initial concentration is parsed properly

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java

@@ -33,6 +33,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
     Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
     try {
       Species result = clazz.getConstructor(String.class).newInstance(species.getId());
+      result.setInitialAmount(species.getInitialAmount());
       assignBioEntityData(species, result);
       if (layout == null) {
         assignCompartment(result, species.getCompartment());

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java

@@ -26,6 +26,7 @@ import lcsb.mapviewer.model.map.species.Phenotype;
 import lcsb.mapviewer.model.map.species.ReceptorProtein;
 import lcsb.mapviewer.model.map.species.Rna;
 import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
 import lcsb.mapviewer.model.map.species.Unknown;
 
 public class SbmlSpeciesParserTest {
@@ -144,4 +145,11 @@ public class SbmlSpeciesParserTest {
     assertTrue(element instanceof Unknown);
     assertEquals(ElementColorEnum.UNKNOWN.getColor(), element.getColor());
   }
+
+  @Test
+  public void testParseInitialAmount() throws Exception {
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/initial_amount.xml"));
+    Species element = model.getElementByElementId("s1");
+    assertEquals((Double)1.0, element.getInitialAmount());
+  }
 }