From 6ca6a3f5001a468c18b5d21eff98d49bc4f5cc7c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 29 Jan 2018 16:53:23 +0100
Subject: [PATCH] support for SBML units and parameters added
---
.../celldesigner/CellDesignerXmlParser.java | 21 +++-
.../function/FunctionCollectionXmlParser.java | 2 +-
.../function/FunctionXmlParser.java | 2 +-
.../ParameterCollectionXmlParser.java | 31 ++++++
.../parameter/ParameterXmlParser.java | 29 +++++
.../unit/UnitCollectionXmlParser.java | 24 ++++
.../celldesigner/unit/UnitXmlParser.java | 70 ++++++++++++
.../celldesigner/AllCellDesignerTests.java | 46 ++++----
.../celldesigner/ComplexParserTests.java | 26 +++++
.../function/FunctionXmlParserTest.java | 2 +-
.../parameter/ParameterXmlParserTest.java | 36 ++++++
.../celldesigner/unit/UnitXmlParserTest.java | 33 ++++++
.../testFiles/parameter.xml | 54 +++++++++
.../testFiles/parameter/simple.xml | 1 +
converter-CellDesigner/testFiles/unit.xml | 31 ++++++
.../testFiles/unit/simple.xml | 5 +
.../map/{ => kinetics}/SbmlFunction.java | 2 +-
.../model/map/kinetics/SbmlParameter.java | 101 +++++++++++++++++
.../model/map/kinetics/SbmlUnit.java | 88 +++++++++++++++
.../model/map/kinetics/SbmlUnitType.java | 36 ++++++
.../map/kinetics/SbmlUnitTypeFactor.java | 103 ++++++++++++++++++
.../lcsb/mapviewer/model/map/model/Model.java | 18 ++-
.../mapviewer/model/map/model/ModelData.java | 32 +++++-
.../model/map/model/ModelFullIndexed.java | 40 ++++++-
.../graphics/PolylineDataComparatorTest.java | 3 +-
.../lcsb/mapviewer/model/map/AllMapTests.java | 54 ++++-----
.../model/map/kinetics/AllKineticsTests.java | 11 ++
.../map/{ => kinetics}/SbmlFunctionTest.java | 2 +-
.../model/map/kinetics/SbmlParameterTest.java | 32 ++++++
.../model/map/kinetics/SbmlUnitTest.java | 33 ++++++
.../map/kinetics/SbmlUnitTypeFactorTest.java | 25 +++++
31 files changed, 934 insertions(+), 59 deletions(-)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
create mode 100644 converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParserTest.java
create mode 100644 converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParserTest.java
create mode 100644 converter-CellDesigner/testFiles/parameter.xml
create mode 100644 converter-CellDesigner/testFiles/parameter/simple.xml
create mode 100644 converter-CellDesigner/testFiles/unit.xml
create mode 100644 converter-CellDesigner/testFiles/unit/simple.xml
rename model/src/main/java/lcsb/mapviewer/model/map/{ => kinetics}/SbmlFunction.java (93%)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitType.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
rename model/src/test/java/lcsb/mapviewer/model/map/{ => kinetics}/SbmlFunctionTest.java (96%)
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 05794c33d6..0178e222c6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -9,7 +9,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
-import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringEscapeUtils;
@@ -30,6 +29,7 @@ import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParse
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.UnknownReactionClassException;
import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
@@ -37,9 +37,9 @@ import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlP
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.unit.UnitCollectionXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.SbmlFunction;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
@@ -110,6 +110,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
CellDesignerElementCollection elements = new CellDesignerElementCollection();
FunctionCollectionXmlParser functionParser = new FunctionCollectionXmlParser();
+ UnitCollectionXmlParser unitParser = new UnitCollectionXmlParser();
Model model = new ModelFullIndexed(null);
@@ -120,6 +121,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+ ParameterCollectionXmlParser parameterParser = new ParameterCollectionXmlParser(model);
+
DOMParser parser = new DOMParser();
try {
parser.parse(params.getSource());
@@ -163,6 +166,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
Node reactionsNode = null;
Node functionsNode = null;
+ Node unitsNode = null;
+ Node parametersNode = null;
NodeList nodes = modelNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
@@ -184,15 +189,25 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
model.setNotes(notes);
} else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
- continue; // we can ignore unit definitions
+ unitsNode = node;
} else if (node.getNodeName().equalsIgnoreCase("listOfFunctionDefinitions")) {
functionsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfParameters")) {
+ parametersNode = node;
} else {
throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
