diff --git a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..6030a1a6f1d798306cccaf5a19e4336926972383
--- /dev/null
+++ b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
@@ -0,0 +1,94 @@
+package lcsb.mapviewer.common;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
+ Logger logger = Logger.getLogger(Comparator.class);
+ private Class<T> comparatorClazz;
+ private boolean exactClassMatch;
+ private List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();
+
+ protected Comparator(Class<T> clazz) {
+ this(clazz, false);
+ }
+
+ protected Comparator(Class<T> clazz, boolean exactClassMatch) {
+ this.comparatorClazz = clazz;
+ this.exactClassMatch = exactClassMatch;
+ }
+
+ @Override
+ public final int compare(T arg0, T arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ if (!arg0.getClass().equals(comparatorClazz)) {
+ Comparator subClassComparator = getSubClassComparatorForClass(arg0.getClass());
+ if (subClassComparator != null) {
+ return subClassComparator.compare(arg0, arg1);
+ } else if (exactClassMatch) {
+ throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ }
+ int result = compareParents(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+ return internalCompare(arg0, arg1);
+ } else {
+ return -1;
+ }
+ }
+
+ private Comparator getSubClassComparatorForClass(Class<? extends Object> clazz) {
+ for (Comparator comparator : subClassComparatorList) {
+ if (comparator.getComparatorClazz().isAssignableFrom(clazz)) {
+ return comparator;
+ }
+ }
+ return null;
+ }
+
+ private int compareParents(T arg0, T arg1) {
+ Comparator parentComparator = getParentComparator();
+ while (parentComparator != null) {
+ int result = parentComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+ parentComparator = parentComparator.getParentComparator();
+ }
+ return 0;
+
+ }
+
+ protected Comparator getParentComparator() {
+ return null;
+ }
+
+ protected abstract int internalCompare(T arg0, T arg1);
+
+ protected void addSubClassComparator(Comparator<? extends T> subClassComparator) {
+ subClassComparatorList.add(subClassComparator);
+ }
+
+ public Class<T> getComparatorClazz() {
+ return comparatorClazz;
+ }
+
+}
diff --git a/converter-sbml/.classpath b/converter-sbml/.classpath
index 121fc2c8190e91386cecbac241fc4a0b7e6bb5ad..ebdb3af0aa2a29bebab2b0565e1f7c49e9d1aec3 100644
--- a/converter-sbml/.classpath
+++ b/converter-sbml/.classpath
@@ -30,6 +30,7 @@
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="org.eclipse.jst.component.nondependency" value=""/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
diff --git a/converter-sbml/.project b/converter-sbml/.project
index 0a5695c6c29ccbc08e4825dbbe3b8aa759daa0f0..6ae989581c3ea83c552dd30b96d1c07ebbe4ee9d 100644
--- a/converter-sbml/.project
+++ b/converter-sbml/.project
@@ -5,6 +5,11 @@
<projects>
</projects>
<buildSpec>
+ <buildCommand>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
@@ -15,9 +20,17 @@
<arguments>
</arguments>
</buildCommand>
+ <buildCommand>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
</buildSpec>
<natures>
+ <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+ <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
+ <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter-sbml/.settings/org.eclipse.jdt.core.prefs b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
index 714351aec195a9a572640e6844dcafd51565a2a5..6e80039d3b822e65e46fbf18906ef652814e9505 100644
--- a/converter-sbml/.settings/org.eclipse.jdt.core.prefs
+++ b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
@@ -1,5 +1,8 @@
eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
index 3d67b7b4f649f6ee77df0c7c651ba33d0fafd899..787d1a4e8313d49c976e531b4070d108f08bbbff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.model.graphics;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -14,87 +13,59 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
* @author Piotr Gawron
*
*/
-public class ArrowTypeDataComparator implements Comparator<ArrowTypeData> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PolylineDataComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ArrowTypeDataComparator(double epsilon) {
- this.epsilon = epsilon;
- }
+public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PolylineDataComparator.class);
- /**
- * Default constructor.
- */
- public ArrowTypeDataComparator() {
- this(Configuration.EPSILON);
- }
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
- @Override
- public int compare(ArrowTypeData arg0, ArrowTypeData arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ArrowTypeDataComparator(double epsilon) {
+ super(ArrowTypeData.class);
+ this.epsilon = epsilon;
+ }
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- return -1;
- }
- }
+ /**
+ * Default constructor.
+ */
+ public ArrowTypeDataComparator() {
+ this(Configuration.EPSILON);
+ }
- /**
- * This method compares only the fields that are defined in ArrowTypeData
- * class in inheritance tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are equal then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(ArrowTypeData arg0, ArrowTypeData arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ @Override
+ protected int internalCompare(ArrowTypeData arg0, ArrowTypeData arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
- logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
- return arg0.getArrowType().compareTo(arg1.getArrowType());
- }
+ if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
+ logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
+ return arg0.getArrowType().compareTo(arg1.getArrowType());
+ }
- if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
- logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
- return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
- }
+ if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
+ logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
+ return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
+ }
- if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
- logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
- return doubleComparator.compare(arg0.getLen(), arg1.getLen());
- }
+ if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
+ logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
+ return doubleComparator.compare(arg0.getLen(), arg1.getLen());
+ }
- if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
- logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
- return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
- }
- return 0;
- }
+ if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
+ logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
+ return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
+ }
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
index d06b841c16046228ec85564ad9a72f35ffe2b27c..12e7bde45dfb098f163d1b7b2772d0be5d4b0455 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -1,13 +1,11 @@
package lcsb.mapviewer.model.graphics;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements comparator interface for {@link PolylineData}. It
@@ -16,7 +14,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class PolylineDataComparator implements Comparator<PolylineData> {
+public class PolylineDataComparator extends Comparator<PolylineData> {
/**
* Default class logger.
*/
@@ -34,6 +32,7 @@ public class PolylineDataComparator implements Comparator<PolylineData> {
* {@link #epsilon}
*/
public PolylineDataComparator(double epsilon) {
+ super(PolylineData.class, true);
this.epsilon = epsilon;
}
@@ -45,53 +44,20 @@ public class PolylineDataComparator implements Comparator<PolylineData> {
}
@Override
- public int compare(PolylineData arg0, PolylineData arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(PolylineData.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link PolylineData}
- * class in inheritance tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are equal then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(PolylineData arg0, PolylineData arg1) {
+ protected int internalCompare(PolylineData arg0, PolylineData arg1) {
IntegerComparator integerComparator = new IntegerComparator();
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
- int different1=0;
- int different2=0;
- for (int i=1;i<arg0.getPoints().size();i++) {
- if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i-1))>Configuration.EPSILON) {
+ int different1 = 0;
+ int different2 = 0;
+ for (int i = 1; i < arg0.getPoints().size(); i++) {
+ if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i - 1)) > Configuration.EPSILON) {
different1++;
}
}
- for (int i=1;i<arg1.getPoints().size();i++) {
- if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i-1))>Configuration.EPSILON) {
+ for (int i = 1; i < arg1.getPoints().size(); i++) {
+ if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i - 1)) > Configuration.EPSILON) {
different2++;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
index 87bfc05c4a9bedcdfb735a1705db60f807a6b2ae..c7d981188407b65cadb177b397061e03a38a6580 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map;
-import java.util.Comparator;
+import lcsb.mapviewer.common.Comparator;
/**
* {@link Comparator} implementation for {@link MiriamType} that uses
@@ -9,21 +9,15 @@ import java.util.Comparator;
* @author Piotr Gawron
*
*/
-public class MiriamTypeNameComparator implements Comparator<MiriamType> {
+public class MiriamTypeNameComparator extends Comparator<MiriamType> {
- @Override
- public int compare(MiriamType arg0, MiriamType arg1) {
- // comparator is null-safe
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
- return arg0.getCommonName().compareTo(arg1.getCommonName());
- }
+ public MiriamTypeNameComparator() {
+ super(MiriamType.class);
+ }
+
+ @Override
+ protected int internalCompare(MiriamType arg0, MiriamType arg1) {
+ return arg0.getCommonName().compareTo(arg1.getCommonName());
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
index 6796e011abf1e305e893255d135e453a00d9e89c..de8391c624b8a30ccc3d4670c0ba1e2a3344f95e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
@@ -1,127 +1,98 @@
package lcsb.mapviewer.model.map;
-import java.util.Comparator;
import java.util.List;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
-import org.apache.log4j.Logger;
-
/**
* This class implements comparator interface for {@link OverviewImage}.
*
* @author Piotr Gawron
*
*/
-public class OverviewImageComparator implements Comparator<OverviewImage> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewImageComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewImageComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public OverviewImageComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(OverviewImage arg0, OverviewImage arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link OverviewImage} class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(OverviewImage arg0, OverviewImage arg1) {
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getFilename(), arg1.getFilename()) != 0) {
- logger.debug("filename different: " + arg0.getFilename() + ", " + arg1.getFilename());
- return stringComparator.compare(arg0.getFilename(), arg1.getFilename());
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return integerComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (integerComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return integerComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (compareLinks(arg0.getLinks(), arg1.getLinks()) != 0) {
- return compareLinks(arg0.getLinks(), arg1.getLinks());
- }
-
- return 0;
- }
-
- /**
- * Compare two list of {@link OverviewLink links}.
- *
- * @param links
- * first list to compare
- * @param links2
- * second list to compare
- * @return 0 if the list are identical, -1/1 otherwise
- */
- private int compareLinks(List<OverviewLink> links, List<OverviewLink> links2) {
- IntegerComparator integerComparator = new IntegerComparator();
- OverviewLinkComparator ovc = new OverviewLinkComparator(epsilon);
- if (integerComparator.compare(links.size(), links2.size()) != 0) {
- return integerComparator.compare(links.size(), links2.size());
- }
- for (int i = 0; i < links.size(); i++) {
- if (ovc.compare(links.get(i), links2.get(i)) != 0) {
- return ovc.compare(links.get(i), links2.get(i));
- }
- }
- return 0;
- }
+public class OverviewImageComparator extends Comparator<OverviewImage> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewImageComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewImageComparator(double epsilon) {
+ super(OverviewImage.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImageComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewImage arg0, OverviewImage arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getFilename(), arg1.getFilename()) != 0) {
+ logger.debug("filename different: " + arg0.getFilename() + ", " + arg1.getFilename());
+ return stringComparator.compare(arg0.getFilename(), arg1.getFilename());
+ }
+
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return integerComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (integerComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return integerComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (compareLinks(arg0.getLinks(), arg1.getLinks()) != 0) {
+ return compareLinks(arg0.getLinks(), arg1.getLinks());
+ }
+
+ return 0;
+ }
+
+ /**
+ * Compare two list of {@link OverviewLink links}.
+ *
+ * @param links
+ * first list to compare
+ * @param links2
+ * second list to compare
+ * @return 0 if the list are identical, -1/1 otherwise
+ */
+ private int compareLinks(List<OverviewLink> links, List<OverviewLink> links2) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ OverviewLinkComparator ovc = new OverviewLinkComparator(epsilon);
+ if (integerComparator.compare(links.size(), links2.size()) != 0) {
+ return integerComparator.compare(links.size(), links2.size());
+ }
+ for (int i = 0; i < links.size(); i++) {
+ if (ovc.compare(links.get(i), links2.get(i)) != 0) {
+ return ovc.compare(links.get(i), links2.get(i));
+ }
+ }
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
index 3ba0b157c6fce7ba885ad3821ff725996147608d..eeb7f3ba0b7034a88c3e7d53267000ce567c70c9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
@@ -1,104 +1,74 @@
package lcsb.mapviewer.model.map;
-import java.util.Comparator;
+import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
-import org.apache.log4j.Logger;
-
/**
* This class implements comparator interface for {@link OverviewImageLink}.
*
* @author Piotr Gawron
*
*/
-public class OverviewImageLinkComparator implements Comparator<OverviewImageLink> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewImageLinkComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewImageLinkComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public OverviewImageLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(OverviewImageLink arg0, OverviewImageLink arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link OverviewImageLink} class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(OverviewImageLink arg0, OverviewImageLink arg1) {
- OverviewLinkComparator overviewLinkComparator = new OverviewLinkComparator(epsilon);
- int result = overviewLinkComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (arg0.getLinkedOverviewImage() == null) {
- if (arg1.getLinkedOverviewImage() == null) {
- result = 0;
- } else {
- result = 1;
- }
- } else if (arg1.getLinkedOverviewImage() == null) {
- result = -1;
- } else {
- result = integerComparator.compare(arg0.getLinkedOverviewImage().getId(), arg1.getLinkedOverviewImage().getId());
- }
-
- if (result != 0) {
- return result;
- }
-
- return 0;
-
- }
+public class OverviewImageLinkComparator extends Comparator<OverviewImageLink> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewImageLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewImageLinkComparator(double epsilon) {
+ super(OverviewImageLink.class);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new OverviewLinkComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImageLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewImageLink arg0, OverviewImageLink arg1) {
+ int result = 0;
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (arg0.getLinkedOverviewImage() == null) {
+ if (arg1.getLinkedOverviewImage() == null) {
+ result = 0;
+ } else {
+ result = 1;
+ }
+ } else if (arg1.getLinkedOverviewImage() == null) {
+ result = -1;
+ } else {
+ result = integerComparator.compare(arg0.getLinkedOverviewImage().getId(), arg1.getLinkedOverviewImage().getId());
+ }
+
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
index a81a46c0e6dd3dadbdbb3702479e69055233af9e..6ea1cc68e505f8b9d6af4360813761e2d05b16d1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.model.map;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements comparator interface for {@link OverviewLink}.
@@ -14,96 +12,51 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class OverviewLinkComparator implements Comparator<OverviewLink> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewLinkComparator.class);
-
- /**
- * Comparator used to compare {@link OverviewModelLink} objects.
- */
- private OverviewModelLinkComparator overviewModelLinkComparator;
-
- /**
- * Comparator used to compare {@link OverviewImageLink} objects.
- */
- private OverviewImageLinkComparator overviewImageLinkComparator;
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- @SuppressWarnings("unused")
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewLinkComparator(double epsilon) {
- this.epsilon = epsilon;
- overviewImageLinkComparator = new OverviewImageLinkComparator(epsilon);
- overviewModelLinkComparator = new OverviewModelLinkComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public OverviewLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(OverviewLink arg0, OverviewLink arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof OverviewImageLink) {
- return overviewImageLinkComparator.compare((OverviewImageLink) arg0, (OverviewImageLink) arg1);
- } else if (arg0 instanceof OverviewModelLink) {
- return overviewModelLinkComparator.compare((OverviewModelLink) arg0, (OverviewModelLink) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link OverviewImage} class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(OverviewLink arg0, OverviewLink arg1) {
-
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getPolygon(), arg1.getPolygon()) != 0) {
- logger.debug("polygon different: " + arg0.getPolygon() + ", " + arg1.getPolygon());
- return stringComparator.compare(arg0.getPolygon(), arg1.getPolygon());
- }
-
- return 0;
-
- }
+public class OverviewLinkComparator extends Comparator<OverviewLink> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ @SuppressWarnings("unused")
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewLinkComparator(double epsilon) {
+ super(OverviewLink.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new OverviewImageLinkComparator(epsilon));
+ addSubClassComparator(new OverviewModelLinkComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewLink arg0, OverviewLink arg1) {
+
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getPolygon(), arg1.getPolygon()) != 0) {
+ logger.debug("polygon different: " + arg0.getPolygon() + ", " + arg1.getPolygon());
+ return stringComparator.compare(arg0.getPolygon(), arg1.getPolygon());
+ }
+
+ return 0;
+
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
index dfa7a9c72c92fed205ffd5012a04a5df96b96085..7adb2b8647c14a4770da68d57bbae0cc0e8cfce3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
@@ -1,120 +1,88 @@
package lcsb.mapviewer.model.map;
-import java.util.Comparator;
+import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
-import org.apache.log4j.Logger;
-
/**
* This class implements comparator interface for {@link OverviewModelLink}.
*
* @author Piotr Gawron
*
*/
-public class OverviewModelLinkComparator implements Comparator<OverviewModelLink> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewModelLinkComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewModelLinkComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public OverviewModelLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(OverviewModelLink arg0, OverviewModelLink arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link OverviewModelLink} class in inheritence tree. It also calls the
- * {@link OverviewLinkComparator} for the super class ({@link OverviewLink}).
