diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 0eb5e5f8634ca3888e7abc88619937417a0938c6..afd349aacbefceb9ab4f0dfb11c9689219ce0587 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -700,9 +700,12 @@ public abstract class AbstractImageGenerator {
for (Layer layer : params.getModel().getLayers()) {
drawLayer(layer);
}
+ closeImageObject();
setDrawn(true);
}
+ protected abstract void closeImageObject();
+
/**
* This method draw layer on the graphics.
*
@@ -840,13 +843,9 @@ public abstract class AbstractImageGenerator {
if (rescale) {
customScale = scale;
}
- try {
- converter.draw(
- species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
- visibleLayouts);
- } catch (Exception e) {
- throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
- }
+ converter.draw(
+ species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
+ visibleLayouts);
// if the species is a complex then we may want to draw children
// objects
@@ -874,8 +873,9 @@ public abstract class AbstractImageGenerator {
* list of {@link ColorSchema} used for coloring reaction in layouts
* @param params
* list of all params to create apropriate image
+ * @throws DrawingException
*/
- protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) {
+ protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
if (!cross(reaction.getLines())) {
return;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
index 142bb59baf31c1dcebdb87bce71b15562b4aeaf2..c903920061e6d139072d4238d6f39fbf417d70b9 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
@@ -77,4 +77,8 @@ public class JpgImageGenerator extends NormalImageGenerator {
return "jpg";
}
+ @Override
+ protected void closeImageObject() {
+ }
+
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
index 61091747ec0731ab0d0b163645d9db2f1c309f79..504b4e2d1cbd31e084318e5ef79474468dbc70f3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
@@ -74,6 +74,10 @@ public class PdfImageGenerator extends AbstractImageGenerator {
*/
public PdfImageGenerator(final Params params) throws DrawingException {
super(params);
+ }
+
+ @Override
+ protected void closeImageObject() {
getGraphics().dispose();
pdfDocument.close();
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
index 50729fb7b580511a62f97b741992f73b0751cf24..77f65da695c922cf7d192656de4907e9b7301dea 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
@@ -43,6 +43,10 @@ public class PngImageGenerator extends NormalImageGenerator {
super(params);
}
+ @Override
+ protected void closeImageObject() {
+ }
+
@Override
public void saveToFileImplementation(String fileName) throws IOException {
FileOutputStream fos = new FileOutputStream(new File(fileName));
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
index ff95faa79d716559593c7f25cc710cc77ec55fca..bf97fec4fdbd82a3f0e544c08deeea55f24c72cf 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
@@ -57,6 +57,10 @@ public class SvgImageGenerator extends AbstractImageGenerator {
super(params);
}
+ @Override
+ protected void closeImageObject() {
+ }
+
@Override
public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
((SVGGraphics2D) getGraphics()).stream(new OutputStreamWriter(os));
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 9575da4d8082aded32214a61a844fba09715c2bf..2bf39b74d6e17b23e67cf08e4f5df83b037dd5e8 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
@@ -60,9 +60,10 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* visuzalization params (like, should the object be filled with
* solid color, etc.), for more information see
* {@link ConverterParams}
+ * @throws DrawingException
*
*/
- public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) {
+ public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
draw(bioEntity, graphics, params, new ArrayList<>());
}
@@ -81,9 +82,10 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* list of {@link ColorSchema} that were used for visualizing this
* bioentity in different data overlays that should be overlayed on
* the alias
+ * @throws DrawingException
*
*/
- public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas);
+ public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas) throws DrawingException;
/**
* This function will find proper font size to display text within it. Then it
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index 6f71c865dce77931cf7c3ebb27c619d3c464a177..ee41d7e57230d4bf9f2d6cd51d5cce7839774117 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -189,9 +189,13 @@ public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
@SuppressWarnings("unchecked")
@Override
- public void draw(BioEntity element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- if (isVisible(element, params)) {
- elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ public void draw(BioEntity element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ try {
+ if (isVisible(element, params)) {
+ elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ }
+ } catch (Exception e) {
+ throw new DrawingException(new ElementUtils().getElementTag(element) + "Problem with drawing element.", e);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index b3291603acb9700c5969164c6950ea93d79c0444..7e3a88ad40c62f07c52b5ecf39596aed225ef92a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
@@ -15,6 +15,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
@@ -179,7 +180,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
}
@Override
- public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
draw(alias, graphics, params);
Color oldColor = graphics.getColor();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 82edaed71deeef1652acfb4d66c4383cdb99e8ef..fb2460619fcd85d355aac51b301c351525d48b53 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -22,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -579,7 +580,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
@Override
