diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..8da925497e5cd4c575fb4dd0a081a194b233a6ee
--- /dev/null
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
@@ -0,0 +1,29 @@
+package lcsb.mapviewer.common.comparator;
+
+import java.awt.Color;
+import java.util.Comparator;
+
+/**
+ * Comparator implementation for {@link Color} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EnumComparator implements Comparator<Enum<?>> {
+
+ @Override
+ public int compare(Enum arg0, Enum arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return arg0.compareTo(arg1);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
index ef661a1cc48fa5639b4357e1c350dac36e61b207..a82e7c0355fa06f80d2068eb7cbdc6e1bee0507e 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
@@ -8,6 +8,7 @@ import org.junit.runners.Suite.SuiteClasses;
@SuiteClasses({ BooleanComparatorTest.class, //
ColorComparatorTest.class, //
DoubleComparatorTest.class, //
+ EnumComparatorTest.class, //
IntegerComparatorTest.class, //
PointComparatorTest.class, //
StringComparatorTest.class, //
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/EnumComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/EnumComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..58c410181b3c25facae0b2d24553fdc3c08b1e7f
--- /dev/null
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/EnumComparatorTest.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.common.MimeType;
+
+public class EnumComparatorTest {
+
+ @Test
+ public void testEquals() {
+ EnumComparator comp = new EnumComparator();
+ assertEquals(0, comp.compare(MimeType.CSS, MimeType.CSS));
+ }
+
+ @Test
+ public void testDifferent() {
+ EnumComparator comp = new EnumComparator();
+ assertTrue(0 != comp.compare(MimeType.CSS, MimeType.JPG));
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
index 4b7a71ad3812c18a195dd0c6d21a8487f314ae2c..d37d8b22910a60238855202514a7549d51f655a0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
@@ -52,7 +52,7 @@ public class SbmlFunction implements Serializable, SbmlArgument {
private String functionId;
private String name;
-
+
@Column(columnDefinition = "TEXT")
private String definition;
@@ -105,5 +105,8 @@ public class SbmlFunction implements Serializable, SbmlArgument {
this.definition = definition;
}
+ public void addArgument(String argument) {
+ arguments.add(argument);
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..30de968a0329cd5c4d0539c5fb39af372d7f03ac
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
@@ -0,0 +1,35 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.StringListComparator;
+
+public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
+
+ protected SbmlFunctionComparator() {
+ super(SbmlFunction.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlFunction arg0, SbmlFunction arg1) {
+ StringComparator stringComparator = new StringComparator();
+ StringListComparator stringListComparator = new StringListComparator();
+ if (stringComparator.compare(arg0.getFunctionId(), arg1.getFunctionId()) != 0) {
+ return stringComparator.compare(arg0.getFunctionId(), arg1.getFunctionId());
+ }
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition()) != 0) {
+ return stringComparator.compare(arg0.getDefinition(), arg1.getDefinition());
+ }
+
+ if (stringListComparator.compare(arg0.getArguments(), arg1.getArguments()) != 0) {
+ return stringListComparator.compare(arg0.getArguments(), arg1.getArguments());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
index 9a4f29f710663a9d7c9a4b2ae05db811ca157649..f02ad1316a93b416f141dfc982afc155af956895 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
@@ -4,7 +4,6 @@ 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;
@@ -53,7 +52,7 @@ public class SbmlKinetics implements Serializable {
@OneToMany(mappedBy = "model", orphanRemoval = true)
private Set<SbmlFunction> functions = new HashSet<>();
- private List<Element> elements = new ArrayList<>();
+ private Set<Element> elements = new HashSet<>();
/**
* Unique database identifier.
