Merge branch 'error-message' into 'master'

Error message improved

See merge request !576

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java

@@ -4,6 +4,7 @@ import org.apache.log4j.Logger;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -150,6 +151,8 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
 
       species.updateModelElementAfterLayoutAdded(result);
       return result;
+    } catch (InvalidArgumentException e) {
+      throw new InvalidXmlSchemaException(errorPrefix + e.getMessage(), e);
     } catch (NotImplementedException e) {
       throw new InvalidXmlSchemaException(errorPrefix + "Problem with creating species", e);
     }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java

@@ -156,8 +156,9 @@ public class ReactionToXml extends XmlParser {
    * @param reaction
    *          reaction for which list is generated
    * @return xml node with list of modification
+   * @throws InconsistentModelException 
    */
-  private String getListOfModificationsXmlStringForReaction(Reaction reaction) {
+  private String getListOfModificationsXmlStringForReaction(Reaction reaction) throws InconsistentModelException {
     StringBuilder sb = new StringBuilder();
     sb.append("<celldesigner:listOfModification>\n");
 
@@ -312,15 +313,16 @@ public class ReactionToXml extends XmlParser {
   }
 
   /**
-   * Creates xml node for given modifer.
+   * Creates xml node for given modifier.
    * 
    * @param modifier
-   *          modifier to be transaformed
+   *          modifier to be transformed
    * @param gate
    *          operator to which modifier is connected (if any)
-   * @return xml node for given modifer
+   * @return xml node for given modifier
+   * @throws InconsistentModelException 
    */
-  private String getModifierXmlString(Modifier modifier, NodeOperator gate) {
+  private String getModifierXmlString(Modifier modifier, NodeOperator gate) throws InconsistentModelException {
     StringBuilder sb = new StringBuilder();
     ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
     sb.append("<celldesigner:modification ");
@@ -340,21 +342,26 @@ public class ReactionToXml extends XmlParser {
       line.setStartPoint(start);
     }
 
-    List<Point2D> points = lineTransformation.getPointsFromLine(line);
-    if (points.size() > 0) {
+    try {
+      List<Point2D> points = lineTransformation.getPointsFromLine(line);
+      if (points.size() > 0) {
 
-      boolean first = true;
-      sb.append(" editPoints=\"");
+        boolean first = true;
+        sb.append(" editPoints=\"");
 
-      for (Point2D point : points) {
-        if (first) {
-          first = false;
-        } else {
-          sb.append(" ");
+        for (Point2D point : points) {
+          if (first) {
+            first = false;
+          } else {
+            sb.append(" ");
+          }
+          sb.append(point.getX() + "," + point.getY());
         }
-        sb.append(point.getX() + "," + point.getY());
+        sb.append("\"");
       }
-      sb.append("\"");
+    } catch (InvalidArgumentException e) {
+      throw new InconsistentModelException(new ElementUtils().getElementTag(modifier) + "Problem with exporting line",
+          e);
     }
 
     sb.append(">\n");
@@ -479,8 +486,9 @@ public class ReactionToXml extends XmlParser {
    * @param reaction
    *          reaction to be processed
    * @return xml node representing annotation part
+   * @throws InconsistentModelException 
    */
-  private String getAnnotationXmlStringForReaction(Reaction reaction) {
+  private String getAnnotationXmlStringForReaction(Reaction reaction) throws InconsistentModelException {
     ReactionLineData rdl = ReactionLineData.getByReactionType(reaction.getClass());
     if (rdl == null) {
       throw new InvalidArgumentException("Unknown reaction type: " + reaction.getClass());

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -135,7 +135,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
       parser.createModel(new ConverterParams().filename("testFiles/invalid/sample10.xml"));
       fail("Exceptin expected");
-    } catch (InvalidArgumentException e) {
+    } catch (InvalidInputDataExecption e) {
       assertTrue(e.getMessage().contains("No type information for modification"));
     } catch (Exception e) {
       e.printStackTrace();

debian/create-debian-pkg.sh

@@ -15,9 +15,6 @@ dbschemadiff=management_scripts/db_schema_and_diff.sh
 #Where source file of the debian package should be placed
 SRC_DIR=debian/src
 
