diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index 60a9e523a44bd658d76b30de7ab3e6ee9c2f2408..29de42936083bc05aabc03ef9853ea2c56d9a1b5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/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);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 93b36d3da15633ba9456a0ba187c5a2b79e05347..aaf6deac15abb02301c9d109aad3d4d678fa26ac 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/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());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 2cefdb5ec198f1385754e9538e8bde15ea3a2ca7..08d31257d193971461c3bade4575d7180ad34a9d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/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();
diff --git a/debian/create-debian-pkg.sh b/debian/create-debian-pkg.sh
index f56f8a9e045a0f40be2f448058b2861d94eec53d..6eef85de2294e01a8bf6b202ae9e1c94ab17395f 100755
--- a/debian/create-debian-pkg.sh
+++ b/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 $SRC_DIR/minerva.txt
#copy configuration of logrotate
diff --git a/debian/description.txt b/debian/description.txt
new file mode 100644
index 0000000000000000000000000000000000000000..786ee1cd6ad012b1cbf42a3416065e159d911af0
--- /dev/null
+++ b/debian/description.txt
@@ -0,0 +1,2 @@
+MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format. After installation, the resource is used and managed via a web browser, under the default address 'http://localhost:8080/minerva/'. You can configure your Tomcat server later to change the address.
+
diff --git a/model-command/pom.xml b/model-command/pom.xml
index df81c883631b7962fb23df500f944a35a3fd1328..a6d6b9166e5e5d8ba19f8ceef4098a0756356950 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -33,6 +33,14 @@
<version>${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
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
index ab6002da40becb5143b83e4a654e27efbc8f82af..db732b843dea35067f42c58c7af2b1b98688064c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ b/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));
+ }
+ }
+ }
+ }
+ }
+ }
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
index 17bb61852042416a7a9606c5d082de6ac04f4b9b..efc14fabd446a75566b134306fdf54b86caedeb7 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
+++ b/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;
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java b/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
index 2cfa3c8905b6cfa9ad2f417de46b495675165d65..b685b338060a4adf6ea4e84ab74a7cb7bdd1738b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
+++ b/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);
}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 5313c5b44f9ddb33b98d4fc1981c46e7e9f43957..932fb236d818ac071d286672d21a0954b40d1bb3 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/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) {