From e5bcb7f429bd786d20aadb5a57219aa6390592ac Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Jun 2017 10:59:03 +0200
Subject: [PATCH] copying adds information about comaprtments properly
---
.../lcsb/mapviewer/commands/CopyCommand.java | 25 ++++---
.../mapviewer/commands/CopyCommandTest.java | 65 ++++++++++++++++++-
2 files changed, 79 insertions(+), 11 deletions(-)
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 3014886559..5ea871caf6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -176,6 +176,7 @@ public class CopyCommand extends NewModelCommand {
if (alias instanceof Compartment) {
Compartment copy = ((Compartment) alias).copy();
copy.getElements().clear();
+ copy.setCompartment(null);
result.addElement(copy);
}
@@ -184,21 +185,25 @@ public class CopyCommand extends NewModelCommand {
for (Element alias : model.getElements()) {
if (alias instanceof Species) {
Species copy = ((Species) alias).copy();
- Compartment ca = copy.getCompartment();
copy.setCompartment(null);
-
- // the trick is that in addAlias also some connections are added, so
- // lets clear info about parents
-
result.addElement(copy);
- if (ca != null) {
- ca = result.getElementByElementId(ca.getElementId());
- copy.setCompartment(ca);
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
}
+
} else if (alias instanceof Compartment) {
- // we already added compartment alias
- continue;
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ Compartment copy = result.getElementByElementId(alias.getElementId());
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
} else {
throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 6b2c37080b..cc78f07b6e 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,8 +1,12 @@
package lcsb.mapviewer.commands;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
@@ -14,8 +18,11 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -23,9 +30,12 @@ import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
@@ -311,4 +321,57 @@ public class CopyCommandTest extends CommandTestFunctions {
}
}
+ @Test
+ public void testCopyModelReaction() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment c1 = new SquareCompartment("c1");
+ Compartment c2 = new SquareCompartment("c2");
+ c1.setSemanticZoomLevelVisibility("2");
+ c2.setSemanticZoomLevelVisibility("3");
+
+ model.addElement(c1);
+ model.addElement(c2);
+
+ GenericProtein s1 = new GenericProtein("s1");
+ s1.setCompartment(c1);
+ model.addElement(s1);
+
+ GenericProtein s2 = new GenericProtein("s2");
+ s2.setCompartment(c2);
+ model.addElement(s2);
+
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ Reactant reactant = new Reactant(s1);
+ reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
+ reaction.addReactant(reactant);
+ Product product = new Product(s2);
+ product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
+ reaction.addProduct(product);
+ reaction.setSemanticZoomLevelVisibility("4");
+
+ model.addReaction(reaction);
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ Model model2 = new CopyCommand(model).execute();
+ Reaction reaction2 = model2.getReactions().iterator().next();
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
+ assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
+
+ assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
+ assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
--
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