Merge branch '1356-reference-to-alias-from-text-glyph' into 'master'

Resolve "reference to alias from textGlyph is taken from wrong attribute"

Closes #1354 and #1356

See merge request !1238

CHANGELOG

+minerva (15.1.0~beta.1) unstable; urgency=medium
+  * Bug fix: SBML import - label aligned to top of species was inproperly drawn
+    (#1354)
+  * Bug fix: SBML text  labels that were referencing layout aliases using
+    layout:graphicalObject attribute were not handled properly (#1356)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 17 Aug 2020 16:00:00 +0200
+
 minerva (15.1.0~beta.0) unstable; urgency=medium
   * Small improvement: annotations are exported in SBGN extension that can be
     opened by newt (#1296)

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java

@@ -162,7 +162,11 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
                 "Don't know what to do with celldesigner:point for class: " + result.getClass());
           }
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:namePoint")) {
-          result.setNamePoint(getCommonParser().getPosition(node));
+          Point2D position = getCommonParser().getPosition(node);
+          result.setNameX(position.getX());
+          result.setNameY(position.getY());
+          result.setNameWidth(result.getWidth() - (result.getNameX() - result.getX()));
+          result.setNameHeight(result.getHeight() - (result.getNameY() - result.getY()));
           result.setNameHorizontalAlign(HorizontalAlign.LEFT);
           result.setNameVerticalAlign(VerticalAlign.TOP);
         } else {
@@ -171,9 +175,13 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
         }
       }
     }
-    if (result.getNamePoint()==null) {
-      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE,result),"Name point is not defined");
-      result.setNamePoint(new Point2D.Double(result.getX(), result.getY()));
+    if (result.getNameX() == null || result.getNameY() == null || result.getNameWidth() == null
+        || result.getNameHeight() == null) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, result), "Name point is not defined");
+      result.setNameX(result.getX());
+      result.setNameY(result.getY());
+      result.setNameWidth(result.getWidth());
+      result.setNameHeight(result.getHeight());
       result.setNameHorizontalAlign(HorizontalAlign.LEFT);
       result.setNameVerticalAlign(VerticalAlign.TOP);
     }
@@ -222,8 +230,8 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
     }
 
     sb.append("<celldesigner:namePoint ");
-    sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
-    sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
+    sb.append("x=\"" + compartment.getNameX() + "\" ");
+    sb.append("y=\"" + compartment.getNameY() + "\"/>\n");
 
     sb.append(getDoubleLineNode(compartment));
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java

 package lcsb.mapviewer.converter.model.celldesigner.alias;
 
-import java.awt.geom.Point2D;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -176,7 +175,10 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
     }
     complexAliasesMapById.put(result.getElementId(), result);
     species.updateModelElementAfterLayoutAdded(result);
-    result.setNamePoint(new Point2D.Double(result.getCenterX(), result.getY() + result.getHeight() - 2));
+    result.setNameX(result.getX());
+    result.setNameY(result.getY());
+    result.setNameWidth(result.getWidth());
+    result.setNameHeight(result.getHeight());
     result.setNameHorizontalAlign(HorizontalAlign.CENTER);
     result.setNameVerticalAlign(VerticalAlign.BOTTOM);
     return result;

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java

@@ -156,7 +156,10 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
       }
 
       species.updateModelElementAfterLayoutAdded(result);
-      result.setNamePoint(result.getCenter());
+      result.setNameX(result.getX());
+      result.setNameY(result.getY());
+      result.setNameWidth(result.getWidth());
+      result.setNameHeight(result.getHeight());
       result.setNameHorizontalAlign(HorizontalAlign.CENTER);
       result.setNameVerticalAlign(VerticalAlign.MIDDLE);
       return result;

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java

@@ -227,10 +227,10 @@ public abstract class CellDesignerTestFunctions {
     Model model2 = serializeModel(model);
 