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(OverviewModelLink arg0, OverviewModelLink arg1) {
- OverviewLinkComparator overviewLinkComparator = new OverviewLinkComparator(epsilon);
- int result = overviewLinkComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- IntegerComparator integerComparator = new IntegerComparator();
- if (integerComparator.compare(arg0.getxCoord(), arg1.getxCoord()) != 0) {
- logger.debug("xCoord different: " + arg0.getxCoord() + ", " + arg1.getxCoord());
- return integerComparator.compare(arg0.getxCoord(), arg1.getxCoord());
- }
-
- if (integerComparator.compare(arg0.getyCoord(), arg1.getyCoord()) != 0) {
- logger.debug("yCoord different: " + arg0.getyCoord() + ", " + arg1.getyCoord());
- return integerComparator.compare(arg0.getyCoord(), arg1.getyCoord());
- }
-
- if (integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel()) != 0) {
- logger.debug("zoomLevel different: " + arg0.getZoomLevel() + ", " + arg1.getZoomLevel());
- return integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel());
- }
-
-
- if (arg0.getLinkedModel() == null) {
- if (arg1.getLinkedModel() == null) {
- result = 0;
- } else {
- result = 1;
- }
- } else if (arg1.getLinkedModel() == null) {
- result = -1;
- } else {
- result = integerComparator.compare(arg0.getLinkedModel().getId(), arg1.getLinkedModel().getId());
- }
-
- if (result != 0) {
- return result;
- }
-
-
- return 0;
-
- }
+public class OverviewModelLinkComparator extends Comparator<OverviewModelLink> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewModelLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewModelLinkComparator(double epsilon) {
+ super(OverviewModelLink.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewModelLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public Comparator<?> getParentComparator() {
+ return new OverviewLinkComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(OverviewModelLink arg0, OverviewModelLink arg1) {
+ int result = 0;
+ IntegerComparator integerComparator = new IntegerComparator();
+ if (integerComparator.compare(arg0.getxCoord(), arg1.getxCoord()) != 0) {
+ logger.debug("xCoord different: " + arg0.getxCoord() + ", " + arg1.getxCoord());
+ return integerComparator.compare(arg0.getxCoord(), arg1.getxCoord());
+ }
+
+ if (integerComparator.compare(arg0.getyCoord(), arg1.getyCoord()) != 0) {
+ logger.debug("yCoord different: " + arg0.getyCoord() + ", " + arg1.getyCoord());
+ return integerComparator.compare(arg0.getyCoord(), arg1.getyCoord());
+ }
+
+ if (integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel()) != 0) {
+ logger.debug("zoomLevel different: " + arg0.getZoomLevel() + ", " + arg1.getZoomLevel());
+ return integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel());
+ }
+
+ if (arg0.getLinkedModel() == null) {
+ if (arg1.getLinkedModel() == null) {
+ result = 0;
+ } else {
+ result = 1;
+ }
+ } else if (arg1.getLinkedModel() == null) {
+ result = -1;
+ } else {
+ result = integerComparator.compare(arg0.getLinkedModel().getId(), arg1.getLinkedModel().getId());
+ }
+
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
index e56a9c0532e64df5fa2f8d48cec9daf9e32081d5..80b2870b9c6a0b29da4ff7ae0d151efb291a8048 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
@@ -1,16 +1,17 @@
package lcsb.mapviewer.model.map.compartment;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.PointComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.reaction.AbstractNodeComparator;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.ElementComparator;
@@ -22,127 +23,99 @@ import lcsb.mapviewer.model.map.species.ElementComparator;
* @see Compartment
*
*/
-public class CompartmentComparator implements Comparator<Compartment> {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CompartmentComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public CompartmentComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public CompartmentComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Compartment arg0, Compartment arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link Compartment} class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Compartment arg0, Compartment arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- int result = elementComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- IntegerComparator integerComparator = new IntegerComparator();
- PointComparator pointComparator = new PointComparator(epsilon);
-
- if (doubleComparator.compare(arg0.getThickness(), arg1.getThickness()) != 0) {
- logger.debug("Thickness different: " + arg0.getThickness() + ", " + arg1.getThickness());
- return doubleComparator.compare(arg0.getThickness(), arg1.getThickness());
- }
-
- if (doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth()) != 0) {
- logger.debug("Outer width different: " + arg0.getOuterWidth() + ", " + arg1.getOuterWidth());
- return doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth());
- }
-
- if (doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth()) != 0) {
- logger.debug("Inner width different: " + arg0.getInnerWidth() + ", " + arg1.getInnerWidth());
- return doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth());
- }
-
- if (pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint()) != 0) {
- logger.debug("NamePoint different: " + arg0.getNamePoint() + ", " + arg1.getNamePoint());
- return pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint());
- }
-
- if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
- logger.debug("Elements number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
- return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
- }
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- for (Element element : arg0.getElements()) {
- if (map1.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : arg1.getElements()) {
- if (map2.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : arg0.getElements()) {
- Element element2 = map2.get(element.getElementId());
- int status = elementComparator.compare(element, element2);
- if (status != 0) {
- logger.debug("Couldn't match element: " + element.getElementId() + ", " + element2);
- return status;
- }
- }
-
- return 0;
- }
+public class CompartmentComparator extends Comparator<Compartment> {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CompartmentComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CompartmentComparator(double epsilon) {
+ super(Compartment.class);
+ this.epsilon = epsilon;
+ }
+
+ protected Comparator<?> getParentComparator() {
+ return new ElementComparator(epsilon);
+ }
+
+
+ /**
+ * Default constructor.
+ */
+ public CompartmentComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Compartment arg0, Compartment arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+ PointComparator pointComparator = new PointComparator(epsilon);
+
+ if (doubleComparator.compare(arg0.getThickness(), arg1.getThickness()) != 0) {
+ logger.debug("Thickness different: " + arg0.getThickness() + ", " + arg1.getThickness());
+ return doubleComparator.compare(arg0.getThickness(), arg1.getThickness());
+ }
+
+ if (doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth()) != 0) {
+ logger.debug("Outer width different: " + arg0.getOuterWidth() + ", " + arg1.getOuterWidth());
+ return doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth()) != 0) {
+ logger.debug("Inner width different: " + arg0.getInnerWidth() + ", " + arg1.getInnerWidth());
+ return doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth());
+ }
+
+ if (pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint()) != 0) {
+ logger.debug("NamePoint different: " + arg0.getNamePoint() + ", " + arg1.getNamePoint());
+ return pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint());
+ }
+
+ if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
+ logger.debug("Elements number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
+ }
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
+ if (status != 0) {
+ logger.debug("Couldn't match element: " + element.getElementId() + ", " + element2);
+ return status;
+ }
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMiningSetComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMiningSetComparator.java
index faed93797389cd29ed81305b87b78290565e8e32..7cb3f086934b312e6b42a403e5f228ccfb7b5e5e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMiningSetComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMiningSetComparator.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.model.map.graph;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator for {@link DataMiningSet} class.
@@ -14,78 +12,46 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class DataMiningSetComparator implements Comparator<DataMiningSet> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(DataMiningSetComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- @SuppressWarnings("unused")
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DataMiningSetComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public DataMiningSetComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(DataMiningSet arg0, DataMiningSet arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass() == DataMiningSet.class) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link DataMiningSet} class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(DataMiningSet arg0, DataMiningSet arg1) {
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- return 0;
- }
+public class DataMiningSetComparator extends Comparator<DataMiningSet> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DataMiningSetComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ @SuppressWarnings("unused")
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DataMiningSetComparator(double epsilon) {
+ super(DataMiningSet.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DataMiningSetComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(DataMiningSet arg0, DataMiningSet arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ return 0;
+ }
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..bee84ba436b5eca70e93e39edd477c841377f504
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
@@ -0,0 +1,16 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import lcsb.mapviewer.common.Comparator;
+
+public class SbmlKineticsComparator extends Comparator<SbmlKinetics> {
+
+ public SbmlKineticsComparator() {
+ super(SbmlKinetics.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlKinetics arg0, SbmlKinetics arg1) {
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
index 147590ff1e6c6fd7c39aea4a714c5d10de5a62be..30055b47f72cdec4a0ca6328ea213a61bd9b4825 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.layout;
-import java.util.Comparator;
-
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements comparator interface for Layout.
@@ -13,80 +11,48 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class LayoutComparator implements Comparator<Layout> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- @SuppressWarnings("unused")
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayoutComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayoutComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * This method compares only the fields that are defined in {@link Layout}
- * class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Layout arg0, Layout arg1) {
- StringComparator stringComparator = new StringComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
- if (stringComparator.compare(arg0.getDirectory(), arg1.getDirectory()) != 0) {
- return stringComparator.compare(arg0.getDirectory(), arg1.getDirectory());
- }
- if (stringComparator.compare(arg0.getTitle(), arg1.getTitle()) != 0) {
- return stringComparator.compare(arg0.getTitle(), arg1.getTitle());
- }
-
- if (booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView()) != 0) {
- return booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView());
- }
-
- return 0;
- }
-
- @Override
- public int compare(Layout arg0, Layout arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass() == Layout.class) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
+public class LayoutComparator extends Comparator<Layout> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ @SuppressWarnings("unused")
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayoutComparator(double epsilon) {
+ super(Layout.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayoutComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Layout arg0, Layout arg1) {
+ StringComparator stringComparator = new StringComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+ if (stringComparator.compare(arg0.getDirectory(), arg1.getDirectory()) != 0) {
+ return stringComparator.compare(arg0.getDirectory(), arg1.getDirectory());
+ }
+ if (stringComparator.compare(arg0.getTitle(), arg1.getTitle()) != 0) {
+ return stringComparator.compare(arg0.getTitle(), arg1.getTitle());
+ }
+
+ if (booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView()) != 0) {
+ return booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
index 536b027b647877562981ceb1474e9071e34f40c6..8f842708acea2ad329ecb5f37d235c8c8dfc32c2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
@@ -12,153 +11,122 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
/**
- * Compparator of {@link Layer} class.
+ * Comparator of {@link Layer} class.
*
* @author Piotr Gawron
*
*
*/
-public class LayerComparator implements Comparator<Layer> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(LayerComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Layer arg0, Layer arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Layer.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares all fields that are defined in Layer class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Layer arg0, Layer arg1) {
- StringComparator stringComparator = new StringComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (stringComparator.compare(arg0.getLayerId(), arg1.getLayerId()) != 0) {
- logger.debug("layer ids different: " + arg0.getLayerId() + ", " + arg1.getLayerId());
- return stringComparator.compare(arg0.getLayerId(), arg1.getLayerId());
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("layer name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (booleanComparator.compare(arg0.isVisible(), arg1.isVisible()) != 0) {
- logger.debug("layer visibility different: " + arg0.isVisible() + ", " + arg1.isVisible());
- return booleanComparator.compare(arg0.isVisible(), arg1.isVisible());
- }
-
- if (booleanComparator.compare(arg0.isLocked(), arg1.isLocked()) != 0) {
- logger.debug("layer locked different: " + arg0.isLocked() + ", " + arg1.isLocked());
- return booleanComparator.compare(arg0.isLocked(), arg1.isLocked());
- }
-
- if (integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size()) != 0) {
- logger.debug("layer texts different: " + arg0.getTexts().size() + ", " + arg1.getTexts().size());
- return integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size());
- }
- if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
- logger.debug("layer lines different: " + arg0.getLines().size() + ", " + arg1.getLines().size());
- return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
- }
- if (integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size()) != 0) {
- logger.debug("layer rectangles different: " + arg0.getRectangles().size() + ", " + arg1.getRectangles().size());
- return integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size());
- }
- if (integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size()) != 0) {
- logger.debug("layer ovals different: " + arg0.getOvals().size() + ", " + arg1.getOvals().size());
- return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
- }
-
- LayerTextComparator textComparator = new LayerTextComparator(epsilon);
- for (int i = 0; i < arg0.getTexts().size(); i++) {
- int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
- if (status != 0) {
- logger.debug("layer texts different");
- return status;
- }
- }
-
- LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
- for (int i = 0; i < arg0.getOvals().size(); i++) {
- int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
- if (status != 0) {
- logger.debug("layer ovals different");
- return status;
- }
- }
-
- LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
- for (int i = 0; i < arg0.getRectangles().size(); i++) {
- int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
- if (status != 0) {
- logger.debug("layer rectangles different ");
- return status;
- }
- }
-
- PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
- for (int i = 0; i < arg0.getLines().size(); i++) {
- int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
- if (status != 0) {
- logger.debug("layer lines different ");
- return status;
- }
- }
-
- return 0;
- }
+public class LayerComparator extends Comparator<Layer> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(LayerComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerComparator(double epsilon) {
+ super(Layer.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Layer arg0, Layer arg1) {
+ StringComparator stringComparator = new StringComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (stringComparator.compare(arg0.getLayerId(), arg1.getLayerId()) != 0) {
+ logger.debug("layer ids different: " + arg0.getLayerId() + ", " + arg1.getLayerId());
+ return stringComparator.compare(arg0.getLayerId(), arg1.getLayerId());
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("layer name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (booleanComparator.compare(arg0.isVisible(), arg1.isVisible()) != 0) {
+ logger.debug("layer visibility different: " + arg0.isVisible() + ", " + arg1.isVisible());
+ return booleanComparator.compare(arg0.isVisible(), arg1.isVisible());
+ }
+
+ if (booleanComparator.compare(arg0.isLocked(), arg1.isLocked()) != 0) {
+ logger.debug("layer locked different: " + arg0.isLocked() + ", " + arg1.isLocked());
+ return booleanComparator.compare(arg0.isLocked(), arg1.isLocked());
+ }
+
+ if (integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size()) != 0) {
+ logger.debug("layer texts different: " + arg0.getTexts().size() + ", " + arg1.getTexts().size());
+ return integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size());
+ }
+ if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
+ logger.debug("layer lines different: " + arg0.getLines().size() + ", " + arg1.getLines().size());
+ return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
+ }
+ if (integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size()) != 0) {
+ logger.debug("layer rectangles different: " + arg0.getRectangles().size() + ", " + arg1.getRectangles().size());
+ return integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size());
+ }
+ if (integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size()) != 0) {
+ logger.debug("layer ovals different: " + arg0.getOvals().size() + ", " + arg1.getOvals().size());
+ return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
+ }
+
+ LayerTextComparator textComparator = new LayerTextComparator(epsilon);
+ for (int i = 0; i < arg0.getTexts().size(); i++) {
+ int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
+ if (status != 0) {
+ logger.debug("layer texts different");
+ return status;
+ }
+ }
+
+ LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
+ for (int i = 0; i < arg0.getOvals().size(); i++) {
+ int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
+ if (status != 0) {
+ logger.debug("layer ovals different");
+ return status;
+ }
+ }
+
+ LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
+ for (int i = 0; i < arg0.getRectangles().size(); i++) {
+ int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
+ if (status != 0) {
+ logger.debug("layer rectangles different ");
+ return status;
+ }
+ }
+
+ PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
+ for (int i = 0; i < arg0.getLines().size(); i++) {
+ int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
+ if (status != 0) {
+ logger.debug("layer lines different ");
+ return status;
+ }
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
index 2e005f1f1b16c451ccd832d51d2999ad91ef9a02..2ef01f855d2c5c4682dd0232b0a6cc4f3f8bee38 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
@@ -1,101 +1,68 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.util.Comparator;
-
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ColorComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * Compparator of {@link LayerOval} class.
+ * Comparator of {@link LayerOval} class.
*
* @author Piotr Gawron
*
*
*/
-public class LayerOvalComparator implements Comparator<LayerOval> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerOvalComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerOvalComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * This method compares all fields that are defined in LayerOval class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(LayerOval arg0, LayerOval arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- return 0;
- }
-
- @Override
- public int compare(LayerOval arg0, LayerOval arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(LayerOval.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
+public class LayerOvalComparator extends Comparator<LayerOval> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerOvalComparator(double epsilon) {
+ super(LayerOval.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerOvalComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerOval arg0, LayerOval arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
index 7d8f14d44263176b4aab77cf6a402eab80a43bcf..b945ac9e012ba0989b0a9fd159516f1547da0069 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.util.Comparator;
-
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ColorComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Compparator of {@link LayerRect} class.
@@ -14,88 +12,57 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*
*/
-public class LayerRectComparator implements Comparator<LayerRect> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerRectComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerRectComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * This method compares all fields that are defined in LayerRect class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(LayerRect arg0, LayerRect arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- return 0;
- }
-
- @Override
- public int compare(LayerRect arg0, LayerRect arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(LayerRect.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
+public class LayerRectComparator extends Comparator<LayerRect> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerRectComparator(double epsilon) {
+ super(LayerRect.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerRectComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerRect arg0, LayerRect arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
index 8f35b4040c6c5c874c69611aea62c957dab8186e..d0371804acbe2519215c5b42e6e9638abd4d7d6a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.model.map.layout.graphics;
-import java.util.Comparator;
-
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ColorComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Compparator of {@link LayerText} class.
@@ -15,97 +13,66 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*
*/
-public class LayerTextComparator implements Comparator<LayerText> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerTextComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerTextComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * This method compares all fields that are defined in LayerText class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(LayerText arg0, LayerText arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- StringComparator stringComparator = new StringComparator();
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
- }
-
- if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
- }
-
- return 0;
- }
-
- @Override
- public int compare(LayerText arg0, LayerText arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(LayerText.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
+public class LayerTextComparator extends Comparator<LayerText> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerTextComparator(double epsilon) {
+ super(LayerText.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerTextComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerText arg0, LayerText arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ StringComparator stringComparator = new StringComparator();
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ }
+
+ if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
+ return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
index c1709b3a29d3298dc9e184fa522981e01710745b..15f64f78e1473d8dfd8ffcd64db8cfe042ae4b49 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
@@ -1,113 +1,81 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Comparator;
+import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.ElementComparator;
-import org.apache.log4j.Logger;
-
/**
- * This class implements comparator interface for {@link ElementSubmodelConnection}.
+ * This class implements comparator interface for
+ * {@link ElementSubmodelConnection}.
