AllFieldTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllFieldTests.class, //
- AntisenseRnaComparatorTest.class, //
- AntisenseRnaTest.class, //
- ChemicalComparatorTest.class, //
- ComplexComparatorTest.class, //
- ComplexTest.class, //
- DegradedComparatorTest.class, //
- DegradedTest.class, //
- DrugComparatorTest.class, //
- DrugTest.class, //
- ElementComparatorTest.class, //
- ElementTest.class, //
- GeneComparatorTest.class, //
- GenericProteinComparatorTest.class, //
- GenericProteinTest.class, //
- GeneTest.class, //
- IonChannelProteinTest.class, //
- IonChannelProteinComparatorTest.class, //
- IonComparatorTest.class, //
- IonTest.class, //
- PhenotypeComparatorTest.class, //
- PhenotypeTest.class, //
- ProteinComparatorTest.class, //
- ProteinTest.class, //
- ReceptorProteinTest.class, //
- ReceptorProteinComparatorTest.class, //
- RnaComparatorTest.class, //
- RnaTest.class, //
- SimpleMoleculeComparatorTest.class, //
- SimpleMoleculeTest.class, //
- SpeciesComparatorTest.class, //
- SpeciesTest.class, //
- TruncatedProteinTest.class, //
- TruncatedProteinComparatorTest.class, //
- UnknownComparatorTest.class, //
- UnknownTest.class, //
+@SuiteClasses({ AllFieldTests.class,
+ AntisenseRnaComparatorTest.class,
+ AntisenseRnaTest.class,
+ ChemicalComparatorTest.class,
+ ComplexComparatorTest.class,
+ ComplexTest.class,
+ DegradedComparatorTest.class,
+ DegradedTest.class,
+ DrugComparatorTest.class,
+ DrugTest.class,
+ ElementComparatorTest.class,
+ ElementTest.class,
+ GeneComparatorTest.class,
+ GenericProteinComparatorTest.class,
+ GenericProteinTest.class,
+ GeneTest.class,
+ IonChannelProteinTest.class,
+ IonChannelProteinComparatorTest.class,
+ IonComparatorTest.class,
+ IonTest.class,
+ PhenotypeComparatorTest.class,
+ PhenotypeTest.class,
+ ProteinComparatorTest.class,
+ ProteinTest.class,
+ ReceptorProteinTest.class,
+ ReceptorProteinComparatorTest.class,
+ RnaComparatorTest.class,
+ RnaTest.class,
+ SimpleMoleculeComparatorTest.class,
+ SimpleMoleculeTest.class,
+ SpeciesComparatorTest.class,
+ SpeciesTest.class,
+ TruncatedProteinTest.class,
+ TruncatedProteinComparatorTest.class,
+ UnknownComparatorTest.class,
+ UnknownTest.class,
})
public class AllSpeciesTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
index afde73415e..48eca26298 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
@@ -5,13 +5,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CodingRegionTest.class, //
- ModificationStateTest.class, //
- ResidueTest.class, //
- PositionToCompartmentTest.class, //
- ProteinBindingDomainTest.class,//
- StructureTest.class,//
- UniprotRecordTest.class,//
+@SuiteClasses({ CodingRegionTest.class,
+ ModificationStateTest.class,
+ ResidueTest.class,
+ PositionToCompartmentTest.class,
+ ProteinBindingDomainTest.class,
+ StructureTest.class,
+ UniprotRecordTest.class,
})
public class AllFieldTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
index 278b07f38d..e212af7b9b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
@@ -5,8 +5,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ SearchHistoryTest.class, //
- SearchTypeTest.class,//
+@SuiteClasses({ SearchHistoryTest.class,
+ SearchTypeTest.class,
})
public class AllStatisticsTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java b/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
index 11d59b900b..9e1f50fef2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
@@ -5,17 +5,17 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BasicPrivilegeTest.class, //
- ConfigurationElementTypeTest.class, //
- ConfigurationElementEditTypeTest.class, //
- ConfigurationTest.class, //
- ObjectPrivilegeTest.class, //
- PrivilegeTypeTest.class, //
- UserAnnotationSchemaTest.class, //
- UserClassAnnotatorsTest.class, //
- UserClassRequiredAnnotationsTest.class, //
- UserClassValidAnnotationsTest.class, //
- UserTest.class,//
+@SuiteClasses({ BasicPrivilegeTest.class,
+ ConfigurationElementTypeTest.class,
+ ConfigurationElementEditTypeTest.class,
+ ConfigurationTest.class,
+ ObjectPrivilegeTest.class,
+ PrivilegeTypeTest.class,
+ UserAnnotationSchemaTest.class,
+ UserClassAnnotatorsTest.class,
+ UserClassRequiredAnnotationsTest.class,
+ UserClassValidAnnotationsTest.class,
+ UserTest.class,
})
public class AllUserTests {
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
index 6e4837f4a5..16ddd95d33 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
@@ -5,9 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ClassTreeNodeTest.class, //
- ElementUtilsTest.class, //
- RequireAnnotationMapTest.class, //
+@SuiteClasses({ ClassTreeNodeTest.class,
+ ElementUtilsTest.class,
+ RequireAnnotationMapTest.class,
})
public class AllMapUtilTests {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index ba5686885f..4c5c2beb9c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -167,8 +167,8 @@ public class GpmlParser {
if ("".equals(style)) {
style = null;
}
- if (style != null && //
- !"Complex".equalsIgnoreCase(style) && //
+ if (style != null &&
+ !"Complex".equalsIgnoreCase(style) &&
!"Group".equalsIgnoreCase(style)) {
throw new UnknownAttributeValueException(
"Unknown value of \"style\" attribute for group node: " + style + ". Only null, Complex, Group are supported.");
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
index 6d2ec1a489..53e55ce336 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
@@ -12,17 +12,17 @@ public enum Direction {
/**
* North.
*/
- NORTH(Axis.NORTH_SOUTH), //
+ NORTH(Axis.NORTH_SOUTH),
/**
* East.
*/
- EAST(Axis.EAST_WEST), //
+ EAST(Axis.EAST_WEST),
/**
* South.
*/
- SOUTH(Axis.NORTH_SOUTH), //
+ SOUTH(Axis.NORTH_SOUTH),
/**
* West.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
index 27c3cbc362..524c0b7e1a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
@@ -11,77 +11,77 @@ public enum GpmlInteractionType {
/**
* Simple line.
*/
- LINE(null), //
+ LINE(null),
/**
* Arrow.
*/
- ARROW("Arrow"), //
+ ARROW("Arrow"),
/**
* T-bar.
*/
- TBAR("TBar"), //
+ TBAR("TBar"),
/**
* Necessary stimulation.
*/
- NECESSARY_STIMULATION("mim-necessary-stimulation"), //
+ NECESSARY_STIMULATION("mim-necessary-stimulation"),
/**
* Binding.
*/
- BINDING("mim-binding"), //
+ BINDING("mim-binding"),
/**
* Conversion.
*/
- CONVERSION("mim-conversion"), //
+ CONVERSION("mim-conversion"),
/**
* Stimulation.
*/
- STIMULATION("mim-stimulation"), //
+ STIMULATION("mim-stimulation"),
/**
* Modification.
*/
- MODIFICATION("mim-modification"), //
+ MODIFICATION("mim-modification"),
/**
* Catalysis.
*/
- CATALYSIS("mim-catalysis"), //
+ CATALYSIS("mim-catalysis"),
/**
* Inhibition.
*/
- INHIBITION("mim-inhibition"), //
+ INHIBITION("mim-inhibition"),
/**
* Cleavage.
*/
- CLEAVAGE("mim-cleavage"), //
+ CLEAVAGE("mim-cleavage"),
/**
* Covalent bond.
*/
- COVALENT_BOND("mim-covalent-bond"), //
+ COVALENT_BOND("mim-covalent-bond"),
/**
* Branching (to the left).
*/
- BRANCHING_LEFT("mim-branching-left"), //
+ BRANCHING_LEFT("mim-branching-left"),
/**
* Branching (to the right).
*/
- BRANCHING_RIGHT("mim-branching-right"), //
+ BRANCHING_RIGHT("mim-branching-right"),
/**
* Transcription, translation.
*/
- TRANSCRIPTION_TRANSLATION("mim-transcription-translation"), //
+ TRANSCRIPTION_TRANSLATION("mim-transcription-translation"),
/**
* Gap.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
index 4724e464ff..8eab165591 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
@@ -11,17 +11,17 @@ public enum GpmlLineConnectorType {
/**
* Line is a curve.
*/
- CURVED("Curved"), //
+ CURVED("Curved"),
/**
* Line is constructed from list of perpendicular segments.
*/
- ELBOW("Elbow"), //
+ ELBOW("Elbow"),
/**
* It's a straight line from start point to the end point.
*/
- STRAIGHT("Straight"), //
+ STRAIGHT("Straight"),
/**
* Line is constructoed from list of segement lines.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
index 6f2c441646..60a07ccd7d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
@@ -13,7 +13,7 @@ public enum GpmlLineType {
/**
* Sold line (global representation: {@link LineType#SOLID}).
*/
- SOLID(null, LineType.SOLID), //
+ SOLID(null, LineType.SOLID),
/**
* Dashed line (global representation: {@link LineType#DASHED}).
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
index 8f63049790..79370f35ab 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
@@ -13,57 +13,57 @@ public enum GpmlModificationType {
/**
* Gpml type representing: {@link ModificationState#PHOSPHORYLATED}.
*/
- PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED), //
+ PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED),
/**
* Gpml type representing: {@link ModificationState#ACETYLATED}.
*/
- ACETYLATED("Ac", ModificationState.ACETYLATED), //
+ ACETYLATED("Ac", ModificationState.ACETYLATED),
/**
* Gpml type representing: {@link ModificationState#UBIQUITINATED}.
*/
- UBIQUITINATED("Ub", ModificationState.UBIQUITINATED), //
+ UBIQUITINATED("Ub", ModificationState.UBIQUITINATED),
/**
* Gpml type representing: {@link ModificationState#METHYLATED}.
*/
- METHYLATED("Me", ModificationState.METHYLATED), //
+ METHYLATED("Me", ModificationState.METHYLATED),
/**
* Gpml type representing: {@link ModificationState#HYDROXYLATED}.
*/
- HYDROXYLATED("OH", ModificationState.HYDROXYLATED), //
+ HYDROXYLATED("OH", ModificationState.HYDROXYLATED),
/**
* Gpml type representing: {@link ModificationState#MYRISTOYLATED}.
*/
- MYRISTOYLATED("My", ModificationState.MYRISTOYLATED), //
+ MYRISTOYLATED("My", ModificationState.MYRISTOYLATED),
/**
* Gpml type representing: {@link ModificationState#SULFATED}.
*/
- SULFATED("S", ModificationState.SULFATED), //
+ SULFATED("S", ModificationState.SULFATED),
/**
* Gpml type representing: {@link ModificationState#PRENYLATED}.
*/
- PRENYLATED("Pr", ModificationState.PRENYLATED), //
+ PRENYLATED("Pr", ModificationState.PRENYLATED),
/**
* Gpml type representing: {@link ModificationState#GLYCOSYLATED}.
*/
- GLYCOSYLATED("G", ModificationState.GLYCOSYLATED), //
+ GLYCOSYLATED("G", ModificationState.GLYCOSYLATED),
/**
* Gpml type representing: {@link ModificationState#PALMYTOYLATED}.
*/
- PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED), //
+ PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED),
/**
* Gpml type representing: {@link ModificationState#UNKNOWN}.
*/
- UNKOWN("", ModificationState.UNKNOWN), //
+ UNKOWN("", ModificationState.UNKNOWN),
/**
* Gpml type representing: {@link ModificationState#PROTONATED}.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
index 87129f1689..feccb7c7fc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
@@ -13,7 +13,7 @@ public enum GpmlStateType {
* {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
* Protein}.