-#where the documentation files are stored
-DOC_DIR=doc
-
 #File that should be deployed on tomcat
 TOMCAT_FILE=web/target/web-1.0.war
 
@@ -42,7 +39,7 @@ mkdir $SRC_DIR
 cp $TOMCAT_FILE $SRC_DIR/minerva.war
 
 #copy manual documentation
-cp $DOC_DIR/description.txt $SRC_DIR/minerva.txt
+cp debian/description.txt $SRC_DIR/minerva.txt
 gzip -n $SRC_DIR/minerva.txt
 
 #copy configuration of logrotate

debian/description.txt

+MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format. After installation, the resource is used and managed via a web browser, under the default address 'http://localhost:8080/minerva/'. You can configure your Tomcat server later to change the address.
+

model-command/pom.xml

@@ -33,6 +33,14 @@
 			<version>${log4j.version}</version>
 		</dependency>
 
+		<!-- mockito used for testing -->
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-core</artifactId>
+			<version>${mockito.version}</version>
+			<scope>test</scope>
+		</dependency>
+
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -40,6 +48,7 @@
 			<scope>test</scope>
 		</dependency>
 
+
 	</dependencies>
 
 </project>
\ No newline at end of file

model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java

@@ -2,12 +2,16 @@ package lcsb.mapviewer.commands;
 
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.log4j.Logger;
+
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -17,8 +21,8 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
 
 /**
  * Command which moves elements in model by dx, dy coordinates.
@@ -28,154 +32,159 @@ import org.apache.log4j.Logger;
  */
 public class MoveElementsCommand extends ModelCommand {
 