     ModelComparator comparator = new ModelComparator();
-    
-    //import of unbounded compartments is problematic
-    for (Compartment compartment :model.getCompartments()) {
-      if (compartment instanceof BottomSquareCompartment || 
+
+    // import of unbounded compartments is problematic
+    for (Compartment compartment : model.getCompartments()) {
+      if (compartment instanceof BottomSquareCompartment ||
           compartment instanceof TopSquareCompartment ||
           compartment instanceof LeftSquareCompartment ||
           compartment instanceof RightSquareCompartment) {
@@ -261,26 +261,39 @@ public abstract class CellDesignerTestFunctions {
     GenericProtein protein = new GenericProtein("id" + (idCounter++));
     protein.setActivity(true);
     protein.setFontSize(4);
-    protein.setHeight(10);
-    protein.setWidth(20);
-    protein.setX(30);
-    protein.setY(40);
     protein.setStateLabel("xxx");
     protein.setStatePrefix("yyy");
-    protein.setNamePoint(protein.getCenter());
-    protein.setNameHorizontalAlign(HorizontalAlign.CENTER);
-    protein.setNameVerticalAlign(VerticalAlign.MIDDLE);
+
+    assignCoordinates(30, 40, 10, 20, protein);
+
     return protein;
   }
 
   protected SimpleMolecule createSimpleMolecule() {
     SimpleMolecule result = new SimpleMolecule("id" + (idCounter++));
-    result.setX(50);
-    result.setY(60);
-    result.setNamePoint(result.getCenter());
-    result.setNameHorizontalAlign(HorizontalAlign.CENTER);
-    result.setNameVerticalAlign(VerticalAlign.MIDDLE);
+    assignCoordinates(50, 60, 20, 20, result);
     return result;
   }
 
+  static int zIndex = 10;
+
+  protected static void assignCoordinates(lcsb.mapviewer.model.map.species.Element element) {
+    assignCoordinates(10, 20, 30, 40, element);
+  }
+
+  protected static void assignCoordinates(double x, double y, double width, double height,
+      lcsb.mapviewer.model.map.species.Element element) {
+    element.setX(x);
+    element.setY(y);
+    element.setZ(zIndex++);
+    element.setWidth(width);
+    element.setHeight(height);
+    element.setNameX(x);
+    element.setNameY(y);
+    element.setNameWidth(width);
+    element.setNameHeight(height);
+    element.setNameVerticalAlign(VerticalAlign.MIDDLE);
+    element.setNameHorizontalAlign(HorizontalAlign.CENTER);
+  }
+
 }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java

@@ -2,7 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.alias;
 
 import static org.junit.Assert.*;
 
-import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -285,11 +284,7 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
   private Compartment createCompartment(String id) {
     Compartment compartment = new SquareCompartment(id);
     compartment.setName("name" + id);
-    compartment.setX(13);
-    compartment.setY(14);
-    compartment.setWidth(100);
-    compartment.setHeight(120);
-    compartment.setNamePoint(new Point2D.Double(0, 1));
+    assignCoordinates(13, 14, 100, 120, compartment);
 
     return compartment;
   }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java

@@ -2,8 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.alias;
 
 import static org.junit.Assert.*;
 
-import java.awt.geom.Point2D;
-
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
@@ -54,8 +52,10 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(compartment.getWidth(), alias2.getWidth(), 1e-6);
     assertEquals(compartment.getX(), alias2.getX(), 1e-6);
     assertEquals(compartment.getY(), alias2.getY(), 1e-6);
-    assertEquals(compartment.getNamePoint().getX(), alias2.getNamePoint().getX(), 1e-6);
-    assertEquals(compartment.getNamePoint().getY(), alias2.getNamePoint().getY(), 1e-6);
+    assertEquals(compartment.getNameX(), alias2.getNameX(), 1e-6);
+    assertEquals(compartment.getNameY(), alias2.getNameY(), 1e-6);
+    assertEquals(compartment.getNameWidth(), alias2.getNameWidth(), 1e-6);
+    assertEquals(compartment.getNameHeight(), alias2.getNameHeight(), 1e-6);
     assertNotNull(alias2.getNameHorizontalAlign());
     assertNotNull(alias2.getNameVerticalAlign());
   }
@@ -63,11 +63,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
   private Compartment createCompartment() {
     Compartment compartment = new SquareCompartment("comp_id");
     compartment.setName("name");
-    compartment.setX(13);
-    compartment.setY(14);
-    compartment.setWidth(100);
-    compartment.setHeight(120);
-    compartment.setNamePoint(new Point2D.Double(0, 1));
+    assignCoordinates(13, 14, 100, 120, compartment);
 
     return compartment;
   }
@@ -127,8 +123,9 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(139.0, alias.getX(), 1e-6);
     assertEquals(55.0, alias.getY(), 1e-6);
     assertEquals(522.0, alias.getWidth(), 1e-6);
-    assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
-    assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
+    assertEquals(392.5, alias.getNameX(), 1e-6);
+    assertEquals(196.5, alias.getNameY(), 1e-6);
+    assertEquals(522.0, alias.getNameWidth(), 1e-6);
     assertEquals(0xffcccc00, alias.getFillColor().getRGB());
   }
 
