diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index 25fbd300a7cc51d34d57a923dc724d6735c3adc8..0f3fbea1f767125d5922bbed62ae53ee300e4999 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -15,6 +15,9 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
+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.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
@@ -164,12 +167,60 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
result &= isVisible(complex, params);
}
}
+ } else if (bioEntity instanceof Reaction) {
+ if (!isAnyProductVisible(((Reaction) bioEntity).getProducts(), params)) {
+ result = false;
+ } else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
+ result = false;
+ }
+
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
}
+
return result;
}
return true;
}
+ /**
+ * Checks if at least one reactant is visible.
+ *
+ * @param reactants
+ * list of reactants
+ * @param params
+ * params against which check is run
+ * @return true if at least one reactant is visible
+ */
+ private boolean isAnyReactantVisible(List<Reactant> reactants, ConverterParams params) {
+ boolean result = false;
+ for (Reactant reactant : reactants) {
+ if (isVisible(reactant, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Checks if at least one product is visible.
+ *
+ * @param products
+ * list of products
+ * @param params
+ * params against which check is run
+ * @return true if at least one product is visible
+ */
+ private boolean isAnyProductVisible(List<Product> products, ConverterParams params) {
+ boolean result = false;
+ for (Product product : products) {
+ if (isVisible(product, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
/**
* Checks if level belongs to the range defined in
* semanticZoomLevelVisibility.
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
index 940785356395983a48c340979d981a2d65ffd175..712c9d780cc68a7801c4536f6d38d703ec5d54e6 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
@@ -1,19 +1,18 @@
package lcsb.mapviewer.converter.graphics;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AllSpeciesConverterTests;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.AllReactionTests;
-import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
-import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
-
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.converter.graphics.bioEntity.AllBioEntityTests;
+import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
+import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
+
@RunWith(Suite.class)
-@SuiteClasses({ AllGeometryTests.class, //
+@SuiteClasses({ //
+ AllBioEntityTests.class, //
+ AllGeometryTests.class, //
AllPlaceFinderTest.class, //
- AllReactionTests.class, //
- AllSpeciesConverterTests.class, //
ConverterTest.class, //
ImageGeneratorsTest.class, //
MapGeneratorTest.class, //
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..4feec5c7d2f55a7a9f1e0888bc0ac822acb149ef
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AllSpeciesConverterTests;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.AllReactionTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ //
+ AllSpeciesConverterTests.class, //
+ AllReactionTests.class, //
+ BioEntityConverterImplTest.class//
+})
+public class AllBioEntityTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8ba25ceb5b694c44954955c85a691d880e1aa439
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -0,0 +1,98 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+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.GenericProtein;
+
+public class BioEntityConverterImplTest {
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ Reaction reaction = createReaction(1.0);
+ reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ private Reaction createReaction(double lineWidth) {
+ Reaction result = new Reaction();
+
+ Modifier modifier = new Catalysis(new GenericProtein("s1"));
+ modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
+ modifier.getLine().setWidth(lineWidth);
+
+ Reactant reactant = new Reactant(new GenericProtein("s2"));
+ reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
+ reactant.getLine().setWidth(lineWidth);
+ Product product = new Product(new GenericProtein("s3"));
+ product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
+ product.getLine().setWidth(lineWidth);
+ result.addModifier(modifier);
+ result.addProduct(product);
+ result.addReactant(reactant);
+ return result;
+ }
+
+}