default populator of z-index implemented

converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java

+package lcsb.mapviewer.converter;
+
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+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.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This util class populate with z-index data if necessary.
+ * 
+ * @author Piotr Gawron
+ *
+ */
+public class ZIndexPopulator {
+
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(ZIndexPopulator.class);
+
+  private DoubleComparator doubleComparator = new DoubleComparator(Configuration.EPSILON);
+  private StringComparator stringComparator = new StringComparator();
+
+  /**
+   * Populate all elements that don't have z-index with valid values. Elements
+   * without z-index would have bigger z-values than elements with existing
+   * z-values.
+   * 
+   * @param model
+   */
+  public void populateZIndex(Model model) {
+    int maxZIndex = 0;
+
+    List<BioEntity> bioEntities = new ArrayList<>();
+    bioEntities.addAll(model.getBioEntities());
+    bioEntities.sort(new Comparator<BioEntity>() {
+      @Override
+      public int compare(BioEntity o1, BioEntity o2) {
+        if (o1 instanceof Reaction) {
+          if (o2 instanceof Reaction) {
+            return stringComparator.compare(o1.getElementId(), o2.getElementId());
+          }
+          return -1;
+        }
+        if (o2 instanceof Reaction) {
+          return 1;
+        }
+        Element e1 = (Element) o1;
+        Element e2 = (Element) o2;
+
+        if (isChildren(e1, e2)) {
+          return -1;
+        }
+        if (isChildren(e2, e1)) {
+          return 1;
+        }
+
+        int result = -doubleComparator.compare(e1.getSize(), e2.getSize());
+        if (result == 0) {
+          result = stringComparator.compare(e1.getElementId(), e2.getElementId());
+        }
+
+        return result;
+      }
+
+      private boolean isChildren(Element e1, Element e2) {
+        if (e1 instanceof Complex && e2 instanceof Species) {
+          Complex parent = (Complex) e1;
+          Species child = (Species) e2;
+          return parent.getAllSimpleChildren().contains(child);
+        }
+        if (e1 instanceof Compartment) {
+          Compartment parent = (Compartment) e1;
+          return parent.getAllSubElements().contains(e2);
+        }
+        return false;
+      }
+    });
+
+    for (BioEntity bioEntity : bioEntities) {
+      if (bioEntity.getZ() != null) {
+        maxZIndex = Math.max(maxZIndex, bioEntity.getZ());
+      }
+    }
+
+    for (BioEntity bioEntity : bioEntities) {
+      if (bioEntity.getZ() == null) {
+        bioEntity.setZ(++maxZIndex);
+      }
+    }
+
+  }
+}

converter/src/test/java/lcsb/mapviewer/converter/AllTests.java

@@ -12,6 +12,7 @@ import lcsb.mapviewer.converter.annotation.XmlAnnotationParserTest;
     OverviewParserTest.class,
     ProjectFactoryTest.class,
     XmlAnnotationParserTest.class,
+    ZIndexPopulatorTest.class
 })
 public class AllTests {
 

converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java

+package lcsb.mapviewer.converter;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ZIndexPopulatorTest {
+
+  Logger logger = Logger.getLogger(ZIndexPopulatorTest.class);
+
+  int identifierCounter = 0;
+
+  @Test
+  public void testMixZIndexValuesInSpecies() {
+    Model model = new ModelFullIndexed(null);
+    Species speciesWithoutZIndex = createProtein();
+    model.addElement(speciesWithoutZIndex);
+
+    Species speciesWithZIndex = createProtein();
+    speciesWithZIndex.setZ(100);
+    model.addElement(speciesWithZIndex);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertNotNull(speciesWithoutZIndex.getZ());
+
+    assertTrue(speciesWithoutZIndex.getZ() > speciesWithZIndex.getZ());
+  }
+
+  @Test
+  public void testZIndexBySpeciesSize() {
+    Model model = new ModelFullIndexed(null);
+    Species microSpecies = createProtein();
+    microSpecies.setWidth(1);
+    microSpecies.setHeight(1);
+    model.addElement(microSpecies);
+
+    Species biggerSpecies = createProtein();
+    biggerSpecies.setWidth(100);
+    biggerSpecies.setHeight(100);
+    model.addElement(biggerSpecies);
+
+    Species smallerSpecies = createProtein();
+    smallerSpecies.setWidth(10);
+    smallerSpecies.setHeight(10);
+    model.addElement(smallerSpecies);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertTrue(biggerSpecies.getZ() < smallerSpecies.getZ());
+    assertTrue(smallerSpecies.getZ() < microSpecies.getZ());
+  }
+
+  @Test
+  public void testZIndexReactionShouldBeBeforeElement() {
+    Model model = new ModelFullIndexed(null);
+    Species species = createProtein();
+    species.setWidth(1);
+    species.setHeight(1);
+    model.addElement(species);
+
+    Reaction reaction = createReaction();
+    model.addReaction(reaction);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertTrue(reaction.getZ() < species.getZ());
+  }
+
+  @Test
+  public void testZIndexEqualSizeByElementId() {
+    Model model = new ModelFullIndexed(null);
+    Species firstSpecies = createProtein();
+    firstSpecies.setWidth(1);
+    firstSpecies.setHeight(1);
+    model.addElement(firstSpecies);
+
+    Species secondSpecies = createProtein();
+    secondSpecies.setWidth(1);
+    secondSpecies.setHeight(1);
+    model.addElement(secondSpecies);
+
+    Species thirdSpecies = createProtein();
+    thirdSpecies.setWidth(1);
+    thirdSpecies.setHeight(1);
+    model.addElement(thirdSpecies);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertTrue(firstSpecies.getZ() < secondSpecies.getZ());
+    assertTrue(secondSpecies.getZ() < thirdSpecies.getZ());
+  }
+
+  @Test
+  public void testZIndexComplexChildren() {
+    Model model = new ModelFullIndexed(null);
+    Complex complex = createComplex();
+    complex.setWidth(1);
+    complex.setHeight(1);
+    model.addElement(complex);
+
+    Species child = createProtein();
+    child.setWidth(10);
+    child.setHeight(10);
+    model.addElement(child);
+
+    complex.addSpecies(child);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertTrue(complex.getZ() < child.getZ());
+  }
+
+  @Test
+  public void testZIndexCompartmentChildren() {
+    Model model = new ModelFullIndexed(null);
+    Compartment compartment = createCompartment();
+    compartment.setWidth(1);
+    compartment.setHeight(1);
+    model.addElement(compartment);
+
+    Compartment childCompartment = createCompartment();
+    childCompartment.setWidth(2);
+    childCompartment.setHeight(2);
+    model.addElement(childCompartment);
+    compartment.addElement(childCompartment);
+
+    Species child = createProtein();
+    child.setWidth(10);
+    child.setHeight(10);
+    model.addElement(child);
+
+    childCompartment.addElement(child);
+
+    ZIndexPopulator populator = new ZIndexPopulator();
+    populator.populateZIndex(model);
+
+    assertTrue(compartment.getZ() < childCompartment.getZ());
+    assertTrue(childCompartment.getZ() < child.getZ());
+  }
+
+  private Species createProtein() {
+    GenericProtein result = new GenericProtein("s" + identifierCounter++);
+    return result;
+  }
+
+  private Complex createComplex() {
+    Complex result = new Complex("s" + identifierCounter++);
+    return result;
+  }
+
+  private Compartment createCompartment() {
+    Compartment result = new Compartment("s" + identifierCounter++);
+    return result;
+  }
+
+  private Reaction createReaction () {
+    Reaction result = new TransportReaction("s" + identifierCounter++);
+    return result;
+  }
+
+
+}