kinetics parser added

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java

+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class KineticsXmlParser extends XmlParser {
+  Logger logger = Logger.getLogger(KineticsXmlParser.class);
+
+  ParameterCollectionXmlParser parameterParser;
+
+  Model model;
+
+  public KineticsXmlParser(Model model) {
+    this.model = model;
+    parameterParser = new ParameterCollectionXmlParser(model);
+  }
+
+  public SbmlKinetics parseKinetics(Node kineticsNode, Map<String, Element> elements) throws InvalidXmlSchemaException {
+    SbmlKinetics result = new SbmlKinetics();
+    Node mathNode = super.getNode("math", kineticsNode);
+    if (mathNode == null) {
+      throw new InvalidXmlSchemaException("kineticLaw node doesn't have math subnode");
+    }
+
+    Node parametersNode = super.getNode("listOfParameters", kineticsNode);
+    if (parametersNode != null) {
+      result.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
+    }
+
+    Set<SbmlArgument> elementsUsedInKinetics = new HashSet<>();
+    for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", mathNode)) {
+      String id = super.getNodeValue(ciNode).trim();
+      SbmlArgument element = elements.get(id);
+      if (element == null) {
+        element = result.getParameterById(id);
+      }
+      if (element == null) {
+        element = model.getParameterById(id);
+      }
+      if (element == null) {
+        element = model.getFunctionById(id);
+      }
+      if (element == null) {
+        throw new InvalidXmlSchemaException("Unknown symbol in kinetics: " + id);
+      }
+      elementsUsedInKinetics.add(element);
+    }
+    result.addArguments(elementsUsedInKinetics);
+
+    return result;
+  }
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java

@@ -5,14 +5,15 @@ import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
-@SuiteClasses({ ReactionCollectionXmlParserTest.class, //
-		ReactionFromXmlTest.class, //
-		ReactionLineDataTest.class, //
-		ReactionParserExceptionTest.class, //
-		ReactionParserTests.class, //
-		ReactionToXmlTest.class, //
-		UnknownModifierClassExceptionTest.class, //
-		UnknownReactionClassExceptionTest.class,//
+@SuiteClasses({ KineticsXmlParserTest.class, //
+    ReactionCollectionXmlParserTest.class, //
+    ReactionFromXmlTest.class, //
+    ReactionLineDataTest.class, //
+    ReactionParserExceptionTest.class, //
+    ReactionParserTests.class, //
+    ReactionToXmlTest.class, //
+    UnknownModifierClassExceptionTest.class, //
+    UnknownReactionClassExceptionTest.class,//
 })
 public class AllReactionTests {
 

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java

+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class KineticsXmlParserTest extends CellDesignerTestFunctions {
+
+  @Test
+  public void testParserElements() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = getTestElementMap();
+    Model model = new ModelFullIndexed(null); 
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/simple.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(2, kinetics.getArguments().size());
+  }
+
+  @Test
+  public void testParserParameters() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = getTestElementMap();
+    Model model = new ModelFullIndexed(null); 
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_parameter.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(1, kinetics.getParameters().size());
+  }
+
+  @Test
+  public void testParserWithUsedParameters() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = getTestElementMap();
+    Model model = new ModelFullIndexed(null); 
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_used_parameter.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(1, kinetics.getParameters().size());
+  }
+
+  @Test
+  public void testParserGlobalParameters() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = getTestElementMap();
+    Model model = new ModelFullIndexed(null);
+    model.addParameter(new SbmlParameter("k1"));
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_global_parameter.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(1, kinetics.getParameters().size());
+  }
+
+  @Test
+  public void testParserGlobalFunction() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = getTestElementMap();
+    Model model = new ModelFullIndexed(null);
+    model.addFunction(new SbmlFunction("fun"));
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_function.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(1, kinetics.getFunctions().size());
+  }
+
+  @Test(expected = InvalidXmlSchemaException.class)
+  public void testParserNonExistingElements() throws InvalidXmlSchemaException, IOException {
+    Map<String, Element> elements = new HashMap<>();
+    Model model = new ModelFullIndexed(null); 
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/simple.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    parser.parseKinetics(node, elements);
+  }
+
+  @Test
+  public void testParserElementDuplicate() throws InvalidXmlSchemaException, IOException {
+    Model model = new ModelFullIndexed(null); 
+    Map<String, Element> elements = getTestElementMap();
+    Node node = super.getXmlDocumentFromFile("testFiles/kinetics/math_using_one_element.xml").getFirstChild();
+
+    KineticsXmlParser parser = new KineticsXmlParser(model);
+    SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+    assertNotNull(kinetics);
+    assertEquals(1, kinetics.getArguments().size());
+  }
+
+  private Map<String, Element> getTestElementMap() {
+    Map<String, Element> elements = new HashMap<>();
+    elements.put("s1", new GenericProtein("s1"));
+    elements.put("s2", new GenericProtein("s2"));
+    return elements;
+  }
+
+}

converter-CellDesigner/testFiles/kinetics/math_using_one_element.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s1 </ci>
+</apply>
+</math>
+</kineticLaw>

converter-CellDesigner/testFiles/kinetics/simple.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>

converter-CellDesigner/testFiles/kinetics/with_function.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> fun </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>

converter-CellDesigner/testFiles/kinetics/with_global_parameter.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> k1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>

converter-CellDesigner/testFiles/kinetics/with_parameter.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+<listOfParameters>
+<parameter metaid="k2" id="k2" name="local param" value="0" units="substance"/>
+</listOfParameters>
+</kineticLaw>

converter-CellDesigner/testFiles/kinetics/with_used_parameter.xml

+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> k2 </ci>
+</apply>
+</math>
+<listOfParameters>
+<parameter metaid="k2" id="k2" name="local param" value="0" units="substance"/>
+</listOfParameters>
+</kineticLaw>

converter-CellDesigner/testFiles/reactions/kinetics.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="67.0" y="151.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="296.0" y="174.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false" fast="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlArgument.java