}
}
}
+ if (unitsNode!=null) {
+ model.addUnits(unitParser.parseXmlUnitCollection(unitsNode));
+ }
+
+ if (parametersNode!=null) {
+ model.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
+ }
+
Node annotationNode = getNode("annotation", modelNode.getChildNodes());
if (annotationNode == null) {
throw new InvalidInputDataExecption("No annotation node in SBML/model");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
index ceeaa4963e..e8ebe8c180 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
@@ -7,7 +7,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
public class FunctionCollectionXmlParser extends XmlParser {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
index b25b2829d1..e5fa4b9379 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
@@ -8,7 +8,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
public class FunctionXmlParser extends XmlParser {
Logger logger = Logger.getLogger(FunctionXmlParser.class);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
new file mode 100644
index 0000000000..cc8d4a3c0e
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterCollectionXmlParser.java
@@ -0,0 +1,31 @@
+package lcsb.mapviewer.converter.model.celldesigner.parameter;
+
+import java.util.HashSet;
+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.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class ParameterCollectionXmlParser extends XmlParser {
+ Logger logger = Logger.getLogger(ParameterCollectionXmlParser.class);
+
+ private ParameterXmlParser parameterParser;
+
+ public ParameterCollectionXmlParser(Model model) {
+ parameterParser = new ParameterXmlParser(model);
+ }
+
+ public Set<SbmlParameter> parseXmlParameterCollection(Node functionsNode) throws InvalidXmlSchemaException {
+ Set<SbmlParameter> result = new HashSet<>();
+ for (Node node : super.getNodes("parameter", functionsNode.getChildNodes())) {
+ result.add(parameterParser.parseFunction(node));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
new file mode 100644
index 0000000000..c0eb0dbaf0
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParser.java
@@ -0,0 +1,29 @@
+package lcsb.mapviewer.converter.model.celldesigner.parameter;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class ParameterXmlParser extends XmlParser {
+ Logger logger = Logger.getLogger(ParameterXmlParser.class);
+
+ private Model model;
+
+ public ParameterXmlParser(Model model) {
+ this.model = model;
+ }
+
+ public SbmlParameter parseFunction(Node unitNode) throws InvalidXmlSchemaException {
+ String parameterId = getNodeAttr("id", unitNode);
+
+ SbmlParameter result = new SbmlParameter(parameterId);
+ result.setName(getNodeAttr("name", unitNode));
+ result.setValue(Double.parseDouble(getNodeAttr("value", unitNode)));
+ result.setUnits(model.getUnitsByUnitId(getNodeAttr("units", unitNode)));
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
new file mode 100644
index 0000000000..1cf70a8067
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitCollectionXmlParser.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.converter.model.celldesigner.unit;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+
+public class UnitCollectionXmlParser extends XmlParser {
+
+ private UnitXmlParser unitParser = new UnitXmlParser();
+
+ public Set<SbmlUnit> parseXmlUnitCollection(Node functionsNode) throws InvalidXmlSchemaException {
+ Set<SbmlUnit> result = new HashSet<>();
+ for (Node node : super.getNodes("unitDefinition", functionsNode.getChildNodes())) {
+ result.add(unitParser.parseFunction(node));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
new file mode 100644
index 0000000000..fe1ca925a0
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParser.java
@@ -0,0 +1,70 @@
+package lcsb.mapviewer.converter.model.celldesigner.unit;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
+
+public class UnitXmlParser extends XmlParser {
+ Logger logger = Logger.getLogger(UnitXmlParser.class);
+
+ public SbmlUnit parseFunction(Node unitNode) throws InvalidXmlSchemaException {
+ String unitId = getNodeAttr("id", unitNode);
+
+ SbmlUnit result = new SbmlUnit(unitId);
+ result.setName(getNodeAttr("name", unitNode));
+ Node factors = getNode("listOfUnits", unitNode);
+ if (factors == null) {
+ throw new InvalidXmlSchemaException(
+ "Unit Definition " + unitId + " doesn't contain information about units (listOfUnits node)");
+ }
+ for (SbmlUnitTypeFactor factor : parseUnitTypeFactors(factors)) {
+ result.addUnitTypeFactor(factor);
+ }
+
+ return result;
+ }
+
+ private List<SbmlUnitTypeFactor> parseUnitTypeFactors(Node factors) throws InvalidXmlSchemaException {
+ List<SbmlUnitTypeFactor> result = new ArrayList<>();