- public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
draw(alias, graphics, params);
Color oldColor = graphics.getColor();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d061d78bbbc99bcd218723ffdd07127bca08cd52
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java
@@ -0,0 +1,114 @@
+package lcsb.mapviewer.converter.graphics;
+
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+import java.awt.Graphics2D;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+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 AbstractImageGeneratorTest extends GraphicsTestFunctions {
+ Logger logger = Logger.getLogger(AbstractImageGeneratorTest.class);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawSimpleMap() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+
+ Model model = createSimpleModel();
+
+ AbstractImageGenerator gen = createAbstractImageGeneratorMock(graphics, model);
+ gen.draw();
+
+ //3 times for proteins and 4 times for reaction
+ verify(graphics, times(7)).draw(any());
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ private Model createSimpleModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(100);
+ model.setHeight(100);
+
+ GenericProtein protein1 = new GenericProtein("s1");
+ protein1.setX(10);
+ protein1.setY(10);
+ protein1.setWidth(10);
+ protein1.setHeight(10);
+ model.addElement(protein1);
+
+ GenericProtein protein2 = new GenericProtein("s2");
+ protein2.setX(30);
+ protein2.setY(10);
+ protein2.setWidth(10);
+ protein2.setHeight(10);
+ model.addElement(protein2);
+
+ GenericProtein protein3 = new GenericProtein("s3");
+ protein3.setX(40);
+ protein3.setY(10);
+ protein3.setWidth(10);
+ protein3.setHeight(10);
+ model.addElement(protein3);
+
+ Reaction reaction = new Reaction();
+
+ Modifier modifier = new Catalysis(protein1);
+ modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
+ modifier.getLine().setWidth(1.0);
+
+ Reactant reactant = new Reactant(protein2);
+ reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
+ reactant.getLine().setWidth(1.0);
+ Product product = new Product(protein3);
+ product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
+ product.getLine().setWidth(1.0);
+ reaction.addModifier(modifier);
+ reaction.addProduct(product);
+ reaction.addReactant(reactant);
+
+ model.addReaction(reaction);
+
+ return model;
+ }
+
+ private AbstractImageGenerator createAbstractImageGeneratorMock(Graphics2D graphics, Model model) throws Exception {
+ AbstractImageGenerator result = Mockito.mock(AbstractImageGenerator.class, Mockito.CALLS_REAL_METHODS);
+ result.setGraphics(graphics);
+ result.setParams(new AbstractImageGenerator.Params().model(model));
+ return result;
+
+ }
+
+}
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 712c9d780cc68a7801c4536f6d38d703ec5d54e6..582a1ddc3925a75f8eed2bb51f74d82a571f8156 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
@@ -10,6 +10,7 @@ import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
@RunWith(Suite.class)
@SuiteClasses({ //
+ AbstractImageGeneratorTest.class, //
AllBioEntityTests.class, //
AllGeometryTests.class, //
AllPlaceFinderTest.class, //
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java
new file mode 100644
index 0000000000000000000000000000000000000000..4cea69b99bf72038251af115595abf4cbd6ef8cb
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java
@@ -0,0 +1,21 @@
+package lcsb.mapviewer.converter.graphics;
+
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.when;
+
+import java.awt.FontMetrics;
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
+
+import org.mockito.Mockito;
+
+public abstract class GraphicsTestFunctions {
+ protected Graphics2D createGraphicsMock() {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ FontMetrics fontMetrics = Mockito.mock(FontMetrics.class);
+ when(fontMetrics.getStringBounds(any(), any())).thenReturn(new Rectangle2D.Double());
+ when(graphics.getFontMetrics()).thenReturn(fontMetrics);
+ return graphics;
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index 2606bb7c8316829dbfbaf55fd27962281de03e56..f5f24088412eedb983923420f2cb1cac7a9f5ea6 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -4,14 +4,11 @@ import static org.junit.Assert.assertTrue;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
import java.awt.Color;
-import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.geom.GeneralPath;
import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.Arrays;
@@ -27,6 +24,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -40,7 +38,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
import lcsb.mapviewer.model.map.species.GenericProtein;
-public class ReactionConverterTest {
+public class ReactionConverterTest extends GraphicsTestFunctions {
ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
@@ -359,14 +357,6 @@ public class ReactionConverterTest {
}
}
- private Graphics2D createGraphicsMock() {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- FontMetrics fontMetrics = Mockito.mock(FontMetrics.class);
- when(fontMetrics.getStringBounds(any(), any())).thenReturn(new Rectangle2D.Double());
- when(graphics.getFontMetrics()).thenReturn(fontMetrics);
- return graphics;
- }
-
@Test
public void testDrawComplexReactionWithSemanticZoomingAndReactantOff() throws Exception {
try {
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/MinervaCanvas.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/MinervaCanvas.java
index 454cdb3aff0a46101091518f3d1ae6d7c4b8591c..7190343e89fedb9dde647437d9ba316d9fd2f0c0 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/MinervaCanvas.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/MinervaCanvas.java
@@ -409,6 +409,10 @@ public class MinervaCanvas extends JComponent {
throw new NotImplementedException();
}
+ @Override
+ protected void closeImageObject() {
+ }
+
}
try {
if (lastBufferedData == null || Math.abs(lastBufferedData.getZoom() - zoom) > Configuration.EPSILON) {