*/
- GTP("GTP", "GTP"), //
+ GTP("GTP", "GTP"),
/**
* Gpml type representing "GDP"
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
index 23123297e1..d8570ebf06 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
@@ -42,267 +42,267 @@ public enum InteractionMapping {
/**
* Default line.
*/
- LINE(GpmlInteractionType.LINE, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
+ LINE(GpmlInteractionType.LINE, GpmlLineType.SOLID,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, false,
+ Reactant.class, false,
+ true),
/**
* Default arrow.
*/
- ARROW(GpmlInteractionType.ARROW, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
+ ARROW(GpmlInteractionType.ARROW, GpmlLineType.SOLID,
+ StateTransitionReaction.class, false,
+ Modulation.class, true,
Product.class, false),
/**
* Dashed line.
*/
- LINE_DASHED(GpmlInteractionType.LINE, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
+ LINE_DASHED(GpmlInteractionType.LINE, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, true,
+ Reactant.class, true,
+ true),
/**
* Dashed arrow.
*/
- ARROW_DASHED(GpmlInteractionType.ARROW, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
+ ARROW_DASHED(GpmlInteractionType.ARROW, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, false,
+ Modulation.class, true,
Product.class, true),
/**
* Line ended with T-bar.
*/
- TBAR(GpmlInteractionType.TBAR, GpmlLineType.SOLID, //
- NegativeInfluenceReaction.class, true, //
- Inhibition.class, false, //
- Product.class, true), //
+ TBAR(GpmlInteractionType.TBAR, GpmlLineType.SOLID,
+ NegativeInfluenceReaction.class, true,
+ Inhibition.class, false,
+ Product.class, true),
/**
* Line ended with T-bar dashed.
*/
- TBAR_DASHED(GpmlInteractionType.TBAR, GpmlLineType.DASHED, //
- UnknownNegativeInfluenceReaction.class, true, //
- UnknownInhibition.class, false, //
- Product.class, true), //
+ TBAR_DASHED(GpmlInteractionType.TBAR, GpmlLineType.DASHED,
+ UnknownNegativeInfluenceReaction.class, true,
+ UnknownInhibition.class, false,
+ Product.class, true),
/**
* Necessary stimulation.
*/
- NECESSARY_STIMULATION(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.SOLID, //
- ReducedPhysicalStimulationReaction.class, false, //
- PhysicalStimulation.class, false, //
- Product.class, true), //
+ NECESSARY_STIMULATION(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.SOLID,
+ ReducedPhysicalStimulationReaction.class, false,
+ PhysicalStimulation.class, false,
+ Product.class, true),
/**
* Necessary stimulation dashed.
*/
- NECESSARY_STIMULATION_DASHED(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
+ NECESSARY_STIMULATION_DASHED(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, true,
+ Modulation.class, true,
+ Product.class, true),
/**
* Binding.
*/
- BINDING(GpmlInteractionType.BINDING, GpmlLineType.SOLID, //
- HeterodimerAssociationReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
+ BINDING(GpmlInteractionType.BINDING, GpmlLineType.SOLID,
+ HeterodimerAssociationReaction.class, false,
+ Modulation.class, true,
+ Product.class, true),
/**
* Binding dashed.
*/
- BINDING_DASHED(GpmlInteractionType.BINDING, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
+ BINDING_DASHED(GpmlInteractionType.BINDING, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, false,
+ Modulation.class, true,
+ Product.class, true),
/**
* Conversion.
*/
- CONVERSION(GpmlInteractionType.CONVERSION, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
- Product.class, false), //
+ CONVERSION(GpmlInteractionType.CONVERSION, GpmlLineType.SOLID,
+ StateTransitionReaction.class, false,
+ Modulation.class, true,
+ Product.class, false),
/**
* Dashed conversion.
*/
- CONVERSION_DASHED(GpmlInteractionType.CONVERSION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
+ CONVERSION_DASHED(GpmlInteractionType.CONVERSION, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, false,
+ Modulation.class, true,
Product.class, true),
/**
* Stimulation.
*/
- STIMULATION(GpmlInteractionType.STIMULATION, GpmlLineType.SOLID, //
- ReducedPhysicalStimulationReaction.class, true, //
- PhysicalStimulation.class, false, //
- Product.class, true), //
+ STIMULATION(GpmlInteractionType.STIMULATION, GpmlLineType.SOLID,
+ ReducedPhysicalStimulationReaction.class, true,
+ PhysicalStimulation.class, false,
+ Product.class, true),
/**
* Stimulation dashed.
*/
- STIMULATION_DASHED(GpmlInteractionType.STIMULATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
+ STIMULATION_DASHED(GpmlInteractionType.STIMULATION, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, true,
+ Modulation.class, true,
+ Product.class, true),
/**
* Modification.
*/
- MODIFICATION(GpmlInteractionType.MODIFICATION, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, false, //
- Product.class, true), //
+ MODIFICATION(GpmlInteractionType.MODIFICATION, GpmlLineType.SOLID,
+ PositiveInfluenceReaction.class, true,
+ Modulation.class, false,
+ Product.class, true),
/**
* Modification dashed.
*/
- MODIFICATION_DASHED(GpmlInteractionType.MODIFICATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
+ MODIFICATION_DASHED(GpmlInteractionType.MODIFICATION, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, false,
+ Modulation.class, true,
+ Product.class, true),
/**
* Catalysis.
*/
- CATALYSIS(GpmlInteractionType.CATALYSIS, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Catalysis.class, false, //
- Product.class, true), //
+ CATALYSIS(GpmlInteractionType.CATALYSIS, GpmlLineType.SOLID,
+ PositiveInfluenceReaction.class, true,
+ Catalysis.class, false,
+ Product.class, true),
/**
* Catalysis dashed.
*/
- CATALYSIS_DASHED(GpmlInteractionType.CATALYSIS, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- UnknownCatalysis.class, false, //
- Product.class, true), //
+ CATALYSIS_DASHED(GpmlInteractionType.CATALYSIS, GpmlLineType.DASHED,
+ UnknownPositiveInfluenceReaction.class, true,
+ UnknownCatalysis.class, false,
+ Product.class, true),
/**
* Inhibition.
*/
- INHIBITION(GpmlInteractionType.INHIBITION, GpmlLineType.SOLID, //
- NegativeInfluenceReaction.class, false, //
- Inhibition.class, false, //
- Product.class, true), //
+ INHIBITION(GpmlInteractionType.INHIBITION, GpmlLineType.SOLID,
+ NegativeInfluenceReaction.class, false,
+ Inhibition.class, false,
+ Product.class, true),
/**
* Inhibition dashed.
*/
- INHIBITION_DASHED(GpmlInteractionType.INHIBITION, GpmlLineType.DASHED, //
- UnknownNegativeInfluenceReaction.class, true, //
- UnknownInhibition.class, true, //
- Product.class, true), //
+ INHIBITION_DASHED(GpmlInteractionType.INHIBITION, GpmlLineType.DASHED,
+ UnknownNegativeInfluenceReaction.class, true,
+ UnknownInhibition.class, true,
+ Product.class, true),
/**
* Cleavage.
*/
- CLEAVAGE(GpmlInteractionType.CLEAVAGE, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
- Product.class, false), //
+ CLEAVAGE(GpmlInteractionType.CLEAVAGE, GpmlLineType.SOLID,
+ StateTransitionReaction.class, false,
+ Modulation.class, true,
+ Product.class, false),
/**
* Cleavage dashed.
*/
- CLEAVAGE_DASHED(GpmlInteractionType.CLEAVAGE, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
+ CLEAVAGE_DASHED(GpmlInteractionType.CLEAVAGE, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Modulation.class, true,
+ Product.class, true),
/**
* Covalent bond.
*/
- COVALENT_BOND(GpmlInteractionType.COVALENT_BOND, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Product.class, true, //
- true), //
+ COVALENT_BOND(GpmlInteractionType.COVALENT_BOND, GpmlLineType.SOLID,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, true,
+ Product.class, true,
+ true),
/**
* Covalent bond dashed.
*/
- COVALENT_BOND_DASHED(GpmlInteractionType.COVALENT_BOND, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Product.class, true, //
- true), //
+ COVALENT_BOND_DASHED(GpmlInteractionType.COVALENT_BOND, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, true,
+ Product.class, true,
+ true),
/**
* Branching left.
*/
- BRANCHING_LEFT(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
+ BRANCHING_LEFT(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.SOLID,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, false,
+ Reactant.class, false,
+ true),
/**
* Branching left dashed.
*/
- BRANCHING_LEFT_DASHED(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
+ BRANCHING_LEFT_DASHED(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, true,
+ Reactant.class, true,
+ true),
/**
* Branching right.
*/
- BRANCHING_RIGHT(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
+ BRANCHING_RIGHT(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.SOLID,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, false,
+ Reactant.class, false,
+ true),
/**
* Branching right dashed.
*/
- BRANCHING_RIGHT_DASHED(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
+ BRANCHING_RIGHT_DASHED(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Reactant.class, true,
+ Reactant.class, true,
+ true),
/**
* Transription-translation.
*/
- TRANSCRIPTION_TRANSLATION(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
+ TRANSCRIPTION_TRANSLATION(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.SOLID,
+ PositiveInfluenceReaction.class, true,
+ Modulation.class, true,
+ Product.class, true),
/**
* Transription-translation dashed.
*/
- TRANSCRIPTION_TRANSLATION_DASHED(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.DASHED, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
+ TRANSCRIPTION_TRANSLATION_DASHED(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.DASHED,
+ PositiveInfluenceReaction.class, true,
+ Modulation.class, true,
+ Product.class, true),
/**
* Gap...
*/
- GAP(GpmlInteractionType.GAP, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true, //
+ GAP(GpmlInteractionType.GAP, GpmlLineType.SOLID,
+ UnknownTransitionReaction.class, true,
+ Modulation.class, true,
+ Product.class, true,
true),
/**
* Gap dashed...
*/
- GAP_DASHED(GpmlInteractionType.GAP, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true, //
+ GAP_DASHED(GpmlInteractionType.GAP, GpmlLineType.DASHED,
+ UnknownTransitionReaction.class, true,
+ Modulation.class, true,
+ Product.class, true,
true);
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
index c945b07a3a..2076bccc08 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
@@ -14,48 +14,48 @@ public enum MergeMapping {
* Merging {@link GpmlInteractionType#LINE} and
* {@link GpmlInteractionType#ARROW} when both of them are in right direction.
*/
- LINE_ARROW_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
+ LINE_ARROW_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false),
/**
* Merging {@link GpmlInteractionType#LINE} and
* {@link GpmlInteractionType#ARROW} when line is reversed (user doesn't see a
* difference) and arrow is in normal direction.
*/
- LINE_ARROW_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
+ LINE_ARROW_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false),
/**
* Merging {@link GpmlInteractionType#ARROW} and
* {@link GpmlInteractionType#LINE} when arrow is reversed and line is in
* normal direction.
*/
- ARROW_LINE_R_N(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, true), //
+ ARROW_LINE_R_N(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, true),
/**
* Merging {@link GpmlInteractionType#ARROW} and
* {@link GpmlInteractionType#LINE} when line is reversed and line is also
* reversed (user doesn't see a difference) .
*/
- ARROW_LINE_R_R(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, true), //
+ ARROW_LINE_R_R(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, true),
/**
* Merging {@link GpmlInteractionType#LINE} and
* {@link GpmlInteractionType#LINE} when both of them are in right direction.
*/
- LINE_LINE_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
+ LINE_LINE_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false),
/**
* Merging {@link GpmlInteractionType#LINE} and
* {@link GpmlInteractionType#LINE} when first of them is reversed and second
* not.