+ List<Node> variables = super.getNodes("unit", factors.getChildNodes());
+ for (Node node : variables) {
+ result.add(parseFactor(node));
+ }
+ return result;
+ }
+
+ private SbmlUnitTypeFactor parseFactor(Node node) throws InvalidXmlSchemaException {
+ String unitTypeString = getNodeAttr("kind", node);
+ SbmlUnitType unitType;
+ try {
+ unitType = SbmlUnitType.valueOf(unitTypeString.toUpperCase());
+ } catch (Exception e) {
+ throw new InvalidXmlSchemaException("Unknown unit kind: " + unitTypeString);
+ }
+ int scale = 0;
+ double multiplier = 1.0;
+ int exponent = 1;
+
+ String scaleString = getNodeAttr("scale", node);
+ if (scaleString != null && !scaleString.isEmpty()) {
+ scale = Integer.parseInt(scaleString);
+ }
+ String exponentString = getNodeAttr("exponent", node);
+ if (exponentString != null && !exponentString.isEmpty()) {
+ exponent = Integer.parseInt(exponentString);
+ }
+ String multiplierString = getNodeAttr("multiplier", node);
+ if (multiplierString != null && !multiplierString.isEmpty()) {
+ multiplier = Double.parseDouble(multiplierString);
+ }
+ return new SbmlUnitTypeFactor(unitType, exponent, scale, multiplier);
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
index 5c6735bb6e..1b78ab1daf 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
@@ -1,36 +1,42 @@
package lcsb.mapviewer.converter.model.celldesigner;
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
import lcsb.mapviewer.converter.model.celldesigner.alias.AllAliasTests;
import lcsb.mapviewer.converter.model.celldesigner.annotation.AllAnnotationTests;
import lcsb.mapviewer.converter.model.celldesigner.compartment.AllCompartmentTests;
+import lcsb.mapviewer.converter.model.celldesigner.function.FunctionXmlParserTest;
import lcsb.mapviewer.converter.model.celldesigner.geometry.AllGeometryTests;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterXmlParserTest;
import lcsb.mapviewer.converter.model.celldesigner.reaction.AllReactionTests;
import lcsb.mapviewer.converter.model.celldesigner.species.AllSpeciesTests;
import lcsb.mapviewer.converter.model.celldesigner.structure.AllStructureTests;
import lcsb.mapviewer.converter.model.celldesigner.types.AllTypesTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
@RunWith(Suite.class)
@SuiteClasses({ //
- AllAnnotationTests.class, //
- AllAliasTests.class, //
- AllCompartmentTests.class, //
- AllGeometryTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStructureTests.class, //
- AllTypesTests.class, //
- CellDesignerElementCollectionTest.class,//
- CellDesignerParserExceptionTest.class, //
- CellDesignerXmlParserTest.class, //
- ComplexParserTests.class, //
- InvalidGroupExceptionTest.class, //
- LayerXmlParserTest.class, //
- NestedComplexParsingTests.class, //
- ReconDataInCellDesignerXmlParserTest.class,//
+ AllAnnotationTests.class, //
+ AllAliasTests.class, //
+ AllCompartmentTests.class, //
+ AllGeometryTests.class, //
+ AllReactionTests.class, //
+ AllSpeciesTests.class, //
+ AllStructureTests.class, //
+ AllTypesTests.class, //
+ CellDesignerElementCollectionTest.class, //
+ CellDesignerParserExceptionTest.class, //
+ CellDesignerXmlParserTest.class, //
+ ComplexParserTests.class, //
+ FunctionXmlParserTest.class, //
+ InvalidGroupExceptionTest.class, //
+ LayerXmlParserTest.class, //
+ NestedComplexParsingTests.class, //
+ ParameterXmlParserTest.class, //
+ ReconDataInCellDesignerXmlParserTest.class, //
+ UnitXmlParserTest.class,//
})
public class AllCellDesignerTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index 6484b40970..b268656012 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -62,6 +62,32 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testParseParameters() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/parameter.xml");
+
+ assertEquals(1, model.getParameters().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseUnits() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/unit.xml");
+
+ assertEquals(1, model.getUnits().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testParseCompartmens() throws Exception {
Model model;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
index 71af481a35..b0dde7d9de 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
public class FunctionXmlParserTest extends CellDesignerTestFunctions {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParserTest.java
new file mode 100644
index 0000000000..ea6201dc17
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/parameter/ParameterXmlParserTest.java
@@ -0,0 +1,36 @@
+package lcsb.mapviewer.converter.model.celldesigner.parameter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class ParameterXmlParserTest extends CellDesignerTestFunctions {
+
+ @Test
+ public void testParseBasicData() throws InvalidXmlSchemaException, IOException {
