diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index 068af61908262d6eca1908b8b53610b2631a7212..4f9d07386c1e8e486295f17835de6c50f797a744 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -157,14 +157,12 @@ public interface BioEntity extends Serializable {
*/
void setVisibilityLevel(Integer zoomLevelVisibility);
- /**
- * Returns semantic zoom level visibility.
- *
- * @return semantic zoom level visibility
- */
- String getVisibilityLevel();
-
- String getElementId();
+ /**
+ * Returns semantic zoom level visibility.
+ *
+ * @return semantic zoom level visibility
+ */
+ String getVisibilityLevel();
/**
* Returns the {@link Model} where BioEntity is located.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java
new file mode 100644
index 0000000000000000000000000000000000000000..fc75944422f6147e87ad2d8d6a55f9f89fd181be
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java
@@ -0,0 +1,109 @@
+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.IndexColumn;
+
+/**
+ * Representation of a single SBML function
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_function")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlFunction implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlFunction.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ private String functionId;
+
+ private String name;
+
+ @Column(columnDefinition = "TEXT")
+ private String definition;
+
+ @ElementCollection
+ @CollectionTable(name = "sbml_function_arguments", joinColumns = @JoinColumn(name = "sbml_function_iddb"))
+ @IndexColumn(name = "idx")
+ @Column(name = "argument_name")
+ private List<String> arguments = new ArrayList<>();
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlFunction() {
+ super();
+ }
+
+ public SbmlFunction(String functionId) {
+ this.functionId = functionId;
+ }
+
+ public String getFunctionId() {
+ return functionId;
+ }
+
+ public void setFunctionId(String functionId) {
+ this.functionId = functionId;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public List<String> getArguments() {
+ return arguments;
+ }
+
+ public void setArguments(List<String> arguments) {
+ this.arguments = arguments;
+ }
+
+ public String getDefinition() {
+ return definition;
+ }
+
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index f20bbd35a49e556693c7d9c318bc700f13c4f258..613c5ce87787ac6a4fc74c6a6a71ff04b0019c36 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -8,6 +8,7 @@ import java.util.Set;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.SbmlFunction;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -588,4 +589,8 @@ public interface Model {
* layout to remove
*/
void removeLayout(Layout dbLayout);
+
+ Set<SbmlFunction> getFunctions();
+
+ void addFunctions(Collection<SbmlFunction> parseXmlFunctionCollection);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index e5c17ee79861f77859bb66464e4be93434ba39d2..95fe2a9fbdf13cef3d5481774cb6f3e7fbfb3d27 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -27,6 +27,7 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.SbmlFunction;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
@@ -101,6 +102,16 @@ public class ModelData implements Serializable {
@OneToMany(mappedBy = "model", orphanRemoval = true)
private Set<Reaction> reactions = new HashSet<>();
+ /**
+ * Collection of SBML functions in the map.
+ *
+ * @see SbmlFunction
+ *
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<SbmlFunction> functions = new HashSet<>();
+
/**
* When the map was created.
*/
@@ -110,7 +121,7 @@ public class ModelData implements Serializable {
* Width of the map.
*/
private Double width;
-
+
/**
* Height of the map.
*/
@@ -120,7 +131,7 @@ public class ModelData implements Serializable {
* X coordinate that should be used when initially showing map.
*/
private Double defaultCenterX;
-
+
/**
* Y coordinate that should be used when initially showing map.
*/
@@ -732,4 +743,8 @@ public class ModelData implements Serializable {
public void setDefaultZoomLevel(Integer defaultZoomLevel) {
this.defaultZoomLevel = defaultZoomLevel;
}
+
+ public Set<SbmlFunction> getFunctions() {
+ return functions;
+ }
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 9a5c504bc38475d5f62cf62d3fd3472628d9d03b..99a09db9a8def3b1d92c7874973690364b455b83 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -16,6 +16,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.SbmlFunction;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -652,4 +653,14 @@ public class ModelFullIndexed implements Model {
public void setDefaultZoomLevel(Integer defaultZoomLevel) {
modelData.setDefaultZoomLevel(defaultZoomLevel);
}
+
+ @Override
+ public Set<SbmlFunction> getFunctions() {
+ return modelData.getFunctions();
+ }
+
+ @Override
+ public void addFunctions(Collection<SbmlFunction> functions) {
+ modelData.getFunctions().addAll(functions);
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index d1139cf5a6c9c26ee6958efc415565b54eb65cbe..eb6e6ccac3b9756e27a3a55be425cc93dc8a2555 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -889,10 +889,4 @@ public class Reaction implements BioEntity {
}
}
-
- @Override
- public String getElementId() {
- return getIdReaction();
- }
-
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..20e3c983f963d874f2a23cb982e3dbb110fcca97
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java
@@ -0,0 +1,45 @@
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.Test;
+
+public class SbmlFunctionTest {
+
+ @Test
+ public void testConstructor() {
+ String id = "function_i";
+ SbmlFunction function = new SbmlFunction(id);
+ assertEquals(id, function.getFunctionId());
+ }
+
+ @Test
+ public void testSetName() {
+ String name = "name";
+ SbmlFunction function = new SbmlFunction("");
+ function.setName(name);
+ assertEquals(name, function.getName());
+ }
+
+ @Test
+ public void testSetDefinition() {
+ String definition = "<lambda><bvar><ci> x </ci></bvar></lambda>";
+ SbmlFunction function = new SbmlFunction("");
+ function.setDefinition(definition);
+ assertEquals(definition, function.getDefinition());
+ }
+
+ @Test
+ public void testGetArguments() {
+ List<String> arguments = new ArrayList<>();
+ arguments.add("x");
+
+ SbmlFunction function = new SbmlFunction("");
+ function.setArguments(arguments);
+ assertEquals(arguments, function.getArguments());
+ }
+
+}