*/
- LINE_LINE_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
+ LINE_LINE_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false),
/**
* Merging {@link GpmlInteractionType#LINE} and
* {@link GpmlInteractionType#LINE} when first is in right direction, but
* second reversed.
*/
- LINE_LINE_N_R(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false), //
+ LINE_LINE_N_R(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false),
/**
* Merging {@link GpmlInteractionType#LINE} and
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
index 236d8c972e..9db45a737d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
@@ -14,177 +14,177 @@ public enum ReferenceMapping {
/**
* {@link MiriamType#CAS}.
*/
- CAS("CAS", MiriamType.CAS), //
+ CAS("CAS", MiriamType.CAS),
/**
* {@link MiriamType#CHEBI}.
*/
- CHEBI("Chebi", MiriamType.CHEBI), //
+ CHEBI("Chebi", MiriamType.CHEBI),
/**
* {@link MiriamType#CHEMBL_COMPOUND}.
*/
- CHEMBL_COMPOUND(null, MiriamType.CHEMBL_COMPOUND), //
+ CHEMBL_COMPOUND(null, MiriamType.CHEMBL_COMPOUND),
/**
* {@link MiriamType#CHEMBL_TARGET}.
*/
- CHEMBL_TARGET(null, MiriamType.CHEMBL_TARGET), //
+ CHEMBL_TARGET(null, MiriamType.CHEMBL_TARGET),
/**
* {@link MiriamType#CHEMSPIDER}.
*/
- CHEMSPIDER("ChemSpider", MiriamType.CHEMSPIDER), //
+ CHEMSPIDER("ChemSpider", MiriamType.CHEMSPIDER),
/**
* {@link MiriamType#EC}.
*/
- EC("Enzyme Nomenclature", MiriamType.EC), //
+ EC("Enzyme Nomenclature", MiriamType.EC),
/**
* {@link MiriamType#ENSEMBL}.
*/
- ENSEMBL("Ensembl", MiriamType.ENSEMBL), //
+ ENSEMBL("Ensembl", MiriamType.ENSEMBL),
/**
* {@link MiriamType#ENTREZ}.
*/
- ENTREZ("Entrez Gene", MiriamType.ENTREZ), //
+ ENTREZ("Entrez Gene", MiriamType.ENTREZ),
/**
* Alternative name for {@link MiriamType#ENTREZ}.
*/
- GEN_BANK("GenBank", MiriamType.ENTREZ), //
+ GEN_BANK("GenBank", MiriamType.ENTREZ),
/**
* {@link MiriamType#GO}.
*/
- GO("GeneOntology", MiriamType.GO), //
+ GO("GeneOntology", MiriamType.GO),
/**
* {@link MiriamType#HGNC}.
*/
- HGNC("HGNC Accession number", MiriamType.HGNC), //
+ HGNC("HGNC Accession number", MiriamType.HGNC),
/**
* {@link MiriamType#HGNC_SYMBOL}.
*/
- HGNC_SYMBOL("HGNC", MiriamType.HGNC_SYMBOL), //
+ HGNC_SYMBOL("HGNC", MiriamType.HGNC_SYMBOL),
/**
* {@link MiriamType#HMDB}.
*/
- HMDB("HMDB", MiriamType.HMDB), //
+ HMDB("HMDB", MiriamType.HMDB),
/**
* {@link MiriamType#INTERPRO}.
*/
- INTERPRO("InterPro", MiriamType.INTERPRO), //
+ INTERPRO("InterPro", MiriamType.INTERPRO),
/**
* {@link MiriamType#MESH_2012}.
*/
- MESH_2012(null, MiriamType.MESH_2012), //
+ MESH_2012(null, MiriamType.MESH_2012),
/**
* {@link MiriamType#MI_RBASE_SEQUENCE}.
*/
- MI_RBASE_SEQUENCE2("miRBase", MiriamType.MI_R_BASE_SEQUENCE), //
+ MI_RBASE_SEQUENCE2("miRBase", MiriamType.MI_R_BASE_SEQUENCE),
/**
* {@link MiriamType#KEGG_COMPOUND}.
*/
- KEGG_COMPOUND("KEGG Compound", MiriamType.KEGG_COMPOUND), //
+ KEGG_COMPOUND("KEGG Compound", MiriamType.KEGG_COMPOUND),
/**
* {@link MiriamType#KEGG_GENES}.
*/
- KEGG_GENES("KEGG Genes", MiriamType.KEGG_GENES), //
+ KEGG_GENES("KEGG Genes", MiriamType.KEGG_GENES),
/**
* {@link MiriamType#KEGG_ORTHOLOGY}.
*/
- KEGG_ORTHOLOGY("Kegg ortholog", MiriamType.KEGG_ORTHOLOGY), //
+ KEGG_ORTHOLOGY("Kegg ortholog", MiriamType.KEGG_ORTHOLOGY),
/**
* {@link MiriamType#KEGG_PATHWAY}.
*/
- KEGG_PATHWAY("KEGG Pathway", MiriamType.KEGG_PATHWAY), //
+ KEGG_PATHWAY("KEGG Pathway", MiriamType.KEGG_PATHWAY),
/**
* {@link MiriamType#KEGG_REACTION}.
*/
- KEGG_REACTION("KEGG Reaction", MiriamType.KEGG_REACTION), //
+ KEGG_REACTION("KEGG Reaction", MiriamType.KEGG_REACTION),
/**
* {@link MiriamType#MGD}.
*/
- MGD("MGI", MiriamType.MGD), //
+ MGD("MGI", MiriamType.MGD),
/**
* {@link MiriamType#MI_RBASE_SEQUENCE}.
*/
- MI_RBASE_SEQUENCE("miRBase Sequence", MiriamType.MI_R_BASE_SEQUENCE), //
+ MI_RBASE_SEQUENCE("miRBase Sequence", MiriamType.MI_R_BASE_SEQUENCE),
/**
* {@link MiriamType#PANTHER}.
*/
- PANTHER(null, MiriamType.PANTHER), //
+ PANTHER(null, MiriamType.PANTHER),
/**
* {@link MiriamType#PFAM}.
*/
- PFAM("Pfam", MiriamType.PFAM), //
+ PFAM("Pfam", MiriamType.PFAM),
/**
* {@link MiriamType#PHARM}.
*/
- PHARM("PharmGKB Pathways", MiriamType.PHARM), //
+ PHARM("PharmGKB Pathways", MiriamType.PHARM),
/**
* {@link MiriamType#PUBCHEM}.
*/
- PUBCHEM("PubChem-compound", MiriamType.PUBCHEM), //
+ PUBCHEM("PubChem-compound", MiriamType.PUBCHEM),
/**
* {@link MiriamType#PUBCHEM_SUBSTANCE}.
*/
- PUBCHEM_SUBSTANCE("PubChem-substance", MiriamType.PUBCHEM_SUBSTANCE), //
+ PUBCHEM_SUBSTANCE("PubChem-substance", MiriamType.PUBCHEM_SUBSTANCE),
/**
* {@link MiriamType#REACTOME}.
*/
- REACTOME("Reactome", MiriamType.REACTOME), //
+ REACTOME("Reactome", MiriamType.REACTOME),
/**
* {@link MiriamType#REFSEQ}.
*/
- REFSEQ("RefSeq", MiriamType.REFSEQ), //
+ REFSEQ("RefSeq", MiriamType.REFSEQ),
/**
* {@link MiriamType#SGD }.
*/
- SGD("SGD", MiriamType.SGD), //
+ SGD("SGD", MiriamType.SGD),
/**
* {@link MiriamType#TAIR_LOCUS}.
*/
- TAIR_LOCUS("TAIR", MiriamType.TAIR_LOCUS), //
+ TAIR_LOCUS("TAIR", MiriamType.TAIR_LOCUS),
/**
* {@link MiriamType#UNIPROT}.
*/
- UNIPROT("Uniprot-TrEMBL", MiriamType.UNIPROT), //
+ UNIPROT("Uniprot-TrEMBL", MiriamType.UNIPROT),
/**
* {@link MiriamType#UNIPROT_ISOFORM}.
*/
- UNIPROT_ISOFORM(null, MiriamType.UNIPROT_ISOFORM), //
+ UNIPROT_ISOFORM(null, MiriamType.UNIPROT_ISOFORM),
/**
* {@link MiriamType#WIKIPATHWAYS}.
*/
- WIKIPATHWAYS("Wikipathways", MiriamType.WIKIPATHWAYS), //
+ WIKIPATHWAYS("Wikipathways", MiriamType.WIKIPATHWAYS),
/**
* {@link MiriamType#WIKIPEDIA}.