+ SbmlUnit volume = new SbmlUnit("volume");
+ Model model = new ModelFullIndexed(null);
+ model.addUnit(volume);
+ ParameterXmlParser parser = new ParameterXmlParser(model);
+ SbmlParameter unit = parser
+ .parseFunction(super.getXmlDocumentFromFile("testFiles/parameter/simple.xml").getFirstChild());
+
+ assertNotNull(unit);
+ assertEquals(unit.getParameterId(), "param_id");
+ assertEquals(unit.getName(), "Parameter name");
+ assertEquals(unit.getValue(), 12.0, Configuration.EPSILON);
+ assertEquals(unit.getUnits(), volume);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParserTest.java
new file mode 100644
index 0000000000..b55724ba11
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/unit/UnitXmlParserTest.java
@@ -0,0 +1,33 @@
+package lcsb.mapviewer.converter.model.celldesigner.unit;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+
+public class UnitXmlParserTest extends CellDesignerTestFunctions {
+
+ UnitXmlParser parser = new UnitXmlParser();
+
+ @Test
+ public void testParseBasicData() throws InvalidXmlSchemaException, IOException {
+ SbmlUnit unit = parser.parseFunction(super.getXmlDocumentFromFile("testFiles/unit/simple.xml").getFirstChild());
+ assertNotNull(unit);
+ assertEquals(unit.getUnitId(), "unit_id");
+ assertEquals(unit.getName(), "unit name");
+ }
+
+ @Test
+ public void testParseUnitTypes() throws InvalidXmlSchemaException, IOException {
+ SbmlUnit unit = parser.parseFunction(super.getXmlDocumentFromFile("testFiles/unit/simple.xml").getFirstChild());
+ assertNotNull(unit);
+ assertEquals(unit.getUnitTypeFactors().size(), 1);
+ }
+
+}
diff --git a/converter-CellDesigner/testFiles/parameter.xml b/converter-CellDesigner/testFiles/parameter.xml
new file mode 100644
index 0000000000..940a6cf422
--- /dev/null
+++ b/converter-CellDesigner/testFiles/parameter.xml
@@ -0,0 +1,54 @@
+<?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:listOfGroups/>
+<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="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfParameters>
+<parameter metaid="param_id" id="param_id" name="Parameter name" value="12" units="volume"/>
+</listOfParameters>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/parameter/simple.xml b/converter-CellDesigner/testFiles/parameter/simple.xml
new file mode 100644
index 0000000000..53a110385b
--- /dev/null
+++ b/converter-CellDesigner/testFiles/parameter/simple.xml
@@ -0,0 +1 @@
+<parameter metaid="param_id" id="param_id" name="Parameter name" value="12" units="volume"/>
diff --git a/converter-CellDesigner/testFiles/unit.xml b/converter-CellDesigner/testFiles/unit.xml
new file mode 100644
index 0000000000..17cb63121b
--- /dev/null
+++ b/converter-CellDesigner/testFiles/unit.xml
@@ -0,0 +1,31 @@
+<?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:listOfGroups/>
+<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>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/unit/simple.xml b/converter-CellDesigner/testFiles/unit/simple.xml
new file mode 100644
index 0000000000..f017bc8652
--- /dev/null
+++ b/converter-CellDesigner/testFiles/unit/simple.xml
@@ -0,0 +1,5 @@
+<unitDefinition metaid="substance" id="unit_id" name="unit name">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java
rename to model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
index fc75944422..f9e067bae5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.model.map.kinetics;
import java.io.Serializable;
import java.util.ArrayList;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
new file mode 100644
index 0000000000..7684fc2f29
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
@@ -0,0 +1,101 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of a single SBML parameter
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_parameter")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlParameter implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlParameter.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 parameterId;
+
+ private String name;
+
+ private Double value;
+ private SbmlUnit units;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlParameter() {
+ super();
+ }
+
+ public SbmlParameter(String parameterId) {
+ this.parameterId = parameterId;
+ }
+
+ public void setFunctionId(String parameterId) {
+ this.parameterId = parameterId;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getParameterId() {
+ return parameterId;
+ }
+
+ public void setParameterId(String parameterId) {
+ this.parameterId = parameterId;
+ }
+
+ public Double getValue() {
+ return value;
+ }
+
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ public SbmlUnit getUnits() {
+ return units;
+ }
+
+ public void setUnits(SbmlUnit units) {
