renaming of methods

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

@@ -84,11 +84,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   protected abstract void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph);
 
   protected AbstractReferenceGlyph createGlyph(T element) {
-    String sbmlCompartmentId = sbmlElementByElementId.get(element.getElementId()).getId();
+    String sbmlElementId = sbmlElementByElementId.get(element.getElementId()).getId();
     String glyphId = element.getElementId();
-    AbstractReferenceGlyph compartmentGlyph = createElementGlyph(sbmlCompartmentId, glyphId);
-    assignLayoutToGlyph(element, compartmentGlyph);
-    return compartmentGlyph;
+    AbstractReferenceGlyph elementGlyph = createElementGlyph(sbmlElementId, glyphId);
+    assignLayoutToGlyph(element, elementGlyph);
+    return elementGlyph;
   }
 
   protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);

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

@@ -17,7 +17,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
     super(sbmlLayout, minervaModel);
   }
 
-  protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph) {
+  protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
     BoundingBox boundingBox = new BoundingBox();
 
     boundingBox.setPosition(new Point(element.getX(), element.getY()));
@@ -26,7 +26,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
     dimensions.setHeight(element.getHeight());
     boundingBox.setDimensions(dimensions);
 
-    compartmentGlyph.setBoundingBox(boundingBox);
+    speciesGlyph.setBoundingBox(boundingBox);
   }
 
 }

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

@@ -3,6 +3,7 @@ package lcsb.mapviewer.converter.model.sbml;
 import javax.xml.stream.XMLStreamException;
 
 import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.apache.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlExporter {
+  Logger logger = Logger.getLogger(SbmlExporter.class);
   public String toXml(lcsb.mapviewer.model.map.model.Model model)
       throws SBMLException, XMLStreamException, InconsistentModelException {
     SBMLDocument doc = new SBMLDocument(3, 1);

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

@@ -89,6 +89,7 @@ public class SbmlParser implements IConverter {
         if (layout.getDimensions() != null) {
           model.setWidth(layout.getDimensions().getWidth());
           model.setHeight(layout.getDimensions().getHeight());
+
         }
         compartmentParser.mergeLayout(model.getCompartments(), layout, sbmlModel);
         speciesParser.mergeLayout(model.getSpeciesList(), layout, sbmlModel);
@@ -117,15 +118,14 @@ public class SbmlParser implements IConverter {
       if (sbmlModel.getRuleCount() > 0) {
         throw new NotImplementedException("Rule not implemented for model");
       }
-
-      createLayout(model, layout);
+      createLayout(model, layout, params.isSizeAutoAdjust());
       return model;
     } catch (XMLStreamException e) {
       throw new InvalidInputDataExecption(e);
     }
   }
 
-  private void createLayout(Model model, Layout layout) throws InvalidInputDataExecption {
+  private void createLayout(Model model, Layout layout, boolean resize) throws InvalidInputDataExecption {
     if (model.getWidth() == null) {
       double maxY = 0;
       double maxX = 0;
@@ -133,8 +133,10 @@ public class SbmlParser implements IConverter {
         maxY = Math.max(maxY, element.getY() + element.getHeight() + 10);
         maxX = Math.max(maxX, element.getX() + element.getWidth() + 10);
       }
-      model.setWidth(maxX);
-      model.setHeight(maxY);
+      if (resize) {
+        model.setWidth(maxX);
+        model.setHeight(maxY);
+      }
     }
     Collection<BioEntity> bioEntitesRequiringLayout = new HashSet<>();
 
@@ -150,7 +152,9 @@ public class SbmlParser implements IConverter {
       }
     }
     try {
-      new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
+      if (bioEntitesRequiringLayout.size() > 0) {
+        new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
+      }
     } catch (CommandExecutionException e) {
       throw new InvalidInputDataExecption("Problem with generating layout", e);
     }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -153,7 +153,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
             nodeClass = Modulation.class;
           }
           if (minervaNode == null) {
-            logger.debug(nodeClass);
             throw new InvalidInputDataExecption(
                 "Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
           }

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

@@ -66,7 +66,7 @@ public class GenericSbmlToXmlParserTest {
       String xmlFilePath = pathWithouExtension.concat(".xml");
       converter.exportModelToFile(model, xmlFilePath);
 
-      Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath));
+      Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
       model2.setName(null);
 
       assertNotNull(model2);