dimer cardinality is drawn twice only when different values are provided from sbgn

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java

@@ -72,14 +72,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
   @Override
   protected void drawImpl(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
 
-    java.util.List<String> unitOfInformationText = new ArrayList<>();
-    if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
-      if (protein.getStatePrefix().equals("free input")) {
-        unitOfInformationText.add(protein.getStateLabel());
-      } else {
-        unitOfInformationText.add(protein.getStatePrefix() + ":" + protein.getStateLabel());
-      }
-    }
+    java.util.List<String> unitOfInformationText = getUnitOfInformation(protein);
 
     int homodir = protein.getHomodimer();
 
@@ -120,6 +113,18 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
     protein.setHeight(protein.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
   }
 
+  protected java.util.List<String> getUnitOfInformation(final Protein protein) {
+    java.util.List<String> unitOfInformationText = new ArrayList<>();
+    if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
+      if (protein.getStatePrefix().equals("free input")) {
+        unitOfInformationText.add(protein.getStateLabel());
+      } else {
+        unitOfInformationText.add(protein.getStatePrefix() + ":" + protein.getStateLabel());
+      }
+    }
+    return unitOfInformationText;
+  }
+
   void drawActivityShape(final Protein protein, final Graphics2D graphics) {
     if (protein instanceof GenericProtein && protein.getActivity()) {
       drawActivityGenericProtein(protein, graphics);

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinSbgnConverter.java

 package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
 
-import java.awt.*;
+import java.awt.Graphics2D;
+import java.awt.Shape;
 import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
@@ -38,14 +38,7 @@ public class ProteinSbgnConverter extends ProteinConverter {
 
   @Override
   protected void drawImpl(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
-    List<String> unitOfInformationText = new ArrayList<>();
-    if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
-      if (protein.getStatePrefix().equals("free input")) {
-        unitOfInformationText.add(protein.getStateLabel());
-      } else {
-        unitOfInformationText.add(protein.getStatePrefix() + ":" + protein.getStateLabel());
-      }
-    }
+    List<String> unitOfInformationText = getUnitOfInformation(protein);
 
     int originalHomodimer = protein.getHomodimer();
     int homodir;
@@ -56,10 +49,15 @@ public class ProteinSbgnConverter extends ProteinConverter {
     }
 
     protein.setHomodimer(homodir);
-
     super.drawImpl(protein, graphics, params);
     protein.setHomodimer(originalHomodimer);
+    
+    drawUnitOfInformation(unitOfInformationText, protein, graphics);
+  }
 
+  @Override
+  protected List<String> getUnitOfInformation(final Protein protein) {
+    List<String> unitOfInformationText = super.getUnitOfInformation(protein);
     if (protein instanceof IonChannelProtein) {
       if (protein.getActivity()) {
         unitOfInformationText.add("open");
@@ -68,20 +66,20 @@ public class ProteinSbgnConverter extends ProteinConverter {
       }
     }
 
-    if (homodir > 1) {
-      unitOfInformationText.add("N:" + Integer.toString(protein.getHomodimer()));
+    if (protein.getHomodimer() > 1) {
+      String unit = "N:" + Integer.toString(protein.getHomodimer());
+      if (!unitOfInformationText.contains(unit)) {
+        unitOfInformationText.add(unit);
+      }
     }
-
-    Color oldColor = graphics.getColor();
-    drawUnitOfInformation(unitOfInformationText, protein, graphics);
-    graphics.setColor(oldColor);
+    return unitOfInformationText;
   }
 
   @Override
   protected Shape getShape(final Protein protein) {
     return getGenericShape(protein);
   }
-  
+
   @Override
   void drawActivityShape(final Protein protein, final Graphics2D graphics) {
   }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -376,6 +376,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
    *          where the drawing should be performed
    */
   protected void drawUnitOfInformation(List<String> units, T species, final Graphics2D graphics) {
+    Color oldColor = graphics.getColor();
     List<String> unitsToDraw = new ArrayList<>();
     for (String text : units) {
       if (text != null && !text.trim().isEmpty()) {
@@ -394,11 +395,11 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
       double height = UNIT_OF_INFORMATION_HEIGHT;
 
       Rectangle2D rectangle = new Rectangle2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
-      Color c = graphics.getColor();
       graphics.setColor(Color.WHITE);
       graphics.fill(rectangle);
-      graphics.setColor(c);
+      graphics.setColor(species.getBorderColor());
       graphics.draw(rectangle);
+      graphics.setColor(species.getFontColor());
       Font font = graphics.getFont();
       graphics.setFont(getUnitOfInformationFont());
 