+ this.units = units;
+
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
new file mode 100644
index 0000000000..38d6347252
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
@@ -0,0 +1,88 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of a single SBML unit
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_unit")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlUnit implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlUnit.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 unitId;
+ private String name;
+
+ private List<SbmlUnitTypeFactor> unitTypeFactors = new ArrayList<>();
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlUnit() {
+ super();
+ }
+
+ public SbmlUnit(String unitId) {
+ this.unitId = unitId;
+ }
+
+ public String getUnitId() {
+ return unitId;
+ }
+
+ public void setUnitId(String unitId) {
+ this.unitId = unitId;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void addUnitTypeFactor(SbmlUnitTypeFactor factor) {
+ unitTypeFactors.add(factor);
+ }
+
+ public List<SbmlUnitTypeFactor> getUnitTypeFactors() {
+ return unitTypeFactors;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitType.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitType.java
new file mode 100644
index 0000000000..9cee1416c9
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitType.java
@@ -0,0 +1,36 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+public enum SbmlUnitType {
+ AMPERE,
+ BECQUEREL,
+ CANDELA,
+ COULUMB,
+ DIMENSIONLESS,
+ FARAD,
+ GRAM,
+ GRAY,
+ HENRY,
+ HERTZ,
+ ITEM,
+ JOULE,
+ KATAL,
+ KELVIN,
+ KILOGRAM,
+ LITRE,
+ LUMEN,
+ LUX,
+ METRE,
+ MOLE,
+ NEWTON,
+ OHM,
+ PASCAL,
+ RADIAN,
+ SECOND,
+ SIEMENS,
+ SIEVERT,
+ STERADIAN,
+ TESLA,
+ VOLT,
+ WATT,
+ WEBER,
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
new file mode 100644
index 0000000000..16f20feb52
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
@@ -0,0 +1,103 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of a single SBML unit factor. For example unit for velocity is
+ * m/s. It means that we have two unit types here:
+ * <ul>
+ * <li>metre^1</li>
+ * <li>second^-1</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_unit_factor")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlUnitTypeFactor implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlUnitTypeFactor.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 SbmlUnitType unitType;
+
+ private int exponent = 1;
+ private int scale = 0;
+ private double multiplier = 1.0;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlUnitTypeFactor() {
+ super();
+ }
+
+ public SbmlUnitTypeFactor(SbmlUnitType unitType, int exponent, int scale, double multiplier) {
+ this.unitType = unitType;
+ this.exponent = exponent;
+ this.scale = scale;
+ this.multiplier = multiplier;
+ }
+
+ public SbmlUnitType getUnitType() {
+ return unitType;
+ }
+
+ public void setUnitType(SbmlUnitType unitType) {
+ this.unitType = unitType;
+ }
+
+ public int getExponent() {
+ return exponent;
+ }
+
+ public void setExponent(int exponent) {
+ this.exponent = exponent;
+ }
+
+ public int getScale() {
+ return scale;
+ }
+
+ public void setScale(int scale) {
+ this.scale = scale;
+ }
+
+ public double getMultiplier() {
+ return multiplier;
+ }
+
+ public void setMultiplier(double multiplier) {
+ this.multiplier = multiplier;
+ }
+
+}
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 613c5ce877..81ac64e4b5 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
@@ -8,9 +8,11 @@ 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.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -592,5 +594,17 @@ public interface Model {
Set<SbmlFunction> getFunctions();
- void addFunctions(Collection<SbmlFunction> parseXmlFunctionCollection);
+ void addFunctions(Collection<SbmlFunction> sbmlFunctions);
+
+ Set<SbmlParameter> getParameters();
+
+ void addUnits(Collection<SbmlUnit> units);
+
+ Set<SbmlUnit> getUnits();
+
+ void addUnit(SbmlUnit volume);
+
+ SbmlUnit getUnitsByUnitId(String unitId);
+
+ void addParameters(Collection<SbmlParameter> sbmlParamters);
}
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 95fe2a9fbd..3970c18f01 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
@@ -27,8 +27,10 @@ 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.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -112,6 +114,14 @@ public class ModelData implements Serializable {
@OneToMany(mappedBy = "model", orphanRemoval = true)
private Set<SbmlFunction> functions = new HashSet<>();
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<SbmlParameter> parameters = new HashSet<>();
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<SbmlUnit> units = new HashSet<>();
+
/**
* When the map was created.