*
* @author Piotr Gawron
*
*/
-public class ElementSubmodelConnectionComparator implements Comparator<ElementSubmodelConnection> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ElementSubmodelConnectionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
+public class ElementSubmodelConnectionComparator extends Comparator<ElementSubmodelConnection> {
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ElementSubmodelConnectionComparator(double epsilon) {
- this.epsilon = epsilon;
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ElementSubmodelConnectionComparator.class);
- /**
- * Default constructor.
- */
- public ElementSubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
- @Override
- public int compare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ElementSubmodelConnectionComparator(double epsilon) {
+ super(ElementSubmodelConnection.class);
+ this.epsilon = epsilon;
+ }
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
+ /**
+ * Default constructor.
+ */
+ public ElementSubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
- /**
- * This method compares only the fields that are defined in
- * {@link ElementSubmodelConnection} class in inheritence tree. It also calls
- * the {@link SubmodelConnectionComparator} for the super class (
- * {@link SubmodelConnection}).
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
- SubmodelConnectionComparator superComparator = new SubmodelConnectionComparator(epsilon);
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SubmodelConnectionComparator(epsilon);
+ }
- int result = superComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- ElementComparator elementComparator = new ElementComparator(epsilon);
- Element element1 = arg0.getFromElement();
- Element element2 = arg1.getFromElement();
- arg0.setFromElement(null);
- arg1.setFromElement(null);
- int status = elementComparator.compare(element1, element2);
- arg0.setFromElement(element1);
- arg1.setFromElement(element2);
- if (status != 0) {
- logger.debug("from element different: " + arg0.getFromElement() + ", " + arg1.getFromElement());
- return status;
- }
- element1 = arg0.getToElement();
- element2 = arg1.getToElement();
- arg0.setToElement(null);
- arg1.setToElement(null);
- status = elementComparator.compare(element1, element2);
- arg0.setToElement(element1);
- arg1.setToElement(element2);
- if (status != 0) {
- logger.debug("to element different: " + arg0.getToElement() + ", " + arg1.getToElement());
- return status;
- }
+ @Override
+ protected int internalCompare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ Element element1 = arg0.getFromElement();
+ Element element2 = arg1.getFromElement();
+ arg0.setFromElement(null);
+ arg1.setFromElement(null);
+ int status = elementComparator.compare(element1, element2);
+ arg0.setFromElement(element1);
+ arg1.setFromElement(element2);
+ if (status != 0) {
+ logger.debug("from element different: " + arg0.getFromElement() + ", " + arg1.getFromElement());
+ return status;
+ }
+ element1 = arg0.getToElement();
+ element2 = arg1.getToElement();
+ arg0.setToElement(null);
+ arg1.setToElement(null);
+ status = elementComparator.compare(element1, element2);
+ arg0.setToElement(element1);
+ arg1.setToElement(element2);
+ if (status != 0) {
+ logger.debug("to element different: " + arg0.getToElement() + ", " + arg1.getToElement());
+ return status;
+ }
- return 0;
- }
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index cd1fee24d3d0081760c6e74233f7871b2ad606ae..dc8eb6f002c64b30c22fa122b153c01e1abeeca1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.model.map.model;
import java.util.Collection;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -9,6 +8,7 @@ import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
@@ -29,377 +29,352 @@ import lcsb.mapviewer.model.map.species.ElementComparator;
* @author Piotr Gawron
*
*/
-public class ModelComparator implements Comparator<Model> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ModelComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ModelComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ModelComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Model arg0, Model arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Model}
- * class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are equal then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Model arg0, Model arg1) {
- StringComparator stringComparator = new StringComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (stringComparator.compare(arg0.getIdModel(), arg1.getIdModel()) != 0) {
- logger.debug("Id different: " + arg0.getIdModel() + ", " + arg1.getIdModel());
- return stringComparator.compare(arg0.getIdModel(), arg1.getIdModel());
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
- logger.debug(arg0.getNotes());
- logger.debug(arg1.getNotes());
- logger.debug("Notes different:\n" + arg0.getNotes() + "\n---\n" + arg1.getNotes() + "\n---");
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true);
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels()) != 0) {
- logger.debug("Zoom levels different: " + arg0.getZoomLevels() + ", " + arg1.getZoomLevels());
- return integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels());
- }
-
- if (integerComparator.compare(arg0.getTileSize(), arg1.getTileSize()) != 0) {
- logger.debug("Tile size different: " + arg0.getTileSize() + ", " + arg1.getTileSize());
- return integerComparator.compare(arg0.getTileSize(), arg1.getTileSize());
- }
-
- int status = compareElements(arg0.getElements(), arg1.getElements());
- if (status != 0) {
- logger.debug("Set of elements different");
- return status;
- }
-
- status = compareLayers(arg0.getLayers(), arg1.getLayers());
- if (status != 0) {
- logger.debug("Set of layers different");
- return status;
- }
-
- status = compareReaction(arg0.getReactions(), arg1.getReactions());
- if (status != 0) {
- logger.debug("Set of reactions different");
- return status;
- }
-
- status = compareLayouts(arg0.getLayouts(), arg1.getLayouts());
- if (status != 0) {
- logger.debug("Set of layouts different");
- return status;
- }
-
- status = compareSubmodels(arg0.getSubmodelConnections(), arg1.getSubmodelConnections());
- if (status != 0) {
- logger.debug("Set of submodels different");
- return status;
- }
-
- status = integerComparator.compare(arg0.getDataMiningSets().size(), arg1.getDataMiningSets().size());
- if (status != 0) {
- logger.debug("Set of data mining sets different");
- return status;
- }
- DataMiningSetComparator dataMiningSetComparator = new DataMiningSetComparator();
- for (int i = 0; i < arg0.getDataMiningSets().size(); i++) {
- status = dataMiningSetComparator.compare(arg0.getDataMiningSets().get(i), arg1.getDataMiningSets().get(i));
- if (status != 0) {
- logger.debug("Set of data mining sets different");
- return status;
- }
-
- }
- return 0;
- }
-
- /**
- * Compares two set of reactions.
- *
- * @param reactions
- * first set of reactions
- * @param reactions2
- * second set of reactions
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
- */
- private int compareReaction(Set<Reaction> reactions, Set<Reaction> reactions2) {
- ReactionComparator comparator = new ReactionComparator(epsilon);
-
- Map<String, Reaction> map = new HashMap<String, Reaction>();
- Map<String, Reaction> map2 = new HashMap<String, Reaction>();
-
- for (Reaction reaction : reactions) {
- map.put(reaction.getIdReaction(), reaction);
- }
- for (Reaction reaction : reactions2) {
- map2.put(reaction.getIdReaction(), reaction);
- }
-
- for (Reaction reaction : reactions) {
- int status = comparator.compare(reaction, map2.get(reaction.getIdReaction()));
- if (status != 0) {
- logger.debug("Different reaction " + reaction.getIdReaction() + ": " + map2.get(reaction.getIdReaction()));
- return status;
- }
- }
-
- for (Reaction reaction : reactions2) {
- int status = comparator.compare(reaction, map.get(reaction.getIdReaction()));
- if (status != 0) {
- logger.debug("Different reaction " + reaction.getIdReaction());
- return status;
- }
- }
- return 0;
- }
-
- /**
- * Compares two sets of layers.
- *
- * @param layers
- * first set of layers
- * @param layers2
- * second set of layers
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
- */
- private int compareLayers(Set<Layer> layers, Set<Layer> layers2) {
- LayerComparator layerComparator = new LayerComparator(epsilon);
- for (Layer layer : layers) {
- boolean found = false;
- for (Layer layer2 : layers2) {
- if (layerComparator.compare(layer, layer2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return 1;
- }
- }
- for (Layer layer : layers2) {
- boolean found = false;
- for (Layer layer2 : layers) {
- if (layerComparator.compare(layer, layer2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return -1;
- }
- }
- return 0;
- }
-
- /**
- * Compares two sets of layouts.
- *
- * @param layouts
- * first set of layouts
- * @param layouts2
- * second set of layouts
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
- */
- private int compareLayouts(List<Layout> layouts, List<Layout> layouts2) {
- LayoutComparator layoutComparator = new LayoutComparator(epsilon);
- for (Layout layout : layouts) {
- boolean found = false;
- for (Layout layout2 : layouts2) {
- if (layoutComparator.compare(layout, layout2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return 1;
- }
- }
- for (Layout layout : layouts2) {
- boolean found = false;
- for (Layout layout2 : layouts) {
- if (layoutComparator.compare(layout, layout2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return -1;
- }
- }
- return 0;
- }
-
- /**
- * Compares two sets of elements.
- *
- * @param elements
- * first set of elements
- * @param elements2
- * second set of elements
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
- */
- private int compareElements(Set<Element> elements, Set<Element> elements2) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- if (elements.size() != elements2.size()) {
- logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
- return ((Integer) elements.size()).compareTo(elements2.size());
- }
-
- for (Element element : elements) {
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : elements2) {
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : elements) {
- int status = elementComparator.compare(element, map2.get(element.getElementId()));
- if (status != 0) {
- logger.debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
- return status;
- }
- }
-
- for (Element element : elements2) {
- int status = elementComparator.compare(element, map1.get(element.getElementId()));
- if (status != 0) {
- logger.debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
- return status;
- }
- }
- return 0;
- }
-
- /**
- * Compares two collection of models.
- *
- * @param collection1
- * first collection to compare
- * @param collection2
- * second collection to compare
- * @return 0 if the collections are identical, -1/1 otherwise
- */
- private int compareSubmodels(Collection<ModelSubmodelConnection> collection1, Collection<ModelSubmodelConnection> collection2) {
- IntegerComparator integerComparator = new IntegerComparator();
- if (integerComparator.compare(collection1.size(), collection2.size()) != 0) {
- logger.debug("collection of submodels doesn't match: " + collection1.size() + ", " + collection2.size());
- return integerComparator.compare(collection1.size(), collection2.size());
- }
- ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator(epsilon);
- for (ModelSubmodelConnection submodel1 : collection1) {
- boolean found = false;
- for (ModelSubmodelConnection submodel2 : collection2) {
- ModelData parent1 = submodel1.getParentModel();
- submodel1.setParentModel((ModelData) null);
- ModelData parent2 = submodel2.getParentModel();
- submodel2.setParentModel((ModelData) null);
-
- if (comparator.compare(submodel1, submodel2) == 0) {
- found = true;
- }
- submodel1.setParentModel(parent1);
- submodel2.setParentModel(parent2);
- if (found) {
- break;
- }
- }
- if (!found) {
- logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the second model");
- return 1;
- }
- }
-
- for (ModelSubmodelConnection submodel1 : collection2) {
- boolean found = false;
- for (ModelSubmodelConnection submodel2 : collection1) {
- ModelData parent1 = submodel1.getParentModel();
- submodel1.setParentModel((ModelData) null);
- ModelData parent2 = submodel2.getParentModel();
- submodel2.setParentModel((ModelData) null);
-
- if (comparator.compare(submodel1, submodel2) == 0) {
- found = true;
- }
- submodel1.setParentModel(parent1);
- submodel2.setParentModel(parent2);
- if (found) {
- break;
- }
- }
- if (!found) {
- logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the first model");
- return -1;
- }
- }
-
- return 0;
- }
+public class ModelComparator extends Comparator<Model> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ModelComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ModelComparator(double epsilon) {
+ super(Model.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ModelComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Model arg0, Model arg1) {
+ StringComparator stringComparator = new StringComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (stringComparator.compare(arg0.getIdModel(), arg1.getIdModel()) != 0) {
+ logger.debug("Id different: " + arg0.getIdModel() + ", " + arg1.getIdModel());
+ return stringComparator.compare(arg0.getIdModel(), arg1.getIdModel());
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
+ logger.debug(arg0.getNotes());
+ logger.debug(arg1.getNotes());
+ logger.debug("Notes different:\n" + arg0.getNotes() + "\n---\n" + arg1.getNotes() + "\n---");
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true);
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels()) != 0) {
+ logger.debug("Zoom levels different: " + arg0.getZoomLevels() + ", " + arg1.getZoomLevels());
+ return integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels());
+ }
+
+ if (integerComparator.compare(arg0.getTileSize(), arg1.getTileSize()) != 0) {
+ logger.debug("Tile size different: " + arg0.getTileSize() + ", " + arg1.getTileSize());
+ return integerComparator.compare(arg0.getTileSize(), arg1.getTileSize());
+ }
+
+ int status = compareElements(arg0.getElements(), arg1.getElements());
+ if (status != 0) {
+ logger.debug("Set of elements different");
+ return status;
+ }
+
+ status = compareLayers(arg0.getLayers(), arg1.getLayers());
+ if (status != 0) {
+ logger.debug("Set of layers different");
+ return status;
+ }
+
+ status = compareReaction(arg0.getReactions(), arg1.getReactions());
+ if (status != 0) {
+ logger.debug("Set of reactions different");
+ return status;
+ }
+
+ status = compareLayouts(arg0.getLayouts(), arg1.getLayouts());
+ if (status != 0) {
+ logger.debug("Set of layouts different");
+ return status;
+ }
+
+ status = compareSubmodels(arg0.getSubmodelConnections(), arg1.getSubmodelConnections());
+ if (status != 0) {
+ logger.debug("Set of submodels different");
+ return status;
+ }
+
+ status = integerComparator.compare(arg0.getDataMiningSets().size(), arg1.getDataMiningSets().size());
+ if (status != 0) {
+ logger.debug("Set of data mining sets different");
+ return status;
+ }
+ DataMiningSetComparator dataMiningSetComparator = new DataMiningSetComparator();
+ for (int i = 0; i < arg0.getDataMiningSets().size(); i++) {
+ status = dataMiningSetComparator.compare(arg0.getDataMiningSets().get(i), arg1.getDataMiningSets().get(i));
+ if (status != 0) {
+ logger.debug("Set of data mining sets different");
+ return status;
+ }
+
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two set of reactions.
+ *
+ * @param reactions
+ * first set of reactions
+ * @param reactions2
+ * second set of reactions
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareReaction(Set<Reaction> reactions, Set<Reaction> reactions2) {
+ ReactionComparator comparator = new ReactionComparator(epsilon);
+
+ Map<String, Reaction> map = new HashMap<String, Reaction>();
+ Map<String, Reaction> map2 = new HashMap<String, Reaction>();
+
+ for (Reaction reaction : reactions) {
+ map.put(reaction.getIdReaction(), reaction);
+ }
+ for (Reaction reaction : reactions2) {
+ map2.put(reaction.getIdReaction(), reaction);
+ }
+
+ for (Reaction reaction : reactions) {
+ int status = comparator.compare(reaction, map2.get(reaction.getIdReaction()));
+ if (status != 0) {
+ logger.debug("Different reaction " + reaction.getIdReaction() + ": " + map2.get(reaction.getIdReaction()));
+ return status;
+ }
+ }
+
+ for (Reaction reaction : reactions2) {
+ int status = comparator.compare(reaction, map.get(reaction.getIdReaction()));
+ if (status != 0) {
+ logger.debug("Different reaction " + reaction.getIdReaction());
+ return status;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of layers.
+ *
+ * @param layers
+ * first set of layers
+ * @param layers2
+ * second set of layers
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareLayers(Set<Layer> layers, Set<Layer> layers2) {
+ LayerComparator layerComparator = new LayerComparator(epsilon);
+ for (Layer layer : layers) {
+ boolean found = false;
+ for (Layer layer2 : layers2) {
+ if (layerComparator.compare(layer, layer2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return 1;
+ }
+ }
+ for (Layer layer : layers2) {
+ boolean found = false;
+ for (Layer layer2 : layers) {
+ if (layerComparator.compare(layer, layer2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return -1;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of layouts.
+ *
+ * @param layouts
+ * first set of layouts
+ * @param layouts2
+ * second set of layouts
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareLayouts(List<Layout> layouts, List<Layout> layouts2) {
+ LayoutComparator layoutComparator = new LayoutComparator(epsilon);
+ for (Layout layout : layouts) {
+ boolean found = false;
+ for (Layout layout2 : layouts2) {
+ if (layoutComparator.compare(layout, layout2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return 1;
+ }
+ }
+ for (Layout layout : layouts2) {
+ boolean found = false;
+ for (Layout layout2 : layouts) {
+ if (layoutComparator.compare(layout, layout2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return -1;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of elements.
+ *
+ * @param elements
+ * first set of elements
+ * @param elements2
+ * second set of elements
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareElements(Set<Element> elements, Set<Element> elements2) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ if (elements.size() != elements2.size()) {
+ logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
+ return ((Integer) elements.size()).compareTo(elements2.size());
+ }
+
+ for (Element element : elements) {
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : elements2) {
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : elements) {
+ int status = elementComparator.compare(element, map2.get(element.getElementId()));
+ if (status != 0) {
+ logger
+ .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
+ return status;
+ }
+ }
+
+ for (Element element : elements2) {
+ int status = elementComparator.compare(element, map1.get(element.getElementId()));
+ if (status != 0) {
+ logger
+ .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
+ return status;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two collection of models.
