simple molecules are visualized as ellipses not circles

CHANGELOG

 minerva (15.0.0~alpha.1) stable; urgency=medium
   * Small improvement: sort order of tables in admin panel is preserved among
     sessions (#836)
+  * Small improvement: simple molecules in sbgn compliant view are drawn as 
+    ellipses not circles (#796)
   * Bug fix: structural states of proteins are imported properly from SBGNML PD
     (#995)
   * Bug fix: clear button icon, refresh comments button and show overview

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

@@ -44,8 +44,7 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
       final ConverterParams params) {
     int homodir;
     if (params.isSbgnFormat()) {
-      // If the SBGN display mode is set, multimer is shown as two stacked
-      // glyphs
+      // If the SBGN display mode is set, multimer is shown as two stacked glyphs
       if (simpleMolecule.getHomodimer() > 1) {
         homodir = 2;
       } else {
@@ -58,12 +57,6 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
     simpleMolecule.setWidth(simpleMolecule.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
     simpleMolecule.setHeight(simpleMolecule.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
 
-    // SBGN view - simple molecules are represented as circles
-    if (params.isSbgnFormat()) {
-      simpleMolecule.setX(simpleMolecule.getX() + (simpleMolecule.getWidth() - simpleMolecule.getHeight()) / 2);
-      simpleMolecule.setWidth(simpleMolecule.getHeight());
-    }
-
     simpleMolecule.setX(simpleMolecule.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
     simpleMolecule.setY(simpleMolecule.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
 
@@ -82,8 +75,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
       graphics.setStroke(stroke);
       graphics.setColor(oldColor);
 
-      // SBGN view - multimers are displayed with a unit of information
-      // containing cardinality
+      // SBGN view - multimers are displayed with a unit of information containing
+      // cardinality
       if (params.isSbgnFormat() && (i == homodir - 1)) {
         String unitOfInformationText = null;
         if (simpleMolecule.getStatePrefix() != null && simpleMolecule.getStateLabel() != null) {

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

@@ -16,8 +16,7 @@ import lcsb.mapviewer.common.UnitTestFailedWatcher;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.modifier.Catalysis;
 import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.*;
 
 public abstract class GraphicsTestFunctions {
 
@@ -89,4 +88,15 @@ public abstract class GraphicsTestFunctions {
     return result;
   }
 
+  protected SimpleMolecule createSimpleMolecule() {
+    SimpleMolecule protein = new SimpleMolecule ("sm" + elementCounter++);
+    protein.setX(10);
+    protein.setY(20);
+    protein.setWidth(100);
+    protein.setHeight(80);
+    protein.setFillColor(Color.WHITE);
+
+    return protein;
+  }
+
 }

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

@@ -6,6 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
 @SuiteClasses({ ComplexConverterTest.class,
+    SimpleMoleculeConverterTest.class,
     SpeciesConverterTest.class,
     SpeciesGenericConverterTests.class })
 public class AllSpeciesConverterTests {

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

+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+public class SimpleMoleculeConverterTest extends GraphicsTestFunctions {
+  Logger logger = LogManager.getLogger();
+
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testDrawText() throws Exception {
+    int size = 200;
+    BufferedImage bi = new BufferedImage(size, size, BufferedImage.TYPE_INT_ARGB);
+    Graphics2D graphics = bi.createGraphics();
+    SimpleMoleculeConverter rc = new SimpleMoleculeConverter(colorExtractor);
+
+    SimpleMolecule simpleMolecule = createSimpleMolecule();
+    double x = simpleMolecule.getX();
+    double width = simpleMolecule.getWidth();
+    rc.drawImpl(simpleMolecule, graphics, new ConverterParams().sbgnFormat(true));
+    assertEquals("Coordinates shouldn't be changed when drawing SBGN-ML", x, simpleMolecule.getX(),
+        Configuration.EPSILON);
+    assertEquals("Width shouldn't be changed when drawing SBGN-ML", width, simpleMolecule.getWidth(),
+        Configuration.EPSILON);
+  }
+}