@@ -142,4 +141,8 @@ public class SbmlKinetics implements Serializable {
return functions;
}
+ public Set<Element> getElements() {
+ return elements;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
index bee84ba436b5eca70e93e39edd477c841377f504..f8e8f30a488918c69496f639d14c0e5ee72dc0f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
@@ -1,6 +1,10 @@
package lcsb.mapviewer.model.map.kinetics;
import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
public class SbmlKineticsComparator extends Comparator<SbmlKinetics> {
@@ -10,6 +14,22 @@ public class SbmlKineticsComparator extends Comparator<SbmlKinetics> {
@Override
protected int internalCompare(SbmlKinetics arg0, SbmlKinetics arg1) {
+ SetComparator<SbmlFunction> functionComparator = new SetComparator<>(new SbmlFunctionComparator());
+ if (functionComparator.compare(arg0.getFunctions(), arg1.getFunctions()) != 0) {
+ return functionComparator.compare(arg0.getFunctions(), arg1.getFunctions());
+ }
+ SetComparator<SbmlParameter> parameterComparator = new SetComparator<>(new SbmlParameterComparator());
+ if (parameterComparator.compare(arg0.getParameters(), arg1.getParameters()) != 0) {
+ return parameterComparator.compare(arg0.getParameters(), arg1.getParameters());
+ }
+ SetComparator<Element> elementComparator = new SetComparator<>(new ElementComparator());
+ if (elementComparator.compare(arg0.getElements(), arg1.getElements()) != 0) {
+ return elementComparator.compare(arg0.getElements(), arg1.getElements());
+ }
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition()) != 0) {
+ return stringComparator.compare(arg0.getDefinition(), arg1.getDefinition());
+ }
return 0;
}
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
index 2f8bd963053c1df5867879a4a2f00971a93694ed..5d535f7cd35ae75ab02e565f0ca0fd03662a0e69 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
@@ -61,10 +61,6 @@ public class SbmlParameter implements Serializable, SbmlArgument {
this.parameterId = parameterId;
}
- public void setFunctionId(String parameterId) {
- this.parameterId = parameterId;
- }
-
public String getName() {
return name;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..6590704a43f4a45a92a639cbc3b795168f2c4a82
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparator.java
@@ -0,0 +1,36 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+public class SbmlParameterComparator extends Comparator<SbmlParameter> {
+
+ protected SbmlParameterComparator() {
+ super(SbmlParameter.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlParameter arg0, SbmlParameter arg1) {
+ StringComparator stringComparator = new StringComparator();
+ DoubleComparator doubleComparator = new DoubleComparator();
+ SbmlUnitComparator unitComparator = new SbmlUnitComparator();
+ if (stringComparator.compare(arg0.getParameterId(), arg1.getParameterId()) != 0) {
+ return stringComparator.compare(arg0.getParameterId(), arg1.getParameterId());
+ }
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (doubleComparator.compare(arg0.getValue(), arg1.getValue()) != 0) {
+ return doubleComparator.compare(arg0.getValue(), arg1.getValue());
+ }
+
+ if (unitComparator.compare(arg0.getUnits(), arg1.getUnits()) != 0) {
+ return unitComparator.compare(arg0.getUnits(), arg1.getUnits());
+ }
+
+ return 0;
+ }
+
+}
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
index 38d63472528b91c45ad523add85f81fba17530b2..004f9c533bf74b1772d239bf779bb18db618fc06 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
@@ -1,8 +1,9 @@
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.Set;
import javax.persistence.Column;
import javax.persistence.Entity;
@@ -48,7 +49,7 @@ public class SbmlUnit implements Serializable {
private String unitId;
private String name;
- private List<SbmlUnitTypeFactor> unitTypeFactors = new ArrayList<>();
+ private Set<SbmlUnitTypeFactor> unitTypeFactors = new HashSet<>();
/**
* Constructor required by hibernate.