+ *
+ * @param collection1
+ * first collection to compare
+ * @param collection2
+ * second collection to compare
+ * @return 0 if the collections are identical, -1/1 otherwise
+ */
+ private int compareSubmodels(Collection<ModelSubmodelConnection> collection1,
+ Collection<ModelSubmodelConnection> collection2) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ if (integerComparator.compare(collection1.size(), collection2.size()) != 0) {
+ logger.debug("collection of submodels doesn't match: " + collection1.size() + ", " + collection2.size());
+ return integerComparator.compare(collection1.size(), collection2.size());
+ }
+ ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator(epsilon);
+ for (ModelSubmodelConnection submodel1 : collection1) {
+ boolean found = false;
+ for (ModelSubmodelConnection submodel2 : collection2) {
+ ModelData parent1 = submodel1.getParentModel();
+ submodel1.setParentModel((ModelData) null);
+ ModelData parent2 = submodel2.getParentModel();
+ submodel2.setParentModel((ModelData) null);
+
+ if (comparator.compare(submodel1, submodel2) == 0) {
+ found = true;
+ }
+ submodel1.setParentModel(parent1);
+ submodel2.setParentModel(parent2);
+ if (found) {
+ break;
+ }
+ }
+ if (!found) {
+ logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the second model");
+ return 1;
+ }
+ }
+
+ for (ModelSubmodelConnection submodel1 : collection2) {
+ boolean found = false;
+ for (ModelSubmodelConnection submodel2 : collection1) {
+ ModelData parent1 = submodel1.getParentModel();
+ submodel1.setParentModel((ModelData) null);
+ ModelData parent2 = submodel2.getParentModel();
+ submodel2.setParentModel((ModelData) null);
+
+ if (comparator.compare(submodel1, submodel2) == 0) {
+ found = true;
+ }
+ submodel1.setParentModel(parent1);
+ submodel2.setParentModel(parent2);
+ if (found) {
+ break;
+ }
+ }
+ if (!found) {
+ logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the first model");
+ return -1;
+ }
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
index a92d69f28aa37ed4614e4d9b9ecaa4bd8ca92c30..f6dff4bdb97f94f8f19e058e72c738d18c7ed876 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
@@ -1,11 +1,10 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Comparator;
+import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import org.apache.log4j.Logger;
-
/**
* This class implements comparator interface for
* {@link ModelSubmodelConnection}.
@@ -13,95 +12,62 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class ModelSubmodelConnectionComparator implements Comparator<ModelSubmodelConnection> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ModelSubmodelConnectionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ModelSubmodelConnectionComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ModelSubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
+public class ModelSubmodelConnectionComparator extends Comparator<ModelSubmodelConnection> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ModelSubmodelConnectionComparator.class);
- @Override
- public int compare(ModelSubmodelConnection arg0, ModelSubmodelConnection arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ModelSubmodelConnectionComparator(double epsilon) {
+ super(ModelSubmodelConnection.class);
+ this.epsilon = epsilon;
+ }
- /**
- * This method compares only the fields that are defined in
- * {@link ModelSubmodelConnection} class in inheritence tree. It also calls
- * the {@link SubmodelConnectionComparator} for the super class (
- * {@link SubmodelConnection}).
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- protected int internalCompare(ModelSubmodelConnection arg0, ModelSubmodelConnection arg1) {
+ /**
+ * Default constructor.
+ */
+ public ModelSubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
- SubmodelConnectionComparator superComparator = new SubmodelConnectionComparator(epsilon);
- int result = superComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SubmodelConnectionComparator(epsilon);
+ }
- ModelComparator comparator = new ModelComparator(epsilon);
+ @Override
+ protected int internalCompare(ModelSubmodelConnection arg0, ModelSubmodelConnection arg1) {
+ ModelComparator comparator = new ModelComparator(epsilon);
- if (arg0.getParentModel() != null && arg1.getParentModel() != null) {
- int status = comparator.compare(arg0.getParentModel().getModel(), arg1.getParentModel().getModel());
- if (status != 0) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return status;
- }
- } else {
- if (arg0.getParentModel() != null) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return -1;
- }
- if (arg1.getParentModel() != null) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return 1;
- }
- }
+ if (arg0.getParentModel() != null && arg1.getParentModel() != null) {
+ int status = comparator.compare(arg0.getParentModel().getModel(), arg1.getParentModel().getModel());
+ if (status != 0) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return status;
+ }
+ } else {
+ if (arg0.getParentModel() != null) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return -1;
+ }
+ if (arg1.getParentModel() != null) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return 1;
+ }
+ }
- return 0;
- }
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
index b4227814d436ef0bdacf79958c5e0a820009a59c..9fc00be4322af6568f0990aefb59de5b3a1dff7e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements comparator interface for {@link SubmodelConnection}. It
@@ -15,136 +13,89 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class SubmodelConnectionComparator implements Comparator<SubmodelConnection> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(SubmodelConnection.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SubmodelConnectionComparator(double epsilon) {
- this.epsilon = epsilon;
- modelSubmodelConnectionComparator = new ModelSubmodelConnectionComparator(epsilon);
- elementSubmodelConnectionComparator = new ElementSubmodelConnectionComparator(epsilon);
- }
-
- /**
- * Comparator used to compare {@link ModelSubmodelConnection} subclasses.
- */
- private ModelSubmodelConnectionComparator modelSubmodelConnectionComparator = null;
-
- /**
- * Comparator used to compare {@link ElementSubmodelConnection} subclasses.
- */
- private ElementSubmodelConnectionComparator elementSubmodelConnectionComparator = null;
-
- /**
- * Default constructor.
- */
- public SubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link SubmodelConnection} class in inheritence tree. It should be called
- * by the super class comparators, like
- * {@link ModelSubmodelConnectionComparator} and
- * {@link ElementSubmodelConnectionComparator}.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- protected int internalCompare(SubmodelConnection arg0, SubmodelConnection arg1) {
- StringComparator stringComparator = new StringComparator();
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (arg0.getType() == null && arg1.getType() != null) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return -1;
- }
- if (arg0.getType() != null) {
- if (arg1.getType() == null) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return -1;
- }
- if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return arg0.getType().compareTo(arg1.getType());
- }
- }
-
- ModelComparator modelComparator = new ModelComparator(epsilon);
- if (arg0.getSubmodel() != null && arg1.getSubmodel() != null) {
- int status = modelComparator.compare(arg0.getSubmodel().getModel(), arg1.getSubmodel().getModel());
- if (status != 0) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return status;
- }
- } else {
- if (arg0.getSubmodel() != null) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return 1;
- }
- if (arg1.getSubmodel() != null) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return -1;
- }
- }
-
- return 0;
- }
-
- @Override
- public int compare(SubmodelConnection arg0, SubmodelConnection arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof ModelSubmodelConnection) {
- return modelSubmodelConnectionComparator.compare((ModelSubmodelConnection) arg0, (ModelSubmodelConnection) arg1);
- } else if (arg0 instanceof ElementSubmodelConnection) {
- return elementSubmodelConnectionComparator.compare((ElementSubmodelConnection) arg0, (ElementSubmodelConnection) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
+public class SubmodelConnectionComparator extends Comparator<SubmodelConnection> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(SubmodelConnection.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SubmodelConnectionComparator(double epsilon) {
+ super(SubmodelConnection.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new ModelSubmodelConnectionComparator(epsilon));
+ addSubClassComparator(new ElementSubmodelConnectionComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(SubmodelConnection arg0, SubmodelConnection arg1) {
+ StringComparator stringComparator = new StringComparator();
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (arg0.getType() == null && arg1.getType() != null) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return -1;
+ }
+ if (arg0.getType() != null) {
+ if (arg1.getType() == null) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return -1;
+ }
+ if (arg0.getType().compareTo(arg1.getType()) != 0) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return arg0.getType().compareTo(arg1.getType());
+ }
+ }
+
+ ModelComparator modelComparator = new ModelComparator(epsilon);
+ if (arg0.getSubmodel() != null && arg1.getSubmodel() != null) {
+ int status = modelComparator.compare(arg0.getSubmodel().getModel(), arg1.getSubmodel().getModel());
+ if (status != 0) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return status;
+ }
+ } else {
+ if (arg0.getSubmodel() != null) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return 1;
+ }
+ if (arg1.getSubmodel() != null) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return -1;
+ }
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
index c51dee52a746d420d5c04c19f39fe0aec62622dd..693855bee60c6b07afb6e7f559f8c58aac4dc2b4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.model.map.reaction;
-import java.util.Comparator;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidClassException;
@@ -15,7 +15,7 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class AbstractNodeComparator implements Comparator<AbstractNode> {
+public class AbstractNodeComparator extends Comparator<AbstractNode> {
/**
* Default class logger.
*/
@@ -33,7 +33,10 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
* {@link #epsilon}
*/
public AbstractNodeComparator(double epsilon) {
+ super(AbstractNode.class, true);
this.epsilon = epsilon;
+ addSubClassComparator(new NodeOperatorComparator(epsilon));
+ addSubClassComparator(new ReactionNodeComparator(epsilon));
}
/**
@@ -44,46 +47,6 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
}
@Override
- public int compare(AbstractNode arg0, AbstractNode arg1) {
- // check null values
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- // now check class types
- if (arg0.getClass().equals(arg1.getClass())) {
- // and call comparator of appropriate subclass
- if (arg0 instanceof NodeOperator) {
- NodeOperatorComparator nodeOperatorComparator = new NodeOperatorComparator(epsilon);
- return nodeOperatorComparator.compare((NodeOperator) arg0, (NodeOperator) arg1);
- } else if (arg0 instanceof ReactionNode) {
- ReactionNodeComparator reactionNodeComparator = new ReactionNodeComparator(epsilon);
- return reactionNodeComparator.compare((ReactionNode) arg0, (ReactionNode) arg1);
- } else {
- throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in AbstractNode class
- * in inheritance tree. By the design it is called by subclass comparator.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are equal then returns 0. If they are different then
- * -1/1 is returned.
- */
protected int internalCompare(AbstractNode arg0, AbstractNode arg1) {
PolylineDataComparator pdComparator = new PolylineDataComparator(epsilon);
if (pdComparator.compare(arg0.getLine(), arg1.getLine()) != 0) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
index 97b0927379243605a7051b4ffb0ae52ab659fc19..cbe96d36925f9deba6a9a9b0e55221763c8655ff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.model.map.reaction;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
@@ -15,121 +14,88 @@ import lcsb.mapviewer.common.comparator.IntegerComparator;
* @author Piotr Gawron
*
*/
-public class NodeOperatorComparator implements Comparator<NodeOperator> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(NodeOperatorComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public NodeOperatorComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public NodeOperatorComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(NodeOperator arg0, NodeOperator arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("Different classes.");
- return -1;
- }
- }
-
- /**
- * This method compare all fields of two node operators and return 0 if they
- * are the same or 1/-1 if the objects are different. Also comparator for
- * super class ({@link AbstractNode}) is called.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return 0 if objects are equal,<br>
- * -1/1 otherwise
- */
-
- private int internalCompare(NodeOperator arg0, NodeOperator arg1) {
- AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
-
- int result = anComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- logger.debug("Different Abstract Nodes: " + arg0 + ", " + arg1);
- return result;
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size()) != 0) {
- logger.debug("Different input size: " + arg0.getInputs().size() + ", " + arg1.getInputs().size());
- return integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size());
- }
- if (integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size()) != 0) {
- logger.debug("Different output size: " + arg0.getOutputs().size() + ", " + arg1.getOutputs().size());
- return integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size());
- }
-
- for (int i = 0; i < arg0.getInputs().size(); i++) {
- AbstractNode node1 = arg0.getInputs().get(i);
- int status = -1;
- for (int j = 0; j < arg1.getInputs().size(); j++) {
- AbstractNode node2 = arg1.getInputs().get(j);
- int tmpStatus = anComparator.compare(node1, node2);
- if (tmpStatus == 0) {
- status = 0;
- break;
- }
- }
- if (status != 0) {
- logger.debug("Can't find match in inputs.");
- return status;
- }
- }
- for (int i = 0; i < arg0.getOutputs().size(); i++) {
- AbstractNode node1 = arg0.getOutputs().get(i);
- int status = -1;
- for (int j = 0; j < arg1.getOutputs().size(); j++) {
- AbstractNode node2 = arg1.getOutputs().get(j);
- int tmpStatus = anComparator.compare(node1, node2);
- if (tmpStatus == 0) {
- status = 0;
- break;
- }
- }
- if (status != 0) {
- logger.debug("Can't find match in outputs.");
- return status;
- }
- }
-
- return 0;
- }
+public class NodeOperatorComparator extends Comparator<NodeOperator> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(NodeOperatorComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public NodeOperatorComparator(double epsilon) {
+ super(NodeOperator.class);
+ this.epsilon = epsilon;
+ }
+
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public NodeOperatorComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(NodeOperator arg0, NodeOperator arg1) {
+ AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
+
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size()) != 0) {
+ logger.debug("Different input size: " + arg0.getInputs().size() + ", " + arg1.getInputs().size());
+ return integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size());
+ }
+ if (integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size()) != 0) {
+ logger.debug("Different output size: " + arg0.getOutputs().size() + ", " + arg1.getOutputs().size());
+ return integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size());
+ }
+
+ for (int i = 0; i < arg0.getInputs().size(); i++) {
+ AbstractNode node1 = arg0.getInputs().get(i);
+ int status = -1;
+ for (int j = 0; j < arg1.getInputs().size(); j++) {
+ AbstractNode node2 = arg1.getInputs().get(j);
+ int tmpStatus = anComparator.compare(node1, node2);
+ if (tmpStatus == 0) {
+ status = 0;
+ break;
+ }
+ }
+ if (status != 0) {
+ logger.debug("Can't find match in inputs.");
+ return status;
+ }
+ }
+ for (int i = 0; i < arg0.getOutputs().size(); i++) {
+ AbstractNode node1 = arg0.getOutputs().get(i);
+ int status = -1;
+ for (int j = 0; j < arg1.getOutputs().size(); j++) {
+ AbstractNode node2 = arg1.getOutputs().get(j);
+ int tmpStatus = anComparator.compare(node1, node2);
+ if (tmpStatus == 0) {
+ status = 0;
+ break;
+ }
+ }
+ if (status != 0) {
+ logger.debug("Can't find match in outputs.");
+ return status;
+ }
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 78691472086ea094781e84009280198703156401..eb812a44ed20d709da02458ba92e4e609c846d39 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -1,11 +1,11 @@
package lcsb.mapviewer.model.map.reaction;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -14,6 +14,7 @@ import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringListComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
/**
* This class implements comparator interface for {@link Reaction}.
@@ -21,7 +22,7 @@ import lcsb.mapviewer.model.map.MiriamData;
* @author Piotr Gawron
*
*/
-public class ReactionComparator implements Comparator<Reaction> {
+public class ReactionComparator extends Comparator<Reaction> {
/**
* Default class logger.
*/
@@ -39,6 +40,7 @@ public class ReactionComparator implements Comparator<Reaction> {
* {@link #epsilon}
*/
public ReactionComparator(double epsilon) {
+ super(Reaction.class);
this.epsilon = epsilon;
}
@@ -50,37 +52,7 @@ public class ReactionComparator implements Comparator<Reaction> {
}
@Override
- public int compare(Reaction arg0, Reaction arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("Different class: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Reaction}
- * class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(Reaction arg0, Reaction arg1) {
+ protected int internalCompare(Reaction arg0, Reaction arg1) {
StringComparator stringComparator = new StringComparator();
BooleanComparator booleanComparator = new BooleanComparator();
AbstractNodeComparator aNodeComparator = new AbstractNodeComparator(epsilon);
@@ -202,6 +174,11 @@ public class ReactionComparator implements Comparator<Reaction> {
}
}
+ SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
+ if (kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics()) != 0) {
+ logger.debug("Kinetics different");
+ return kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics());
+ }
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
index 5c22f844761ec30af1c7402ed80d0cfbbeb73e66..7abecd825ce3a0932e7c9b28dbec1a1940e7eefc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.model.map.reaction;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.species.ElementComparator;
@@ -15,80 +14,54 @@ import lcsb.mapviewer.model.map.species.ElementComparator;
* @author Piotr Gawron
*
*/
-public class ReactionNodeComparator implements Comparator<ReactionNode> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ReactionNodeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
+public class ReactionNodeComparator extends Comparator<ReactionNode> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ReactionNodeComparator.class);
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ReactionNodeComparator(double epsilon) {
- this.epsilon = epsilon;
- }
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
- /**
- * Default constructor.
- */
- public ReactionNodeComparator() {
- this(Configuration.EPSILON);
- }
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ReactionNodeComparator(double epsilon) {
+ super(ReactionNode.class);
+ this.epsilon = epsilon;
+ }
- @Override
- public int compare(ReactionNode arg0, ReactionNode arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon);
+ }
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("Different classes.");
- return -1;
- }
- }
+ /**
+ * Default constructor.