@@ -142,7 +139,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
   @Test
   public void testLeftToXml() throws Exception {
     Compartment alias = new LeftSquareCompartment("id");
-    alias.setNamePoint(new Point2D.Double());
+    assignCoordinates(alias);
     String xml = parser.toXml(alias);
     assertNotNull(xml);
   }
@@ -150,7 +147,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
   @Test
   public void testRightToXml() throws Exception {
     Compartment alias = new RightSquareCompartment("id");
-    alias.setNamePoint(new Point2D.Double());
+    assignCoordinates(alias);
     String xml = parser.toXml(alias);
     assertNotNull(xml);
   }
@@ -158,7 +155,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
   @Test
   public void testTopToXml() throws Exception {
     Compartment alias = new TopSquareCompartment("id");
-    alias.setNamePoint(new Point2D.Double());
+    assignCoordinates(alias);
     String xml = parser.toXml(alias);
     assertNotNull(xml);
   }
@@ -166,7 +163,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
   @Test
   public void testBotttomToXml() throws Exception {
     Compartment alias = new BottomSquareCompartment("id");
-    alias.setNamePoint(new Point2D.Double());
+    assignCoordinates(alias);
     String xml = parser.toXml(alias);
     assertNotNull(xml);
   }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java

@@ -73,7 +73,10 @@ public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(100.0, alias.getWidth(), Configuration.EPSILON);
     assertEquals(744.0, alias.getX(), Configuration.EPSILON);
     assertEquals(0.0, alias.getY(), Configuration.EPSILON);
-    assertNotNull(alias.getNamePoint());
+    assertNotNull(alias.getNameX());
+    assertNotNull(alias.getNameY());
+    assertNotNull(alias.getNameWidth());
+    assertNotNull(alias.getNameHeight());
     assertNotNull(alias.getNameHorizontalAlign());
     assertNotNull(alias.getNameVerticalAlign());
   }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java

@@ -67,7 +67,10 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(11813.0, alias.getX(), 1e-6);
     assertEquals(2840.5, alias.getY(), 1e-6);
     assertEquals("ca1", alias.getCompartment().getElementId());
-    assertNotNull(alias.getNamePoint());
+    assertNotNull(alias.getNameX());
+    assertNotNull(alias.getNameY());
+    assertNotNull(alias.getNameWidth());
+    assertNotNull(alias.getNameHeight());
     assertNotNull(alias.getNameHorizontalAlign());
     assertNotNull(alias.getNameVerticalAlign());
   }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java

@@ -19,7 +19,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.model.map.*;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java

@@ -2,8 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.compartment;
 
 import static org.junit.Assert.*;
 
-import java.awt.geom.Point2D;
-
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
@@ -137,7 +135,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
     Model model = new ModelFullIndexed(null);
     Compartment compartment = new SquareCompartment("c");
     compartment.setName("xyz");
-    compartment.setNamePoint(new Point2D.Double());
+    assignCoordinates(compartment);
     model.addElement(compartment);
 
     Model model2 = super.serializeModel(model);
@@ -148,7 +146,7 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
   public void testToXmlWithCompartmentIdNotRecognizedByCellDesignerAndChildren() throws Exception {
     Model model = new ModelFullIndexed(null);
     Compartment compartment = new SquareCompartment("c");
-    compartment.setNamePoint(new Point2D.Double());
+    assignCoordinates(compartment);
     compartment.setName("xyz");
     model.addElement(compartment);
 

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java

@@ -17,7 +17,6 @@ import org.xml.sax.InputSource;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.species.ProteinXmlParserTest;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java

@@ -3,18 +3,14 @@ package lcsb.mapviewer.converter.model.celldesigner.types;
 import static org.junit.Assert.*;
 
 import java.awt.geom.Point2D;
-import java.lang.reflect.Field;
 
 import org.junit.*;
 import org.mockito.Mockito;
 
