From ad998297b35dd99ec92dff4a079cf7d0e3f7f648 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Mon, 3 Oct 2016 15:14:43 +0200
Subject: [PATCH] old CD structures don't refer to db anymore
---
.../services/ModelAnnotatorTest.java | 1 -
.../lcsb/mapviewer/run/ConsoleConverter.java | 1 -
.../celldesigner/structure/AntisenseRna.java | 17 +-
.../structure/AntisenseRnaRegion.java | 40 +-
.../celldesigner/structure/Chemical.java | 8 -
.../celldesigner/structure/Compartment.java | 11 +-
.../structure/ComplexSpecies.java | 9 -
.../celldesigner/structure/Degraded.java | 5 -
.../model/celldesigner/structure/Drug.java | 7 +-
.../model/celldesigner/structure/Element.java | 69 +--
.../model/celldesigner/structure/Gene.java | 23 +-
.../structure/GenericProtein.java | 12 +-
.../model/celldesigner/structure/Ion.java | 5 -
.../structure/IonChannelProtein.java | 5 -
.../structure/ModificationResidue.java | 46 --
.../celldesigner/structure/Phenotype.java | 5 -
.../model/celldesigner/structure/Protein.java | 15 -
.../structure/ReceptorProtein.java | 5 -
.../model/celldesigner/structure/Rna.java | 15 +-
.../celldesigner/structure/RnaRegion.java | 58 +-
.../structure/SimpleMolecule.java | 5 -
.../model/celldesigner/structure/Species.java | 8 -
.../structure/TruncatedProtein.java | 7 +-
.../model/celldesigner/structure/Unknown.java | 7 +-
.../model/celldesigner/species/ModelMock.java | 540 ------------------
.../structure/AntisenseRnaComparatorTest.java | 2 +-
.../structure/AntisenseRnaRegionTest.java | 2 +-
.../structure/CompartmentComparatorTest.java | 2 +-
.../ComplexSpeciesComparatorTest.java | 2 +-
.../structure/DegradedComparatorTest.java | 2 +-
.../structure/DrugComparatorTest.java | 2 +-
.../celldesigner/structure/ElementTest.java | 3 -
.../structure/GeneComparatorTest.java | 2 +-
.../structure/IonComparatorTest.java | 2 +-
.../structure/ModificationResidueTest.java | 4 -
.../structure/PhenotypeComparatorTest.java | 2 +-
.../structure/ProteinComparatorTest.java | 2 +-
.../structure/RnaComparatorTest.java | 2 +-
.../celldesigner/structure/RnaRegionTest.java | 5 +-
.../SimpleMoleculeComparatorTest.java | 2 +-
.../structure/UnknownComparatorTest.java | 2 +-
.../DrugAndCatalystComparator.java | 5 +-
.../GeneAndDefinedSetComparator.java | 5 +-
.../GeneAndOtherEntityComparator.java | 9 +-
.../comparators/IonAndComplexComparator.java | 5 +-
.../IonAndDefinedSetComparator.java | 4 +-
...tityWithAccessionedSequenceComparator.java | 6 +-
.../MoleculeAndCatalystComparator.java | 1 -
.../MoleculeAndComplexComparator.java | 1 -
.../MoleculeAndDefinedSetComparator.java | 1 -
...tityWithAccessionedSequenceComparator.java | 1 -
.../services/impl/LayoutServiceTest2.java | 1 -
.../services/impl/ProjectServiceTest.java | 1 -
.../search/data/FullAliasViewFactoryTest.java | 1 -
54 files changed, 60 insertions(+), 943 deletions(-)
delete mode 100644 converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index bcfae07154..bba1c52d6f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index bb4a7bea76..5aa503bf51 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
index dbe7dc37c5..d1aa4bfb89 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
@@ -3,15 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
@@ -22,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Antisense RNA")
public class AntisenseRna extends Species<AntisenseRnaAlias> {
/**
@@ -40,9 +30,6 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
/**
* List of antisense rna regions (some rna sequences) in this object.