+ */
+ public ReactionNodeComparator() {
+ this(Configuration.EPSILON);
+ }
- /**
- * This method compare all fields of two node operators and return 0 if they
- * are the same or 1/-1 if the objects are different. Also comparator for
- * super class ({@link AbstractNode}) is called.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return 0 if objects are equal,<br>
- * -1/1 otherwise
- */
- private int internalCompare(ReactionNode arg0, ReactionNode arg1) {
- AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
- ElementComparator elementComparator = new ElementComparator(epsilon);
+ @Override
+ protected int internalCompare(ReactionNode arg0, ReactionNode arg1) {
+ AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
- int result = anComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
+ int result = anComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
- if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
- logger.debug("Element different");
- return elementComparator.compare(arg0.getElement(), arg1.getElement());
- }
+ if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
+ logger.debug("Element different");
+ return elementComparator.compare(arg0.getElement(), arg1.getElement());
+ }
- return 0;
- }
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index e5c2a69cfba58e0b861e9cf25481313289cb5a36..95e2a358541cc7f2eec77865c0aeb23607793708 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
/**
@@ -17,94 +16,61 @@ import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
* @author Piotr Gawron
*
*/
-public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public AntisenseRnaComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public AntisenseRnaComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(AntisenseRna arg0, AntisenseRna arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(AntisenseRna.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link AntisenseRna} class in inheritence tree. By the design it calls also
- * comparator of the upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<String>();
- Set<String> set2 = new HashSet<String>();
-
- for (AntisenseRnaRegion region : arg0.getRegions()) {
- set1.add(region.toString());
- }
-
- for (AntisenseRnaRegion region : arg1.getRegions()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
+public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AntisenseRnaComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public AntisenseRnaComparator(double epsilon) {
+ super(AntisenseRna.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AntisenseRnaComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<String>();
+ Set<String> set2 = new HashSet<String>();
+
+ for (AntisenseRnaRegion region : arg0.getRegions()) {
+ set1.add(region.toString());
+ }
+
+ for (AntisenseRnaRegion region : arg1.getRegions()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
index ec844f1f271432853edebf005b0b110e4c7af641..14601f6a0fd3a43105361382ad16c51afa64e999 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
@@ -1,12 +1,10 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Chemical} objects.
@@ -14,107 +12,62 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class ChemicalComparator implements Comparator<Chemical> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ChemicalComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Comparator for {@link Ion} implementation of {@link Chemical}.
- */
- private IonComparator ionComparator;
-
- /**
- * Comparator for {@link SimpleMolecule} implementation of {@link Chemical}.
- */
- private SimpleMoleculeComparator simpleMoleculeComparator;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ChemicalComparator(double epsilon) {
- this.epsilon = epsilon;
- ionComparator = new IonComparator(epsilon);
- simpleMoleculeComparator = new SimpleMoleculeComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public ChemicalComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Chemical arg0, Chemical arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Ion.class)) {
- return ionComparator.compare((Ion) arg0, (Ion) arg1);
- } else if (arg0.getClass().equals(SimpleMolecule.class)) {
- return simpleMoleculeComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Chemical}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- int internalCompare(Chemical arg0, Chemical arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
- logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
- return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
- }
-
- if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
- logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
- return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
- }
-
- if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
- logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
- return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
- }
-
- return 0;
- }
+public class ChemicalComparator extends Comparator<Chemical> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ChemicalComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ChemicalComparator(double epsilon) {
+ super(Chemical.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new IonComparator(epsilon));
+ addSubClassComparator(new SimpleMoleculeComparator(epsilon));
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ChemicalComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Chemical arg0, Chemical arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
+ logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
+ return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
+ }
+
+ if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
+ logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
+ return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
+ }
+
+ if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
+ logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
+ return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index e7a29c9ddbc43e583a4808e471c4c316c05cae8b..b452ec2ceac2ebdf836befe1ed5b4c910505e1c1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -1,16 +1,15 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements comparator interface for {@link Complex}.
@@ -18,117 +17,84 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class ComplexComparator implements Comparator<Complex> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ComplexComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ComplexComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ComplexComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Complex arg0, Complex arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Complex.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Complex}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Complex arg0, Complex arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- ElementComparator elementComparator = new ElementComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
- logger.debug("children elements size different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
- return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
- }
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- for (Element element : arg0.getElements()) {
- if (map1.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : arg1.getElements()) {
- if (map2.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : arg0.getElements()) {
- Element element2 = map2.get(element.getElementId());
- int status = elementComparator.compare(element, element2);
- if (status != 0) {
- logger.debug("child doesn't have a match: " + element.getElementId());
- return status;
- }
- }
-
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
- logger.debug("Species structuralState different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
- }
-
- return 0;
- }
+public class ComplexComparator extends Comparator<Complex> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ComplexComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ComplexComparator(double epsilon) {
+ super(Complex.class, true);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ComplexComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Complex arg0, Complex arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
+ logger.debug("children elements size different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
+ }
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
+ if (status != 0) {
+ logger.debug("child doesn't have a match: " + element.getElementId());
+ return status;
+ }
+ }
+
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ logger
+ .debug("Species structuralState different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
+ return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
index e7161064267021662914e55ac0c1fc7e346a1bce..51333b2e03ff566ce3ff47b8d304e923ea342aae 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Degraded} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class DegradedComparator implements Comparator<Degraded> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DegradedComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DegradedComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public DegradedComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Degraded arg0, Degraded arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Degraded.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Degraded}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Degraded arg0, Degraded arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class DegradedComparator extends Comparator<Degraded> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DegradedComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DegradedComparator(double epsilon) {
+ super(Degraded.class, true);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DegradedComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Degraded arg0, Degraded arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
index 3732d4c347db1d63d8e8129ee733aa586f49cedd..7f0173f5f44056acb09d8ee849a8953f67147556 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Drug} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class DrugComparator implements Comparator<Drug> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DrugComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public DrugComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Drug arg0, Drug arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Drug.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Drug} class
- * in inheritence tree. By the design it calls also comparator of the upper (
- * {@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Drug arg0, Drug arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class DrugComparator extends Comparator<Drug> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DrugComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DrugComparator(double epsilon) {
+ super(Drug.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DrugComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Drug arg0, Drug arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index a462b0538a649343670dab32c89c2862997da132..098c7d1f679bea0fb9e0d617ad77d2e4dd745f09 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -1,20 +1,19 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.ColorComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringListComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
@@ -24,218 +23,181 @@ import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
* @author Piotr Gawron
*
*/
-public class ElementComparator implements Comparator<Element> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ElementComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ElementComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ElementComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Element arg0, Element arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof Complex) {
- ComplexComparator caComparator = new ComplexComparator(epsilon);
- return caComparator.compare((Complex) arg0, (Complex) arg1);
- } else if (arg0 instanceof Compartment) {
- CompartmentComparator caComparator = new CompartmentComparator(epsilon);
- return caComparator.compare((Compartment) arg0, (Compartment) arg1);
- } else if (arg0 instanceof Species) {
- SpeciesComparator caComparator = new SpeciesComparator(epsilon);
- return caComparator.compare((Species) arg0, (Species) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- logger.debug("Mismatch class type: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Element}
- * class in inheritence tree. By the design it is called by subclass
- * comparator.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(Element arg0, Element arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- StringComparator stringComparator = new StringComparator();
- IntegerComparator integerComparator = new IntegerComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
-
- if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
- logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
- return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- logger.debug("X different: " + arg0.getX() + ", " + arg1.getX());
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- logger.debug("Y different: " + arg0.getY() + ", " + arg1.getY());
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- logger.debug("Font size different: " + arg0.getFontSize() + ", " + arg1.getFontSize());
- return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
- }
-
- if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
- logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
- return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
- }
-
- if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
- logger.debug("Color different: " + arg0.getColor().getRGB() + ", " + arg1.getColor().getRGB());
- return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
- }
-
- // this should be somehow modified, because it can create a situation where
- // comparison will fall into infinite loop (in cyclic submodels)
- ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
- int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
- if (status != 0) {
- logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return status;
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
- logger.debug("notes different: \n\"" + arg0.getNotes() + "\"\n\"" + arg1.getNotes() + "\"");
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
- }
-
- if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
- logger.debug("symbol different: \"" + arg0.getSymbol() + "\", \"" + arg1.getSymbol() + "\"");
- return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
- }
-
- if (stringComparator.compare(arg0.getFullName(), arg1.getFullName()) != 0) {
- logger.debug("full name different: \"" + arg0.getFullName() + "\", \"" + arg1.getFullName() + "\"");
- return stringComparator.compare(arg0.getFullName(), arg1.getFullName());
- }
-
- if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
- logger.debug("Abbreviation different: \"" + arg0.getAbbreviation() + "\", \"" + arg1.getAbbreviation() + "\"");
- return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
- }
-
- if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
- logger.debug("formula different: \"" + arg0.getFormula() + "\", \"" + arg1.getFormula() + "\"");
- return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
- StringListComparator stringListComparator = new StringListComparator();
-
- if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
- logger.debug("List of synonyms different");
- return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
- }
-
- if (stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols()) != 0) {
- logger.debug("List of former symbols different");
- return stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols());
- }
-
- Set<String> hashCode1 = new HashSet<>();
- Set<String> hashCode2 = new HashSet<>();
-
- if (arg0.getMiriamData().size() != arg1.getMiriamData().size()) {
- logger.debug("different number of annotations: " + arg0.getMiriamData().size() + ", " + arg1.getMiriamData().size());
- return ((Integer) arg0.getMiriamData().size()).compareTo(arg1.getMiriamData().size());
- }
-
- for (MiriamData md : arg0.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode1.add(hash);
- }
-
- for (MiriamData md : arg1.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode2.add(hash);
- }
-
- if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
- logger.debug("different annotations: ");
- logger.debug("A:");
- for (String string : hashCode1) {
- logger.debug("|" + string + "|");
- }
- logger.debug("B:");
- for (String string : hashCode2) {
- logger.debug("|" + string + "|");
- }
- logger.debug("--");
- return stringSetComparator.compare(hashCode1, hashCode2);
-
- }
-
- return 0;
- }
+public class ElementComparator extends Comparator<Element> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ElementComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ElementComparator(double epsilon) {
+ super(Element.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new ComplexComparator(epsilon));
+ addSubClassComparator(new CompartmentComparator(epsilon));
+ addSubClassComparator(new SpeciesComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ElementComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Element arg0, Element arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ StringComparator stringComparator = new StringComparator();
+ ColorComparator colorComparator = new ColorComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+
+ if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
+ logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
+ return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ logger.debug("X different: " + arg0.getX() + ", " + arg1.getX());
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ logger.debug("Y different: " + arg0.getY() + ", " + arg1.getY());
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
+ logger.debug("Font size different: " + arg0.getFontSize() + ", " + arg1.getFontSize());
+ return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+ }
+
+ if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
+ logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
+ return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ logger.debug("Color different: " + arg0.getColor() + ", " + arg1.getColor());
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ // this should be somehow modified, because it can create a situation where
+ // comparison will fall into infinite loop (in cyclic submodels)
+ ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
+ int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
+ if (status != 0) {
+ logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return status;
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
+ logger.debug("notes different: \n\"" + arg0.getNotes() + "\"\n\"" + arg1.getNotes() + "\"");
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ }
+
+ if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
+ logger.debug("symbol different: \"" + arg0.getSymbol() + "\", \"" + arg1.getSymbol() + "\"");
+ return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
+ }
+
+ if (stringComparator.compare(arg0.getFullName(), arg1.getFullName()) != 0) {
+ logger.debug("full name different: \"" + arg0.getFullName() + "\", \"" + arg1.getFullName() + "\"");
+ return stringComparator.compare(arg0.getFullName(), arg1.getFullName());
+ }
+
+ if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
+ logger.debug("Abbreviation different: \"" + arg0.getAbbreviation() + "\", \"" + arg1.getAbbreviation() + "\"");
+ return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
+ }
+
+ if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
+ logger.debug("formula different: \"" + arg0.getFormula() + "\", \"" + arg1.getFormula() + "\"");
+ return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
+ }
+
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ StringListComparator stringListComparator = new StringListComparator();
+
+ if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
+ logger.debug("List of synonyms different");
+ return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
+ }
+
+ if (stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols()) != 0) {
+ logger.debug("List of former symbols different");
+ return stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols());
+ }
+
+ Set<String> hashCode1 = new HashSet<>();
+ Set<String> hashCode2 = new HashSet<>();
+
+ if (arg0.getMiriamData().size() != arg1.getMiriamData().size()) {
+ logger.debug(
+ "different number of annotations: " + arg0.getMiriamData().size() + ", " + arg1.getMiriamData().size());
+ return ((Integer) arg0.getMiriamData().size()).compareTo(arg1.getMiriamData().size());
+ }
+
+ for (MiriamData md : arg0.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode1.add(hash);
+ }
+
+ for (MiriamData md : arg1.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode2.add(hash);
+ }
+
+ if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
+ logger.debug("different annotations: ");
+ logger.debug("A:");
+ for (String string : hashCode1) {
+ logger.debug("|" + string + "|");
+ }
+ logger.debug("B:");
+ for (String string : hashCode2) {
+ logger.debug("|" + string + "|");
+ }
+ logger.debug("--");
+ return stringSetComparator.compare(hashCode1, hashCode2);
+
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index 044e7f059f66da106463734a55716c220b541bb8..89b0aa38e0296cdd2206d121d925d35e6fafbfc5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
@@ -17,95 +16,61 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
* @author Piotr Gawron
*
*/
-public class GeneComparator implements Comparator<Gene> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public GeneComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public GeneComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Gene arg0, Gene arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Gene.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Gene} class
- * in inheritence tree. By the design it calls also comparator of the upper (
- * {@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Gene arg0, Gene arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getModificationResidues()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getModificationResidues()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
+public class GeneComparator extends Comparator<Gene> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GeneComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public GeneComparator(double epsilon) {
+ super(Gene.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public GeneComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Gene arg0, Gene arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getModificationResidues()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getModificationResidues()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
index ce6e0c5c2cafa37934e9ace0ccfda9b2a9d27eb8..694a41e8d6a7d61785e84aa63f9a088f31f9f937 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link GenericProtein} objects.
@@ -13,78 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class GenericProteinComparator implements Comparator<GenericProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GenericProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public GenericProteinComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public GenericProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(GenericProtein arg0, GenericProtein arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(GenericProtein.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link GenericProtein} class in inheritence tree. By the design it
- * calls also comparator of the upper ({@link Protein}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(GenericProtein arg0, GenericProtein arg1) {
- ProteinComparator proteinComparator = new ProteinComparator(epsilon);
- int result = proteinComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class GenericProteinComparator extends Comparator<GenericProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GenericProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public GenericProteinComparator(double epsilon) {
+ super(GenericProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public GenericProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(GenericProtein arg0, GenericProtein arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
index 8f6c3f4b8a27d76c615cf75f445f9bc18c98327d..3fead0056fb3b28bfca446c01f83c48cfe18ca5e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link IonChannelProtein} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class IonChannelProteinComparator implements Comparator<IonChannelProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonChannelProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public IonChannelProteinComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public IonChannelProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(IonChannelProtein arg0, IonChannelProtein arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(IonChannelProtein.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link IonChannelProtein} class in inheritence tree. By the design it calls
- * also comparator of the upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class IonChannelProteinComparator extends Comparator<IonChannelProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(IonChannelProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public IonChannelProteinComparator(double epsilon) {
+ super(IonChannelProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public IonChannelProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
index 365f5de9f8fe5995b90e9b62e3c07410f005e194..d1a1f8ec3be548b36c65edd88d1a410ee4749a3a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Ion} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class IonComparator implements Comparator<Ion> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public IonComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public IonComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Ion arg0, Ion arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Ion.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Ion} class
- * in inheritence tree. By the design it calls also comparator of the upper
- * {@link Chemical} class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Ion arg0, Ion arg1) {
- ChemicalComparator speciesComparator = new ChemicalComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class IonComparator extends Comparator<Ion> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(IonComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public IonComparator(double epsilon) {
+ super(Ion.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public IonComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ChemicalComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Ion arg0, Ion arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
index 8b7af90f58594eaffed7cd61baff51b04a13f3b2..93be6412390919aa06374fc459ac8b38a4e1c840 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Phenotype} objects.
@@ -13,77 +11,45 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class PhenotypeComparator implements Comparator<Phenotype> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public PhenotypeComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public PhenotypeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Phenotype arg0, Phenotype arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Phenotype.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Phenotype}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Phenotype arg0, Phenotype arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class PhenotypeComparator extends Comparator<Phenotype> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PhenotypeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public PhenotypeComparator(double epsilon) {
+ super(Phenotype.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PhenotypeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+
+ @Override
+ protected int internalCompare(Phenotype arg0, Phenotype arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index 53cee7bdba96b9f0268509e390073158ab466fb7..b397b9b4f3b38f956c0a93a9232b45cc6e9e5fb8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -1,15 +1,14 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
@@ -18,131 +17,71 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
* @author Piotr Gawron
*
*/
-public class ProteinComparator implements Comparator<Protein> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Comparator for {@link GenericProtein} implementation of {@link Protein}.
- */
- private GenericProteinComparator genericProteinComparator;
-
- /**
- * Comparator for {@link IonChannelProtein} implementation of {@link Protein}.
- */
- private IonChannelProteinComparator ionChannelProteinComparator;
-
- /**
- * Comparator for {@link ReceptorProtein} implementation of {@link Protein}.
- */
- private ReceptorProteinComparator receptorProteinComparator;
-
- /**
- * Comparator for {@link TruncatedProtein} implementation of {@link Protein}.