-	/**
-	 * Default class logger.
-	 */
-	private final Logger logger				= Logger.getLogger(MoveElementsCommand.class);
-
-	/**
-	 * Delta x.
-	 */
-	private double			 dx;
-
-	/**
-	 * Delta y.
-	 */
-	private double			 dy;
-
-	/**
-	 * List of objects to move.
-	 */
-	private List<Object> objectsToMove = new ArrayList<>();
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param model
-	 *          model to move
-	 * @param elements
-	 *          elements that should be moved
-	 * @param dx
-	 *          delta x
-	 * @param dy
-	 *          delat y
-	 */
-	public MoveElementsCommand(Model model, List<Object> elements, double dx, double dy) {
-		super(model);
-		this.dx = dx;
-		this.dy = dy;
-		for (Object object : elements) {
-			if (object instanceof Element) {
-				if (((Element) object).getModel() != model) {
-					throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
-				}
-			} else if (object instanceof Reaction) {
-				if (((Reaction) object).getModel() != model) {
-					throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
-				}
-			} else {
-				throw new InvalidArgumentException("Cannot move element: " + object);
-			}
-		}
-		objectsToMove = elements;
-	}
-
-	@Override
-	protected void undoImplementation() {
-		dx = -dx;
-		dy = -dy;
-		executeImplementation();
-		dx = -dx;
-		dy = -dy;
-		setStatus(ModelCommandStatus.UNDONE);
-	}
-
-	@Override
-	protected void redoImplementation() {
-		executeImplementation();
-		setStatus(ModelCommandStatus.EXECUTED);
-	}
-
-	@Override
-	protected void executeImplementation() {
-		Set<Element> aliases = new HashSet<>();
-
-		for (Object object : objectsToMove) {
-			if (object instanceof Element) {
-				Element alias = (Element) object;
-
-				includeInAffectedRegion(alias);
-
-				alias.setX(alias.getX() + dx);
-				alias.setY(alias.getY() + dy);
-				if (alias instanceof Compartment) {
-					((Compartment) alias)
-							.setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
-				}
-
-				includeInAffectedRegion(alias);
-
-				aliases.add(alias);
-			} else if (object instanceof Reaction) {
-				Reaction reaction = (Reaction) object;
-				for (Reactant node : reaction.getReactants()) {
-					for (int i = 1; i < node.getLine().getPoints().size(); i++) {
-						Point2D point = node.getLine().getPoints().get(i);
-						logger.debug("Moving point: " + point);
-						point.setLocation(point.getX() + dx, point.getY() + dy);
-					}
-				}
-				for (Product node : reaction.getProducts()) {
-					for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
-						Point2D point = node.getLine().getPoints().get(i);
-						point.setLocation(point.getX() + dx, point.getY() + dy);
-					}
-				}
-				for (Modifier node : reaction.getModifiers()) {
-					for (int i = 1; i < node.getLine().getPoints().size(); i++) {
-						Point2D point = node.getLine().getPoints().get(i);
-						point.setLocation(point.getX() + dx, point.getY() + dy);
-					}
-				}
-				for (NodeOperator node : reaction.getOperators()) {
-					for (int i = 0; i < node.getLine().getPoints().size(); i++) {
-						Point2D point = node.getLine().getPoints().get(i);
-						point.setLocation(point.getX() + dx, point.getY() + dy);
-					}
-				}
-				includeInAffectedRegion(reaction);
-			} else {
-				throw new InvalidStateException("Unknown class type: " + object);
-			}
-		}
-		if (aliases.size() > 0) {
-			// TODO this must be improved, we cannot do full search on every move
-			for (Reaction reaction : getModel().getReactions()) {
-				for (ReactionNode node : reaction.getReactionNodes()) {
-					if (aliases.contains(node.getElement())) {
-						if (node instanceof Reactant) {
-							Point2D point = node.getLine().getBeginPoint();
-							point.setLocation(point.getX() + dx, point.getY() + dy);
-
-							// we don't have to include point that we change as it's already
-							// on the border of the element
-							includeInAffectedRegion(node.getLine().getPoints().get(1));
-						} else if (node instanceof Modifier) {
-							Point2D point = node.getLine().getBeginPoint();
-							point.setLocation(point.getX() + dx, point.getY() + dy);
-							// we don't have to include point that we change as it's already
-							// on the border of the element
-							includeInAffectedRegion(node.getLine().getPoints().get(1));
-						} else if (node instanceof Product) {
-							Point2D point = node.getLine().getEndPoint();
-							point.setLocation(point.getX() + dx, point.getY() + dy);
-							// we don't have to include point that we change as it's already
-							// on the border of the element
-							includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
-						}
-					}
-				}
-			}
-		}
-	}
+  /**
+   * Default class logger.
+   */
+  private final Logger logger = Logger.getLogger(MoveElementsCommand.class);
+
+  /**
+   * Delta x.
+   */
+  private double dx;
+
+  /**
+   * Delta y.
+   */
+  private double dy;
+
+  /**
+   * List of objects to move.
+   */
+  private List<Object> objectsToMove = new ArrayList<>();
+
+  /**
+   * Default constructor.
+   * 
+   * @param model
+   *          model to move
+   * @param elements
+   *          elements that should be moved