*/
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species")
- @LazyCollection(LazyCollectionOption.FALSE)
private List<AntisenseRnaRegion> regions = new ArrayList<AntisenseRnaRegion>();
/**
@@ -51,7 +38,7 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* @param species
* parent species from which we want to copy data
*/
- public AntisenseRna(Species species) {
+ public AntisenseRna(Species<?> species) {
super(species);
if (species instanceof AntisenseRna) {
AntisenseRna asRna = (AntisenseRna) species;
@@ -104,7 +91,7 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
}
@Override
- public void update(Species sp) {
+ public void update(Species<?> sp) {
super.update(sp);
if (sp instanceof AntisenseRna) {
AntisenseRna rna = (AntisenseRna) sp;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
index 8966d67425..8ec3bb9181 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
@@ -2,43 +2,29 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
/**
* This structure contains information about antisense rna region (rna fragment
* of interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna AntisenseRna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
+ * AntisenseRna}.
*
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "antisense_rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class AntisenseRnaRegion implements Serializable {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default size of the object (in graphical representation).
@@ -54,21 +40,16 @@ public class AntisenseRnaRegion implements Serializable {
/**
* Unique identifier in the database.
*/
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
private int id;
/**
* String identifier of the element. Unique in the model.
*/
- @Column(name = "idantisensernaregion")
private String idAntisenseRnaRegion = "";
/**
* Name of the region.
*/
- @Column(name = "name")
private String name = "";
/**
@@ -76,7 +57,6 @@ public class AntisenseRnaRegion implements Serializable {
*
* @see ModificationState
*/
- @Column(name = "state")
private ModificationState state = null;
/**
@@ -87,28 +67,22 @@ public class AntisenseRnaRegion implements Serializable {
* <li>Modification site.</li>
* </ul>
*/
- @Column(name = "type")
private AntisenseRnaRegionType type;
/**
* Size of the region in the graphic representation.
*/
- @Column(name = "size")
private double size = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
*/
- @Column(name = "pos")
private Double pos;
/**
* Defines a species where the region belongs to.
*/
- @Cascade({ CascadeType.ALL })
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private Species species;
+ private AntisenseRna species;
/**
* Default constructor.
@@ -311,7 +285,7 @@ public class AntisenseRnaRegion implements Serializable {
* @return the species
* @see #species
*/
- public Species getSpecies() {
+ public AntisenseRna getSpecies() {
return species;
}
@@ -320,7 +294,7 @@ public class AntisenseRnaRegion implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(Species species) {
+ public void setSpecies(AntisenseRna species) {
this.species = species;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
index 0a910c01ac..200e0d5882 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
@@ -1,9 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
/**
@@ -12,8 +8,6 @@ import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Chemical")
public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
/**
@@ -26,7 +20,6 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
* "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
* >Smiles</a> parameter for the chemical.
*/
- @Column(name = "smiles", columnDefinition = "TEXT")
private String smiles;
/**
@@ -34,7 +27,6 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
* InChI</a> parameter for the chemical.
*/
- @Column(name = "inchi", columnDefinition = "TEXT")
private String inChI;
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
index 28f3d50dee..bd710e3e22 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
@@ -3,11 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -19,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Compartment")
public class Compartment extends Element<CompartmentAlias> implements Comparable<Compartment> {
/**
@@ -37,14 +30,12 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
/**
* Identifier of the compartment. Unique in the model
*/
- @Column(name = "compartmentId")
private String compartmentId = "";
/**
* List of agregated elements.
*/
- @OneToMany(mappedBy = "parent")
- private Set<Element<?>> elements = new HashSet<>();
+ private Set<Element<?>> elements = new HashSet<>();
/**
* Default constructor with identifier given as a parameter.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
index 387fa80916..2da11f9215 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
@@ -3,11 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -20,8 +15,6 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("COMPLEX_SPECIES")
public class ComplexSpecies extends Species<ComplexAlias> {
/**
@@ -37,13 +30,11 @@ public class ComplexSpecies extends Species<ComplexAlias> {
/**
* Elements that exists in this complex.