- */
- private TruncatedProteinComparator truncatedProteinComparator;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ProteinComparator(double epsilon) {
- this.epsilon = epsilon;
- genericProteinComparator = new GenericProteinComparator(epsilon);
- ionChannelProteinComparator = new IonChannelProteinComparator(epsilon);
- receptorProteinComparator = new ReceptorProteinComparator(epsilon);
- truncatedProteinComparator = new TruncatedProteinComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public ProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Protein arg0, Protein arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(GenericProtein.class)) {
- return genericProteinComparator.compare((GenericProtein) arg0, (GenericProtein) arg1);
- } else if (arg0.getClass().equals(IonChannelProtein.class)) {
- return ionChannelProteinComparator.compare((IonChannelProtein) arg0, (IonChannelProtein) arg1);
- } else if (arg0.getClass().equals(ReceptorProtein.class)) {
- return receptorProteinComparator.compare((ReceptorProtein) arg0, (ReceptorProtein) arg1);
- } else if (arg0.getClass().equals(TruncatedProtein.class)) {
- return truncatedProteinComparator.compare((TruncatedProtein) arg0, (TruncatedProtein) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Protein}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- int internalCompare(Protein arg0, Protein arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- StringComparator stringComparator = new StringComparator();
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
- logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
- }
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getModificationResidues()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getModificationResidues()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.debug("modification residues different");
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
+public class ProteinComparator extends Comparator<Protein> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ProteinComparator(double epsilon) {
+ super(Protein.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new GenericProteinComparator(epsilon));
+ addSubClassComparator(new IonChannelProteinComparator(epsilon));
+ addSubClassComparator(new ReceptorProteinComparator(epsilon));
+ addSubClassComparator(new TruncatedProteinComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Protein arg0, Protein arg1) {
+ StringComparator stringComparator = new StringComparator();
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
+ return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ }
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getModificationResidues()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getModificationResidues()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug("modification residues different");
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
index 186498d9fc344c043ca46a0995ed35dec8e28873..8fef3d5d0c0db03c28cb7887ed00229111654ef9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link ReceptorProtein} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ReceptorProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ReceptorProteinComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ReceptorProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(ReceptorProtein arg0, ReceptorProtein arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ReceptorProtein.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link ReceptorProtein} class in inheritence tree. By the design it calls
- * also comparator of the upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
- ProteinComparator proteinComparator = new ProteinComparator(epsilon);
- int result = proteinComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class ReceptorProteinComparator extends Comparator<ReceptorProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ReceptorProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ReceptorProteinComparator(double epsilon) {
+ super(ReceptorProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ReceptorProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index 25f8e4de9bbef561513dc0df1ae16418407b2efc..a16fbb967e9cdc64cb31a4f67b8bb8aecb0c0f54 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -1,14 +1,13 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
@@ -17,95 +16,61 @@ import lcsb.mapviewer.model.map.species.field.RnaRegion;
* @author Piotr Gawron
*
*/
-public class RnaComparator implements Comparator<Rna> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public RnaComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public RnaComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Rna arg0, Rna arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Rna.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Rna} class
- * in inheritence tree. By the design it calls also comparator of the upper (
- * {@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Rna arg0, Rna arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (RnaRegion region : arg0.getRegions()) {
- set1.add(region.toString());
- }
-
- for (RnaRegion region : arg1.getRegions()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
+public class RnaComparator extends Comparator<Rna> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RnaComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public RnaComparator(double epsilon) {
+ super(Rna.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public RnaComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Rna arg0, Rna arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (RnaRegion region : arg0.getRegions()) {
+ set1.add(region.toString());
+ }
+
+ for (RnaRegion region : arg1.getRegions()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
index 776941b69814e3149d406cabace5b98f4479041d..ef10a99608a1c8a8c893dd680031b9a4c4cab191 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link SimpleMolecule} objects.
@@ -13,78 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SimpleMoleculeComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public SimpleMoleculeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(SimpleMolecule arg0, SimpleMolecule arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(SimpleMolecule.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link SimpleMolecule} class in inheritence tree. By the design it calls
- * also comparator of the upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
- ChemicalComparator chemicalComparator = new ChemicalComparator(epsilon);
- int result = chemicalComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- return 0;
- }
+public class SimpleMoleculeComparator extends Comparator<SimpleMolecule> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SimpleMoleculeComparator(double epsilon) {
+ super(SimpleMolecule.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SimpleMoleculeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ChemicalComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index c790a81e46fcdd8804b20a707db94e389894eefd..c3e6141b3b7c8a617dabd4e661ea7d8cfa2b5b3e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -1,15 +1,13 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Species} objects.
@@ -17,224 +15,126 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class SpeciesComparator implements Comparator<Species> {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SpeciesComparator.class);
-
- /**
- * Comparator for {@link AntisenseRna} implementation of {@link Species}.
- */
- private AntisenseRnaComparator antisenseRnaComparator;
-
- /**
- * Comparator for {@link Chemical} implementation of {@link Species}.
- */
- private ChemicalComparator chemicalComparator;
-
- /**
- * Comparator for {@link Complex} implementation of {@link Species}.
- */
- private ComplexComparator complexComparator;
-
- /**
- * Comparator for {@link Degraded} implementation of {@link Species}.
- */
- private DegradedComparator degradedComparator;
-
- /**
- * Comparator for {@link Drug} implementation of {@link Species}.
- */
- private DrugComparator drugComparator;
-
- /**
- * Comparator for {@link Gene} implementation of {@link Species}.
- */
- private GeneComparator geneComparator;
-
- /**
- * Comparator for {@link Phenotype} implementation of {@link Species}.
- */
- private PhenotypeComparator phenotypeComparator;
-
- /**
- * Comparator for {@link Protein} implementation of {@link Species}.
- */
- private ProteinComparator proteinComparator;
-
- /**
- * Comparator for {@link Rna} implementation of {@link Species}.
- */
- private RnaComparator rnaComparator;
-
- /**
- * Comparator for {@link Unknown} implementation of {@link Species}.
- */
- private UnknownComparator unknownComparator;
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SpeciesComparator(double epsilon) {
- this.epsilon = epsilon;
- antisenseRnaComparator = new AntisenseRnaComparator(epsilon);
- chemicalComparator = new ChemicalComparator(epsilon);
- complexComparator = new ComplexComparator(epsilon);
- degradedComparator = new DegradedComparator(epsilon);
- drugComparator = new DrugComparator(epsilon);
- geneComparator = new GeneComparator(epsilon);
- phenotypeComparator = new PhenotypeComparator(epsilon);
- proteinComparator = new ProteinComparator(epsilon);
- rnaComparator = new RnaComparator(epsilon);
- unknownComparator = new UnknownComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public SpeciesComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Species arg0, Species arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(AntisenseRna.class)) {
- return antisenseRnaComparator.compare((AntisenseRna) arg0, (AntisenseRna) arg1);
- } else if (arg0 instanceof Chemical) {
- return chemicalComparator.compare((Chemical) arg0, (Chemical) arg1);
- } else if (arg0.getClass().equals(Complex.class)) {
- return complexComparator.compare((Complex) arg0, (Complex) arg1);
- } else if (arg0.getClass().equals(Degraded.class)) {
- return degradedComparator.compare((Degraded) arg0, (Degraded) arg1);
- } else if (arg0.getClass().equals(Drug.class)) {
- return drugComparator.compare((Drug) arg0, (Drug) arg1);
- } else if (arg0.getClass().equals(Gene.class)) {
- return geneComparator.compare((Gene) arg0, (Gene) arg1);
- } else if (arg0.getClass().equals(Phenotype.class)) {
- return phenotypeComparator.compare((Phenotype) arg0, (Phenotype) arg1);
- } else if (arg0 instanceof Protein) {
- return proteinComparator.compare((Protein) arg0, (Protein) arg1);
- } else if (arg0.getClass().equals(Rna.class)) {
- return rnaComparator.compare((Rna) arg0, (Rna) arg1);
- } else if (arg0.getClass().equals(Unknown.class)) {
- return unknownComparator.compare((Unknown) arg0, (Unknown) arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Species}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Element}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- int internalCompare(Species arg0, Species arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- int result = elementComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- BooleanComparator booleanComparator = new BooleanComparator();
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (booleanComparator.compare(arg0.getActivity(), arg1.getActivity()) != 0) {
- logger.debug("activity different: " + arg0.getActivity() + ", " + arg1.getActivity());
- return booleanComparator.compare(arg0.getActivity(), arg1.getActivity());
- }
-
- if (doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth()) != 0) {
- logger.debug("line width different: " + arg0.getLineWidth() + ", " + arg1.getLineWidth());
- return doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
- }
- StringComparator stringComparator = new StringComparator();
- if (stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel()) != 0) {
- logger.debug("state label different: " + arg0.getStateLabel() + ", " + arg1.getStateLabel());
- return stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel());
- }
-
- if (stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix()) != 0) {
- logger.debug("state prefix different: " + arg0.getStatePrefix() + ", " + arg1.getStatePrefix());
- return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
- }
-
- if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
- logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
- return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
- }
-
- if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
- logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
- return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
- }
-
- if (integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer()) != 0) {
- logger.debug("Homodimer different: " + arg0.getHomodimer() + ", " + arg1.getHomodimer());
- return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
- }
-
- if (integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
- logger.debug("Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
- return integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
- }
-
- if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
- logger.debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
- return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
- }
-
- if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
- Integer pos0 = null;
- Integer pos1 = null;
- if (arg0.getPositionToCompartment() != null) {
- pos0 = arg0.getPositionToCompartment().ordinal();
- }
- if (arg1.getPositionToCompartment() != null) {
- pos1 = arg1.getPositionToCompartment().ordinal();
- }
- if (integerComparator.compare(pos0, pos1) != 0) {
- logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \"" + arg1.getPositionToCompartment() + "\"");
- return integerComparator.compare(pos0, pos1);
- }
- }
-
- if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
- logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
- return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
- }
-
- return 0;
- }
+public class SpeciesComparator extends Comparator<Species> {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SpeciesComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SpeciesComparator(double epsilon) {
+ super(Species.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new AntisenseRnaComparator(epsilon));
+ addSubClassComparator(new ChemicalComparator(epsilon));
+ addSubClassComparator(new ComplexComparator(epsilon));
+ addSubClassComparator(new DegradedComparator(epsilon));
+ addSubClassComparator(new DrugComparator(epsilon));
+ addSubClassComparator(new GeneComparator(epsilon));
+ addSubClassComparator(new PhenotypeComparator(epsilon));
+ addSubClassComparator(new ProteinComparator(epsilon));
+ addSubClassComparator(new RnaComparator(epsilon));
+ addSubClassComparator(new UnknownComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SpeciesComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Species arg0, Species arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ int result = elementComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ BooleanComparator booleanComparator = new BooleanComparator();
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (booleanComparator.compare(arg0.getActivity(), arg1.getActivity()) != 0) {
+ logger.debug("activity different: " + arg0.getActivity() + ", " + arg1.getActivity());
+ return booleanComparator.compare(arg0.getActivity(), arg1.getActivity());
+ }
+
+ if (doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth()) != 0) {
+ logger.debug("line width different: " + arg0.getLineWidth() + ", " + arg1.getLineWidth());
+ return doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
+ }
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel()) != 0) {
+ logger.debug("state label different: " + arg0.getStateLabel() + ", " + arg1.getStateLabel());
+ return stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel());
+ }
+
+ if (stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix()) != 0) {
+ logger.debug("state prefix different: " + arg0.getStatePrefix() + ", " + arg1.getStatePrefix());
+ return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
+ }
+
+ if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
+ logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
+ return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
+ }
+
+ if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
+ logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
+ return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
+ }
+
+ if (integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer()) != 0) {
+ logger.debug("Homodimer different: " + arg0.getHomodimer() + ", " + arg1.getHomodimer());
+ return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
+ }
+
+ if (integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
+ logger.debug(
+ "Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
+ return integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
+ }
+
+ if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
+ logger
+ .debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
+ return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
+ }
+
+ if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
+ Integer pos0 = null;
+ Integer pos1 = null;
+ if (arg0.getPositionToCompartment() != null) {
+ pos0 = arg0.getPositionToCompartment().ordinal();
+ }
+ if (arg1.getPositionToCompartment() != null) {
+ pos1 = arg1.getPositionToCompartment().ordinal();
+ }
+ if (integerComparator.compare(pos0, pos1) != 0) {
+ logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \""
+ + arg1.getPositionToCompartment() + "\"");
+ return integerComparator.compare(pos0, pos1);
+ }
+ }
+
+ if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
+ logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
+ return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
index 22483ca6f5a916c633f3b8076d971aa610881758..e05a1edf0e0efd006b2b273d473d77aeb392ec9a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link TruncatedProtein} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class TruncatedProteinComparator implements Comparator<TruncatedProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TruncatedProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public TruncatedProteinComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public TruncatedProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(TruncatedProtein arg0, TruncatedProtein arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(TruncatedProtein.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link TruncatedProtein} class in inheritence tree. By the design it calls
- * also comparator of the upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class TruncatedProteinComparator extends Comparator<TruncatedProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TruncatedProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public TruncatedProteinComparator(double epsilon) {
+ super(TruncatedProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public TruncatedProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
index 96c0edce8513f350cf3a87dc5d4b3a4f57e44117..1c45054aea17468b8dbc9cbba15902311cc42c8b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
@@ -1,11 +1,9 @@
package lcsb.mapviewer.model.map.species;
-import java.util.Comparator;
-
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* Comparator class used for comparing {@link Unknown} objects.