+   * @param dx
+   *          delta x
+   * @param dy
+   *          delta y
+   */
+  public MoveElementsCommand(Model model, Collection<? extends BioEntity> elements, double dx, double dy) {
+    super(model);
+    this.dx = dx;
+    this.dy = dy;
+    for (Object object : elements) {
+      if (object instanceof Element) {
+        if (((Element) object).getModel() != model) {
+          throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+        }
+      } else if (object instanceof Reaction) {
+        if (((Reaction) object).getModel() != model) {
+          throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+        }
+      } else {
+        throw new InvalidArgumentException("Cannot move element: " + object);
+      }
+    }
+    objectsToMove.addAll(elements);
+  }
+
+  @Override
+  protected void undoImplementation() {
+    dx = -dx;
+    dy = -dy;
+    executeImplementation();
+    dx = -dx;
+    dy = -dy;
+    setStatus(ModelCommandStatus.UNDONE);
+  }
+
+  @Override
+  protected void redoImplementation() {
+    executeImplementation();
+    setStatus(ModelCommandStatus.EXECUTED);
+  }
+
+  @Override
+  protected void executeImplementation() {
+    Set<Element> aliases = new HashSet<>();
+
+    for (Object object : objectsToMove) {
+      if (object instanceof Element) {
+        Element alias = (Element) object;
+
+        includeInAffectedRegion(alias);
+
+        alias.setX(alias.getX() + dx);
+        alias.setY(alias.getY() + dy);
+        if (alias instanceof Compartment) {
+          ((Compartment) alias)
+              .setNamePoint(((Compartment) alias).getNamePoint().getX() + dx,
+                  ((Compartment) alias).getNamePoint().getY() + dy);
+        }
+        if (alias instanceof SpeciesWithModificationResidue) {
+          for (ModificationResidue mr : ((SpeciesWithModificationResidue) alias).getModificationResidues()) {
+            Point2D position = mr.getPosition();
+            position.setLocation(position.getX() + dx, position.getY() + dy);
+          }
+        }
+        includeInAffectedRegion(alias);
+
+        aliases.add(alias);
+      } else if (object instanceof Reaction) {
+        Reaction reaction = (Reaction) object;
+        for (Reactant node : reaction.getReactants()) {
+          for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+            Point2D point = node.getLine().getPoints().get(i);
+            node.getLine().getPoints().set(i, new Point2D.Double(point.getX() + dx, point.getY() + dy));
+          }
+        }
+        for (Product node : reaction.getProducts()) {
+          for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
+            Point2D point = node.getLine().getPoints().get(i);
+            node.getLine().getPoints().set(i, new Point2D.Double(point.getX() + dx, point.getY() + dy));
+          }
+        }
+        for (Modifier node : reaction.getModifiers()) {
+          for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+            Point2D point = node.getLine().getPoints().get(i);
+            node.getLine().getPoints().set(i, new Point2D.Double(point.getX() + dx, point.getY() + dy));
+          }
+        }
+        for (NodeOperator node : reaction.getOperators()) {
+          for (int i = 0; i < node.getLine().getPoints().size(); i++) {
+            Point2D point = node.getLine().getPoints().get(i);
+            node.getLine().getPoints().set(i, new Point2D.Double(point.getX() + dx, point.getY() + dy));
+          }
+        }
+        includeInAffectedRegion(reaction);
+      } else {
+        throw new InvalidStateException("Unknown class type: " + object);
+      }
+    }
+    if (aliases.size() > 0) {
+      // TODO this must be improved, we cannot do full search on every move
+      for (Reaction reaction : getModel().getReactions()) {
+        for (ReactionNode node : reaction.getReactionNodes()) {
+          if (aliases.contains(node.getElement())) {
+            if (node instanceof Reactant) {
+              Point2D point = node.getLine().getBeginPoint();
+              point.setLocation(point.getX() + dx, point.getY() + dy);
+
+              // we don't have to include point that we change as it's already
+              // on the border of the element
+              includeInAffectedRegion(node.getLine().getPoints().get(1));
+            } else if (node instanceof Modifier) {
+              Point2D point = node.getLine().getBeginPoint();
+              point.setLocation(point.getX() + dx, point.getY() + dy);
+              // we don't have to include point that we change as it's already
+              // on the border of the element
+              includeInAffectedRegion(node.getLine().getPoints().get(1));
+            } else if (node instanceof Product) {
+              Point2D point = node.getLine().getEndPoint();
+              point.setLocation(point.getX() + dx, point.getY() + dy);
+              // we don't have to include point that we change as it's already
+              // on the border of the element
+              includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
+            }
+          }
+        }
+      }
+    }
+  }
 }