@@ -81,7 +82,7 @@ public class SbmlUnit implements Serializable {
unitTypeFactors.add(factor);
}
- public List<SbmlUnitTypeFactor> getUnitTypeFactors() {
+ public Set<SbmlUnitTypeFactor> getUnitTypeFactors() {
return unitTypeFactors;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..4ac63392e0b22c1ad915e425f394ef71ee3fede8
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
@@ -0,0 +1,38 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+public class SbmlUnitComparator extends Comparator<SbmlUnit> {
+
+ protected SbmlUnitComparator() {
+ super(SbmlUnit.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlUnit arg0, SbmlUnit arg1) {
+ StringComparator stringComparator = new StringComparator();
+ SetComparator<SbmlUnitTypeFactor> unitTypeFactorComparator = new SetComparator<>(
+ new SbmlUnitTypeFactorComparator());
+ if (stringComparator.compare(arg0.getUnitId(), arg1.getUnitId()) != 0) {
+ return stringComparator.compare(arg0.getUnitId(), arg1.getUnitId());
+ }
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (unitTypeFactorComparator.compare(arg0.getUnitTypeFactors(), arg1.getUnitTypeFactors()) != 0) {
+ return unitTypeFactorComparator.compare(arg0.getUnitTypeFactors(), arg1.getUnitTypeFactors());
+ }
+ //
+ // if (stringListComparator.compare(arg0.getArguments(), arg1.getArguments()) !=
+ // 0) {
+ // return stringListComparator.compare(arg0.getArguments(),
+ // arg1.getArguments());
+ // }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c585a94b81b67e8ae7f04697f9d9442ea5fa5d12
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparator.java
@@ -0,0 +1,37 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.EnumComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+public class SbmlUnitTypeFactorComparator extends Comparator<SbmlUnitTypeFactor> {
+
+ protected SbmlUnitTypeFactorComparator() {
+ super(SbmlUnitTypeFactor.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlUnitTypeFactor arg0, SbmlUnitTypeFactor arg1) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ DoubleComparator doubleComparator = new DoubleComparator();
+ EnumComparator enumComparator = new EnumComparator();
+ if (integerComparator.compare(arg0.getExponent(), arg1.getExponent()) != 0) {
+ return integerComparator.compare(arg0.getExponent(), arg1.getExponent());
+ }
+ if (integerComparator.compare(arg0.getScale(), arg1.getScale()) != 0) {
+ return integerComparator.compare(arg0.getScale(), arg1.getScale());
+ }
+
+ if (doubleComparator.compare(arg0.getMultiplier(), arg1.getMultiplier()) != 0) {
+ return doubleComparator.compare(arg0.getMultiplier(), arg1.getMultiplier());
+ }
+
+ if (enumComparator.compare(arg0.getUnitType(), arg1.getUnitType()) != 0) {
+ return enumComparator.compare(arg0.getUnitType(), arg1.getUnitType());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
index 956076bdf28df445a890d95ddc35d956a77c8930..5509035aac6c8c93a2ea1ca8af66b80a09dd504f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
@@ -6,10 +6,16 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ SbmlFunctionTest.class, //
+ SbmlFunctionComparatorTest.class, //
SbmlKineticsTest.class, //
+ SbmlKineticsComparatorTest.class, //
SbmlParameterTest.class, //
+ SbmlParameterComparatorTest.class, //
SbmlUnitTest.class, //
- SbmlUnitTypeFactorTest.class })
+ SbmlUnitComparatorTest.class, //
+ SbmlUnitTypeFactorTest.class,//
+ SbmlUnitTypeFactorComparatorTest.class, //
+ })
public class AllKineticsTests {
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..dd6e4d9f6ac6ad5ca6cdea145795fca85c0f8441
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparatorTest.java
@@ -0,0 +1,59 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+public class SbmlFunctionComparatorTest {
+ SbmlFunctionComparator comparator = new SbmlFunctionComparator();
+
+ @Test
+ public void testCompareEqual() {
+ SbmlFunction Function = createFunction();
+ SbmlFunction Function2 = createFunction();
+ assertEquals(0, comparator.compare(Function, Function2));
+ }
+
+ @Test
+ public void testCompareDifferentFunctionId() {
+ SbmlFunction function = createFunction();
+ SbmlFunction function2 = createFunction();
+ function.setFunctionId("xxx");
+ assertTrue("Function object have different id but comparison returned equal",
+ comparator.compare(function, function2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentName() {
+ SbmlFunction function = createFunction();
+ SbmlFunction function2 = createFunction();
+ function.setName("xxx");
+ assertTrue("Function object have different name but comparison returned equal",
+ comparator.compare(function, function2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentDefinition() {
+ SbmlFunction function = createFunction();