-import lcsb.mapviewer.common.exception.*;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
 
 public class ModifierTypeUtilsTest extends CellDesignerTestFunctions {
 

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -494,6 +494,12 @@ public class SbgnmlXmlExporter {
   private Label getGlyphLabelFromAlias(Element element) {
     Label label = new Label();
     label.setText(element.getName());
+    Bbox box = new Bbox();
+    box.setX(element.getNameX().floatValue());
+    box.setY(element.getNameY().floatValue());
+    box.setW(element.getNameWidth().floatValue());
+    box.setH(element.getNameHeight().floatValue());
+    label.setBbox(box);
     return label;
   }
 

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -761,13 +761,17 @@ public class SbgnmlXmlParser {
     if (g.getLabel() != null) {
       newSpecies.setName(g.getLabel().getText());
       if (g.getLabel().getBbox() != null) {
-        double x = g.getLabel().getBbox().getX() + g.getLabel().getBbox().getW() / 2;
-        double y = g.getLabel().getBbox().getY() + g.getLabel().getBbox().getH() / 2;
-        newSpecies.setNamePoint(x, y);
+        newSpecies.setNameX(g.getLabel().getBbox().getX());
+        newSpecies.setNameY(g.getLabel().getBbox().getY());
+        newSpecies.setNameWidth(g.getLabel().getBbox().getW());
+        newSpecies.setNameHeight(g.getLabel().getBbox().getH());
         newSpecies.setNameHorizontalAlign(HorizontalAlign.CENTER);
-        newSpecies.setNameVerticalAlign(VerticalAlign.MIDDLE);
+        if (newSpecies instanceof Complex) {
+          newSpecies.setNameVerticalAlign(VerticalAlign.BOTTOM);
+        } else {
+          newSpecies.setNameVerticalAlign(VerticalAlign.MIDDLE);
+        }
       }
-
     } else {
       newSpecies.setName("");
     }
@@ -918,13 +922,16 @@ public class SbgnmlXmlParser {
     species.setWidth(new Double(glyph.getBbox().getW()));
     species.setX(new Double(glyph.getBbox().getX()));
     species.setY(new Double(glyph.getBbox().getY()));
-    if (species.getNamePoint() == null) {
+    if (species.getNameX() == null || species.getNameY() == null) {
+      species.setNameX(species.getX());
+      species.setNameY(species.getY());
+      species.setNameWidth(species.getWidth());
       species.setNameHorizontalAlign(HorizontalAlign.CENTER);
       if (species instanceof Complex) {
-        species.setNamePoint(new Point2D.Double(species.getCenterX(), species.getY() + species.getHeight() - 2));
         species.setNameVerticalAlign(VerticalAlign.BOTTOM);
+        species.setNameHeight(species.getHeight() - 2);
       } else {
-        species.setNamePoint(species.getCenter());
+        species.setNameHeight(species.getHeight());
         species.setNameVerticalAlign(VerticalAlign.MIDDLE);
       }
     }
@@ -1067,7 +1074,10 @@ public class SbgnmlXmlParser {
     nullParent.setHeight(Double.MAX_VALUE);
     nullParent.setX(0.0);
     nullParent.setY(0.0);
-    nullParent.setNamePoint(new Point2D.Double(10, 10));
+    nullParent.setNameX(10);
+    nullParent.setNameY(10);
+    nullParent.setNameWidth(Double.MAX_VALUE);
+    nullParent.setNameHeight(Double.MAX_VALUE);
     nullParent.setNameHorizontalAlign(HorizontalAlign.LEFT);
     nullParent.setNameVerticalAlign(VerticalAlign.TOP);
     Compartment parent = nullParent;
@@ -1986,12 +1996,18 @@ public class SbgnmlXmlParser {
     compartment.setBorderColor(COMPARTMENT_COLOR);
 