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
index 2f098eb7e2..fee29d20bc 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
@@ -8,14 +8,14 @@ import lcsb.mapviewer.wikipathway.XML.AllXmlTests;
import lcsb.mapviewer.wikipathway.model.AllModelTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class, //
- AllXmlTests.class, //
- ComplexReactionToModelTest.class, //
- GPMLToModelTest.class, //
- ReactionElbowsTest.class, //
- ReactionGpmlInputToModelTest.class, //
- ReactionGpmlOutputToModelTest.class, //
- ReactionGpmlToModelTest.class, //
+@SuiteClasses({ AllModelTests.class,
+ AllXmlTests.class,
+ ComplexReactionToModelTest.class,
+ GPMLToModelTest.class,
+ ReactionElbowsTest.class,
+ ReactionGpmlInputToModelTest.class,
+ ReactionGpmlOutputToModelTest.class,
+ ReactionGpmlToModelTest.class,
})
public class AllWikipathwaysTests {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
index 0fbf211664..563d471d1f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
@@ -5,17 +5,17 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BiopaxParserTest.class,//
- DataNodeParserTest.class,//
- BugTest.class,//
- EdgeLineParserTest.class,//
- GpmlParserTest.class,//
- LabelParserTest.class,//
- ReferenceParserTest.class,//
- ModelToGPMLTest.class,//
- ModelContructorTest.class,//
- ShapeParserTest.class,//
- StateParserTest.class,//
+@SuiteClasses({ BiopaxParserTest.class,
+ DataNodeParserTest.class,
+ BugTest.class,
+ EdgeLineParserTest.class,
+ GpmlParserTest.class,
+ LabelParserTest.class,
+ ReferenceParserTest.class,
+ ModelToGPMLTest.class,
+ ModelContructorTest.class,
+ ShapeParserTest.class,
+ StateParserTest.class,
})
public class AllXmlTests {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
index 9a4e932e88..940702b474 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
@@ -7,15 +7,15 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllBiopaxTests.class,//
- DataNodeTest.class,//
- EdgeTest.class,//
- GraphTest.class,//
- GroupTest.class,//
- InteractionTest.class,//
- LabelTest.class,//
- PointDataTest.class,//
- ShapeTest.class,//
+@SuiteClasses({ AllBiopaxTests.class,
+ DataNodeTest.class,
+ EdgeTest.class,
+ GraphTest.class,
+ GroupTest.class,
+ InteractionTest.class,
+ LabelTest.class,
+ PointDataTest.class,
+ ShapeTest.class,
StateTest.class })
public class AllModelTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
index b93bf18b8d..ea10a931c1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
@@ -7,11 +7,11 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ ApplicationContextLoaderTest.class, //
- AllDaoTests.class, //
- DbUtilsTest.class, //
- Point2DMapperTest.class, //
- SpringApplicationContextTest.class,//
+@Suite.SuiteClasses({ ApplicationContextLoaderTest.class,
+ AllDaoTests.class,
+ DbUtilsTest.class,
+ Point2DMapperTest.class,
+ SpringApplicationContextTest.class,
})
public class AllDbTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
index a0fb28df6b..bbeed51632 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
@@ -56,9 +56,9 @@ import lcsb.mapviewer.persist.dao.user.UserDao;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml" //
+@ContextConfiguration(locations = { "/applicationContext-persist.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml"
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class PersistTestFunctions {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
index 40344ac58c..1aa38d0378 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
@@ -11,15 +11,15 @@ import lcsb.mapviewer.persist.dao.plugin.AllPluginTests;
import lcsb.mapviewer.persist.dao.user.AllUserTests;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ AllCacheDbTests.class, //
- AllGraphicsDaoTests.class, //
- AllLogTests.class, //
- AllMapDaoTests.class, //
- AllPluginTests.class, //
- AllUserTests.class, //
- BaseDaoTest.class, //
- ConfigurationDaoTest.class, //
- ProjectDaoTest.class, //
+@Suite.SuiteClasses({ AllCacheDbTests.class,
+ AllGraphicsDaoTests.class,
+ AllLogTests.class,
+ AllMapDaoTests.class,
+ AllPluginTests.class,
+ AllUserTests.class,
+ BaseDaoTest.class,
+ ConfigurationDaoTest.class,
+ ProjectDaoTest.class,
})
public class AllDaoTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
index 3c2a221595..774531dd15 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
@@ -5,10 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BigFileEntryDaoTest.class, //
- CacheTypeDaoTest.class, //
- CacheQueryDaoTest.class, //
- UploadedFileEntryDaoTest.class,//
+@SuiteClasses({ BigFileEntryDaoTest.class,
+ CacheTypeDaoTest.class,
+ CacheQueryDaoTest.class,
+ UploadedFileEntryDaoTest.class,
})
public class AllCacheDbTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
index 0e635258bc..2bb1a3edf2 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ LogDaoTest.class,//
+@SuiteClasses({ LogDaoTest.class,
})
public class AllLogTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
index 19c30d3e5b..5ec0b873ca 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
@@ -8,12 +8,12 @@ import lcsb.mapviewer.persist.dao.map.layout.AllLayoutTests;
import lcsb.mapviewer.persist.dao.map.statistics.StatisticsAllTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllLayoutTests.class, //
- CommentDaoTest.class, //
- FeedbackTest.class, //
- LayoutDaoTest.class, //
- ModelDaoTest.class, //
- StatisticsAllTests.class, //
+@SuiteClasses({ AllLayoutTests.class,
+ CommentDaoTest.class,
+ FeedbackTest.class,
+ LayoutDaoTest.class,
+ ModelDaoTest.class,
+ StatisticsAllTests.class,
})
public class AllMapDaoTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
index 944cbb34d9..fb3285bb7d 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
@@ -7,9 +7,9 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.persist.dao.map.layout.alias.AllAliasTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllAliasTests.class, //
- ReferenceGenomeDaoTest.class, //
- ReferenceGenomeGeneMappingDaoTest.class,//
+@SuiteClasses({ AllAliasTests.class,
+ ReferenceGenomeDaoTest.class,
+ ReferenceGenomeGeneMappingDaoTest.class,
})
public class AllLayoutTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
index a2c62e35b1..b9751d8156 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
@@ -5,10 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AliasDaoTest.class, //
- AliasDaoTest2.class, //
- AntisenseRnaTest.class, //
- RnaTest.class, //
+@SuiteClasses({ AliasDaoTest.class,
+ AliasDaoTest2.class,
+ AntisenseRnaTest.class,
+ RnaTest.class,
})
public class AllAliasTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
index 75664e9ccb..5615a52363 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ PluginDaoTest.class, //
+@SuiteClasses({ PluginDaoTest.class,
PluginDataEntryDaoTest.class })
public class AllPluginTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
index dd2ee9fc3c..9521ac690a 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ UserDaoTest.class, //
+@SuiteClasses({ UserDaoTest.class,
})
public class AllUserTests {
diff --git a/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java b/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
index 3ce6491167..ac180b8682 100644
--- a/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
+++ b/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
@@ -188,11 +188,11 @@ public class PointQuadTree {
* @return size of map within model.
*/
private MyRectangle getWholeField(IRectangleShape model) {
- // ////////////////
+ // //////////////
int height, width = height = Math.max((int) (double) model.getHeight(), (int) (double) model.getWidth());
int x = 0;
int y = 0;
- // ////////////////
+ // //////////////
Point tmp = new Point(x, y);
return new MyRectangle(tmp, width, height);
}
@@ -204,12 +204,12 @@ public class PointQuadTree {
* @return
*/
private MyRectangle getWholeField() {
- // ////////////////
+ // //////////////
int height = DEFAULT_RECT_SIZE;
int width = DEFAULT_RECT_SIZE;
int x = 0;
int y = 0;
- // ////////////////
+ // //////////////
Point tmp = new Point(x, y);
return new MyRectangle(tmp, width, height);
}
diff --git a/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java b/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
index dfce7fce92..7d6ec9b179 100644
--- a/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
+++ b/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
@@ -12,12 +12,12 @@ import org.junit.runners.Suite;
public class SuitedTests {
}
-// //////////////////////////////////////////////////////
-// //
-// TODO TODO TODO TODO TODO TODO TODO TODO TODO //
-// //
-// TESTOWAĆTESTOWAĆTESTOWAĆTESTOWAĆTESTOWAĆ//
-// //
-// TODO TODO TODO TODO TODO TODO TODO TODO TODO //
-// //
-// //////////////////////////////////////////////////////
\ No newline at end of file
+// ////////////////////////////////////////////////////
+//
+// TODO TODO TODO TODO TODO TODO TODO TODO TODO
+//
+// TESTOWAĆTESTOWAĆTESTOWAĆTESTOWAĆTESTOWAÄâ€
+//
+// TODO TODO TODO TODO TODO TODO TODO TODO TODO
+//
+// ////////////////////////////////////////////////////
\ No newline at end of file
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
index 3c0984bea4..5a1bb6274c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
@@ -583,9 +583,9 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
}
// ------------------------------------------------
- //
+
// Methods that directly connect to reactome database (via restfull API)
- //
+
// ------------------------------------------------
/**
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/AllReactomeTests.java b/reactome/src/test/java/lcsb/mapviewer/reactome/AllReactomeTests.java
index d874c211a0..23fce328c5 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/AllReactomeTests.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/AllReactomeTests.java
@@ -8,8 +8,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllReactomeUtilsTests.class,//
- AllReactomeXmlTests.class,//
+@SuiteClasses({ AllReactomeUtilsTests.class,
+ AllReactomeXmlTests.class,
})
public class AllReactomeTests {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
index 80019a0fd6..3ed00dea33 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
@@ -51,11 +51,11 @@ import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
@Transactional(value = "txManager")
@Rollback(false)
-@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
- "/applicationContext-reactome.xml", //
- "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+@ContextConfiguration(locations = { "/applicationContext-annotation.xml",
+ "/applicationContext-reactome.xml",
+ "/applicationContext-persist.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml",
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class ReactomeTestFunctions {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/AllReactomeUtilsTests.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/AllReactomeUtilsTests.java
index fd37a493d8..9d86939027 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/AllReactomeUtilsTests.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/AllReactomeUtilsTests.java
@@ -7,10 +7,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ NodeComparatorTest.class, //
- ReactionComparatorTest.class,//
- ReactomeConnectorTest.class, //
- ReactomeQueryUtilTest.class, //
+@SuiteClasses({ NodeComparatorTest.class,
+ ReactionComparatorTest.class,
+ ReactomeConnectorTest.class,
+ ReactomeQueryUtilTest.class,
})
public class AllReactomeUtilsTests {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/AllReactomeXmlTests.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/AllReactomeXmlTests.java
index 421d88c561..3ec8fd60ac 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/AllReactomeXmlTests.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/AllReactomeXmlTests.java
@@ -5,39 +5,39 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ReactomeBlackBoxEventParserTest.class,//
- ReactomeCatalystActivityParserTest.class,//
- ReactomeCandidateSetParserTest.class,//
- ReactomeCompartmentParserTest.class,//
- ReactomeComplexParserTest.class,//
- ReactomeDatabaseIdentifierParserTest.class,//
- ReactomeDatabaseObjectParserTest.class,//
- ReactomeDefinedSetParserTest.class,//
- ReactomeDiseaseParserTest.class,//
- ReactomeEntityCompartmentParserTest.class,//
- ReactomeEntityWithAccessionedSequenceParserTest.class,//
- ReactomeFigureParserTest.class,//
- ReactomeGenomeEncodedEntityParserTest.class,//
- ReactomeGoBiologicalProcessParserTest.class,//
- ReactomeGoMolecularFunctionParserTest.class,//
- ReactomeInstanceEditParserTest.class,//
- ReactomeLiteratureReferenceParserTest.class,//
- ReactomeOtherEntityParserTest.class,//
- ReactomeParserFactoryTest.class,//
- ReactomePathwayParserTest.class,//
- ReactomePersonParserTest.class,//
- ReactomePolymerParserTest.class,//
- ReactomeReactionParserTest.class,//
- ReactomeReferenceDatabaseParserTest.class,//
- ReactomeReferenceGeneProductParserTest.class,//
- ReactomeReferenceIsoformParserTest.class,//
- ReactomeReferenceMoleculeParserTest.class,//
- ReactomeSimpleEntityParserTest.class,//
- ReactomeSpeciesParserTest.class,//
- ReactomeStableIdentifierParserTest.class,//
- ReactomeSummationParserTest.class,//
- ReactomeURLParserTest.class,//
- GeneralTests.class,//
+@SuiteClasses({ ReactomeBlackBoxEventParserTest.class,
+ ReactomeCatalystActivityParserTest.class,
+ ReactomeCandidateSetParserTest.class,
+ ReactomeCompartmentParserTest.class,
+ ReactomeComplexParserTest.class,
+ ReactomeDatabaseIdentifierParserTest.class,
+ ReactomeDatabaseObjectParserTest.class,
+ ReactomeDefinedSetParserTest.class,
+ ReactomeDiseaseParserTest.class,
+ ReactomeEntityCompartmentParserTest.class,
+ ReactomeEntityWithAccessionedSequenceParserTest.class,
+ ReactomeFigureParserTest.class,
+ ReactomeGenomeEncodedEntityParserTest.class,
+ ReactomeGoBiologicalProcessParserTest.class,
+ ReactomeGoMolecularFunctionParserTest.class,
+ ReactomeInstanceEditParserTest.class,
+ ReactomeLiteratureReferenceParserTest.class,
+ ReactomeOtherEntityParserTest.class,
+ ReactomeParserFactoryTest.class,
+ ReactomePathwayParserTest.class,
+ ReactomePersonParserTest.class,
+ ReactomePolymerParserTest.class,
+ ReactomeReactionParserTest.class,
+ ReactomeReferenceDatabaseParserTest.class,
+ ReactomeReferenceGeneProductParserTest.class,
+ ReactomeReferenceIsoformParserTest.class,
+ ReactomeReferenceMoleculeParserTest.class,
+ ReactomeSimpleEntityParserTest.class,
+ ReactomeSpeciesParserTest.class,
+ ReactomeStableIdentifierParserTest.class,
+ ReactomeSummationParserTest.class,
+ ReactomeURLParserTest.class,
+ GeneralTests.class,
})
public class AllReactomeXmlTests {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index 9c231fdbc3..1f4a69ac43 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -71,10 +71,10 @@ public class ConfigurationController extends BaseController {
@RequestMapping(value = "/configuration/options/{option}", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getOption( //
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "option") String option //
+ public Map<String, Object> getOption(
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "option") String option
) throws SecurityException, JsonParseException, JsonMappingException, IOException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "option");
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
index 001221d256..0433a052a5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
@@ -41,11 +41,11 @@ public class ConvertController extends BaseController {
@RequestMapping(value = "/convert/{fromFormat}:{toFormat}",
produces = {MediaType.APPLICATION_XML_VALUE},
method = { RequestMethod.POST })
- public String convertInput(//
- @PathVariable(value = "fromFormat") String fromFormat, //
- @PathVariable(value = "toFormat") String toFormat, //
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public String convertInput(
+ @PathVariable(value = "fromFormat") String fromFormat,
+ @PathVariable(value = "toFormat") String toFormat,
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
)
throws SecurityException, IOException, QueryException, SBMLException,
InvalidInputDataExecption, InconsistentModelException, ConverterException,
@@ -56,13 +56,13 @@ public class ConvertController extends BaseController {
}
@RequestMapping(value = "/convert/image/{fromFormat}:{toFormat}", method = { RequestMethod.POST })
- public @ResponseBody ResponseEntity<byte[]> convertInputToImage(//
- @PathVariable(value = "fromFormat") String fromFormat, //
- @PathVariable(value = "toFormat") String toFormat, //
- //@RequestParam(value = "targetWidth", defaultValue = "0") Double targetWidth, //
- //@RequestParam(value = "targetHeight", defaultValue = "0") Double targetHeight, //
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public @ResponseBody ResponseEntity<byte[]> convertInputToImage(
+ @PathVariable(value = "fromFormat") String fromFormat,
+ @PathVariable(value = "toFormat") String toFormat,
+ //@RequestParam(value = "targetWidth", defaultValue = "0") Double targetWidth,
+ //@RequestParam(value = "targetHeight", defaultValue = "0") Double targetHeight,
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
)
throws SecurityException, IOException, QueryException, SBMLException,
InvalidInputDataExecption, InconsistentModelException, ConverterException,
@@ -79,7 +79,7 @@ public class ConvertController extends BaseController {
@RequestMapping(value = "/convert/", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getInformation(
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException
{
return convertController.getInformation(token);
@@ -88,7 +88,7 @@ public class ConvertController extends BaseController {
@RequestMapping(value = "/convert/image/", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getInformationImage(
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException
{
return convertController.getInformationImage(token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
index a3e16c1516..0f22c5ccc4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
@@ -184,10 +184,10 @@ public class ConvertRestImpl extends BaseRestImpl {
Double wScaled = w*scale;
Double hScaled = h*scale;
- return new AbstractImageGenerator.Params().//
- model(model).//
- width(wScaled + padding).//
- height(hScaled + padding).//
+ return new AbstractImageGenerator.Params().