@@ -13,77 +11,44 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class UnknownComparator implements Comparator<Unknown> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(UnknownComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public UnknownComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public UnknownComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Unknown arg0, Unknown arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Unknown.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Unknown}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper ({@link Species}) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(Unknown arg0, Unknown arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
+public class UnknownComparator extends Comparator<Unknown> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(UnknownComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public UnknownComparator(double epsilon) {
+ super(Unknown.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public UnknownComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Unknown arg0, Unknown arg1) {
+ return 0;
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
index 06a28a73d76151f01aa5bc8ac93c5c498a23a444..9e8cd8147268616b186edf5577bf353144ecd037 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
@@ -8,71 +8,90 @@ import org.junit.Test;
public class OverviewImageLinkComparatorTest {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
-
- OverviewImageLink oi = new OverviewImageLink();
- OverviewImageLink oi2 = new OverviewImageLink();
-
- assertEquals(0, oic.compare(oi, oi2));
- assertEquals(0, oic.compare(null, null));
-
- oi2.setLinkedOverviewImage(new OverviewImage());
- oi.setLinkedOverviewImage(new OverviewImage());
- assertEquals(0, oic.compare(oi, oi2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
-
- OverviewImageLink oi = new OverviewImageLink();
-
- OverviewImageLink oi2 = new OverviewImageLink();
- oi2.setLinkedOverviewImage(new OverviewImage());
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi2, oi));
-
- oi2 = new OverviewImageLink();
- oi2.setLinkedOverviewImage(new OverviewImage());
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi2, oi));
-
- oi2 = new OverviewImageLink();
- oi2.setPolygon("AS");
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi, null));
- assertTrue(0 != oic.compare(null, oi2));
- assertTrue(0 != oic.compare(new OverviewImageLink(){
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;}, oi2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
+
+ OverviewImageLink oi = new OverviewImageLink();
+ OverviewImageLink oi2 = new OverviewImageLink();
+
+ assertEquals(0, oic.compare(oi, oi2));
+ assertEquals(0, oic.compare(null, null));
+
+ oi2.setLinkedOverviewImage(new OverviewImage());
+ oi.setLinkedOverviewImage(new OverviewImage());
+ assertEquals(0, oic.compare(oi, oi2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
+
+ OverviewImageLink oi = new OverviewImageLink();
+
+ OverviewImageLink oi2 = new OverviewImageLink();
+ oi2.setLinkedOverviewImage(new OverviewImage());
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi2, oi));
+
+ oi2 = new OverviewImageLink();
+ oi2.setLinkedOverviewImage(new OverviewImage());
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi2, oi));
+
+ oi2 = new OverviewImageLink();
+ oi2.setPolygon("AS");
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi, null));
+ assertTrue(0 != oic.compare(null, oi2));
+ assertTrue(0 != oic.compare(new OverviewImageLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }, oi2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentPolygon() throws Exception {
+ try {
+ OverviewImageLinkComparator comparator = new OverviewImageLinkComparator();
+
+ OverviewImageLink iml1 = new OverviewImageLink();
+ OverviewImageLink iml2 = new OverviewImageLink();
+ iml2.setPolygon("1,2");
+
+ assertTrue(0 != comparator.compare(iml1, iml2));
+ assertTrue(0 != comparator.compare(iml2, iml1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
index 8902796c1dffe30e1b636ad30a6525e35a2f6494..a328f37ae680ab6602c5ab0bdaed0f0bd2c88646 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
@@ -14,80 +14,80 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class OverviewLinkComparatorTest {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewModelLink oml = new OverviewModelLink();
- OverviewModelLink oml2 = new OverviewModelLink();
-
- assertEquals(0, omlc.compare(oml, oml2));
- assertEquals(0, omlc.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() throws Exception {
- try {
- class Tmp extends OverviewLink {
- private static final long serialVersionUID = 1L;
-
- @Override
- public OverviewLink copy() {
- return null;
- }
- }
- ;
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewLink oml = new Tmp();
- OverviewLink oml2 = new Tmp();
-
- omlc.compare(oml, oml2);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewModelLink oml = new OverviewModelLink();
- OverviewImageLink iml = new OverviewImageLink();
-
- assertTrue(0 != omlc.compare(oml, iml));
- assertTrue(0 != omlc.compare(oml, null));
- assertTrue(0 != omlc.compare(null, iml));
-
- oml = new OverviewModelLink();
- OverviewModelLink oml2 = new OverviewModelLink();
- oml2.setLinkedModel(new ModelFullIndexed(new ModelData()));
-
- assertTrue(0 != omlc.compare(oml, oml2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewModelLink oml = new OverviewModelLink();
+ OverviewModelLink oml2 = new OverviewModelLink();
+
+ assertEquals(0, omlc.compare(oml, oml2));
+ assertEquals(0, omlc.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() throws Exception {
+ try {
+ class Tmp extends OverviewLink {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public OverviewLink copy() {
+ return null;
+ }
+ }
+ ;
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewLink oml = new Tmp();
+ OverviewLink oml2 = new Tmp();
+
+ omlc.compare(oml, oml2);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewModelLink oml = new OverviewModelLink();
+ OverviewImageLink iml = new OverviewImageLink();
+
+ assertTrue(0 != omlc.compare(oml, iml));
+ assertTrue(0 != omlc.compare(oml, null));
+ assertTrue(0 != omlc.compare(null, iml));
+
+ oml = new OverviewModelLink();
+ OverviewModelLink oml2 = new OverviewModelLink();
+ oml2.setLinkedModel(new ModelFullIndexed(new ModelData()));
+
+ assertTrue(0 != omlc.compare(oml, oml2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
index 578e6a92ce78fe07f5288ce4425a41d6ecea7013..b060511d7077b9ce222e6c2f57f2693ce3325999 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
@@ -86,4 +86,22 @@ public class OverviewModelLinkComparatorTest {
}
}
+ @Test
+ public void testDifferentPolygon() throws Exception {
+ try {
+ OverviewModelLinkComparator comparator = new OverviewModelLinkComparator();
+
+ OverviewModelLink iml1 = new OverviewModelLink();
+ OverviewModelLink iml2 = new OverviewModelLink();
+ iml2.setPolygon("1,2");
+
+ assertTrue(0 != comparator.compare(iml1, iml2));
+ assertTrue(0 != comparator.compare(iml2, iml1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
index 3df3ef0c801f092b454fb9b6c0f2ccf5a1067403..535233b7c002d864b0cf48d37890651af07d4831 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
@@ -18,202 +18,205 @@ import lcsb.mapviewer.model.map.species.Species;
public class CompartmentComparatorTest {
- Logger logger = Logger.getLogger(CompartmentComparatorTest.class);
-
- CompartmentComparator comparator = new CompartmentComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- assertEquals(0, comparator.compare(compartment1, compartment2));
-
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- Compartment compartment = createCompartment();
-
- assertTrue(comparator.compare(compartment, new PathwayCompartment()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- GenericProtein protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
- protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
-
- compartment2.getElements().add(new GenericProtein("b"));
- compartment2.getElements().add(new GenericProtein("a"));
-
- comparator.compare(compartment1, compartment2);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid2() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
+ Logger logger = Logger.getLogger(CompartmentComparatorTest.class);
+
+ CompartmentComparator comparator = new CompartmentComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ assertEquals(0, comparator.compare(compartment1, compartment2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ Compartment compartment = createCompartment();
+
+ assertTrue(comparator.compare(compartment, new PathwayCompartment()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ GenericProtein protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+
+ compartment2.getElements().add(new GenericProtein("b"));
+ compartment2.getElements().add(new GenericProtein("a"));
+
+ comparator.compare(compartment1, compartment2);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Species protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
- protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
+ @Test
+ public void testInvalid2() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- compartment2.getElements().add(new GenericProtein("A"));
- compartment2.getElements().add(new GenericProtein("B"));
+ Species protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
- comparator.compare(compartment2, compartment1);
- fail("Exception expected");
+ compartment2.getElements().add(new GenericProtein("A"));
+ compartment2.getElements().add(new GenericProtein("B"));
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ comparator.compare(compartment2, compartment1);
+ fail("Exception expected");
- private Compartment createCompartment() {
- Compartment result = new Compartment();
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel("14");
- result.setThickness(998);
- result.setOuterWidth(45);
- result.setInnerWidth(65);
- result.setNamePoint(new Point2D.Double(9, 2));
+ private Compartment createCompartment() {
+ Compartment result = new Compartment();
- GenericProtein protein = new GenericProtein("S");
- protein.setName("a");
- result.addElement(protein);
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel("14");
+ result.setThickness(998);
+ result.setOuterWidth(45);
+ result.setInnerWidth(65);
+ result.setNamePoint(new Point2D.Double(9, 2));
- return result;
- }
+ GenericProtein protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addElement(protein);
- @Test
- public void testDifferentElementList() {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
+ return result;
+ }
- compartment1.addElement(new GenericProtein("idd"));
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
- }
+ @Test
+ public void testDifferentElementList() {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- @Test
- public void testDifferent() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
+ compartment1.addElement(new GenericProtein("idd"));
- assertTrue(comparator.compare(compartment1, null) != 0);
- assertTrue(comparator.compare(null, compartment1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ }
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ @Test
+ public void testDifferentElementId() {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- compartment1.setElementId("tmp");
+ compartment1.setElementId("tmp");
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ }
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ @Test
+ public void testDifferent() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
- compartment1.setThickness(11111);
+ assertTrue(comparator.compare(compartment1, null) != 0);
+ assertTrue(comparator.compare(null, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ compartment1.setThickness(11111);
- compartment1.setNamePoint(new Point2D.Double(9, 999));
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ compartment1.setNamePoint(new Point2D.Double(9, 999));
- compartment1.getElements().iterator().next().setElementId("bnu");
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ compartment1.getElements().iterator().next().setElementId("bnu");
- Species species = (Species) compartment1.getElements().iterator().next();
- species.setName("new namne");
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ Species species = (Species) compartment1.getElements().iterator().next();
+ species.setName("new namne");
- compartment1.setOuterWidth(2);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ compartment1.setOuterWidth(2);
- compartment1.setInnerWidth(2);
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
- compartment1 = createCompartment();
- compartment2 = createCompartment();
+ compartment1.setInnerWidth(2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
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 d97dc565279aadcf3329ea4cc9361fc9c4d7d848..956076bdf28df445a890d95ddc35d956a77c8930 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
@@ -6,7 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ SbmlFunctionTest.class, //
- SbmlKinetics.class, //
+ SbmlKineticsTest.class, //
SbmlParameterTest.class, //
SbmlUnitTest.class, //
SbmlUnitTypeFactorTest.class })
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
index acd1b7899841235abc1d2fdda17551ca848ddcb6..d8e2ed5174f59b31b6a5a3b46a6fabbbc4ec78a5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
@@ -2,14 +2,13 @@ package lcsb.mapviewer.model.map.reaction;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
-import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
public class AbstractNodeComparatorTest {
@@ -23,20 +22,10 @@ public class AbstractNodeComparatorTest {
public void tearDown() throws Exception {
}
- @Test
+ @Test(expected = NotImplementedException.class)
public void testCompareException() {
- try {
-
- comparator.compare(Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS),
- Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS));
-
- fail("Exception should occur");
- } catch (InvalidClassException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
+ comparator.compare(Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS),
+ Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS));
}
@Test
@@ -46,7 +35,6 @@ public class AbstractNodeComparatorTest {
assertEquals(0, comparator.compare(null, null));
} catch (Exception e) {
e.printStackTrace();
- fail("Unkowne exception");
}
}
@@ -57,7 +45,7 @@ public class AbstractNodeComparatorTest {
assertTrue(comparator.compare(null, new AndOperator()) != 0);
} catch (Exception e) {
e.printStackTrace();
- fail("Unkowne exception");
+ throw e;
}
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
index 080daf032159959393a5cc7fd42afee9c965f6c3..e7e4afecb4bd4d2ab97117163e30cf5de06167e7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
@@ -16,138 +16,141 @@ import lcsb.mapviewer.model.map.species.Species;
public class NodeOperatorComparatorTest {
- NodeOperatorComparator comparator = new NodeOperatorComparator();
+ NodeOperatorComparator comparator = new NodeOperatorComparator();
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testEquals() {
- try {
- assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
+ @Test
+ public void testEquals() {
+ try {
+ assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
- NodeOperator operator1 = createNodeOperator();
- NodeOperator operator2 = createNodeOperator();
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
- assertEquals(0, comparator.compare(operator1, operator2));
+ assertEquals(0, comparator.compare(operator1, operator2));
- assertEquals(0, comparator.compare(operator1, operator1));
+ assertEquals(0, comparator.compare(operator1, operator1));
- assertEquals(0, comparator.compare(null, null));
+ assertEquals(0, comparator.compare(null, null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testDifferent() {
- try {
- NodeOperator operator1 = createNodeOperator();
- NodeOperator operator2 = createNodeOperator();
+ @Test
+ public void testDifferentElement() {
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
- operator1.getLine().addPoint(new Point2D.Double(1, 1));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ Reactant reactant = (Reactant) operator1.getInputs().get(0);
+ reactant.setElement(new GenericProtein("id666"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+ }
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
+ @Test
+ public void testDifferent() {
+ try {
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
- operator1.addInput(new Reactant());
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ operator1.getLine().addPoint(new Point2D.Double(1, 1));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
- operator1.addOutput(new Product());
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ operator1.addInput(new Reactant());
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
- Reactant reactant = (Reactant) operator1.getInputs().get(0);
- reactant.setElement(new GenericProtein("id666"));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ operator1.addOutput(new Product());
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
- Product product= (Product) operator1.getOutputs().get(0);
- product.setElement(new GenericProtein("id666"));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ Product product = (Product) operator1.getOutputs().get(0);
+ product.setElement(new GenericProtein("id666"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
- reactant = (Reactant) operator1.getInputs().get(0);
- reactant.getElement().setName("bla");
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
+ Reactant reactant = (Reactant) operator1.getInputs().get(0);
+ reactant.getElement().setName("bla");
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
- assertTrue(comparator.compare(null, operator1) != 0);
- assertTrue(comparator.compare(operator2, null) != 0);
+ assertTrue(comparator.compare(null, operator1) != 0);
+ assertTrue(comparator.compare(operator2, null) != 0);
- assertTrue(comparator.compare(operator2, new OrOperator()) != 0);
+ assertTrue(comparator.compare(operator2, new OrOperator()) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private NodeOperator createNodeOperator() {
- AndOperator result = new AndOperator();
+ private NodeOperator createNodeOperator() {
+ AndOperator result = new AndOperator();
- Species protein0 = new GenericProtein("id0");
- protein0.setName("protein a");
- protein0.setX(12.0);
- protein0.setY(1.0);
- protein0.setWidth(2.0);
- protein0.setHeight(3.0);
+ Species protein0 = new GenericProtein("id0");
+ protein0.setName("protein a");
+ protein0.setX(12.0);
+ protein0.setY(1.0);
+ protein0.setWidth(2.0);
+ protein0.setHeight(3.0);
- Product product = new Product(protein0);
+ Product product = new Product(protein0);
- result.addOutput(product);
+ result.addOutput(product);
- Species protein1 = new GenericProtein("id1");
- protein1.setName("protein b");
- protein1.setX(120.0);
- protein1.setY(10.0);
- protein1.setWidth(20.0);
- protein1.setHeight(30.0);
+ Species protein1 = new GenericProtein("id1");
+ protein1.setName("protein b");
+ protein1.setX(120.0);
+ protein1.setY(10.0);
+ protein1.setWidth(20.0);
+ protein1.setHeight(30.0);
- Reactant reactant = new Reactant(protein1);
+ Reactant reactant = new Reactant(protein1);
- result.addInput(reactant);
+ result.addInput(reactant);
- Species protein2 = new Gene("id2");
- protein2.setName("gene b");
- protein2.setX(320.0);
- protein2.setY(30.0);
- protein2.setWidth(30.0);
- protein2.setHeight(40.0);
+ Species protein2 = new Gene("id2");
+ protein2.setName("gene b");
+ protein2.setX(320.0);
+ protein2.setY(30.0);
+ protein2.setWidth(30.0);
+ protein2.setHeight(40.0);
- Modifier modifier = new Modifier(protein2);
+ Modifier modifier = new Modifier(protein2);
- result.addInput(modifier);
+ result.addInput(modifier);
- PolylineData pd = new PolylineData();
- pd.addPoint(new Point2D.Double(1, 2));
- pd.addPoint(new Point2D.Double(1, 22));
- pd.addPoint(new Point2D.Double(10, 22));
- result.setLine(pd);
+ PolylineData pd = new PolylineData();
+ pd.addPoint(new Point2D.Double(1, 2));
+ pd.addPoint(new Point2D.Double(1, 22));
+ pd.addPoint(new Point2D.Double(10, 22));
+ result.setLine(pd);
- return result;
- }
+ return result;
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index 5f1f3ee27934a0111f3a32147e665a079c21e756..06403a2233525dbf816523c3dba0efb16371ce35 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -13,6 +13,7 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
@@ -23,266 +24,275 @@ import lcsb.mapviewer.model.map.species.Unknown;
public class ReactionComparatorTest {
- ReactionComparator comparator = new ReactionComparator();
+ ReactionComparator comparator = new ReactionComparator();
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testEquals() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- assertEquals(0, comparator.compare(reaction1, reaction2));
- assertEquals(0, comparator.compare(reaction2, reaction1));
- assertEquals(0, comparator.compare(reaction1, reaction1));
- assertEquals(0, comparator.compare(null, null));
+ @Test
+ public void testEquals() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ assertEquals(0, comparator.compare(reaction1, reaction2));
+ assertEquals(0, comparator.compare(reaction2, reaction1));
+ assertEquals(0, comparator.compare(reaction1, reaction1));
+ assertEquals(0, comparator.compare(null, null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testDifferent3() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setNotes("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setIdReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSymbol("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ @Test
+ public void testDifferent3() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setNotes("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setIdReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSymbol("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setFormula("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setFormula("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSubsystem("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSubsystem("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setGeneProteinReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setGeneProteinReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
+ reaction1 = createReaction();
+ reaction2 = createReaction();
- reaction1.setMechanicalConfidenceScore(1);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.setMechanicalConfidenceScore(1);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
+ reaction1 = createReaction();
+ reaction2 = createReaction();
- reaction1.setLowerBound(1.2);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.setLowerBound(1.2);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
+ reaction1 = createReaction();
+ reaction2 = createReaction();
- reaction1.setUpperBound(4.3);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.setUpperBound(4.3);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
+ reaction1 = createReaction();
+ reaction2 = createReaction();
- reaction1.addSynonym("syn");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.addSynonym("syn");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- reaction1 = createReaction();
- reaction2 = createReaction();
+ reaction1 = createReaction();
+ reaction2 = createReaction();
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testDifferent4() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
+ @Test
+ public void testDifferent4() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testDifferent2() {
- try {
- Reaction reaction1 = createReaction();
- assertTrue(comparator.compare(reaction1, null) != 0);
- assertTrue(comparator.compare(null, reaction1) != 0);
+ @Test
+ public void testDifferent2() {
+ try {
+ Reaction reaction1 = createReaction();
+ assertTrue(comparator.compare(reaction1, null) != 0);
+ assertTrue(comparator.compare(null, reaction1) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testDifferent() {
- try {
+ @Test
+ public void testDifferent() {
+ try {
- assertTrue(comparator.compare(new TransportReaction(), new StateTransitionReaction()) != 0);
+ assertTrue(comparator.compare(new TransportReaction(), new StateTransitionReaction()) != 0);
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
- reaction1.setReversible(true);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addModifier(new Modifier());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getModifiers().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addReactant(new Reactant());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getReactants().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addProduct(new Product());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getProducts().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Reaction createReaction() {
- Reaction reaction = new Reaction();
- Species protein = new GenericProtein("id1");
- protein.setName("ASD");