     if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
-      compartment.setNamePoint(glyph.getLabel().getBbox().getX(), glyph.getLabel().getBbox().getY());
+      compartment.setNameX(glyph.getLabel().getBbox().getX());
+      compartment.setNameY(glyph.getLabel().getBbox().getY());
+      compartment.setNameWidth(glyph.getLabel().getBbox().getW());
+      compartment.setNameHeight(glyph.getLabel().getBbox().getH());
       compartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
       compartment.setNameVerticalAlign(VerticalAlign.TOP);
     } else {
-      compartment.setNamePoint(compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN,
-          compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
+      compartment.setNameX(compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
+      compartment.setNameY(compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
+      compartment.setNameWidth(compartment.getWidth() - 2 * (compartment.getThickness() + CONTAINER_NAME_MARGIN));
+      compartment.setNameHeight(compartment.getHeight() - 2 * (compartment.getThickness() + CONTAINER_NAME_MARGIN));
+
       compartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
       compartment.setNameVerticalAlign(VerticalAlign.TOP);
     }

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlSerializationTest.java

@@ -80,7 +80,7 @@ public class SbgnmlSerializationTest extends SbgnmlTestFunctions {
       e.setPositionToCompartment(null);
     }
     
-    assertEquals("Import/export shouldn't produce any wanrnings", 0, super.getWarnings().size());
+    assertEquals("Import/export shouldn't produce any warnings", 0, super.getWarnings().size());
     ModelComparator mc = new ModelComparator(0.001);
     assertEquals(0, mc.compare(model, model2));
   }

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java

@@ -118,6 +118,7 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
     ion.setHeight(100);
     ion.setX(200 * (id % 2 + 1));
     ion.setY(50 * (id / 2 + 1));
+    ion.setNameBorder(ion.getBorder());
     ion.setOnlySubstanceUnits(true);
     ion.setConstant(true);
     ion.setInitialAmount(2.0);

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java

@@ -95,12 +95,18 @@ public class SbgnmlXmlParserTest extends SbgnmlTestFunctions {
     model2.setNotes(model.getNotes());
 
     for (Element element : model.getElements()) {
-      element.setNamePoint(null);
+      element.setNameX(0);
+      element.setNameY(0);
+      element.setNameWidth(0);
+      element.setNameHeight(0);
       element.setNameHorizontalAlign(null);
       element.setNameVerticalAlign(null);
     }
     for (Element element : model2.getElements()) {
-      element.setNamePoint(null);
+      element.setNameX(0);
+      element.setNameY(0);
+      element.setNameWidth(0);
+      element.setNameHeight(0);
       element.setNameHorizontalAlign(null);
       element.setNameVerticalAlign(null);
     }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java

 package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.*;
-import java.awt.geom.*;
+import java.awt.geom.Area;
+import java.awt.geom.Rectangle2D;
 import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
@@ -154,10 +155,10 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
 
     // draw description
     if (fill) {
-      Point2D tmpPoint = compartment.getNamePoint();
-      compartment.setNamePoint(compartment.getCenter());
+      Rectangle2D tmpBorder = compartment.getNameBorder();
+      compartment.setNameBorder(compartment.getBorder());
       drawText(compartment, graphics, params);
-      compartment.setNamePoint(tmpPoint);
+      compartment.setNameBorder(tmpBorder);
     }
   }
 
@@ -223,9 +224,8 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
       }
     } else {
       border = new Rectangle2D.Double(
-          compartment.getNamePoint().getX(), compartment.getNamePoint().getY(),
-          compartment.getWidth() - (compartment.getNamePoint().getX() - compartment.getX()),
-          compartment.getHeight() - (compartment.getNamePoint().getY() - compartment.getY()));
+          compartment.getNameX(), compartment.getNameY(),
+          compartment.getNameWidth(), compartment.getNameHeight());
 
     }
     double fontSize = compartment.getFontSize() * params.getScale();

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java

 package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.*;
-import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
 
 import lcsb.mapviewer.commands.ColorExtractor;
@@ -61,10 +60,10 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
 
     // draw description of the compartment
     if (fill) {
-      Point2D tmpPoint = compartment.getNamePoint();
-      compartment.setNamePoint(compartment.getCenter());
+      Rectangle2D tmpBorder = compartment.getNameBorder();
+      compartment.setNameBorder(compartment.getBorder());
       drawText(compartment, graphics, params);
-      compartment.setNamePoint(tmpPoint);
+      compartment.setNameBorder(tmpBorder);
     } else {
       if (!compartment.containsIdenticalSpecies()) {
         drawText(compartment, graphics, params);