+ model(model).
+ width(wScaled + padding).
+ height(hScaled + padding).
scale(1/scale)
.x(0);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
index 820c35bbce..8a95cd8032 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
@@ -30,28 +30,28 @@ public class FileController extends BaseController {
private FileRestImpl fileRest;
@RequestMapping(value = "/files/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "filename") String filename, //
- @RequestParam(value = "length") String length //
+ public Map<String, Object> createFile(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "filename") String filename,
+ @RequestParam(value = "length") String length
) throws SecurityException {
return fileRest.createFile(token, filename, length);
}
@RequestMapping(value = "/files/{id}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id //
+ public Map<String, Object> getFile(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "id") String id
) throws SecurityException, ObjectNotFoundException {
return fileRest.getFile(token, id);
}
@RequestMapping(value = "/files/{id}:uploadContent", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> uploadContent(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id, //
+ public Map<String, Object> uploadContent(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "id") String id,
@RequestBody byte[] data) throws SecurityException, ObjectNotFoundException {
return fileRest.uploadContent(token, id, data);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 5a8dab518f..8d2b45df8b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -29,94 +29,94 @@ public class ReferenceGenomeController extends BaseController {
@RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getGenomesByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type, //
- @PathVariable(value = "version") String version//
+ public Map<String, Object> getGenomesByQuery(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "organismId") String organism,
+ @PathVariable(value = "type") String type,
+ @PathVariable(value = "version") String version
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenome(token, organism, type, version);
}
@RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}:getAvailableRemoteUrls", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getRemoteUrls(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type, //
- @PathVariable(value = "version") String version//
+ public List<Map<String, Object>> getRemoteUrls(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "organismId") String organism,
+ @PathVariable(value = "type") String type,
+ @PathVariable(value = "version") String version
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getRemoteUrls(token, organism, type, version);
}
@RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeTaxonomies(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getGenomeTaxonomies(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomeTaxonomies(token);
}
@RequestMapping(value = "/genomics/", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addGenome(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> addGenome(
+ @RequestBody MultiValueMap<String, Object> formData,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
return referenceGenomeController.addReferenceGenome(formData, token);
}
@RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeTaxonomyTypes(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism //
+ public List<Map<String, Object>> getGenomeTaxonomyTypes(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "organismId") String organism
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomeTypes(token, organism);
}
@RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeVersion(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type //
+ public List<Map<String, Object>> getGenomeVersion(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "organismId") String organism,
+ @PathVariable(value = "type") String type
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomeVersions(token, organism, type);
}
@RequestMapping(value = "/genomics/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getDownloaded(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getDownloaded(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenomes(token);
}
@RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeGenome(//
- @PathVariable(value = "genomeId") String genomeId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> removeGenome(
+ @PathVariable(value = "genomeId") String genomeId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException {
return referenceGenomeController.removeGenome(genomeId, token);
}
@RequestMapping(value = "/genomics/{genomeId}/geneMapping/{mappingId}/", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeGeneMapping(//
- @PathVariable(value = "genomeId") String genomeId, //
- @PathVariable(value = "mappingId") String mappingId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> removeGeneMapping(
+ @PathVariable(value = "genomeId") String genomeId,
+ @PathVariable(value = "mappingId") String mappingId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException, lcsb.mapviewer.api.ObjectNotFoundException {
return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
}
@RequestMapping(value = "/genomics/{genomeId}/geneMapping/", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addGeneMapping(//
- @PathVariable(value = "genomeId") String genomeId, //
- @RequestBody MultiValueMap<String, Object> formData, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> addGeneMapping(
+ @PathVariable(value = "genomeId") String genomeId,
+ @RequestBody MultiValueMap<String, Object> formData,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
return referenceGenomeController.addGeneMapping(formData, genomeId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
index a5937dbfbd..3bd73e4267 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
@@ -27,9 +27,9 @@ public class MeshController extends BaseController {
@RequestMapping(value = "/mesh/{id:.+}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getMesh(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id //
+ public Map<String, Object> getMesh(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "id") String id
) throws Exception {
return userRest.getMesh(token, id);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
index cf3de095bd..c7f87d2332 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
@@ -30,83 +30,83 @@ public class PluginController extends BaseController {
private PluginRestImpl pluginRest;
@RequestMapping(value = "/plugins/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPlugin(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "hash") String hash, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "version") String version, //
- @RequestParam(value = "isPublic", defaultValue = "false") String isPublic, //
- @RequestParam(value = "url", defaultValue = "") String url //
+ public Map<String, Object> createPlugin(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "hash") String hash,
+ @RequestParam(value = "name") String name,
+ @RequestParam(value = "version") String version,
+ @RequestParam(value = "isPublic", defaultValue = "false") String isPublic,
+ @RequestParam(value = "url", defaultValue = "") String url
) throws SecurityException {
return pluginRest.createPlugin(token, hash, name, version, url, isPublic);
}
@RequestMapping(value = "/plugins/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getPlugins(//
- @RequestParam(value = "onlyPublic", defaultValue = "false") String onlyPublic, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getPlugins(
+ @RequestParam(value = "onlyPublic", defaultValue = "false") String onlyPublic,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException {
return pluginRest.getPlugins(token, onlyPublic.equalsIgnoreCase("true"));
}
@RequestMapping(value = "/plugins/{hash}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash //
+ public Map<String, Object> getFile(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash
) throws SecurityException, ObjectNotFoundException {
return pluginRest.getPlugin(token, hash);
}
@RequestMapping(value = "/plugins/{hash}", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removePlugin(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash //
+ public Map<String, Object> removePlugin(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash
) throws SecurityException, ObjectNotFoundException {
return pluginRest.removePlugin(token, hash);
}
@RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "login") String login, //
- @PathVariable(value = "key") String key, //
- @RequestParam(value = "value", defaultValue = "") String value //
+ public Map<String, Object> createPluginDataEntry(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash,
+ @PathVariable(value = "login") String login,
+ @PathVariable(value = "key") String key,
+ @RequestParam(value = "value", defaultValue = "") String value
) throws SecurityException, ObjectNotFoundException {
return pluginRest.createPluginDataEntry(token, hash, login, key, value);
}
@RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "login") String login, //
- @PathVariable(value = "key") String key //
+ public Map<String, Object> getPluginDataEntry(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash,
+ @PathVariable(value = "login") String login,
+ @PathVariable(value = "key") String key
) throws SecurityException, ObjectNotFoundException {
return pluginRest.getPluginDataEntry(token, hash, login, key);
}
@RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "key") String key, //
- @RequestParam(value = "value", defaultValue = "") String value //
+ public Map<String, Object> createPluginDataEntry(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash,
+ @PathVariable(value = "key") String key,
+ @RequestParam(value = "value", defaultValue = "") String value
) throws SecurityException, ObjectNotFoundException {
return pluginRest.createPluginDataEntry(token, hash, null, key, value);
}
@RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "key") String key //
+ public Map<String, Object> getPluginDataEntry(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "hash") String hash,
+ @PathVariable(value = "key") String key
) throws SecurityException, ObjectNotFoundException {
return pluginRest.getPluginDataEntry(token, hash, null, key);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index 974a595098..e054daf40e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -39,19 +39,19 @@ public class ProjectController extends BaseController {
@RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> getProject(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException {
return projectController.getProject(projectId, token);
}
@RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateProject(//
- @RequestBody String body, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> updateProject(
+ @RequestBody String body,
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException, QueryException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "project");
@@ -61,10 +61,10 @@ public class ProjectController extends BaseController {
@RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addProject(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> addProject(
+ @RequestBody MultiValueMap<String, Object> formData,
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException, QueryException {
return projectController.addProject(token, projectId, formData, context.getRealPath("/"));
@@ -72,35 +72,35 @@ public class ProjectController extends BaseController {
@RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> removeProject(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException, QueryException {
return projectController.removeProject(token, projectId, context.getRealPath("/"));
}
@RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getProjects(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getProjects(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException {
return projectController.getProjects(token);
}
@RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Object getStatistics(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Object getStatistics(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException {
return projectController.getStatistics(projectId, token);
}
@RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getProjectSource(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId //
+ public ResponseEntity<byte[]> getProjectSource(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId
) throws SecurityException, QueryException {
FileEntry file = projectController.getSource(token, projectId);
@@ -117,15 +117,15 @@ public class ProjectController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/logs/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getLogs(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "level", defaultValue = "warning") String level, //
- @RequestParam(value = "start", defaultValue = "0") String start, //
- @RequestParam(value = "length", defaultValue = "10") Integer length, //
- @RequestParam(value = "sortColumn", defaultValue = "id") String sortColumn, //
- @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
- @RequestParam(value = "search", defaultValue = "") String search//
+ public Map<String, Object> getLogs(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "level", defaultValue = "warning") String level,
+ @RequestParam(value = "start", defaultValue = "0") String start,
+ @RequestParam(value = "length", defaultValue = "10") Integer length,
+ @RequestParam(value = "sortColumn", defaultValue = "id") String sortColumn,
+ @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder,
+ @RequestParam(value = "search", defaultValue = "") String search
) throws QueryException, SecurityException {
return projectController.getLogs(projectId, level, token, start, length, sortColumn, sortOrder, search);
}
@@ -149,9 +149,9 @@ public class ProjectController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/submapConnections", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getSubmapConnections(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId //
+ public List<Map<String, Object>> getSubmapConnections(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId
) throws SecurityException, QueryException {
return projectController.getSubmapConnections(token, projectId);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 528c189b5d..0d1c66e019 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -500,8 +500,8 @@ public class ProjectRestImpl extends BaseRestImpl {
}
private enum LogSortColumn {
- ID("id"), //
- CONTENT("content"); //
+ ID("id"),
+ CONTENT("content");
private String commonName;
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 4b72c31db3..e904309314 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
@@ -27,12 +27,12 @@ public class ChemicalController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/chemicals:search", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getChemicalsByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
+ public List<Map<String, Object>> getChemicalsByQuery(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @RequestParam(value = "query", defaultValue = "") String query,
+ @RequestParam(value = "target", defaultValue = "") String target
) throws SecurityException, QueryException {
if (!query.equals("")) {
return chemicalController.getChemicalsByQuery(token, projectId, columns, query);
@@ -47,9 +47,9 @@ public class ChemicalController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/chemicals/suggestedQueryList", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ public List<String> getSuggestedQueryList(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ChemicalSearchException {
return chemicalController.getSuggestedQueryList(projectId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
index 512d760e82..4d411fdb3b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
@@ -32,22 +32,22 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getComments(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
+ public List<Map<String, Object>> getComments(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @RequestParam(value = "removed", defaultValue = "") String removed
) throws SecurityException, QueryException {
return commentController.getCommentList(token, projectId, columns, "", "", removed);
}
@RequestMapping(value = "/projects/{projectId}/comments/{commentId}/", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeComment(//
- @RequestBody(required = false) String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "commentId") String commentId //
+ public Map<String, Object> removeComment(
+ @RequestBody(required = false) String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "commentId") String commentId
) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
Map<String, Object> node = parseBody(body);
String reason = (String) node.get("reason");
@@ -56,12 +56,12 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
+ public List<Map<String, Object>> getCommentsByReaction(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @PathVariable(value = "reactionId") String reactionId,
+ @RequestParam(value = "removed", defaultValue = "") String removed
) throws SecurityException, QueryException {
return commentController.getCommentList(token, projectId, columns, reactionId,
ElementIdentifierType.REACTION.getJsName(), removed);
@@ -69,12 +69,12 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByElement(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "elementId") String elementId, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
+ public List<Map<String, Object>> getCommentsByElement(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @PathVariable(value = "elementId") String elementId,
+ @RequestParam(value = "removed", defaultValue = "") String removed
) throws SecurityException, QueryException {
return commentController.getCommentList(token, projectId, columns, elementId,
ElementIdentifierType.ALIAS.getJsName(), removed);
@@ -82,12 +82,12 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates:.+}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByPoint(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "coordinates") String coordinates, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
+ public List<Map<String, Object>> getCommentsByPoint(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @PathVariable(value = "coordinates") String coordinates,
+ @RequestParam(value = "removed", defaultValue = "") String removed
) throws SecurityException, QueryException {
return commentController.getCommentList(token, projectId, columns, coordinates,
ElementIdentifierType.POINT.getJsName(), removed);
@@ -95,16 +95,16 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForElement(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "elementId") String elementId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @RequestParam(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
+ public Map<String, Object> addCommentForElement(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "elementId") String elementId,
+ @RequestParam(value = "name") String name,
+ @RequestParam(value = "email") String email,
+ @RequestParam(value = "content") String content,
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned,
+ @RequestParam(value = "coordinates") String coordinates,
+ @PathVariable(value = "modelId") String modelId
) throws SecurityException, QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(token, projectId, ElementIdentifierType.ALIAS.getJsName(), elementId, name,
@@ -113,16 +113,16 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @RequestParam(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
+ public Map<String, Object> addCommentForReaction(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "reactionId") String reactionId,
+ @RequestParam(value = "name") String name,
+ @RequestParam(value = "email") String email,
+ @RequestParam(value = "content") String content,
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned,
+ @RequestParam(value = "coordinates") String coordinates,
+ @PathVariable(value = "modelId") String modelId
) throws SecurityException, QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(token, projectId, ElementIdentifierType.REACTION.getJsName(), reactionId, name,
@@ -131,15 +131,15 @@ public class CommentController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates}", method = {
RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForPoint(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @PathVariable(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
+ public Map<String, Object> addCommentForPoint(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "name") String name,
+ @RequestParam(value = "email") String email,
+ @RequestParam(value = "content") String content,
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned,
+ @PathVariable(value = "coordinates") String coordinates,
+ @PathVariable(value = "modelId") String modelId
) throws SecurityException, QueryException {
Point2D pointCoordinates = parseCoordinates(coordinates);
return commentController.addComment(token, projectId, ElementIdentifierType.POINT.getJsName(), coordinates, name,
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
index c4a084cddd..bf052f0bc7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
@@ -27,12 +27,12 @@ public class DrugController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/drugs:search", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getDrugsByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
+ public List<Map<String, Object>> getDrugsByQuery(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @RequestParam(value = "query", defaultValue = "") String query,
+ @RequestParam(value = "target", defaultValue = "") String target
) throws SecurityException, QueryException {
if (!query.equals("")) {
return drugController.getDrugsByQuery(token, projectId, columns, query);
@@ -47,9 +47,9 @@ public class DrugController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/drugs/suggestedQueryList", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ public List<String> getSuggestedQueryList(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, DrugSearchException {
return drugController.getSuggestedQueryList(projectId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
index 51fdd905a2..e4fdb42163 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
@@ -27,12 +27,12 @@ public class MiRnaController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/miRnas:search", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getMiRnasByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
+ public List<Map<String, Object>> getMiRnasByQuery(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @RequestParam(value = "query", defaultValue = "") String query,
+ @RequestParam(value = "target", defaultValue = "") String target
) throws SecurityException, QueryException {
if (!query.equals("")) {
return miRnaController.getMiRnasByQuery(token, projectId, columns, query);
@@ -47,9 +47,9 @@ public class MiRnaController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/miRnas/suggestedQueryList", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ public List<String> getSuggestedQueryList(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, MiRNASearchException {
return miRnaController.getSuggestedQueryList(projectId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index c726047536..a7d4b8e08c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -37,19 +37,19 @@ public class ModelController extends BaseController {
@RequestMapping(value = "/projects/{projectId:.+}/models/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getModels(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getModels(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException {
return modelController.getModels(projectId, token);
}
@RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Object getModel(//
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Object getModel(
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, ObjectNotFoundException {
if (modelId.equals("*")) {
return modelController.getModels(projectId, token);
@@ -60,11 +60,11 @@ public class ModelController extends BaseController {
@RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Object updateModel(//
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Object updateModel(
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "model");
@@ -73,15 +73,15 @@ public class ModelController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsImage(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ public ResponseEntity<byte[]> getModelAsImage(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @RequestParam(value = "handlerClass") String handlerClass,
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId,
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds,
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel,
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString
) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
DrawingException {
@@ -95,17 +95,17 @@ public class ModelController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = { RequestMethod.GET,
RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsModelFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString, //
- @RequestParam(value = "elementIds", defaultValue = "") String elementIds, //
- @RequestParam(value = "reactionIds", defaultValue = "") String reactionIds //
+ public ResponseEntity<byte[]> getModelAsModelFile(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @RequestParam(value = "handlerClass") String handlerClass,
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId,
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds,
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel,
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString,
+ @RequestParam(value = "elementIds", defaultValue = "") String elementIds,
+ @RequestParam(value = "reactionIds", defaultValue = "") String reactionIds
) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
ConverterException, InconsistentModelException {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index bf5adaf692..94c9f9d47f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -371,16 +371,16 @@ public class ModelRestImpl extends BaseRestImpl {
ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
- Params params = new Params().//
- x(minX).//
- y(minY).//
- height((maxY - minY) / scale).//
- width((maxX - minX) / scale).//
- level(level - Configuration.MIN_ZOOM_LEVEL).//
+ Params params = new Params().
+ x(minX).
+ y(minY).
+ height((maxY - minY) / scale).
+ width((maxX - minX) / scale).
+ level(level - Configuration.MIN_ZOOM_LEVEL).
nested(false).// automatically set nested view as invalid
- scale(scale).//
- colorExtractor(colorExtractor).//
- sbgn(topModel.getProject().isSbgnFormat()).//
+ scale(scale).
+ colorExtractor(colorExtractor).
+ sbgn(topModel.getProject().isSbgnFormat()).
model(colorModel);
if (overlay != null) {
params.nested(overlay.isHierarchicalView());
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 891e8871b4..f7e50c6597 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
@@ -26,15 +26,15 @@ public class BioEntitiesController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities:search", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getClosestElementsByCoordinates(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "coordinates", defaultValue = "") String coordinates, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "count", defaultValue = "") String count, //
- @RequestParam(value = "type", defaultValue = "") String type, //
- @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch//
+ public List<Map<String, Object>> getClosestElementsByCoordinates(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "coordinates", defaultValue = "") String coordinates,
+ @RequestParam(value = "query", defaultValue = "") String query,
+ @RequestParam(value = "count", defaultValue = "") String count,
+ @RequestParam(value = "type", defaultValue = "") String type,
+ @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch
) throws QueryException, SecurityException {
if (!coordinates.trim().isEmpty()) {
if (modelId.equals("*")) {
@@ -71,9 +71,9 @@ 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(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ public String[] getSuggestedQueryList(
+ @PathVariable(value = "projectId") String projectId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException {
return bioEntitiesRestImpl.getSuggestedQueryList(projectId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index d5e58fdbb4..4518368710 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -24,15 +24,15 @@ public class ElementsController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements/", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getElements(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "id", defaultValue = "") String id, //
- @RequestParam(value = "type", defaultValue = "") String type, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds, //
- @RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ public List<Map<String, Object>> getElements(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @RequestParam(value = "id", defaultValue = "") String id,
+ @RequestParam(value = "type", defaultValue = "") String type,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds,
+ @RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException {
return projectController.getElements(projectId, id, columns, modelId, token, type, includedCompartmentIds, excludedCompartmentIds);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
index 06c2d1390e..272fff6fc4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
@@ -24,13 +24,13 @@ public class ReactionsController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/reactions/", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getReactions(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "id", defaultValue = "") String id, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "participantId", defaultValue = "") String participantId//
+ public List<Map<String, Object>> getReactions(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @RequestParam(value = "id", defaultValue = "") String id,
+ @RequestParam(value = "columns", defaultValue = "") String columns,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "participantId", defaultValue = "") String participantId
) throws SecurityException,QueryException {
return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
index 163b6bf66c..ccb7f4f14d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
@@ -23,21 +23,21 @@ public class FunctionsController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/{functionId}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFunction(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "functionId") String functionId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> getFunction(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "functionId") String functionId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return functionController.getFunction(projectId, modelId, token, functionId);
}
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getFunctions(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getFunctions(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return functionController.getFunctions(projectId, modelId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
index f4caca35ec..9567b62032 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
@@ -23,21 +23,21 @@ public class ParametersController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/{parameterId}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getParameter(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "parameterId") String parameterId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> getParameter(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "parameterId") String parameterId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return parameterController.getParameter(projectId, modelId, token, parameterId);
}
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getParameters(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getParameters(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return parameterController.getParameters(projectId, modelId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
index 311c327b3a..37681154d8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
@@ -23,15 +23,15 @@ public class PublicationsController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications/", method = { RequestMethod.GET },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPublications(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "start", defaultValue = "0") String start, //
- @RequestParam(value = "length", defaultValue = "10") Integer length, //
- @RequestParam(value = "sortColumn", defaultValue = "pubmedId") String sortColumn, //
- @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
- @RequestParam(value = "search", defaultValue = "") String search//
+ public Map<String, Object> getPublications(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "start", defaultValue = "0") String start,
+ @RequestParam(value = "length", defaultValue = "10") Integer length,
+ @RequestParam(value = "sortColumn", defaultValue = "pubmedId") String sortColumn,
+ @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder,