+ SbmlFunction function2 = createFunction();
+ function.setDefinition("xxx");
+ assertTrue("Function object have different name but comparison returned equal",
+ comparator.compare(function, function2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentArguments() {
+ SbmlFunction function = createFunction();
+ SbmlFunction function2 = createFunction();
+ function.addArgument("x");
+ assertTrue("Function object have different name but comparison returned equal",
+ comparator.compare(function, function2) != 0);
+ }
+
+ private SbmlFunction createFunction() {
+ SbmlFunction result = new SbmlFunction("fun_id");
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..6528daf0d83126caed16ef043850ce75a17a966d
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparatorTest.java
@@ -0,0 +1,65 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class SbmlKineticsComparatorTest {
+ SbmlKineticsComparator comparator = new SbmlKineticsComparator();
+
+ @Test
+ public void testCompareEqual() {
+ SbmlKinetics kinetics = createKinetics();
+ SbmlKinetics kinetics2 = createKinetics();
+ assertEquals(0, comparator.compare(kinetics, kinetics2));
+ }
+
+ @Test
+ public void testCompareDifferentFunction() {
+ SbmlKinetics kinetics = createKinetics();
+ SbmlKinetics kinetics2 = createKinetics();
+ kinetics2.getFunctions().iterator().next().setFunctionId("new_fun_id");
+ assertTrue("Kinetics object have different functions but comparison returned equal",
+ comparator.compare(kinetics, kinetics2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentParameters() {
+ SbmlKinetics kinetics = createKinetics();
+ SbmlKinetics kinetics2 = createKinetics();
+ kinetics2.getParameters().iterator().next().setParameterId("new_fun_id");
+ assertTrue("Kinetics object have different functions but comparison returned equal",
+ comparator.compare(kinetics, kinetics2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentDefinition() {
+ SbmlKinetics kinetics = createKinetics();
+ SbmlKinetics kinetics2 = createKinetics();
+ kinetics2.setDefinition("xxx");
+ assertTrue("Kinetics object have different definition but comparison returned equal",
+ comparator.compare(kinetics, kinetics2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentElements() {
+ SbmlKinetics kinetics = createKinetics();
+ SbmlKinetics kinetics2 = createKinetics();
+ kinetics2.addElement(new GenericProtein("x1"));
+ assertTrue("Kinetics object have different elements but comparison returned equal",
+ comparator.compare(kinetics, kinetics2) != 0);
+ }
+
+ private SbmlKinetics createKinetics() {
+ SbmlKinetics result = new SbmlKinetics();
+ result.addElement(new GenericProtein("protein_id"));
+ result.addFunction(new SbmlFunction("fun_id"));
+ result.addParameter(new SbmlParameter("param_id"));
+ result.setDefinition("<xml/>");
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..e803cbd9caa17af6cf9d097206bdc1104bcece36
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlParameterComparatorTest.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class SbmlParameterComparatorTest {
+ SbmlParameterComparator comparator = new SbmlParameterComparator();
+
+ private SbmlParameter createParameter() {
+ SbmlParameter result = new SbmlParameter("param_id");
+ return result;
+ }
+
+ @Test
+ public void testCompareEqual() {
+ SbmlParameter parameter = createParameter();
+ SbmlParameter parameter2 = createParameter();
+ assertEquals(0, comparator.compare(parameter, parameter2));
+ }
+
+ @Test
+ public void testCompareDifferentParameterId() {
+ SbmlParameter parameter = createParameter();
+ SbmlParameter parameter2 = createParameter();
+ parameter.setParameterId("xxx");
+ assertTrue("Parameter object have different id but comparison returned equal",
+ comparator.compare(parameter, parameter2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentName() {
+ SbmlParameter parameter = createParameter();
+ SbmlParameter parameter2 = createParameter();
+ parameter.setName("xxx");
+ assertTrue("Parameter object have different name but comparison returned equal",
+ comparator.compare(parameter, parameter2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentDefinition() {
+ SbmlParameter parameter = createParameter();
+ SbmlParameter parameter2 = createParameter();
+ parameter.setValue(13.0);
+ assertTrue("Parameter object have different value but comparison returned equal",
+ comparator.compare(parameter, parameter2) != 0);
+ }
+
+ @Test
+ public void testCompareDifferentArguments() {
+ SbmlParameter parameter = createParameter();
+ SbmlParameter parameter2 = createParameter();
+ parameter.setUnits(new SbmlUnit("x"));
+ assertTrue("Parameter object have different unit but comparison returned equal",