*/
- @OneToMany(mappedBy = "complex")
private Set<Element<?>> elements = new HashSet<>();
/**
* State of the complex species.
*/
- @Column(name = "structuralState")
private String structuralState = null;
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
index 3f4935ffb2..5d0ef0d4c4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Degraded")
public class Degraded extends Species<DegradedAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
index 977bca234d..b3d86a5568 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
@@ -12,14 +9,12 @@ import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Drug")
public class Drug extends Species<DrugAlias> {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Constructor that copies the data from species given in the argument.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
index fa575b156c..fadaa2a653 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
@@ -7,28 +7,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import javax.persistence.CascadeType;
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
@@ -43,11 +22,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "species_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "species_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_ELEMENT")
public abstract class Element<T extends Alias> implements Serializable {
/**
@@ -65,18 +39,9 @@ public abstract class Element<T extends Alias> implements Serializable {
*/
private static Logger logger = Logger.getLogger(Element.class);
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
/**
* Notes describing this element.
*/
- @Column(name = "notes", columnDefinition = "TEXT")
private String notes;
/**
@@ -102,48 +67,37 @@ public abstract class Element<T extends Alias> implements Serializable {
/**
* Short name of the element.
*/
- @Column(name = "name")
private String name = "";
/**
* Lists of all synonyms used for describing this element.
*/
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "element_synonyms", joinColumns = @JoinColumn(name = "idDb"))
- @Column(name = "synonym")
- @IndexColumn(name = "idx")
- @Cascade({ org.hibernate.annotations.CascadeType.ALL })
- private List<String> synonyms = new ArrayList<String>();
+ private List<String> synonyms = new ArrayList<>();
/**
* List of former symbols used to describe this element.
*/
- @Transient
- private List<String> formerSymbols = new ArrayList<String>();
+ private List<String> formerSymbols = new ArrayList<>();
/**
* Where this element lies on.
*/
- @ManyToOne(cascade = { CascadeType.ALL })
private Compartment parent;
/**
* In which complex this element is located.
*/
- @ManyToOne(cascade = { CascadeType.ALL })
private ComplexSpecies complex;
/**
* In which model this element is located.
*/
- @ManyToOne(fetch = FetchType.LAZY)
private ModelData model;
/**
* Set of miriam annotations for this element.
*/
- @Transient
- private Set<MiriamData> miriamData = new HashSet<MiriamData>();
+ private Set<MiriamData> miriamData = new HashSet<>();
/**
* Default constructor that initialize the data with the information given in
@@ -234,23 +188,6 @@ public abstract class Element<T extends Alias> implements Serializable {
*/
public abstract String getStringType();
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
public String getNotes() {
return notes;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
index bd9660cdbb..d573c97bc9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
@@ -3,15 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
@@ -21,22 +12,17 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Gene")
public class Gene extends Species<GeneAlias> {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* List of modifications for the Gene.
*/
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<ModificationResidue>();
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
/**
* Constructor that initializes gene with the data passed in the argument.
@@ -122,15 +108,14 @@ public class Gene extends Species<GeneAlias> {
this.modificationResidues = modificationResidues;
}
-
@Override
public GeneAlias createAlias(String aliasId) {
GeneAlias result = new GeneAlias(aliasId);
super.setAliasFields(result);
- for (ModificationResidue mr: modificationResidues) {
+ for (ModificationResidue mr : modificationResidues) {
result.addModificationResidue(mr.createModificationResidueAlias());
}
return result;
-
+
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
index 7161bcfe86..54ba04d6a5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
@@ -12,14 +9,12 @@ import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("GENERIC_PROTEIN")
public class GenericProtein extends Protein<GenericProteinAlias> {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default constructor.
@@ -31,7 +26,8 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
/**
* Constructor that creates a copy of species.