*/
@@ -747,4 +757,24 @@ public class ModelData implements Serializable {
public Set<SbmlFunction> getFunctions() {
return functions;
}
+
+ public Set<SbmlParameter> getParameters() {
+ return parameters;
+ }
+
+ public void addUnits(Collection<SbmlUnit> units) {
+ this.units.addAll(units);
+ }
+
+ public Set<SbmlUnit> getUnits() {
+ return units;
+ }
+
+ public void addUnit(SbmlUnit unit) {
+ this.units.add(unit);
+ }
+
+ public void addParameters(Collection<SbmlParameter> sbmlParamters) {
+ this.parameters.addAll(sbmlParamters);
+ }
}
\ 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 99a09db9a8..6cfd3c14a6 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
@@ -16,9 +16,11 @@ 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.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -663,4 +665,40 @@ public class ModelFullIndexed implements Model {
public void addFunctions(Collection<SbmlFunction> functions) {
modelData.getFunctions().addAll(functions);
}
+
+ @Override
+ public Set<SbmlParameter> getParameters() {
+ return modelData.getParameters();
+ }
+
+ @Override
+ public void addUnits(Collection<SbmlUnit> units) {
+ modelData.addUnits(units);
+ }
+
+ @Override
+ public Set<SbmlUnit> getUnits() {
+ return modelData.getUnits();
+ }
+
+ @Override
+ public void addUnit(SbmlUnit unit) {
+ modelData.addUnit(unit);
+
+ }
+
+ @Override
+ public SbmlUnit getUnitsByUnitId(String unitId) {
+ for (SbmlUnit unit : getUnits()) {
+ if (unit.getUnitId().equals(unitId)) {
+ return unit;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void addParameters(Collection<SbmlParameter> sbmlParamters) {
+ modelData.addParameters(sbmlParamters);
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
index fef2e47552..2348b1ca8c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
@@ -66,7 +66,8 @@ public class PolylineDataComparatorTest {
pd1 = new PolylineData();
pd2 = new PolylineData();
- pd2.addPoint(new Point2D.Double(1, 2));
+ pd2.addPoint(new Point2D.Double(1, 2));
+ pd2.addPoint(new Point2D.Double(1, 3));
assertTrue(comparator.compare(pd1, pd2) != 0);
assertTrue(comparator.compare(pd2, pd1) != 0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
index 3d0f487666..83b9a41a35 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -6,6 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.model.map.compartment.AllCompartmentTests;
import lcsb.mapviewer.model.map.graph.AllGraphTests;
+import lcsb.mapviewer.model.map.kinetics.AllKineticsTests;
import lcsb.mapviewer.model.map.layout.AllLayoutTests;
import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
import lcsb.mapviewer.model.map.model.AllModelTests;
@@ -16,32 +17,33 @@ import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
@RunWith(Suite.class)
@SuiteClasses({ AllCompartmentTests.class, //
- ElementInFewParentsExceptionTest.class, //
- AllGraphTests.class, //
- AllGraphicsTests.class, //
- AllLayoutTests.class, //
- AllModelTests.class, //
- AllModifierTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStatisticsTests.class, //
- CommentTest.class, //
- InconsistentModelExceptionTest.class, //
- LayoutComparatorTest.class, //
- MiriamDataTest.class, //
- MiriamRelationTypeTest.class, //
- MiriamTypeTest.class, //
- MiriamTypeNameComparatorTest.class, //
- OverviewImageComparatorTest.class, //
- OverviewImageLinkComparatorTest.class, //
- OverviewImageLinkTest.class, //
- OverviewImageTest.class, //
- OverviewLinkComparatorTest.class, //
- OverviewLinkTest.class, //
- OverviewModelLinkComparatorTest.class, //
- OverviewModelLinkTest.class, //
- OverviewSearchLinkTest.class, //
- SearchIndexTest.class,//
+ ElementInFewParentsExceptionTest.class, //
+ AllGraphTests.class, //
+ AllGraphicsTests.class, //
+ AllKineticsTests.class, //
+ AllLayoutTests.class, //
+ AllModelTests.class, //