+ @RequestParam(value = "search", defaultValue = "") String search
) throws QueryException, SecurityException {
return projectController.getPublications(projectId, modelId, token, start, length, sortColumn, sortOrder, search);
}
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 b45034dfaf..bec7b1463f 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
@@ -84,10 +84,10 @@ public class PublicationsRestImpl extends BaseRestImpl {
}
private enum SortColumn {
- PUBMED_ID("pubmedId"), //
- YEAR("year"), //
- JOURNAL("journal"), //
- TITLE("title"), //
+ PUBMED_ID("pubmedId"),
+ YEAR("year"),
+ JOURNAL("journal"),
+ TITLE("title"),
AUTHORS("authors");
private String commonName;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
index 7f7b035060..5d1f200bab 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
@@ -23,21 +23,21 @@ public class UnitsController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/{unitId}", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getUnit(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "unitId") String unitId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> getUnit(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "unitId") String unitId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return unitController.getUnit(projectId, modelId, token, unitId);
}
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getUnits(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public List<Map<String, Object>> getUnits(
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws QueryException, SecurityException {
return unitController.getUnits(projectId, modelId, token);
}
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 26865a0295..6fc3eeb591 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
@@ -39,30 +39,30 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getOverlayList(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "creator", defaultValue = "") String creator, //
- @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay //
+ public List<Map<String, Object>> getOverlayList(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "creator", defaultValue = "") String creator,
+ @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay
) throws SecurityException, QueryException {
return overlayRestImp.getOverlayList(token, projectId, creator, publicOverlay);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getOverlayById(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId//
+ public Map<String, Object> getOverlayById(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "overlayId") String overlayId
) throws SecurityException, QueryException {
return overlayRestImp.getOverlayById(token, projectId, overlayId);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getOverlayElements(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
+ public List<Map<String, Object>> getOverlayElements(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
@PathVariable(value = "overlayId") String overlayId,
@RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
return overlayRestImp.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
@@ -70,13 +70,13 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFullReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "columns", defaultValue = "") String columns //
+ public Map<String, Object> getFullReaction(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "overlayId") String overlayId,
+ @PathVariable(value = "reactionId") String reactionId,
+ @RequestParam(value = "columns", defaultValue = "") String columns
) throws SecurityException, QueryException {
return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
Integer.valueOf(reactionId), "REACTION", columns);
@@ -84,13 +84,13 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFullSpecies(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @PathVariable(value = "elementId") String reactionId, //
- @RequestParam(value = "columns", defaultValue = "") String columns //
+ public Map<String, Object> getFullSpecies(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "overlayId") String overlayId,
+ @PathVariable(value = "elementId") String reactionId,
+ @RequestParam(value = "columns", defaultValue = "") String columns
) throws SecurityException, QueryException {
return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
Integer.valueOf(reactionId), "ALIAS", columns);
@@ -98,37 +98,37 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addOverlay(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "description") String description, //
- @RequestParam(value = "content", defaultValue = "") String content, //
- @RequestParam(value = "fileId", defaultValue = "") String fileId, //
- @RequestParam(value = "filename") String filename, //
- @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent, //
- @RequestParam(value = "type", defaultValue = "") String type //
+ public Map<String, Object> addOverlay(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @RequestParam(value = "name") String name,
+ @RequestParam(value = "description") String description,
+ @RequestParam(value = "content", defaultValue = "") String content,
+ @RequestParam(value = "fileId", defaultValue = "") String fileId,
+ @RequestParam(value = "filename") String filename,
+ @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent,
+ @RequestParam(value = "type", defaultValue = "") String type
) throws SecurityException, QueryException, IOException {
return overlayRestImp.addOverlay(token, projectId, name, description, content, fileId, filename, type, googleLicenseConsent);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeOverlay(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId //
+ public Map<String, Object> removeOverlay(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "overlayId") String overlayId
) throws SecurityException, QueryException, IOException {
return overlayRestImp.removeOverlay(token, projectId, overlayId);
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateOverlay(//
- @RequestBody String body, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> updateOverlay(
+ @RequestBody String body,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "overlayId") String overlayId,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, IOException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "overlay");
@@ -137,10 +137,10 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}:downloadSource", method = {
RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getOverlaySource(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId //
+ public ResponseEntity<byte[]> getOverlaySource(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "projectId") String projectId,
+ @PathVariable(value = "overlayId") String overlayId
) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
FileEntry file = overlayRestImp.getOverlaySource(token, projectId, overlayId);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 75bd99587a..7094b6ee26 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -57,11 +57,11 @@ public class UserController extends BaseController {
@RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> login(//
- @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
- @RequestParam(value = "password", defaultValue = "") String password, //
- HttpServletResponse response, //
- HttpServletRequest request//
+ public Map<String, Object> login(
+ @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login,
+ @RequestParam(value = "password", defaultValue = "") String password,
+ HttpServletResponse response,
+ HttpServletRequest request
) throws SecurityException, IOException {
try {
UsernamePasswordAuthenticationToken springToken = new UsernamePasswordAuthenticationToken(login, password);
@@ -99,20 +99,20 @@ public class UserController extends BaseController {
@RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getUser(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login, //
- @RequestParam(value = "columns", defaultValue = "") String columns//
+ public Map<String, Object> getUser(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "login") String login,
+ @RequestParam(value = "columns", defaultValue = "") String columns
) throws SecurityException, ObjectNotFoundException {
return userRest.getUser(token, login, columns);
}
@RequestMapping(value = "/users/{login}:updatePrivileges", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updatePrivileges(//
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login //
+ public Map<String, Object> updatePrivileges(
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "login") String login
) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "privileges");
@@ -121,10 +121,10 @@ public class UserController extends BaseController {
@RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updatePreferences(//
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login //
+ public Map<String, Object> updatePreferences(
+ @RequestBody String body,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @PathVariable(value = "login") String login
) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "preferences");
@@ -132,9 +132,9 @@ public class UserController extends BaseController {
}
@RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getUsers(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "columns", defaultValue = "") String columns//
+ public List<Map<String, Object>> getUsers(
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ @RequestParam(value = "columns", defaultValue = "") String columns
) throws SecurityException, ObjectNotFoundException {
return userRest.getUsers(token, columns);
}
@@ -142,7 +142,7 @@ public class UserController extends BaseController {
@RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
- HttpServletRequest request, HttpServletResponse response //
+ HttpServletRequest request, HttpServletResponse response
) throws SecurityException, IOException {
// spring logout
Authentication auth = SecurityContextHolder.getContext().getAuthentication();
@@ -169,10 +169,10 @@ public class UserController extends BaseController {
@RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.PATCH }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateUser(//
- @RequestBody String body, //
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> updateUser(
+ @RequestBody String body,
+ @PathVariable(value = "login") String login,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, QueryException, IOException {
Map<String, Object> node = parseBody(body);
Map<String, Object> data = getData(node, "user");
@@ -181,10 +181,10 @@ public class UserController extends BaseController {
@RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addOverlay(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ public Map<String, Object> addOverlay(
+ @RequestBody MultiValueMap<String, Object> formData,
+ @PathVariable(value = "login") String login,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token
) throws SecurityException, IOException, QueryException {
return userRest.addProject(token, login, formData);
@@ -192,10 +192,10 @@ public class UserController extends BaseController {
@RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.DELETE }, produces = {
MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeUser(//
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- HttpServletRequest request, HttpServletResponse response //
+ public Map<String, Object> removeUser(
+ @PathVariable(value = "login") String login,
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ HttpServletRequest request, HttpServletResponse response
) throws SecurityException, IOException, QueryException {
String currentUserLogin = getUserService().getUserByToken(token).getLogin();
Map<String, Object> result = userRest.removeUser(token, login);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
index e52dc9bb7a..771abeede1 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
@@ -14,14 +14,14 @@ import lcsb.mapviewer.api.projects.AllProjectTests;
import lcsb.mapviewer.api.users.AllUserTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllConfigurationTests.class, //
- AllConvertTests.class, //
- AllFileTests.class, //
- AllGenomicsTests.class, //
- AllMeshTests.class, //
- AllPluginsTests.class, //
- AllProjectTests.class, //
- AllUserTests.class,//
+@SuiteClasses({ AllConfigurationTests.class,
+ AllConvertTests.class,
+ AllFileTests.class,
+ AllGenomicsTests.class,
+ AllMeshTests.class,
+ AllPluginsTests.class,
+ AllProjectTests.class,
+ AllUserTests.class,
})
public class AllRestTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index 9b9be9a835..4d816d3e55 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -62,12 +62,12 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/applicationContext-annotation.xml", //
- "/applicationContext-service.xml", //
- "/applicationContext-rest.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+@ContextConfiguration(locations = { "/applicationContext-persist.xml",
+ "/applicationContext-annotation.xml",
+ "/applicationContext-service.xml",
+ "/applicationContext-rest.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml",
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
index 7219f18b9b..dc06efddf7 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
@@ -11,11 +11,11 @@ import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllChemicalTests.class, //
- AllCommentTests.class, //
- AllDrugTests.class, //
- AllMiRnaTests.class, //
- AllModelsTests.class, //
+@SuiteClasses({ AllChemicalTests.class,
+ AllCommentTests.class,
+ AllDrugTests.class,
+ AllMiRnaTests.class,
+ AllModelsTests.class,
ProjectRestImplTest.class })
public class AllProjectTests {
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 5d24a34c55..3684e07c22 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
@@ -9,11 +9,11 @@ import lcsb.mapviewer.api.projects.models.functions.AllFunctionsTests;
import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
@RunWith(Suite.class)
-@SuiteClasses({ //
- AllBioeEntitiesTests.class, //
- AllFunctionsTests.class, //
- AllPublicationsTests.class, //
- ModelRestImplTest.class,//
+@SuiteClasses({
+ AllBioeEntitiesTests.class,
+ AllFunctionsTests.class,
+ AllPublicationsTests.class,
+ ModelRestImplTest.class,
})
public class AllModelsTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java
index 48a870c00f..c3738214b1 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java
@@ -7,9 +7,9 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.projects.models.bioEntities.elements.AllElementsTests;
@RunWith(Suite.class)
-@SuiteClasses({ //
- AllElementsTests.class, //
- BioEntitiesControllerTest.class //
+@SuiteClasses({
+ AllElementsTests.class,
+ BioEntitiesControllerTest.class
})
public class AllBioeEntitiesTests {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java b/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
index cbcb2a57e6..0e7d0cfce8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
@@ -114,11 +114,11 @@ public class EmailSender {
* email account
*/
public EmailSender(IConfigurationService configurationService) {
- this(configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_LOGIN), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_PASSWORD), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_SERVER), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_IMAP_SERVER), //
+ this(configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS),
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_LOGIN),
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_PASSWORD),
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_SERVER),
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_IMAP_SERVER),
configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_PORT));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index 3a54c156fb..617981dc0f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -7,36 +7,36 @@ package lcsb.mapviewer.services.utils.data;
* @author Piotr Gawron
*
*/
-public enum BuildInLayout { //
+public enum BuildInLayout {
/**
* Normal strainghtforward visualization.
*/
- NORMAL("Network", "_normal", null, false), //
+ NORMAL("Network", "_normal", null, false),
// /**
// * Set of data containing Substantia Nigra data for Parkinson Disease (false
// * discovery ratio 0.01).
// */
// FDR_001("PD Substantia Nigra FDR=0.01", "_001", "/enricoData/ge001.txt",
- // false), //
+ // false),
// /**
// * Set of data containing Substantia Nigra data for Parkinson Disease (false
// * discovery ratio 0.05).
// */
// FDR_005("PD Substantia Nigra FDR=0.05", "_005", "/enricoData/ge005.txt",
- // false), //
+ // false),
// /**
// * Set of data containing aging data for Parkinson Disease .
// */
- // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false), //
+ // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false),
/**
* Standard visualization with hierarchical view.