*
- * @param species original species
+ * @param species
+ * original species
*/
public GenericProtein(Species<?> species) {
super(species);
@@ -53,7 +49,7 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
public GenericProteinAlias createAlias(String aliasId) {
GenericProteinAlias result = new GenericProteinAlias(aliasId);
super.setAliasFields(result);
-
+
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
index 13198e509d..7fc1abda1d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.IonAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Ion")
public class Ion extends Chemical<IonAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
index c0189b97eb..9bfe21e7d8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("ION_CHANNEL_PROTEIN")
public class IonChannelProtein extends Protein<IonChannelProteinAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
index 37e5683269..6d78eb82d1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
@@ -2,16 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -27,9 +17,6 @@ import lcsb.mapviewer.model.map.layout.alias.ModificationState;
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "modification_residue_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class ModificationResidue implements Serializable {
/**
@@ -43,56 +30,40 @@ public class ModificationResidue implements Serializable {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
/**
* Identifier of the modification. Must be unique in single map model.
*/
- @Column(name = "idModificationResidue")
private String idModificationResidue = "";
/**
* Name of the modification.
*/
- @Column(name = "name")
private String name = "";
/**
* Some strange param in CellDesigner. No idea what is it for.
*/
- @Column(name = "side")
private String side = "";
/**
* State in which this modification is.
*/
- @Column(name = "state")
private ModificationState state = null;
/**
* Where this modification is located (on which side of the border).
*/
- @Column(name = "angle")
private Double angle = null;
/**
* How big is this modification (used only for some types of the
* modification).
*/
- @Column(name = "size")
private Double size = null;
/**
* Species to which this modification belong to.
*/
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb", nullable = false)
private Species species;
/**
@@ -206,23 +177,6 @@ public class ModificationResidue implements Serializable {
}
}
- /**
- * @return the idModificationResidue
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idModificationResidue to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
/**
* @return the id
* @see #idModificationResidue
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
index b43dac692f..ddb9639f1c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Phenotype")
public class Phenotype extends Species<PhenotypeAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
index be2562cff6..afecc5eb38 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
@@ -3,16 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
@@ -23,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Protein")
public class Protein<T extends ProteinAlias> extends Species<T> {
/**
*
@@ -39,15 +28,11 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
/**
* State of the protein.
*/
- @Column(name = "structuralState")
private String structuralState = null;
/**
* List of modifications for the Protein.
*/
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
private List<ModificationResidue> modificationResidues = new ArrayList<ModificationResidue>();
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
index 82a4e23eb4..a3cb1b0446 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("RECEPTOR_PROTEIN")
public class ReceptorProtein extends Protein<ReceptorProteinAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
index e0bdfba4dd..95ad0b3e7f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
@@ -3,15 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
@@ -22,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("RNA")
public class Rna extends Species<RnaAlias> {
/**
@@ -40,10 +30,7 @@ public class Rna extends Species<RnaAlias> {
/**
* List of rna regions (some rna sequences) in this object.
*/
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<RnaRegion> regions = new ArrayList<RnaRegion>();
+ private List<RnaRegion> regions = new ArrayList<>();
/**
* Constructor that initializes rna with the data passed in the argument.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
index 128dcfe834..7846d84e8c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
@@ -2,16 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -20,14 +10,12 @@ import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
/**
* This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
+ * interest) for a specific
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
*
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class RnaRegion implements Serializable {
/**
@@ -46,20 +34,12 @@ public class RnaRegion implements Serializable {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(RnaRegion.class.getName());
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
/**
* Identifier of the region. Unique in the
* {@link lcsb.mapviewer.model.map.model.Model}.
*/
- @Column(name = "idrnaregion")
private String idRnaRegion = "";
+
/**
* Type of the region in the rna. There are three possible values:
* <ul>
@@ -68,8 +48,6 @@ public class RnaRegion implements Serializable {
* <li>Modification site.</li>
* </ul>
*/
-
- @Column(name = "type")
private String type = "";
/**
@@ -77,33 +55,27 @@ public class RnaRegion implements Serializable {
*
* @see ModificationState
*/
- @Column(name = "state")
private ModificationState state = null;
/**
* Name of the region.
*/
- @Column(name = "name")
private String name = "";
/**
* Size of the region in the graphic representation.