+ comparator.compare(parameter, parameter2) != 0);
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..284f89a936d656c2a893fef7dcc6353e27f5bd6f
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparatorTest.java
@@ -0,0 +1,46 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class SbmlUnitComparatorTest {
+ SbmlUnitComparator comparator = new SbmlUnitComparator();
+
+ private SbmlUnit createUnit() {
+ SbmlUnit result = new SbmlUnit("unit_id");
+ return result;
+ }
+
+ @Test
+ public void testCompareEqual() {
+ SbmlUnit parameter = createUnit();
+ SbmlUnit parameter2 = createUnit();
+ assertEquals(0, comparator.compare(parameter, parameter2));
+ }
+
+ @Test
+ public void testCompareUnitId() {
+ SbmlUnit parameter = createUnit();
+ SbmlUnit parameter2 = createUnit();
+ parameter.setUnitId("xxx");
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ }
+
+ @Test
+ public void testCompareName() {
+ SbmlUnit parameter = createUnit();
+ SbmlUnit parameter2 = createUnit();
+ parameter.setName("xxx");
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ }
+
+ @Test
+ public void testCompareUnitTypes() {
+ SbmlUnit parameter = createUnit();
+ SbmlUnit parameter2 = createUnit();
+ parameter.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 1, 1));;
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ }
+
+}
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
index a6cdd5328b0126b3c47c9c3444b7be5dbe62e0ab..3e1d4e4f8785f4ac012ae54f058805b6cde06777 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
@@ -27,7 +27,7 @@ public class SbmlUnitTest {
SbmlUnit unit = new SbmlUnit("");
unit.addUnitTypeFactor(factor);
assertEquals(unit.getUnitTypeFactors().size(), 1);
- assertEquals(unit.getUnitTypeFactors().get(0), factor);
+ assertEquals(unit.getUnitTypeFactors().iterator().next(), factor);
}
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f7a9e32159d83caafa499c76476e75ec0740bb41
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactorComparatorTest.java
@@ -0,0 +1,60 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+public class SbmlUnitTypeFactorComparatorTest {
+
+ SbmlUnitTypeFactorComparator comparator = new SbmlUnitTypeFactorComparator();
+
+ private SbmlUnitTypeFactor createUnitTypeFactor() {
+ SbmlUnitTypeFactor result = new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 1, 1);
+ return result;
+ }
+
+ @Test
+ public void testCompareEqual() {
+ SbmlUnitTypeFactor parameter = createUnitTypeFactor();
+ SbmlUnitTypeFactor parameter2 = createUnitTypeFactor();
+ assertEquals(0, comparator.compare(parameter, parameter2));
+ }
+
+ @Test
+ public void testCompareDifferentUnitType() {
+ SbmlUnitTypeFactor parameter = createUnitTypeFactor();
+ SbmlUnitTypeFactor parameter2 = createUnitTypeFactor();
+ parameter.setUnitType(SbmlUnitType.BECQUEREL);
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ assertTrue(0 != comparator.compare(parameter2, parameter));
+ }
+
+ @Test
+ public void testCompareDifferentExponent() {
+ SbmlUnitTypeFactor parameter = createUnitTypeFactor();
+ SbmlUnitTypeFactor parameter2 = createUnitTypeFactor();
+ parameter.setExponent(2);
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ assertTrue(0 != comparator.compare(parameter2, parameter));
+ }
+
+ @Test
+ public void testCompareDifferentMultiplier() {
+ SbmlUnitTypeFactor parameter = createUnitTypeFactor();
+ SbmlUnitTypeFactor parameter2 = createUnitTypeFactor();
+ parameter.setMultiplier(2);
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ assertTrue(0 != comparator.compare(parameter2, parameter));
+ }
+
+ @Test
+ public void testCompareDifferentScale() {
+ SbmlUnitTypeFactor parameter = createUnitTypeFactor();
+ SbmlUnitTypeFactor parameter2 = createUnitTypeFactor();
+ parameter.setScale(3);
+ assertTrue(0 != comparator.compare(parameter, parameter2));
+ assertTrue(0 != comparator.compare(parameter2, parameter));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index aa53199703a30f5f0e014af4166f89aa7cbeed29..1593310311473a379dcfac70b6c245798c82dd02 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -36,372 +36,377 @@ import lcsb.mapviewer.model.map.species.Species;
public class ReactionTest extends ModelTestFunctions {
- Logger logger = Logger.getLogger(ReactantTest.class);
-
- private Species species;
-
- @Before
- public void setUp() throws Exception {
- species = new GenericProtein("sa1");
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testContainsElement() {
- try {
- Reaction reaction = new Reaction();
- assertFalse(reaction.containsElement(species));
- Modifier modifier = new Catalysis(species);
- reaction.addModifier(modifier);
- assertTrue(reaction.containsElement(species));