+package lcsb.mapviewer.model.map.kinetics;
+
+public interface SbmlArgument {
+
+}

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java

@@ -28,7 +28,7 @@ import org.hibernate.annotations.IndexColumn;
 @Table(name = "sbml_function")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
-public class SbmlFunction implements Serializable {
+public class SbmlFunction implements Serializable, SbmlArgument {
 
   /**
    * Default class logger.

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java

+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Representation of a single SBML function
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+@Entity
+@Table(name = "sbml_kinetics")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlKinetics implements Serializable {
+
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(SbmlKinetics.class);
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  private Set<SbmlParameter> parameters = new HashSet<>();
+
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  private Set<SbmlFunction> functions = new HashSet<>();
+
+  private List<Element> elements = new ArrayList<>();
+
+  /**
+   * Unique database identifier.
+   */
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  @Column(name = "idDb", unique = true, nullable = false)
+  private int id;
+
+  @Column(columnDefinition = "TEXT")
+  private String definition;
+
+  public void addParameter(SbmlParameter parameter) {
+    parameters.add(parameter);
+  }
+
+  public Set<SbmlParameter> getParameters() {
+    return parameters;
+  }
+
+  public List<SbmlArgument> getArguments() {
+    List<SbmlArgument> arguments = new ArrayList<>();
+    arguments.addAll(parameters);
+    arguments.addAll(elements);
+    arguments.addAll(functions);
+    return arguments;
+  }
+
+  public void addElement(Element element) {
+    this.elements.add(element);
+  }
+
+  public String getDefinition() {
+    return definition;
+  }
+
+  public void setDefinition(String definition) {
+    this.definition = definition;
+  }
+
+  public void addElements(Set<Element> elements) {
+    for (Element element : elements) {
+      addElement(element);
+    }
+  }
+
+  public void addParameters(Set<SbmlParameter> parameters) {
+    for (SbmlParameter parameter : parameters) {
+      addParameter(parameter);
+    }
+
+  }
+
+  public void addArguments(Set<SbmlArgument> elementsUsedInKinetics) {
+    for (SbmlArgument argument : elementsUsedInKinetics) {
+      addArgument(argument);
+    }
+
+  }
+
+  public void addArgument(SbmlArgument argument) {
+    if (argument instanceof SbmlParameter) {
+      addParameter((SbmlParameter) argument);
+    } else if (argument instanceof SbmlFunction) {
+      addFunction((SbmlFunction) argument);
+    } else {
+      addElement((Element) argument);
+    }
+
+  }
+
+  public void addFunction(SbmlFunction argument) {
+    functions.add(argument);
+  }
+
+  public SbmlParameter getParameterById(String id) {
+    for (SbmlParameter parameter : parameters) {
+      if (parameter.getParameterId().equals(id)) {
+        return parameter;
+      }
+    }
+    return null;
+  }
+
+  public Set<SbmlFunction> getFunctions() {
+    return functions;
+  }
+
+}

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java

@@ -22,7 +22,7 @@ import org.apache.log4j.Logger;
 @Table(name = "sbml_parameter")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
-public class SbmlParameter implements Serializable {
+public class SbmlParameter implements Serializable, SbmlArgument {
 
   /**
    * Default class logger.

model/src/main/java/lcsb/mapviewer/model/map/model/Model.java

@@ -10,6 +10,7 @@ import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
 import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
 import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -607,4 +608,12 @@ public interface Model {
   SbmlUnit getUnitsByUnitId(String unitId);
 
   void addParameters(Collection<SbmlParameter> sbmlParamters);
+
+  void addParameter(SbmlParameter sbmlParameter);
+
+  SbmlParameter getParameterById(String parameterId);
+
+  void addFunction(SbmlFunction sbmlFunction);
+
+  SbmlArgument getFunctionById(String id);
 }

model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java

@@ -774,7 +774,15 @@ public class ModelData implements Serializable {
     this.units.add(unit);
   }
 
-  public void addParameters(Collection<SbmlParameter> sbmlParamters) {
-    this.parameters.addAll(sbmlParamters);
+  public void addParameters(Collection<SbmlParameter> sbmlParameters) {
+    this.parameters.addAll(sbmlParameters);
+  }
+
+  public void addParameter(SbmlParameter sbmlParameter) {
+    this.parameters.add(sbmlParameter);
+  }
+
+  public void addFunction(SbmlFunction sbmlFunction) {
+    this.functions.add(sbmlFunction);
   }
 }
\ No newline at end of file