*/
- @Column(name = "size")
private double size = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
*/
- @Column(name = "pos")
private Double pos;
/**
* Defines a species where the region belongs to.
*/
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private Species species;
+ private Rna species;
/**
* Default constructor.
@@ -119,7 +91,6 @@ public class RnaRegion implements Serializable {
* original {@link RnaRegion}
*/
public RnaRegion(RnaRegion mr) {
- this.id = mr.id;
this.idRnaRegion = mr.idRnaRegion;
this.size = mr.size;
setPos(mr.getPos());
@@ -189,23 +160,6 @@ public class RnaRegion implements Serializable {
}
- /**
- * @return the idRnaRegion
- * @see #idRnaRegion
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idRnaRegion to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
/**
* @return the id
* @see #id
@@ -312,7 +266,7 @@ public class RnaRegion implements Serializable {
* @return the species
* @see #species
*/
- public Species getSpecies() {
+ public Rna getSpecies() {
return species;
}
@@ -321,7 +275,7 @@ public class RnaRegion implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(Species species) {
+ public void setSpecies(Rna species) {
this.species = species;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
index 64ca650675..75f255eaa8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -14,8 +11,6 @@ import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("SimpleMolecule")
public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
index 4a79d01566..0066fb92cc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
@@ -1,10 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -19,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("SPECIES")
public class Species<T extends SpeciesAlias> extends Element<T> {
/**
*
@@ -65,7 +58,6 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
/**
* Position on the compartment.
*/
- @Enumerated(EnumType.STRING)
private PositionToCompartment positionToCompartment = null;
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
index 2a1ebc5dfe..c05d481c5b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("TRUNCATED_PROTEIN")
public class TruncatedProtein extends Protein {
/**
@@ -51,7 +46,7 @@ public class TruncatedProtein extends Protein {
public TruncatedProteinAlias createAlias(String aliasId) {
TruncatedProteinAlias result = new TruncatedProteinAlias(aliasId);
super.setAliasFields(result);
-
+
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
index 1c1d8077a9..4fc711dffd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
* @author Piotr Gawron
*
*/
-@Entity
-@DiscriminatorValue("Unknown")
public class Unknown extends Species<UnknownAlias> {
/**
*
@@ -52,7 +47,7 @@ public class Unknown extends Species<UnknownAlias> {
@Override
public UnknownAlias createAlias(String aliasId) {
- UnknownAlias result = new UnknownAlias(aliasId);
+ UnknownAlias result = new UnknownAlias(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
deleted file mode 100644
index 35b82545c2..0000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
+++ /dev/null
@@ -1,540 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ModelMock implements Model {
- private Logger logger = Logger.getLogger(SpeciesAlias.class.getName());
-
- Map<String, Species> species = new HashMap<String, Species>();
-
- public void addSpecies(Species sp) {
- species.put(sp.getElementId(), sp);
- }
-
- @Override
- public Double getWidth() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void setWidth(Double width) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public Double getHeight() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void setHeight(Double height) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setWidth(String nodeAttr) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setHeight(String nodeAttr) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public Set<Alias> getAliases() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public SpeciesAlias getAliasByAliasId(String idAlias) {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addReaction(Reaction reaction) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public Set<Reaction> getReactions() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public CompartmentAlias getCompartmentAliasByCompartmentAliasId(String id) {
- CompartmentAlias alias = new CompartmentAlias(id);
- return alias;
- }
-
- @Override
- public List<CompartmentAlias> getCompartmentsAliases() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addLayer(Layer layer) {
- logger.error("Not implemented in mock object");
-
- }
-
- @Override
- public Set<Layer> getLayers() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addAliases(List<? extends Alias> aliases) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setNotes(String notes) {
- logger.error("Not implemented in mock object");
-
- }
-
- @Override
- public String getNotes() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public Reaction getReactionByReactionId(String idReaction) {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public String getMapVersion() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void setMapVersion(String version) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void addLayers(Collection<Layer> parseLayers) {
- logger.error("Not implemented in mock object");
-
- }
-
- @Override
- public void addAliasGroup(AliasGroup aliasGroup) {
- logger.error("Not implemented in mock object");
-
- }
-
- @Override