+ AllModifierTests.class, //
+ AllReactionTests.class, //
+ AllSpeciesTests.class, //
+ AllStatisticsTests.class, //
+ CommentTest.class, //
+ InconsistentModelExceptionTest.class, //
+ LayoutComparatorTest.class, //
+ MiriamDataTest.class, //
+ MiriamRelationTypeTest.class, //
+ MiriamTypeTest.class, //
+ MiriamTypeNameComparatorTest.class, //
+ OverviewImageComparatorTest.class, //
+ OverviewImageLinkComparatorTest.class, //
+ OverviewImageLinkTest.class, //
+ OverviewImageTest.class, //
+ OverviewLinkComparatorTest.class, //
+ OverviewLinkTest.class, //
+ OverviewModelLinkComparatorTest.class, //
+ OverviewModelLinkTest.class, //
+ OverviewSearchLinkTest.class, //
+ SearchIndexTest.class,//
})
public class AllMapTests {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
new file mode 100644
index 0000000000..b699ac87b8
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SbmlFunctionTest.class, SbmlParameterTest.class, SbmlUnitTest.class, SbmlUnitTypeFactorTest.class })
+public class AllKineticsTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
similarity index 96%
rename from model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
index 20e3c983f9..5ea1f583d7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.model.map.kinetics;
import static org.junit.Assert.*;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
new file mode 100644
index 0000000000..374f97100d
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterTest.java
@@ -0,0 +1,32 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class SbmlParameterTest {
+
+ @Test
+ public void testConstructor() {
+ String id = "param_id";
+ SbmlParameter parameter = new SbmlParameter(id);
+ assertEquals(id, parameter.getParameterId());
+ }
+
+ @Test
+ public void testSetName() {
+ String name= "name";
+ SbmlParameter parameter = new SbmlParameter("");
+ parameter.setName(name);
+ assertEquals(name, parameter.getName());
+ }
+
+ @Test
+ public void testSetValue() {
+ Double value= 13.0;
+ SbmlParameter parameter = new SbmlParameter("");
+ parameter.setValue(value);
+ assertEquals(value, parameter.getValue());
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
new file mode 100644
index 0000000000..a6cdd5328b
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
@@ -0,0 +1,33 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.Test;
+
+public class SbmlUnitTest {
+
+ @Test
+ public void testConstructor() {
+ String id = "id";
+ SbmlUnit unit = new SbmlUnit(id);
+ assertEquals(unit.getUnitId(), id);
+ }
+
+ @Test
+ public void testSetName() {
+ String name= "id";
+ SbmlUnit unit = new SbmlUnit("");
+ unit.setName(name);
+ assertEquals(unit.getName(), name);
+ }
+
+ @Test
+ public void testAddUnitTypeFactor() {
+ SbmlUnitTypeFactor factor = new SbmlUnitTypeFactor(SbmlUnitType.METRE, 2, 0, 1.0);
+ SbmlUnit unit = new SbmlUnit("");
+ unit.addUnitTypeFactor(factor);
+ assertEquals(unit.getUnitTypeFactors().size(), 1);
+ assertEquals(unit.getUnitTypeFactors().get(0), factor);
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
new file mode 100644
index 0000000000..83ec875f1f
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorTest.java
@@ -0,0 +1,25 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+
+public class SbmlUnitTypeFactorTest {
+
+ @Test
+ public void testConstructor() {
+ int exponent = 1;
+ int scale = 1;
+ double multiplier = 1.0;
+ SbmlUnitType unitType = SbmlUnitType.METRE;
+ SbmlUnitTypeFactor factor = new SbmlUnitTypeFactor(unitType, exponent, scale, multiplier);
+ assertEquals(factor.getUnitType(), unitType);
+ assertEquals(factor.getExponent(), exponent);
+ assertEquals(factor.getScale(), scale);
+ assertEquals(factor.getMultiplier(), multiplier, Configuration.EPSILON);
+
+ }
+
+}
--
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