- assertFalse(reaction.containsElement(new GenericProtein("id")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparator() {
- try {
- Reaction reaction1 = new Reaction();
- reaction1.setIdReaction("2");
- Reaction reaction2 = new Reaction();
- reaction2.setIdReaction("1");
- Reaction reaction3 = new Reaction();
- reaction3.setIdReaction("3");
- List<Reaction> reactions = new ArrayList<>();
- reactions.add(reaction1);
- reactions.add(reaction2);
- reactions.add(reaction3);
- Collections.sort(reactions, Reaction.ID_COMPARATOR);
- assertEquals(reaction2, reactions.get(0));
- assertEquals(reaction1, reactions.get(1));
- assertEquals(reaction3, reactions.get(2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction1 = new Reaction();
- reaction1.addMiriamData(new MiriamData());
- reaction1.addSynonym("s");
- Reaction reaction2 = new Reaction(reaction1);
-
- assertEquals(1, reaction2.getMiriamData().size());
- assertEquals(1, reaction2.getSynonyms().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDistanceFromPoint() {
- try {
- Reaction reaction1 = new Reaction();
- Reactant reactant = new Reactant();
- PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
- reactant.setLine(line);
- reaction1.addReactant(reactant);
-
- assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(0.0, 0.0)), Configuration.EPSILON);
- assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
- assertEquals(1.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 1.0)), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetClosestPointTo() {
- try {
- Reaction reaction1 = new Reaction();
- Reactant reactant = new Reactant();
- PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
- reactant.setLine(line);
- reaction1.addReactant(reactant);
-
- assertEquals(0.0, reaction1.getClosestPointTo(new Point2D.Double(0.0, 0.0)).distance(new Point2D.Double(0.0, 0.0)), Configuration.EPSILON);
- assertEquals(0.0, reaction1.getClosestPointTo(new Point2D.Double(1.0, 0.0)).distance(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
- assertEquals(0.0, reaction1.getClosestPointTo(new Point2D.Double(1.0, 1.0)).distance(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddMiriam() {
- try {
- Reaction reaction1 = new Reaction();
-
- MiriamData md = new MiriamData(MiriamType.CAS, "1");
- reaction1.addMiriamData(md);
-
- assertEquals(1, reaction1.getMiriamData().size());
-
- reaction1.addMiriamData(md);
- assertEquals(1, reaction1.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
- List<MiriamData> list = new ArrayList<>();
- list.add(md);
-
- reaction1.addMiriamData(list);
- assertEquals(2, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction1 = new Reaction();
-
- assertNotNull(reaction1.getStringType());
- assertNull(reaction1.getReactionRect());
-
- int id = 61;
- List<AbstractNode> nodes = new ArrayList<>();
- String notes = "dfp";
-
- boolean kineticLaw = true;
- ModelData data = new ModelData();
- Model model = new ModelFullIndexed(data);
- String symbol = "sybm";
- String formula = "form";
- Integer mechanicalConfidenceScore = 9908;
- Double lowerBound = 9.2;
- Double upperBound = 9.2;
- String subsystem = "ssyst";
- String geneProteinReaction = "GPR";
- List<String> synonyms = new ArrayList<>();
-
- reaction1.setId(id);
- reaction1.setNodes(nodes);
- reaction1.setNotes(notes);
- reaction1.setModel(model);
- assertEquals(model, reaction1.getModel());
- reaction1.setModelData(data);
- assertEquals(data, reaction1.getModelData());
- reaction1.setSymbol(symbol);
- assertEquals(symbol, reaction1.getSymbol());
- reaction1.setFormula(formula);
- assertEquals(formula, reaction1.getFormula());
- reaction1.setMechanicalConfidenceScore(mechanicalConfidenceScore);
- assertEquals(mechanicalConfidenceScore, reaction1.getMechanicalConfidenceScore());
- reaction1.setLowerBound(lowerBound);
- assertEquals(lowerBound, reaction1.getLowerBound());
- reaction1.setUpperBound(upperBound);
- assertEquals(upperBound, reaction1.getUpperBound());
- reaction1.setSubsystem(subsystem);
- assertEquals(subsystem, reaction1.getSubsystem());
- reaction1.setGeneProteinReaction(geneProteinReaction);
- assertEquals(geneProteinReaction, reaction1.getGeneProteinReaction());
- reaction1.setSynonyms(synonyms);
- assertEquals(synonyms, reaction1.getSynonyms());
-
- assertEquals(id, reaction1.getId());
- assertEquals(nodes, reaction1.getNodes());
- assertEquals(notes, reaction1.getNotes());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testVisibilityLevel() {
- try {
- Reaction reaction1 = new Reaction();
- assertEquals("", reaction1.getVisibilityLevel());
-
- reaction1.setVisibilityLevel(1);
- assertEquals("1", reaction1.getVisibilityLevel());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine() {