- public void addBlockDiagream(BlockDiagram blockDiagram) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setSbgnFormat(boolean sbgnFormat) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void addCreationWarnings(List<String> warnings) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public List<String> getCreationWarnings() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void addCreationWarning(String warning) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setNotifyEmail(String notifyEmail) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String getNotifyEmail() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setIdModel(String idModel) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String getIdModel() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setTileSize(int tileSize) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public int getTileSize() {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public void setZoomLevels(int zoomLevels) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public int getZoomLevels() {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public void removeReaction(Reaction reaction) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void removeAlias(Alias alias) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public List<Reaction> getSortedReactions() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public List<Alias> getSortedAliases() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Collection<SpeciesAlias> getNotComplexSpeciesAliases() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Collection<ComplexAlias> getComplexAliases() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void addReactions(List<Reaction> reactions2) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setHeight(int height) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setWidth(int width) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void addLayout(Layout layout) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setLayouts(List<Layout> layouts) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public List<Layout> getLayouts() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setCreationDate(Calendar creationDate) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Calendar getCreationDate() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Alias getAliasByDbId(Integer dbId) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Reaction getReactionByDbId(Integer dbId) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public List<CompartmentAlias> getSortedCompartmentsAliases() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public List<Alias> getAliasesSortedBySize() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setProject(Project project) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Project getProject() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setAliases(Set<Alias> aliases) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public ModelData getModelData() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Integer getId() {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public void addSubmodelConnection(ModelSubmodelConnection submodel) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public List<ModelSubmodelConnection> getSubmodelConnections() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getName() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setName(String name) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Model getSubmodelById(Integer idObject) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Collection<SubmodelConnection> getParentModels() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Model getSubmodelByConnectionName(String name) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public SubmodelConnection getSubmodelConnectionById(Integer idObject) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Model getSubmodelById(String modelIdentifier) {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public Collection<Model> getSubmodels() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public Model getSubmodelByName(String selectedModelString) {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public List<OverviewImage> getOverviewImages() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addOverviewImage(OverviewImage overviewImage) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setOverviewImages(List<OverviewImage> parseOverviewLinks) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public OverviewImage getTopOverviewImage() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public boolean isSbgnFormat() {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public void addLayout(int index, Layout layout) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void addDataMiningSet(DataMiningSet dataMiningSet) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public List<DataMiningSet> getDataMiningSets() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addDataMiningSets(Collection<DataMiningSet> dataMiningSets) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public Layout getLayoutByIdentifier(Integer layoutIdentfier) {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addAlias(Alias alias) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public void setId(int id) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public List<AnnotatedObject> getAnnotatedObjects() {
- logger.error("Not implemented in mock object");
- return null;
- }
-
- @Override
- public void addLoggingInfo(EventStorageLoggerAppender appender) {
- logger.error("Not implemented in mock object");
- }
-
- @Override