model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java

@@ -13,9 +13,11 @@ import java.util.List;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
+import org.mockito.Mockito;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -23,255 +25,255 @@ import lcsb.mapviewer.model.map.species.Element;
 
 public class MoveElementsCommandTest extends CommandTestFunctions {
 
-	ModelComparator modelComparator = new ModelComparator();
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testMoveAlias() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Element alias = model.getElementByElementId("sa2");
-			Element alias2 = model.getElementByElementId("sa1");
-			double anotherAliasX = alias2.getX();
-			double anotherAliasY = alias2.getY();
-
-			List<Object> list = new ArrayList<>();
-			list.add(alias);
-			double x = alias.getX();
-			double y = alias.getY();
-
-			double dx = 10;
-			double dy = 2;
-
-			// models should be equal before move
-			assertEquals(0, modelComparator.compare(model, model2));
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
-			moveCommand.execute();
-
-			// after move models should be different
-			assertTrue(0 != modelComparator.compare(model, model2));
-
-			// check new coordinates
-			assertEquals(x + dx, alias.getX(), Configuration.EPSILON);
-			assertEquals(y + dy, alias.getY(), Configuration.EPSILON);
-
-			// and check if another alias didn't change coordinates
-			assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
-			assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
-			list = new ArrayList<>();
-			list.add(model2.getElementByElementId("sa2"));
-			MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
-			moveCommand2.execute();
-
-			// if we perfomr the same operator on the second model then they should be
-			// equal
-			assertEquals(0, modelComparator.compare(model, model2));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testMoveSpecies() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			List<Object> list = new ArrayList<>();
-			list.add(new Object());
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, 10, 10);
-			moveCommand.execute();
-			fail("Exception expected");
-
-		} catch (InvalidArgumentException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testAliasWithReaction() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Element alias = model.getElementByElementId("sa1");
-			Element alias2 = model.getElementByElementId("sa2");
-			double anotherAliasX = alias2.getX();
-			double anotherAliasY = alias2.getY();
-			Reaction reaction = model.getReactionByReactionId("re1");
-
-			List<Object> list = new ArrayList<>();
-			list.add(alias);
-			double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
-			double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
-
-			double dx = 10;
-			double dy = 2;
-
-			// models should be equal before move
-			assertEquals(0, modelComparator.compare(model, model2));
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
-			moveCommand.execute();
-
-			// after move models should be different
-			assertTrue(0 != modelComparator.compare(model, model2));
-
-			// check new coordinates of reaction
-			assertEquals(x + dx, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
-			assertEquals(y + dy, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
-
-			// and check if another alias didn't change coordinates
-			assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
-			assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
-			list = new ArrayList<>();
-			list.add(model2.getElementByElementId("sa1"));
-			MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
-			moveCommand2.execute();
-
-			// if we perfomr the same operator on the second model then they should be
-			// equal
-			assertEquals(0, modelComparator.compare(model, model2));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testMoveReaction() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Element alias2 = model.getElementByElementId("sa1");
-			double anotherAliasX = alias2.getX();
-			double anotherAliasY = alias2.getY();
-			Reaction reaction = model.getReactionByReactionId("re1");
-
-			List<Object> list = new ArrayList<>();
-			list.add(reaction);
-			double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
-			double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
-
-			double x2 = reaction.getReactants().get(0).getLine().getEndPoint().getX();
-			double y2 = reaction.getReactants().get(0).getLine().getEndPoint().getY();
-
-			double dx = 10;
-			double dy = 2;
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
-			moveCommand.execute();
-
-			// check new coordinates of reaction (point attached to alias shouldn't
-			// move, the one not attached should move)
-			assertEquals(x, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
-			assertEquals(y, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
-			assertEquals(x2 + dx, reaction.getReactants().get(0).getLine().getEndPoint().getX(), Configuration.EPSILON);
-			assertEquals(y2 + dy, reaction.getReactants().get(0).getLine().getEndPoint().getY(), Configuration.EPSILON);
-
-			// and check if another alias didn't change coordinates
-			assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