@@ -410,6 +411,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
 
       count++;
     }
+    graphics.setColor(oldColor);
   }
 
   @Override

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java

@@ -6,9 +6,16 @@ import static org.mockito.Mockito.when;
 import java.awt.*;
 import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.imageio.ImageIO;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.junit.Rule;
 import org.mockito.Mockito;
 
@@ -65,6 +72,9 @@ public abstract class GraphicsTestFunctions {
 
   protected GenericProtein createProtein() {
     GenericProtein result = new GenericProtein("s" + elementCounter++);
+    result.setFillColor(Color.YELLOW);
+    result.setBorderColor(Color.BLUE);
+    result.setFontColor(Color.DARK_GRAY);
     assignCoordinates(10, 10, 40, 40, result);
     return result;
   }
@@ -145,4 +155,15 @@ public abstract class GraphicsTestFunctions {
     return pathway;
   }
 
+  protected void showImage(BufferedImage bi) throws IOException {
+    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+    ImageIO.write(bi, "PNG", outputStream);
+    byte[] output2 = outputStream.toByteArray();
+
+    FileUtils.writeByteArrayToFile(new File("tmp.png"), output2);
+
+    Desktop.getDesktop().open(new File("tmp.png"));
+  }
+
+
 }

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinSbgnConverterTest.java

 package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
 
-import static org.mockito.ArgumentMatchers.any;
+import static org.junit.Assert.assertEquals;
+import static org.mockito.ArgumentMatchers.*;
 import static org.mockito.Mockito.atLeastOnce;
 import static org.mockito.Mockito.times;
 
@@ -8,6 +9,7 @@ import java.awt.Color;
 import java.awt.Graphics2D;
 import java.awt.geom.*;
 import java.awt.image.BufferedImage;
+import java.util.Arrays;
 
 import org.junit.Test;
 import org.mockito.Mockito;
@@ -54,4 +56,58 @@ public class ProteinSbgnConverterTest extends GraphicsTestFunctions {
     Mockito.verify(graphics, times(2)).draw(any(Rectangle2D.class));
   }
 
+  @Test
+  public void testDrawUnitOfInformation() throws Exception {
+    int size = 200;
+    BufferedImage bi = new BufferedImage(size, size, BufferedImage.TYPE_INT_ARGB);
+    Graphics2D graphics = Mockito.spy(bi.createGraphics());
+    ProteinConverter rc = new ProteinSbgnConverter(colorExtractor);
+
+    Protein protein = createProtein();
+    protein.setHomodimer(22);
+    protein.setStatePrefix("bla");
+    protein.setStateLabel("xxx");
+    graphics.setColor(Color.CYAN);
+    rc.drawUnitOfInformation(Arrays.asList("test"), protein, graphics);
+
+    Mockito.verify(graphics, times(1)).drawString(anyString(), anyInt(), anyInt());
+    Mockito.verify(graphics, times(1)).setColor(protein.getBorderColor());
+    Mockito.verify(graphics, times(1)).setColor(protein.getFontColor());
+    assertEquals(Color.CYAN, graphics.getColor());
+  }
+
+  @Test
+  public void testDrawHomodimerInformationTogetherWithCardinality() throws Exception {
+    int size = 200;
+    BufferedImage bi = new BufferedImage(size, size, BufferedImage.TYPE_INT_ARGB);
+    Graphics2D graphics = Mockito.spy(bi.createGraphics());
+    ProteinConverter rc = new ProteinSbgnConverter(colorExtractor);
+
+    Protein protein = createProtein();
+    protein.setHomodimer(4);
+    protein.setStatePrefix("N");
+    protein.setStateLabel("4");
+    rc.drawImpl(protein, graphics, new ConverterParams().sbgnFormat(true));
+
+    Mockito.verify(graphics, times(2)).drawString(anyString(), anyInt(), anyInt());
+    Mockito.verify(graphics, times(1)).draw(any(Rectangle2D.class));
+  }
+
+  @Test
+  public void testDrawHomodimerInformationTogetherWithDifferentCardinality() throws Exception {
+    int size = 200;
+    BufferedImage bi = new BufferedImage(size, size, BufferedImage.TYPE_INT_ARGB);
+    Graphics2D graphics = Mockito.spy(bi.createGraphics());
+    ProteinConverter rc = new ProteinSbgnConverter(colorExtractor);
+
+    Protein protein = createProtein();
+    protein.setHomodimer(4);
+    protein.setStatePrefix("N");
+    protein.setStateLabel("14");
+    rc.drawImpl(protein, graphics, new ConverterParams().sbgnFormat(true));
+
+    Mockito.verify(graphics, times(3)).drawString(anyString(), anyInt(), anyInt());
+    Mockito.verify(graphics, times(2)).draw(any(Rectangle2D.class));
+  }
+
 }