- try {
- Reaction reaction1 = new Reaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(4.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterPoint() {
- try {
- Reaction reaction1 = new Reaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- assertEquals(0.0, reaction1.getCenterPoint().distance(new Point2D.Double(2.0, 0.0)), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine2() {
- try {
- Reaction reaction1 = new HeterodimerAssociationReaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Reactant reactant2 = new Reactant();
- PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant2.setLine(line3);
- reaction1.addReactant(reactant2);
- AndOperator operator = new AndOperator();
- operator.addInput(reactant);
- operator.addInput(reactant2);
- PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 11.0));
- operator.setLine(line4);
- reaction1.addNode(operator);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(6.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine3() {
- try {
- Reaction reaction1 = new DissociationReaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Product product2 = new Product();
- PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- product2.setLine(line3);
- reaction1.addProduct(product2);
- SplitOperator operator = new SplitOperator();
- operator.addOutput(product);
- operator.addOutput(product2);
- PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 0.0));
- operator.setLine(line4);
- reaction1.addNode(operator);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(10.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Reaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveModifier() {
- try {
- Reaction reaction = new Reaction();
- Modifier modifier = new Modifier();
- reaction.addModifier(modifier);
- assertEquals(1, reaction.getModifiers().size());
- reaction.removeModifier(modifier);
- assertEquals(0, reaction.getModifiers().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Reaction original = new Reaction();
- Reaction reactant = original.copy();
- assertNotNull(reactant);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new Reaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ReactantTest.class);
+
+ private Species species;
+
+ @Before
+ public void setUp() throws Exception {
+ species = new GenericProtein("sa1");
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testContainsElement() {
+ try {
+ Reaction reaction = new Reaction();
+ assertFalse(reaction.containsElement(species));
+ Modifier modifier = new Catalysis(species);
+ reaction.addModifier(modifier);
+ assertTrue(reaction.containsElement(species));
+ assertFalse(reaction.containsElement(new GenericProtein("id")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparator() {
+ try {
+ Reaction reaction1 = new Reaction();
+ reaction1.setIdReaction("2");
+ Reaction reaction2 = new Reaction();
+ reaction2.setIdReaction("1");
+ Reaction reaction3 = new Reaction();
+ reaction3.setIdReaction("3");
+ List<Reaction> reactions = new ArrayList<>();
+ reactions.add(reaction1);
+ reactions.add(reaction2);
+ reactions.add(reaction3);
+ Collections.sort(reactions, Reaction.ID_COMPARATOR);
+ assertEquals(reaction2, reactions.get(0));
+ assertEquals(reaction1, reactions.get(1));
+ assertEquals(reaction3, reactions.get(2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction1 = new Reaction();
+ reaction1.addMiriamData(new MiriamData());
+ reaction1.addSynonym("s");
+ Reaction reaction2 = new Reaction(reaction1);
+
+ assertEquals(1, reaction2.getMiriamData().size());
+ assertEquals(1, reaction2.getSynonyms().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDistanceFromPoint() {
+ try {
+ Reaction reaction1 = new Reaction();
+ Reactant reactant = new Reactant();
+ PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
+ reactant.setLine(line);
+ reaction1.addReactant(reactant);
+
+ assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(0.0, 0.0)), Configuration.EPSILON);
+ assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
+ assertEquals(1.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 1.0)), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetClosestPointTo() {
+ try {
+ Reaction reaction1 = new Reaction();
+ Reactant reactant = new Reactant();
+ PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
+ reactant.setLine(line);
+ reaction1.addReactant(reactant);
+
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(0.0, 0.0)).distance(new Point2D.Double(0.0, 0.0)),
+ Configuration.EPSILON);
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(1.0, 0.0)).distance(new Point2D.Double(1.0, 0.0)),
+ Configuration.EPSILON);