-			assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testUndo() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Element alias = model.getElementByElementId("sa2");
-
-			List<Object> list = new ArrayList<>();
-			list.add(alias);
-
-			double dx = 10;
-			double dy = 2;
-
-			// models should be equal before move
-			assertEquals(0, modelComparator.compare(model, model2));
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
-			moveCommand.execute();
-
-			// after move models should be different
-			assertTrue(0 != modelComparator.compare(model, model2));
-
-			// undo command
-			moveCommand.undo();
-
-			// after undo they should be the same again
-			assertEquals(0, modelComparator.compare(model, model2));
-
-			moveCommand.redo();
-
-			// after redo they should be different again
-			assertTrue(0 != modelComparator.compare(model, model2));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetAffectedRegion() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
-			Element alias = model.getElementByElementId("sa2");
-
-			List<Object> list = new ArrayList<>();
-			list.add(alias);
-			double x = alias.getX();
-			double y = alias.getY();
-
-			double dx = 10;
-			double dy = 2;
-
-			double minx = x;
-			double maxx = alias.getWidth() + x + dx;
-
-			double miny = y;
-			double maxy = alias.getHeight() + y + dy;
-
-			MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
-			assertNull(moveCommand.getAffectedRegion());
-			moveCommand.execute();
-			assertNotNull(moveCommand.getAffectedRegion());
-			Rectangle2D affectedRegion = moveCommand.getAffectedRegion();
-			assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
-			assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
-			assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
-			assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
-
-			moveCommand.undo();
-
-			affectedRegion = moveCommand.getAffectedRegion();
-			assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
-			assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
-			assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
-			assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
+  ModelComparator modelComparator = new ModelComparator();
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testMoveAlias() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Element alias = model.getElementByElementId("sa2");
+      Element alias2 = model.getElementByElementId("sa1");
+      double anotherAliasX = alias2.getX();
+      double anotherAliasY = alias2.getY();
+
+      List<BioEntity> list = new ArrayList<>();
+      list.add(alias);
+      double x = alias.getX();
+      double y = alias.getY();
+
+      double dx = 10;
+      double dy = 2;
+
+      // models should be equal before move
+      assertEquals(0, modelComparator.compare(model, model2));
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+      moveCommand.execute();
+
+      // after move models should be different
+      assertTrue(0 != modelComparator.compare(model, model2));
+
+      // check new coordinates
+      assertEquals(x + dx, alias.getX(), Configuration.EPSILON);
+      assertEquals(y + dy, alias.getY(), Configuration.EPSILON);
+
+      // and check if another alias didn't change coordinates
+      assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+      assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+      list = new ArrayList<>();
+      list.add(model2.getElementByElementId("sa2"));
+      MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
+      moveCommand2.execute();
+
+      // if we perfomr the same operator on the second model then they should be
+      // equal
+      assertEquals(0, modelComparator.compare(model, model2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testMoveSpecies() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      List<BioEntity> list = new ArrayList<>();
+      list.add(Mockito.mock(BioEntity.class));
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, 10, 10);
+      moveCommand.execute();
+      fail("Exception expected");
+
+    } catch (InvalidArgumentException e) {
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testAliasWithReaction() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Element alias = model.getElementByElementId("sa1");
+      Element alias2 = model.getElementByElementId("sa2");
+      double anotherAliasX = alias2.getX();
+      double anotherAliasY = alias2.getY();
+      Reaction reaction = model.getReactionByReactionId("re1");
+
+      List<BioEntity> list = new ArrayList<>();
+      list.add(alias);
+      double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
+      double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
+
+      double dx = 10;
+      double dy = 2;
+
+      // models should be equal before move
+      assertEquals(0, modelComparator.compare(model, model2));
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+      moveCommand.execute();
+
+      // after move models should be different
+      assertTrue(0 != modelComparator.compare(model, model2));
+
+      // check new coordinates of reaction
+      assertEquals(x + dx, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
+      assertEquals(y + dy, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
