From b5e0e7f2125c713a6e623d9ec6e5176430d460a4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 18 Dec 2017 17:03:00 +0100
Subject: [PATCH] when no information about modifier is provided then
Modulation is used as default
---
.../celldesigner/types/ModifierTypeUtils.java | 3 +-
.../converter/model/sbml/SbmlParser.java | 18 +++-
.../model/sbml/GenericSbmlParserTest.java | 1 -
.../model/map/modifier/Catalysis.java | 82 +++++++++----------
.../model/map/modifier/Inhibition.java | 5 +-
.../model/map/modifier/Modulation.java | 5 +-
.../map/modifier/PhysicalStimulation.java | 5 +-
.../mapviewer/model/map/modifier/Trigger.java | 5 +-
.../model/map/modifier/UnknownCatalysis.java | 5 +-
.../model/map/modifier/UnknownInhibition.java | 5 +-
.../model/map/reaction/Modifier.java | 5 +-
11 files changed, 81 insertions(+), 58 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
index dda0a2c6a9..5b4f536996 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -79,7 +80,7 @@ public class ModifierTypeUtils {
throw new InvalidArgumentException("Unknown modifier type: " + type);
}
try {
- Modifier mod = modType.getClazz().getConstructor(Species.class).newInstance(alias);
+ Modifier mod = modType.getClazz().getConstructor(Element.class).newInstance(alias);
return mod;
} catch (Exception e) {
throw new InvalidStateException("Problem with instantiation of Modifier class: " + type);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 0b8b1e4c24..bbfbd3b22d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -5,6 +5,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
+import java.util.HashSet;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
@@ -30,6 +31,7 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -220,12 +222,26 @@ public class SbmlParser implements IConverter {
operator.setLine(line);
reaction.addNode(operator);
}
+ Set<Modifier> modifiersToBeRemoved = new HashSet<>();
+ Set<Modifier> modifiersToBeAdded = new HashSet<>();
+ for (Modifier modifier : reaction.getModifiers()) {
+ if (modifier.getClass() == Modifier.class) {
+ modifiersToBeRemoved.add(modifier);
+ modifiersToBeAdded.add(new Modulation(modifier.getElement()));
+ }
+ }
+ for (Modifier modifier : modifiersToBeRemoved) {
+ reaction.removeModifier(modifier);
+ }
+ for (Modifier modifier : modifiersToBeAdded) {
+ reaction.addModifier(modifier);
+ }
for (Modifier modifier : reaction.getModifiers()) {
PolylineData line = new PolylineData();
line.addPoint(modifier.getElement().getCenter());
line.addPoint(center);
modifier.setLine(line);
- if (modifier.getClass() == Modifier.class) {
+ if (modifier.getClass() == Modulation.class) {
line.setEndAtd(ModifierType.MODULATION_STRING.getAtd());
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index 252a952df8..28a13cca23 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -61,7 +61,6 @@ public class GenericSbmlParserTest {
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
- logger.debug(model.getElements().size());
// Create and display image of parsed map
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
index d5fa8d1a50..f93e8502a9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
@@ -5,7 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This class defines catalysis modifier in the reaction.
@@ -17,45 +17,45 @@ import lcsb.mapviewer.model.map.species.Species;
@DiscriminatorValue("CATALYSIS_MODIFIER")
public class Catalysis extends Modifier {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Catalysis() {
- super();
- }
-
- /**
- * Constructor that creates {@link Catalysis} modifier for given element.
- *
- * @param element
- * element object to which this modifiar is assigned
- */
- public Catalysis(Species element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter catalysis.
- *
- * @param catalysis
- * object from which data are initialized
- */
- public Catalysis(Catalysis catalysis) {
- super(catalysis);
- }
-
- @Override
- public Catalysis copy() {
- if (this.getClass() == Catalysis.class) {
- return new Catalysis(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Catalysis() {
+ super();
+ }
+
+ /**
+ * Constructor that creates {@link Catalysis} modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public Catalysis(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter catalysis.
+ *
+ * @param catalysis
+ * object from which data are initialized
+ */
+ public Catalysis(Catalysis catalysis) {
+ super(catalysis);
+ }
+
+ @Override
+ public Catalysis copy() {
+ if (this.getClass() == Catalysis.class) {
+ return new Catalysis(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
index 5eb71a10f1..a7ee536523 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -33,9 +34,9 @@ public class Inhibition extends Modifier {
* Constructor that creates inhibition modifier for given element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public Inhibition(Species element) {
+ public Inhibition(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
index 3cc706b094..b909f91c2a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -33,9 +34,9 @@ public class Modulation extends Modifier {
* Constructor that creates modulation modifier for given element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public Modulation(Species element) {
+ public Modulation(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
index ca7fcb28cc..40114e8b15 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -33,9 +34,9 @@ public class PhysicalStimulation extends Modifier {
* Constructor that creates physical stimulation modifier for given element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public PhysicalStimulation(Species element) {
+ public PhysicalStimulation(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
index 642f15c1b4..99baa3f051 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -33,9 +34,9 @@ public class Trigger extends Modifier {
* Constructor that creates trigger modifier for given element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public Trigger(Species element) {
+ public Trigger(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
index eba97a06f2..6fd3092453 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -33,9 +34,9 @@ public class UnknownCatalysis extends Modifier {
* Constructor that creates unknown catalysis modifier for given element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public UnknownCatalysis(Species element) {
+ public UnknownCatalysis(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
index 938249078a..05c76708f7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
@@ -5,6 +5,7 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -34,9 +35,9 @@ public class UnknownInhibition extends Modifier {
* element.
*
* @param element
- * element object to which this modifiar is assigned
+ * element object to which this modifier is assigned
*/
- public UnknownInhibition(Species element) {
+ public UnknownInhibition(Element element) {
super(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
index d97dba4887..39d96b497b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
@@ -4,6 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -38,7 +39,7 @@ public class Modifier extends ReactionNode {
* @param element
* element that represent this modifier
*/
- public Modifier(Species element) {
+ public Modifier(Element element) {
super(element);
}
@@ -46,7 +47,7 @@ public class Modifier extends ReactionNode {
* Constructor that initialize the modifier with data from parameter.
*
* @param original
- * original modifier used for data initalization
+ * original modifier used for data initialization
*/
protected Modifier(Modifier original) {
super(original);
--
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