- Reactant reactant = new Reactant(protein);
-
- Species protein2 = new GenericProtein("id2");
- protein2.setName("ASD2");
- Reactant reactant2 = new Reactant(protein2);
-
- Species simpleMolecule = new SimpleMolecule("id3");
- simpleMolecule.setName("mol");
- Product product = new Product(simpleMolecule);
-
- Species unknown = new Unknown("id4");
- unknown.setName("unk");
- Modifier modifier = new Catalysis(unknown);
-
- AndOperator operator = new AndOperator();
- operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
- operator.addInput(reactant);
- operator.addInput(reactant2);
-
- reaction.addModifier(modifier);
- reaction.addReactant(reactant);
- reaction.addReactant(reactant2);
- reaction.addProduct(product);
- reaction.addNode(operator);
- return reaction;
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- reaction2.setAbbreviation("ABRR");
-
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ reaction1.setReversible(true);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+ reaction1.addModifier(new Modifier());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getModifiers().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addReactant(new Reactant());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getReactants().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addProduct(new Product());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getProducts().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Reaction createReaction() {
+ Reaction reaction = new Reaction();
+ Species protein = new GenericProtein("id1");
+ protein.setName("ASD");
+ Reactant reactant = new Reactant(protein);
+
+ Species protein2 = new GenericProtein("id2");
+ protein2.setName("ASD2");
+ Reactant reactant2 = new Reactant(protein2);
+
+ Species simpleMolecule = new SimpleMolecule("id3");
+ simpleMolecule.setName("mol");
+ Product product = new Product(simpleMolecule);
+
+ Species unknown = new Unknown("id4");
+ unknown.setName("unk");
+ Modifier modifier = new Catalysis(unknown);
+
+ AndOperator operator = new AndOperator();
+ operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
+ operator.addInput(reactant);
+ operator.addInput(reactant2);
+
+ reaction.addModifier(modifier);
+ reaction.addReactant(reactant);
+ reaction.addReactant(reactant2);
+ reaction.addProduct(product);
+ reaction.addNode(operator);
+ return reaction;
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ reaction2.setAbbreviation("ABRR");
+
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentKinetics() {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setKinetics(new SbmlKinetics());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index 09242c650680a3c287d436785cbf077a5ae504bc..690e5c3e23d2e03934ca30e16ceeedd2feede7bd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -15,90 +15,81 @@ import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
public class AntisenseRnaComparatorTest {
- AntisenseRnaComparator comparator = new AntisenseRnaComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
-
- assertEquals(0, comparator.compare(aRna1, aRna1));
-
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
- aRna1.getRegions().get(0).setName("bla");
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createAntisenseRna();
- aRna2 = createAntisenseRna();
- aRna1.getRegions().clear();
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createAntisenseRna();
- aRna2 = createAntisenseRna();
- assertTrue(comparator.compare(null, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- AntisenseRna unknown = createAntisenseRna();
- unknown.setName("n");
- assertTrue(comparator.compare(unknown, aRna2) != 0);
-
- assertTrue(comparator.compare(unknown, Mockito.mock(AntisenseRna.class)) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public AntisenseRna createAntisenseRna() {
- AntisenseRna result = new AntisenseRna();
-
- AntisenseRnaRegion region1 = new AntisenseRnaRegion();
- result.addRegion(region1);
- region1.setIdAntisenseRnaRegion("a");
- region1.setName("name");
- region1.setPos("1");
- region1.setSize("2");
- region1.setType(AntisenseRnaRegionType.CODING_REGION);
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- AntisenseRna element = Mockito.mock(AntisenseRna.class);
- comparator.compare(element, element);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
+ AntisenseRnaComparator comparator = new AntisenseRnaComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ AntisenseRna aRna1 = createAntisenseRna();
+ AntisenseRna aRna2 = createAntisenseRna();
+
+ assertEquals(0, comparator.compare(aRna1, aRna1));
+
+ assertEquals(0, comparator.compare(aRna1, aRna2));
+ assertEquals(0, comparator.compare(aRna2, aRna1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ AntisenseRna aRna1 = createAntisenseRna();
+ AntisenseRna aRna2 = createAntisenseRna();
+ aRna1.getRegions().get(0).setName("bla");
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createAntisenseRna();
+ aRna2 = createAntisenseRna();
+ aRna1.getRegions().clear();
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createAntisenseRna();
+ aRna2 = createAntisenseRna();
+ assertTrue(comparator.compare(null, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ AntisenseRna unknown = createAntisenseRna();
+ unknown.setName("n");
+ assertTrue(comparator.compare(unknown, aRna2) != 0);
+
+ assertTrue(comparator.compare(unknown, Mockito.mock(AntisenseRna.class)) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public AntisenseRna createAntisenseRna() {
+ AntisenseRna result = new AntisenseRna();
+
+ AntisenseRnaRegion region1 = new AntisenseRnaRegion();
+ result.addRegion(region1);
+ region1.setIdAntisenseRnaRegion("a");
+ region1.setName("name");
+ region1.setPos("1");
+ region1.setSize("2");
+ region1.setType(AntisenseRnaRegionType.CODING_REGION);
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ AntisenseRna element = Mockito.mock(AntisenseRna.class);
+ comparator.compare(element, element);
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
index b024670527ba887aa5ecd161c17b01ae145ea05a..ccf0fe04d016481dc37f57c87082d721cc0e82db 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
@@ -13,72 +13,62 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
public class ChemicalComparatorTest {
- ChemicalComparator comparator = new ChemicalComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Chemical drug1 = createChemical();
- Chemical drug2 = createChemical();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Chemical drug2 = createChemical();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Chemical drug = createChemical();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(Chemical.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Chemical createChemical() {
- Chemical result = new Ion();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Chemical object = Mockito.mock(Chemical.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
+ ChemicalComparator comparator = new ChemicalComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Chemical drug1 = createChemical();
+ Chemical drug2 = createChemical();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Chemical drug2 = createChemical();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Chemical drug = createChemical();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(Chemical.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Chemical createChemical() {
+ Chemical result = new Ion();
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Chemical object = Mockito.mock(Chemical.class);
+ comparator.compare(object, object);
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 907dfeeef5ca93a46aa8d67aea5dd8934cdda857..227e98136781369806e1386fadb3d013768e6050 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -18,373 +18,366 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
public class ComplexComparatorTest {
- Logger logger = Logger.getLogger(ComplexComparatorTest.class);
- ComplexComparator comparator = new ComplexComparator();
+ Logger logger = Logger.getLogger(ComplexComparatorTest.class);
+ ComplexComparator comparator = new ComplexComparator();
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testEquals() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
+ @Test
+ public void testEquals() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- assertEquals(0, comparator.compare(complex1, complex2));
+ assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(null, null));
+ assertEquals(0, comparator.compare(null, null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private Complex createComplex2() {
- Complex result = new Complex();
- result.setName("complex");
+ private Complex createComplex2() {
+ Complex result = new Complex();
+ result.setName("complex");
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel("14");
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel("14");
- Species protein = new GenericProtein("S");
- protein.setName("a");
- result.addSpecies(protein);
+ Species protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addSpecies(protein);
- return result;
- }
+ return result;
+ }
- @Test
- public void testDifferent() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
+ @Test
+ public void testDifferent() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
- assertTrue(comparator.compare(complex1, null) != 0);
- assertTrue(comparator.compare(null, complex1) != 0);
+ assertTrue(comparator.compare(complex1, null) != 0);
+ assertTrue(comparator.compare(null, complex1) != 0);
- complex1 = createComplex2();
- complex2 = createComplex2();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- complex1.setElementId("tmp");
+ complex1.setElementId("tmp");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- complex1 = createComplex2();
- complex2 = createComplex2();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- complex1.addSpecies(new GenericProtein("id"));
+ complex1.addSpecies(new GenericProtein("id"));
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- complex1 = createComplex2();
- complex2 = createComplex2();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- complex1.getElements().iterator().next().setElementId("bnu");
+ complex1.getElements().iterator().next().setElementId("bnu");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
- complex1 = createComplex2();
- complex2 = createComplex2();
+ complex1 = createComplex2();
+ complex2 = createComplex2();
- Species species = (Species) complex1.getElements().iterator().next();
- species.setName("new namne");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- complex1.setName("new namne");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- GenericProtein protein = new GenericProtein("1");
- complex1.getElements().add(protein);
- protein = new GenericProtein("1");
- complex1.getElements().add(protein);
-
- complex2.getElements().add(new GenericProtein("b"));
- complex2.getElements().add(new GenericProtein("a"));
-
- comparator.compare(complex1, complex2);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid3() {
- try {
- Complex invalidComplex = Mockito.mock(Complex.class);
-
- comparator.compare(invalidComplex, invalidComplex);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- @Test
- public void testInvalid2() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- Species protein = new GenericProtein("1");
- complex1.getElements().add(protein);
- protein = new GenericProtein("1");
- complex1.getElements().add(protein);
-
- complex2.getElements().add(new GenericProtein("A"));
- complex2.getElements().add(new GenericProtein("B"));
-
- comparator.compare(complex2, complex1);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEquals2() {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
-
- assertEquals(0, comparator.compare(complex1, complex1));
-
- assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(complex2, complex1));
-
- complex2.addSpecies(new GenericProtein("test"));
- complex1.addSpecies(new GenericProtein("test"));
- assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(complex2, complex1));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testInvalidComp2() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
-
- Species mock = Mockito.mock(Species.class);
- when(mock.getElementId()).thenReturn("id");
- complex1.addSpecies(mock);
- complex2.addSpecies(mock);
- comparator.compare(complex1, complex2);
- comparator.compare(complex2, complex1);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInvalidComp3() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein c = new GenericProtein("test");
- complex2.addSpecies(c);
- complex1.addSpecies(new GenericProtein("test"));
- Species mock = Mockito.mock(Species.class);
- when(mock.getElementId()).thenReturn("id");
- complex1.addSpecies(mock);
- complex2.addSpecies(mock);
- comparator.compare(complex2, complex1);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testDifferent5() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- complex1.setHomodimer(123);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.getElements().iterator().next().setNotes("bla");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.getElements().clear();
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- assertTrue(comparator.compare(null, complex2) != 0);
- assertTrue(comparator.compare(complex2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- Complex child = (Complex) complex1.getElements().iterator().next();
- child.getElements().iterator().next().setNotes("grand child notes");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- Protein prot = new GenericProtein();
- prot.setElementId("test");
- complex1.addSpecies(prot);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.setStructuralState("str");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- assertTrue(comparator.compare(new Complex(), Mockito.mock(Complex.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent3() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein prot = new GenericProtein();
- prot.setElementId("test");
- complex1.addSpecies(prot);
- prot = new GenericProtein();
- prot.setElementId("test2");
- complex2.addSpecies(prot);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent4() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein c = new GenericProtein("test");
- c.setName("a");
- complex2.addSpecies(c);
- complex2.addSpecies(new GenericProtein("test"));
- c.setName("");
-
- complex1.addSpecies(new GenericProtein("test"));
- GenericProtein d = new GenericProtein("test2");
- d.setName("a");
- complex1.addSpecies(d);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein comp = new GenericProtein("test");
- comp.setFullName("X");
- complex1.addSpecies(comp);
- complex2.addSpecies(new GenericProtein("test"));
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public Complex createComplex() {
- Complex result = new Complex();
-
- result.setHypothetical(true);
- result.setHomodimer(3);
-
- Complex child = new Complex();
- result.addSpecies(child);
- child.setCharge(12);
- child.setName("buu");
- child.setNotes("hey, hi, hello");
-
- Complex grandChild = new Complex();
- child.addSpecies(grandChild);
- child.setCharge(123);
- child.setName("buus");
- child.setNotes("hey, hi, hello !!");
-
- return result;
- }
+ Species species = (Species) complex1.getElements().iterator().next();
+ species.setName("new namne");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ complex1.setName("new namne");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ GenericProtein protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+
+ complex2.getElements().add(new GenericProtein("b"));
+ complex2.getElements().add(new GenericProtein("a"));
+
+ comparator.compare(complex1, complex2);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid3() {
+ Complex invalidComplex = Mockito.mock(Complex.class);
+
+ comparator.compare(invalidComplex, invalidComplex);
+
+ }
+
+ @Test
+ public void testInvalid2() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ Species protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+
+ complex2.getElements().add(new GenericProtein("A"));
+ complex2.getElements().add(new GenericProtein("B"));
+
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEquals2() {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+
+ assertEquals(0, comparator.compare(complex1, complex1));
+
+ assertEquals(0, comparator.compare(complex1, complex2));
+ assertEquals(0, comparator.compare(complex2, complex1));
+
+ complex2.addSpecies(new GenericProtein("test"));
+ complex1.addSpecies(new GenericProtein("test"));
+ assertEquals(0, comparator.compare(complex1, complex2));
+ assertEquals(0, comparator.compare(complex2, complex1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testInvalidComp2() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+
+ Species mock = Mockito.mock(Species.class);
+ when(mock.getElementId()).thenReturn("id");
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
+ comparator.compare(complex1, complex2);
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInvalidComp3() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein c = new GenericProtein("test");
+ complex2.addSpecies(c);
+ complex1.addSpecies(new GenericProtein("test"));
+ Species mock = Mockito.mock(Species.class);
+ when(mock.getElementId()).thenReturn("id");
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testDifferent5() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ complex1.setHomodimer(123);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.getElements().iterator().next().setNotes("bla");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.getElements().clear();
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ assertTrue(comparator.compare(null, complex2) != 0);
+ assertTrue(comparator.compare(complex2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ Complex child = (Complex) complex1.getElements().iterator().next();
+ child.getElements().iterator().next().setNotes("grand child notes");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ Protein prot = new GenericProtein();
+ prot.setElementId("test");
+ complex1.addSpecies(prot);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.setStructuralState("str");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ assertTrue(comparator.compare(new Complex(), Mockito.mock(Complex.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent3() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein prot = new GenericProtein();
+ prot.setElementId("test");
+ complex1.addSpecies(prot);
+ prot = new GenericProtein();
+ prot.setElementId("test2");
+ complex2.addSpecies(prot);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent4() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein c = new GenericProtein("test");
+ c.setName("a");
+ complex2.addSpecies(c);
+ complex2.addSpecies(new GenericProtein("test"));
+ c.setName("");
+
+ complex1.addSpecies(new GenericProtein("test"));
+ GenericProtein d = new GenericProtein("test2");
+ d.setName("a");
+ complex1.addSpecies(d);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein comp = new GenericProtein("test");
+ comp.setFullName("X");
+ complex1.addSpecies(comp);
+ complex2.addSpecies(new GenericProtein("test"));
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public Complex createComplex() {
+ Complex result = new Complex();
+
+ result.setHypothetical(true);
+ result.setHomodimer(3);
+
+ Complex child = new Complex();
+ result.addSpecies(child);
+ child.setCharge(12);
+ child.setName("buu");
+ child.setNotes("hey, hi, hello");
+
+ Complex grandChild = new Complex();
+ child.addSpecies(grandChild);
+ child.setCharge(123);
+ child.setName("buus");
+ child.setNotes("hey, hi, hello !!");
+
+ return result;
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
index 9256b2a65aeb279d2f5fb642df7266ec57c726fb..e21a9162f1fac2c131410b269af2ebf42241b0ae 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
@@ -13,80 +13,71 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
public class DegradedComparatorTest {
- DegradedComparator comparator = new DegradedComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
-
- assertEquals(0, comparator.compare(degraded1, degraded1));
-
- assertEquals(0, comparator.compare(degraded1, degraded2));
- assertEquals(0, comparator.compare(degraded2, degraded1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
- degraded1 = createDegraded();
- degraded2 = createDegraded();
- degraded1.setCharge(54);
- assertTrue(comparator.compare(degraded1, degraded2) != 0);
- assertTrue(comparator.compare(degraded2, degraded1) != 0);
-
- degraded1 = createDegraded();
- degraded2 = createDegraded();
- assertTrue(comparator.compare(null, degraded2) != 0);
- assertTrue(comparator.compare(degraded2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Degraded degraded = createDegraded();
- degraded.setName("n");
- assertTrue(comparator.compare(degraded, degraded1) != 0);
-
- assertTrue(comparator.compare(degraded, Mockito.mock(Degraded.class)) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Degraded createDegraded() {
- Degraded result = new Degraded();
- result.setCharge(12);
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Degraded object = Mockito.mock(Degraded.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
+ DegradedComparator comparator = new DegradedComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Degraded degraded1 = createDegraded();
+ Degraded degraded2 = createDegraded();
+
+ assertEquals(0, comparator.compare(degraded1, degraded1));
+
+ assertEquals(0, comparator.compare(degraded1, degraded2));
+ assertEquals(0, comparator.compare(degraded2, degraded1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Degraded degraded1 = createDegraded();
+ Degraded degraded2 = createDegraded();
+ degraded1 = createDegraded();
+ degraded2 = createDegraded();
+ degraded1.setCharge(54);
+ assertTrue(comparator.compare(degraded1, degraded2) != 0);
+ assertTrue(comparator.compare(degraded2, degraded1) != 0);
+
+ degraded1 = createDegraded();
+ degraded2 = createDegraded();
+ assertTrue(comparator.compare(null, degraded2) != 0);
+ assertTrue(comparator.compare(degraded2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Degraded degraded = createDegraded();
+ degraded.setName("n");
+ assertTrue(comparator.compare(degraded, degraded1) != 0);
+
+ assertTrue(comparator.compare(degraded, Mockito.mock(Degraded.class)) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Degraded createDegraded() {
+ Degraded result = new Degraded();
+ result.setCharge(12);
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Degraded object = Mockito.mock(Degraded.class);
+
+ comparator.compare(object, object);
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
index f0568d1dec016cf63130318485ce8f3cf07dd6b9..266e2dcb248710c454987c2c1c765c4ccb39d38e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
@@ -13,72 +13,63 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
public class DrugComparatorTest {
- DrugComparator comparator = new DrugComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Drug drug1 = createDrug();
- Drug drug2 = createDrug();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Drug drug2 = createDrug();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Drug drug = createDrug();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(Drug.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Drug createDrug() {
- Drug result = new Drug();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Drug object = Mockito.mock(Drug.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
+ DrugComparator comparator = new DrugComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Drug drug1 = createDrug();
+ Drug drug2 = createDrug();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Drug drug2 = createDrug();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Drug drug = createDrug();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(Drug.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Drug createDrug() {
+ Drug result = new Drug();
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Drug object = Mockito.mock(Drug.class);
+
+ comparator.compare(object, object);
+ }
}
diff --git a/web/.settings/org.eclipse.wst.common.component b/web/.settings/org.eclipse.wst.common.component
index 2c2e2c8b85f16344550cbaac6ff5482a76560f0d..969429923156e2c3a4fb1892eeda3a20a2d72eac 100644
--- a/web/.settings/org.eclipse.wst.common.component
+++ b/web/.settings/org.eclipse.wst.common.component
@@ -37,6 +37,9 @@
<dependent-module archiveName="rest-api-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/rest-api/rest-api">
<dependency-type>uses</dependency-type>
</dependent-module>
+ <dependent-module archiveName="converter-sbml-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-sbml/converter-sbml">
+ <dependency-type>uses</dependency-type>
+ </dependent-module>
<dependent-module archiveName="frontend-js-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/frontend-js/frontend-js">
<dependency-type>uses</dependency-type>
</dependent-module>