comparison against null filxed

CHANGELOG

 minerva (14.0.3) stable; urgency=medium
+  * Bug fix: sbml parser had sometimes problems with combining layout and multi 
+    packages (#966)
   * Bug fix: parsing of CellDesigner files that contained substanceUnits could
     crash the upload (#985)
   * Bug fix: verificatin of version length added when uploading project 

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

@@ -13,6 +13,8 @@ import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.multi.*;
 import org.sbml.jsbml.ext.render.LocalStyle;
 
+import com.google.common.base.Objects;
+
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -317,7 +319,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
           if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
             // find a reference to the alias in layout, so we know it's the proper value
             ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
-            if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
+            if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
+//            if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
               residueGlyph = (GeneralGlyph) graphicalObject;
             }
           } else {

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

@@ -62,6 +62,13 @@ public class SbmlParserTest extends SbmlTestFunctions {
     assertEquals(2, model.getMiriamData().size());
   }
 
+  @Test
+  public void testParseProblematicMultiLayout() throws FileNotFoundException, InvalidInputDataExecption {
+    Model model = parser.createModel(
+        new ConverterParams().filename("testFiles/small/problematic_inflamation_sbml_layout.xml"));
+    assertNotNull(model);
+  }
+
   @Test
   public void testParseKinetics() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/SBML.xml"));