- public List<Alias> getAliasByName(String name) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public List<SpeciesAlias> getSpeciesAliases() {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
index fa649ac8af..842bdd559e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
@@ -37,7 +37,7 @@ public class AntisenseRnaComparatorTest {
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setId(-1);
+ aRna1.setElementId("AAA");
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
index 0564a8bc98..12841cda2a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
@@ -113,7 +113,7 @@ public class AntisenseRnaRegionTest {
try {
AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
int id = 91;
- Species species = new Species();
+ AntisenseRna species = new AntisenseRna();
double pos = 4.6;
double size = 5.3;
AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
index 5e52e347f9..2bd397c337 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
@@ -33,7 +33,7 @@ public class CompartmentComparatorTest {
assertEquals(0, comparator.compare(comp1, comp2));
assertEquals(0, comparator.compare(comp2, comp1));
- comp1.setId(-1);
+ comp1.setElementId("AAA");
assertEquals(0, comparator.compare(comp1, comp2));
assertEquals(0, comparator.compare(comp2, comp1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
index 8decad505f..0f9d38dd02 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
@@ -42,7 +42,7 @@ public class ComplexSpeciesComparatorTest {
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
- complex1.setId(-1);
+ complex1.setElementId("AAA");
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
index 0d15ec6b2a..50364bb452 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
@@ -35,7 +35,7 @@ public class DegradedComparatorTest {
assertEquals(0, comparator.compare(degraded1, degraded2));
assertEquals(0, comparator.compare(degraded2, degraded1));
- degraded1.setId(-1);
+ degraded1.setElementId("AAA");
assertEquals(0, comparator.compare(degraded1, degraded2));
assertEquals(0, comparator.compare(degraded2, degraded1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
index 84c3de7bec..c478814faa 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
@@ -35,7 +35,7 @@ public class DrugComparatorTest {
assertEquals(0, comparator.compare(drug1, drug2));
assertEquals(0, comparator.compare(drug2, drug1));
- drug1.setId(-1);
+ drug1.setElementId("AAA");
assertEquals(0, comparator.compare(drug1, drug2));
assertEquals(0, comparator.compare(drug2, drug1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index b88371676a..7eac4d04d4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -104,21 +104,18 @@ public class ElementTest extends CellDesignerTestFunctions {
public void testGetters() {
try {
Element<?> element = Mockito.spy(Element.class);
- int id = 4;
List<String> synonyms = new ArrayList<>();
List<String> formerSymbols = new ArrayList<>();
ComplexSpecies complex = new ComplexSpecies();
Model model = new ModelFullIndexed(null);
String formula = "str";
- element.setId(id);
element.setSynonyms(synonyms);
element.setFormerSymbols(formerSymbols);
element.setComplex(complex);
element.setModel(model);
element.setFormula(formula);
- assertEquals(id, element.getId());
assertEquals(synonyms, element.getSynonyms());
assertEquals(formerSymbols, element.getFormerSymbols());
assertEquals(complex, element.getComplex());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
index d93122574d..7e4ded16e3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
@@ -34,7 +34,7 @@ public class GeneComparatorTest {
assertEquals(0, comparator.compare(gene1, gene2));
assertEquals(0, comparator.compare(gene2, gene1));
- gene1.setId(-1);
+ gene1.setElementId("AAA");
assertEquals(0, comparator.compare(gene1, gene2));
assertEquals(0, comparator.compare(gene2, gene1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
index a55e4fb58c..d30536e668 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
@@ -35,7 +35,7 @@ public class IonComparatorTest {
assertEquals(0, comparator.compare(ion1, ion2));
assertEquals(0, comparator.compare(ion2, ion1));
- ion1.setId(-1);
+ ion1.setElementId("AAA");
assertEquals(0, comparator.compare(ion1, ion2));
assertEquals(0, comparator.compare(ion2, ion1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
index 1690e144ac..9f3f99119e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
@@ -88,7 +88,6 @@ public class ModificationResidueTest {
String nullStr = null;
Double angle = 2.0;
Species species = new Species();
- int id = 5;
original.setAngle(doubleStr);
assertEquals(angle, original.getAngle(), Configuration.EPSILON);
@@ -111,9 +110,6 @@ public class ModificationResidueTest {
original.setSize(nullStr);
assertNull(original.getSize());
- original.setId(id);
- assertEquals(id, original.getId());
-
original.setSpecies(species);
assertEquals(species, original.getSpecies());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
index f734a14617..11e30dd99c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
@@ -33,7 +33,7 @@ public class PhenotypeComparatorTest {
assertEquals(0, comparator.compare(phenotype1, phenotype2));
assertEquals(0, comparator.compare(phenotype2, phenotype1));
- phenotype1.setId(-1);
+ phenotype1.setElementId("AAA");
assertEquals(0, comparator.compare(phenotype1, phenotype2));
assertEquals(0, comparator.compare(phenotype2, phenotype1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
index b9684ca5b2..48bdfbb22e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
@@ -33,7 +33,7 @@ public class ProteinComparatorTest {
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setId(-1);
+ aRna1.setElementId("AAA");
