export/import of border color works the same as before introducing border color

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

@@ -1514,6 +1514,7 @@ public class SbgnmlXmlParser {
     compartment.setY(new Double(glyph.getBbox().getY()));
     compartment.setThickness(1.0);
     compartment.setFillColor(COMPARTMENT_COLOR);
+    compartment.setBorderColor(COMPARTMENT_COLOR);
 
     if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
       compartment.setNamePoint(glyph.getLabel().getBbox().getX(), glyph.getLabel().getBbox().getY());

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java

@@ -21,6 +21,7 @@ import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Author;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.Element;
@@ -147,6 +148,9 @@ public class SbmlBioEntityParser {
     if (result instanceof Element) {
       Element element = (Element) result;
       element.setFillColor(ElementColorEnum.getColorByClass(element.getClass()));
+      if (result instanceof Compartment) {
+        element.setBorderColor(ElementColorEnum.getColorByClass(element.getClass()));
+      }
     }
   }
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java

@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.render.LocalStyle;
 
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.species.Element;
 
 public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends SbmlBioEntityParser {
@@ -116,6 +117,9 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
     if (style.getGroup().isSetFill()) {
       Color backgroundColor = getColorByColorDefinition(style.getGroup().getFill());
       elementWithLayout.setFillColor(backgroundColor);
+      if (elementWithLayout instanceof Compartment) {
+        elementWithLayout.setBorderColor(backgroundColor);
+      }
     }
     if (style.getGroup().isSetFontSize()) {
       elementWithLayout.setFontSize(style.getGroup().getFontSize());

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java

@@ -81,6 +81,9 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
     if (!style.getGroup().isSetFill() && style.getGroup().isSetStroke()) {
       Color backgroundColor = getColorByColorDefinition(style.getGroup().getStroke());
       elementWithLayout.setFillColor(backgroundColor);
+      if (elementWithLayout instanceof Compartment) {
+        elementWithLayout.setBorderColor(backgroundColor);
+      }
     }
   }
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -242,7 +242,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
   @Test
   public void testColorParsing() throws Exception {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
-    for (Element element : model.getElements()) {
+    for (Species element : model.getSpeciesList()) {
       element.setFillColor(Color.BLUE);
     }
     Model model2 = getModelAfterSerializing(model);