*/
- NESTED("Pathways and compartments", "_nested", null, true), //
+ NESTED("Pathways and compartments", "_nested", null, true),
SEMANTIC("Semantic zoom", "_semantic", null, true),
/**
* Clean visualization (with colors reset to black and white).
*/
- CLEAN("Empty", "_empty", null, false); //
+ CLEAN("Empty", "_empty", null, false);
/**
* Title of the layout.
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 67c7eaa840..46e8b0356a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -18,113 +18,113 @@ public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
- GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Name of the element.
*/
- MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Value that will be transformed into new color.
*
* @see ColorSchemaColumn#COLOR
*/
- VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* In which compartment the element should be located.
*/
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Class type of the element.
*/
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* New element/reaction color.
*/
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Identifier of the element.
*/
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Element identifier.
*/
- ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Element identifier.
*/
@Deprecated
- REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* New line width of the reaction.
*/
- LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Position where gene variants starts.
*/
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Original DNA of the variant.
*/
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Alternative DNA of the variant.
*/
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Short description of the entry.
*/
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
+ DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
/**
* Variant references.
*/
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* What's the {@link ReferenceGenomeType}.
*/
- REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* {@link ReferenceGenome#version Version} of the reference genome.
*/
- REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Contig where variant was observed.
*/
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Should the direction of reaction be reversed.
*/
- REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Optional amino acid change in the variant.
*/
- AMINO_ACID_CHANGE("amino_acid_change", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }); //
+ AMINO_ACID_CHANGE("amino_acid_change", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT });
/**
* Default constructor that creates enum entry.
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
index 721e9eee4d..a5e48ef710 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
@@ -14,57 +14,57 @@ public enum ExportColumn {
/**
* Name of the species.
*/
- NAME("Name", Species.class), //
+ NAME("Name", Species.class),
/**
* Name of compartment.
*/
- COMPARTMENT_NAME("Compartment", Species.class), //
+ COMPARTMENT_NAME("Compartment", Species.class),
/**
* Name of compartment.
*/
- POSITION_TO_COMPARTMENT("Position to compartment", Species.class), //
+ POSITION_TO_COMPARTMENT("Position to compartment", Species.class),
/**
* Name of pathway.
*/
- COMPONENT_NAME("Pathway", Species.class), //
+ COMPONENT_NAME("Pathway", Species.class),
/**
* Type of the species.
*/
- TYPE("Type", Species.class), //
+ TYPE("Type", Species.class),
/**
* Identifier.
*/
- ID("Id", Object.class), //
+ ID("Id", Object.class),
/**
* Complex in which element is localized.
*/
- COMPLEX("Parent complex", Species.class), //
+ COMPLEX("Parent complex", Species.class),
/**
* Complex in which element is localized.
*/
- SUBMODEL("Submodel", Species.class), //
+ SUBMODEL("Submodel", Species.class),
/**
* Reaction identifier.
*/
- REACTION_ID("Reaction id", Reaction.class), //
+ REACTION_ID("Reaction id", Reaction.class),
/**
* Reaction type.
*/
- REACTION_TYPE("Reaction type", Reaction.class), //
+ REACTION_TYPE("Reaction type", Reaction.class),
/**
* Information if reaction is reversible.
*/
- REACTION_REVERSIBLE("Reversible", Reaction.class), //
+ REACTION_REVERSIBLE("Reversible", Reaction.class),
/**
* Every reaction is split into two elements interactions.
diff --git a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
index fa417aad64..fe703ed386 100644
--- a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
@@ -10,10 +10,10 @@ import lcsb.mapviewer.services.search.AllSearchTests;
import lcsb.mapviewer.services.utils.AllUtilsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllImplServiceTests.class, //
- AllOverlayTests.class, //
- AllSearchTests.class, //
- AllUtilsTests.class, //
+@SuiteClasses({ AllImplServiceTests.class,
+ AllOverlayTests.class,
+ AllSearchTests.class,
+ AllUtilsTests.class,
})
public class AllServicesTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index 0957a91b2e..919f9575d2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -82,11 +82,11 @@ import lcsb.mapviewer.services.search.drug.IDrugService;
@Transactional(value = "txManager")
@Rollback(false)
-@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
- "/applicationContext-persist.xml", //
- "/applicationContext-service.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+@ContextConfiguration(locations = { "/applicationContext-annotation.xml",
+ "/applicationContext-persist.xml",
+ "/applicationContext-service.xml",
+ "/test-applicationContext.xml",
+ "/test-dataSource.xml",
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class ServiceTestFunctions {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
index 383ad23d91..cc2d3256ee 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
@@ -5,15 +5,15 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ CommentServiceTest.class, //
- ConfigurationServiceTest.class, //
- ExternalServicesServiceTest.class, //
- LayoutServiceTest.class, //
- LdapServiceTest.class, //
- Md5PasswordEncoderTest.class, //
- ProjectServiceTest.class, //
- SearchServiceTest.class, //
- UserServiceTest.class,//
+@SuiteClasses({ CommentServiceTest.class,
+ ConfigurationServiceTest.class,
+ ExternalServicesServiceTest.class,
+ LayoutServiceTest.class,
+ LdapServiceTest.class,
+ Md5PasswordEncoderTest.class,
+ ProjectServiceTest.class,
+ SearchServiceTest.class,
+ UserServiceTest.class,
})
public class AllImplServiceTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 7076c0c4c0..0521504d11 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -127,10 +127,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertTrue(layoutService.userCanAddLayout(model, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -162,10 +162,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
assertEquals(1, layoutService.getAvailableCustomLayoutsNumber(user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -197,10 +197,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -231,10 +231,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -266,11 +266,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertEquals(0, layouts.size());
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
+ user(user).
async(true);
long logCounter = logDao.getCount();
@@ -329,10 +329,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
userService.setUserPrivilege(user, new ObjectPrivilege(localProject, 1, PrivilegeType.VIEW_PROJECT, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(localModel).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(localModel).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
layoutService.createLayout(params);
@@ -367,11 +367,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertEquals(0, layouts.size());
userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
+ user(user).
async(false);
Layout row = layoutService.createLayout(params);
@@ -403,11 +403,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
ByteArrayInputStream bais = new ByteArrayInputStream(
"name reactionIdentifier Color\ns1 #CC0000\ns2 #CCCC00\n re1 #CCCC00\n"
.getBytes(StandardCharsets.UTF_8));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(bais).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(bais).
+ user(user).
async(false);
Layout row = layoutService.createLayout(params);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 1f80000e20..c66a9ddd1f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -207,10 +207,10 @@ public class LayoutServiceTest2 {
.createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(fis).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(fis).
async(false);
ColorSchemaReader reader = new ColorSchemaReader();
final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index f3d3b7240c..d56d4befe0 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -129,16 +129,16 @@ public class ProjectServiceTest extends ServiceTestFunctions {
public void testUpdater() throws Exception {
try {
String project_id = "test_id";
- projectService.createProject(new CreateProjectParams().//
- authenticationToken(adminToken).//
- projectId(project_id).//
- version("").//
- projectFile("testFiles/centeredAnchorInModifier.xml").//
- annotations(true).//
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(new CreateProjectParams().
+ authenticationToken(adminToken).
+ projectId(project_id).
+ version("").
+ projectFile("testFiles/centeredAnchorInModifier.xml").
+ annotations(true).
+ images(true).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(project_id, adminToken);
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -158,24 +158,24 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ZipEntryFile entry3 = new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- projectService.createProject(new CreateProjectParams().//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile("testFiles/complexModel/complex_model.zip").//
- addZipEntry(entry1).//
- addZipEntry(entry2).//
- addZipEntry(entry3).//
- addZipEntry(entry4).//
- addZipEntry(entry5).//
- annotations(true).//
- semanticZoom(true).//
+ projectService.createProject(new CreateProjectParams().
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile("testFiles/complexModel/complex_model.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ annotations(true).
+ semanticZoom(true).
semanticZoomContainsMultipleLayouts(true).
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ images(true).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
@@ -268,7 +268,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
model.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal", false));
model.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested", false));
- CreateProjectParams params = new CreateProjectParams().images(true).//
+ CreateProjectParams params = new CreateProjectParams().images(true).
projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
@@ -304,7 +304,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "name"));
- CreateProjectParams params = new CreateProjectParams().images(true).//
+ CreateProjectParams params = new CreateProjectParams().images(true).
projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
@@ -335,20 +335,20 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- CreateProjectParams params = new CreateProjectParams().//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile("testFiles/complexModel/complex_model_with_compartment.zip").//
- addZipEntry(entry1).//
- addZipEntry(entry2).//
- addZipEntry(entry3).//
- addZipEntry(entry4).//
- addZipEntry(entry5).//
- annotations(false).//
- images(false).//
- async(false).//
- projectDir(tmpResultDir).//
+ CreateProjectParams params = new CreateProjectParams().
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile("testFiles/complexModel/complex_model_with_compartment.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ annotations(false).
+ images(false).
+ async(false).
+ projectDir(tmpResultDir).
analyzeAnnotations(false);
ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
@@ -583,17 +583,17 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(params.
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile(filename).
+ annotations(true).
+ images(false).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
return project;
@@ -634,18 +634,18 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- networkLayoutAsDefault(true).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(params.
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile(filename).
+ annotations(true).
+ images(false).
+ async(false).
+ networkLayoutAsDefault(true).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
diff --git a/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java b/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
index 4812f764fd..0f5eedc188 100644
--- a/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
@@ -5,9 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AnnotatedObjectTreeRowTest.class, //
- ChebiTreeRowTest.class,//
- IconManagerTest.class, //
+@SuiteClasses({ AnnotatedObjectTreeRowTest.class,
+ ChebiTreeRowTest.class,
+ IconManagerTest.class,
})
public class AllOverlayTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
index d3350d52e7..68d0b5f605 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
@@ -9,11 +9,11 @@ import lcsb.mapviewer.services.search.drug.AllSearchDrugTests;
import lcsb.mapviewer.services.search.mirna.MiRNAServiceTest;
@RunWith(Suite.class)
-@SuiteClasses({ AllSearchDrugTests.class, //
- ChemicalServiceTest.class, //
- DbSearchServiceTest.class, //
- ElementMatcherTest.class, //
- MiRNAServiceTest.class, //
+@SuiteClasses({ AllSearchDrugTests.class,
+ ChemicalServiceTest.class,
+ DbSearchServiceTest.class,
+ ElementMatcherTest.class,
+ MiRNAServiceTest.class,
})
public class AllSearchTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java b/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
index bd40b9629d..ed091619dc 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
@@ -5,7 +5,7 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ DrugServiceTest.class, //
+@SuiteClasses({ DrugServiceTest.class,
})
public class AllSearchDrugTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java b/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
index 3d06600136..716bea85de 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
@@ -5,10 +5,10 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ColorSchemaReaderTest.class, //
- ColorSchemaReaderXlsTest.class, //
- ColorSchemaReaderXlsxTest.class, //
- EmailSenderTest.class,//
+@SuiteClasses({ ColorSchemaReaderTest.class,
+ ColorSchemaReaderXlsTest.class,
+ ColorSchemaReaderXlsxTest.class,
+ EmailSenderTest.class,
})
public class AllUtilsTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 31dbbefc6b..3a7d0ace0e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -331,8 +331,8 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
- String input = "name\tcolor\tvalue\n" + //
- "s1\t#ff0000\t\n" + //
+ String input = "name\tcolor\tvalue\n" +
+ "s1\t#ff0000\t\n" +
"s2\t\t1.0\n";
Collection<ColorSchema> schemas = reader
.readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params);
@@ -350,7 +350,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
- String input = "type\tname\tvalue\n" + //
+ String input = "type\tname\tvalue\n" +
"protein\t\t1.0\n";
Collection<ColorSchema> schemas = reader
.readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params);
--
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