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
index 2b19c81e5c..e2aca98f8e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
@@ -34,7 +34,7 @@ public class RnaComparatorTest {
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setId(-1);
+ aRna1.setElementId("AAA");
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
index b40f127fe2..fe45169fc0 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
@@ -116,13 +116,10 @@ public class RnaRegionTest {
public void testGetters() {
try {
RnaRegion region = new RnaRegion();
- int id = 47;
double size = 2.5;
- Species species = new GenericProtein();
- region.setId(id);
+ Rna species = new Rna();
region.setSize(size);
region.setSpecies(species);
- assertEquals(id, region.getId());
assertEquals(size, region.getSize(), Configuration.EPSILON);
assertEquals(species, region.getSpecies());
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
index 06e688cf76..05dbd82998 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
@@ -35,7 +35,7 @@ public class SimpleMoleculeComparatorTest {
assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
- simpleMolecule1.setId(-1);
+ simpleMolecule1.setElementId("AAA");
assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
index 009dd1d89e..f09907eb61 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
@@ -35,7 +35,7 @@ public class UnknownComparatorTest {
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setId(-1);
+ aRna1.setElementId("AAA");
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
index fc0b0cc738..b053e372fd 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
@@ -2,13 +2,12 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
/**
- * This class allows to compare {@link DrugAlias} element (internal representation)
- * and {@link ReactomeCatalystActivity} (reactome model).
+ * This class allows to compare {@link DrugAlias} element (internal
+ * representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
index 4807cee4ce..e399fcca7e 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
@@ -2,13 +2,12 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
/**
- * This class allows to compare {@link GeneAlias} element (internal representation)
- * and {@link ReactomeDefinedSet} (reactome model).
+ * This class allows to compare {@link GeneAlias} element (internal
+ * representation) and {@link ReactomeDefinedSet} (reactome model).
*
* @author Piotr Gawron
*
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
index d17cc13191..d43765ed4d 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
-import org.apache.log4j.Logger;
-
/**
- * This class allows to compare {@link GeneAlias} element (internal representation)
- * and {@link ReactomeOtherEntity} (reactome model).
+ * This class allows to compare {@link GeneAlias} element (internal
+ * representation) and {@link ReactomeOtherEntity} (reactome model).
*
* @author Piotr Gawron
*
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
index 526d85dec6..061b4ef15b 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
@@ -4,7 +4,6 @@ import java.util.List;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
@@ -17,8 +16,8 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link IonAlias} element (internal representation)
- * and {@link ReactomeComplex} (reactome model).
+ * This class allows to compare {@link IonAlias} element (internal
+ * representation) and {@link ReactomeComplex} (reactome model).
*
* @author Piotr Gawron
*
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
index f16d5afaa5..104b0ddffc 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
@@ -37,7 +36,8 @@ public class IonAndDefinedSetComparator extends ANodeComparator<IonAlias, Reacto
} else if (entity instanceof ReactomeEntityWithAccessionedSequence) {
result |= getGlobalComparator().compareNodes(species, (ReactomeEntityWithAccessionedSequence) entity);
} else {
- throw new InvalidArgumentException("Cannot determine the way of comparison for provided class types: " + species.getClass() + ", " + entity.getClass());
+ throw new InvalidArgumentException(
+ "Cannot determine the way of comparison for provided class types: " + species.getClass() + ", " + entity.getClass());
}
}
return result;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
index e387838a8c..9c6df33aa6 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
- * This class allows to compare {@link IonAlias} element (internal representation)
- * and {@link ReactomeEntityWithAccessionedSequence} (reactome model).
+ * This class allows to compare {@link IonAlias} element (internal
+ * representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
+ * model).
*
* @author Piotr Gawron
*
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
index 53f3f62a1a..dd64991b26 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
index 483803281c..0221ea8f21 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
index bce2b67b54..3cbd349b76 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
index ad23aa7fd8..20d37fad35 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
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 478e70e648..222ab908db 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
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 e445ef52df..74b3894831 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
index b163c56301..69386a73bf 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
@@ -21,7 +21,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.Chebi;
import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
--
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