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(1.0, 1.0)).distance(new Point2D.Double(1.0, 0.0)),
+ Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddMiriam() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ MiriamData md = new MiriamData(MiriamType.CAS, "1");
+ reaction1.addMiriamData(md);
+
+ assertEquals(1, reaction1.getMiriamData().size());
+
+ reaction1.addMiriamData(md);
+ assertEquals(1, reaction1.getMiriamData().size());
+ assertEquals(1, getWarnings().size());
+
+ List<MiriamData> list = new ArrayList<>();
+ list.add(md);
+
+ reaction1.addMiriamData(list);
+ assertEquals(2, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ assertNotNull(reaction1.getStringType());
+ assertNull(reaction1.getReactionRect());
+
+ int id = 61;
+ List<AbstractNode> nodes = new ArrayList<>();
+ String notes = "dfp";
+
+ ModelData data = new ModelData();
+ Model model = new ModelFullIndexed(data);
+ String symbol = "sybm";
+ String formula = "form";
+ Integer mechanicalConfidenceScore = 9908;
+ Double lowerBound = 9.2;
+ Double upperBound = 9.2;
+ String subsystem = "ssyst";
+ String geneProteinReaction = "GPR";
+ List<String> synonyms = new ArrayList<>();
+
+ reaction1.setId(id);
+ reaction1.setNodes(nodes);
+ reaction1.setNotes(notes);
+ reaction1.setModel(model);
+ assertEquals(model, reaction1.getModel());
+ reaction1.setModelData(data);
+ assertEquals(data, reaction1.getModelData());
+ reaction1.setSymbol(symbol);
+ assertEquals(symbol, reaction1.getSymbol());
+ reaction1.setFormula(formula);
+ assertEquals(formula, reaction1.getFormula());
+ reaction1.setMechanicalConfidenceScore(mechanicalConfidenceScore);
+ assertEquals(mechanicalConfidenceScore, reaction1.getMechanicalConfidenceScore());
+ reaction1.setLowerBound(lowerBound);
+ assertEquals(lowerBound, reaction1.getLowerBound());
+ reaction1.setUpperBound(upperBound);
+ assertEquals(upperBound, reaction1.getUpperBound());
+ reaction1.setSubsystem(subsystem);
+ assertEquals(subsystem, reaction1.getSubsystem());
+ reaction1.setGeneProteinReaction(geneProteinReaction);
+ assertEquals(geneProteinReaction, reaction1.getGeneProteinReaction());
+ reaction1.setSynonyms(synonyms);
+ assertEquals(synonyms, reaction1.getSynonyms());
+
+ assertEquals(id, reaction1.getId());
+ assertEquals(nodes, reaction1.getNodes());
+ assertEquals(notes, reaction1.getNotes());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testVisibilityLevel() {
+ try {
+ Reaction reaction1 = new Reaction();
+ assertEquals("", reaction1.getVisibilityLevel());
+
+ reaction1.setVisibilityLevel(1);
+ assertEquals("1", reaction1.getVisibilityLevel());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(4.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterPoint() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ assertEquals(0.0, reaction1.getCenterPoint().distance(new Point2D.Double(2.0, 0.0)), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine2() {
+ try {
+ Reaction reaction1 = new HeterodimerAssociationReaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Reactant reactant2 = new Reactant();
+ PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant2.setLine(line3);
+ reaction1.addReactant(reactant2);
+ AndOperator operator = new AndOperator();
+ operator.addInput(reactant);
+ operator.addInput(reactant2);
+ PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 11.0));
+ operator.setLine(line4);
+ reaction1.addNode(operator);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(6.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine3() {
+ try {
+ Reaction reaction1 = new DissociationReaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Product product2 = new Product();
+ PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ product2.setLine(line3);
+ reaction1.addProduct(product2);
+ SplitOperator operator = new SplitOperator();
+ operator.addOutput(product);
+ operator.addOutput(product2);
+ PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 0.0));
+ operator.setLine(line4);
+ reaction1.addNode(operator);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(10.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Reaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveModifier() {
+ try {
+ Reaction reaction = new Reaction();
+ Modifier modifier = new Modifier();
+ reaction.addModifier(modifier);
+ assertEquals(1, reaction.getModifiers().size());
+ reaction.removeModifier(modifier);
+ assertEquals(0, reaction.getModifiers().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Reaction original = new Reaction();
+ Reaction reactant = original.copy();
+ assertNotNull(reactant);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new Reaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}