celldesigner provides z-index when parsing

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

@@ -22,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
@@ -236,6 +237,7 @@ public class CellDesignerXmlParser extends Converter {
         model.setWidth(width);
         model.setHeight(height);
       }
+      new ZIndexPopulator().populateZIndex(model);
     } catch (InvalidXmlSchemaException e) {
       throw new InvalidInputDataExecption(e);
     } catch (CellDesignerParserException e) {

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

@@ -36,6 +36,7 @@ import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.layout.graphics.Layer;
 import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
@@ -82,6 +83,20 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testZIndexAvailableForBioEntities() throws Exception {
+    try {
+      CellDesignerXmlParser parser = new CellDesignerXmlParser();
+      Model model = parser.createModel(new ConverterParams().filename("testFiles/sample.xml"));
+      for (BioEntity bioEntity : model.getBioEntities()) {
+        assertNotNull(bioEntity.getZ());
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testOpenFromFile() throws Exception {
     try {
@@ -1068,7 +1083,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is));
-      
+
       assertEquals(0, modelComparator.compare(model, model2));
 
     } catch (Exception e) {