+
+      // and check if another alias didn't change coordinates
+      assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+      assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+      list = new ArrayList<>();
+      list.add(model2.getElementByElementId("sa1"));
+      MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
+      moveCommand2.execute();
+
+      // if we perfomr the same operator on the second model then they should be
+      // equal
+      assertEquals(0, modelComparator.compare(model, model2));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testMoveReaction() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Element alias2 = model.getElementByElementId("sa1");
+      double anotherAliasX = alias2.getX();
+      double anotherAliasY = alias2.getY();
+      Reaction reaction = model.getReactionByReactionId("re1");
+
+      List<BioEntity> list = new ArrayList<>();
+      list.add(reaction);
+      double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
+      double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
+
+      double x2 = reaction.getReactants().get(0).getLine().getEndPoint().getX();
+      double y2 = reaction.getReactants().get(0).getLine().getEndPoint().getY();
+
+      double dx = 10;
+      double dy = 2;
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+      moveCommand.execute();
+
+      // check new coordinates of reaction (point attached to alias shouldn't
+      // move, the one not attached should move)
+      assertEquals(x, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
+      assertEquals(y, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
+      assertEquals(x2 + dx, reaction.getReactants().get(0).getLine().getEndPoint().getX(), Configuration.EPSILON);
+      assertEquals(y2 + dy, reaction.getReactants().get(0).getLine().getEndPoint().getY(), Configuration.EPSILON);
+
+      // and check if another alias didn't change coordinates
+      assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+      assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testUndo() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Element alias = model.getElementByElementId("sa2");
+
+      List<BioEntity> list = new ArrayList<>();
+      list.add(alias);
+
+      double dx = 10;
+      double dy = 2;
+
+      // models should be equal before move
+      assertEquals(0, modelComparator.compare(model, model2));
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+      moveCommand.execute();
+
+      // after move models should be different
+      assertTrue(0 != modelComparator.compare(model, model2));
+
+      // undo command
+      moveCommand.undo();
+
+      // after undo they should be the same again
+      assertEquals(0, modelComparator.compare(model, model2));
+
+      moveCommand.redo();
+
+      // after redo they should be different again
+      assertTrue(0 != modelComparator.compare(model, model2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testGetAffectedRegion() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+      Element alias = model.getElementByElementId("sa2");
+
+      List<BioEntity> list = new ArrayList<>();
+      list.add(alias);
+      double x = alias.getX();
+      double y = alias.getY();
+
+      double dx = 10;
+      double dy = 2;
+
+      double minx = x;
+      double maxx = alias.getWidth() + x + dx;
+
+      double miny = y;
+      double maxy = alias.getHeight() + y + dy;
+
+      MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+      assertNull(moveCommand.getAffectedRegion());
+      moveCommand.execute();
+      assertNotNull(moveCommand.getAffectedRegion());
+      Rectangle2D affectedRegion = moveCommand.getAffectedRegion();
+      assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
+      assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
+      assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
+      assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
+
+      moveCommand.undo();
+
+      affectedRegion = moveCommand.getAffectedRegion();
+      assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
+      assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
+      assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
+      assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
 
 }

model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java

@@ -22,6 +22,10 @@ public class InconsistentModelException extends Exception {
     super(message);
   }
 
+  public InconsistentModelException(String message, Throwable e) {
+    super(message, e);
+  }
+
   public InconsistentModelException(Exception e) {
     super(e);
   }

model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java

@@ -260,7 +260,11 @@ public final class ElementUtils {
   }
 
   public String getElementTag(ReactionNode node) {
-    return "[" + node.getClass().getSimpleName() + "]" + getElementTag(node.getElement());
+    String reactionPrefix = "";
+    if (node.getReaction() != null) {
+      reactionPrefix = getElementTag(node.getReaction()).replaceAll("\t", "");
+    }
+    return reactionPrefix + "[" + node.getClass().getSimpleName() + "]" + getElementTag(node.getElement());
   }
 
   public String getElementTag(ModificationResidue mr) {