z-index can be passed as a parameter in cell designer file

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

@@ -13,6 +13,7 @@ import org.w3c.dom.NodeList;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.LineType;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -522,6 +523,7 @@ public class LayerXmlParser {
         }
       }
     }
+    new RestAnnotationParser().processNotes(result.getNotes(), result);
     return result;
   }
 

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

+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+@Retention(RUNTIME)
+@Target(FIELD)
+public @interface ImportOnly {
+
+}

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

@@ -135,7 +135,11 @@ public enum NoteField {
      */
     @Deprecated
     TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD("TransparencyZoomLevelVisibility", Element.class, null),
-	;
+
+    @ImportOnly
+    Z_INDEX("Z-Index", BioEntity.class, null),
+
+    ;
 
 	/**
 	 * Name used in the notes to distinguish fields.

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

@@ -23,9 +23,11 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
@@ -702,6 +704,24 @@ public class RestAnnotationParser {
     }
   }
 
+  private void setZIndex(Drawable element, String annotationString) {
+    String zIndex = getParamByPrefix(annotationString,
+        NoteField.Z_INDEX.getCommonName() + ":");
+    if (zIndex != null) {
+      try {
+        Integer z = Integer.valueOf(zIndex);
+        if (element.getZ() == null) {
+          element.setZ(z);
+        } else if (!element.getZ().equals(z)) {
+          logger.warn(elementUtils.getElementTag(element) + " New " + NoteField.Z_INDEX.getCommonName()
+              + " different than default [" + zIndex + "][" + element.getZ() + "]. Ignoring.");
+        }
+      } catch (NumberFormatException e) {
+        logger.warn("Invalid e index", e);
+      }
+    }
+  }
+
   /**
    * Assigns notes to the element from notes string. This might look strange. The
    * idea is that sometimes we have notes from more then one source. And the data
@@ -739,7 +759,7 @@ public class RestAnnotationParser {
    * @param object
    *          where the structural data should be put
    */
-  public void processNotes(String notes, BioEntity object) {
+  public void processNotes(String notes, Drawable object) {
     StringBuilder annotations = new StringBuilder();
 
     String[] string = notes.split("\n");
@@ -758,38 +778,45 @@ public class RestAnnotationParser {
         newNotes.append(string2 + "\n");
       }
     }
-    object.setNotes(newNotes.toString().trim());
-
     String ann = annotations.toString();
-    setNotes(object, ann);
-    setSymbol(object, ann);
-    setSynonyms(object, ann);
-    setSemanticZoomLevelVisibility(object, ann);
-    setAbbreviation(object, ann);
-    setFormula(object, ann);
-    if (object instanceof Reaction) {
-      Reaction reaction = (Reaction) object;
-      setMechanicalConfidenceScoreToReaction(reaction, ann);
-      setLowerBoundToReaction(reaction, ann);
-      setUpperBoundToReaction(reaction, ann);
-      setSubsystemToReaction(reaction, ann);
-      setGeneProteinReactionToReaction(reaction, ann);
-    } else if (object instanceof Element) {
-      setTransparencyZoomLevelVisibility((Element) object, ann);
-      setFullNameToSpecies((Element) object, ann);
-      setFormerSymbolsToSpecies((Element) object, ann);
-      if (object instanceof Species) {
-        setCharge((Species) object, ann);
+    setZIndex(object, ann);
+    if (object instanceof LayerText) {
+      ((LayerText) object).setNotes(newNotes.toString().trim());
+    }
+    if (object instanceof BioEntity) {
+      BioEntity bioEntity = (BioEntity) object;
+      bioEntity.setNotes(newNotes.toString().trim());
+
+      setNotes(bioEntity, ann);
+      setSymbol(bioEntity, ann);
+      setSynonyms(bioEntity, ann);
+      setSemanticZoomLevelVisibility(bioEntity, ann);
+      setAbbreviation(bioEntity, ann);
+      setFormula(bioEntity, ann);
+      if (object instanceof Reaction) {
+        Reaction reaction = (Reaction) object;
+        setMechanicalConfidenceScoreToReaction(reaction, ann);
+        setLowerBoundToReaction(reaction, ann);
+        setUpperBoundToReaction(reaction, ann);
+        setSubsystemToReaction(reaction, ann);
+        setGeneProteinReactionToReaction(reaction, ann);
+      } else if (object instanceof Element) {
+        setTransparencyZoomLevelVisibility((Element) object, ann);
+        setFullNameToSpecies((Element) object, ann);
+        setFormerSymbolsToSpecies((Element) object, ann);
+        if (object instanceof Species) {
+          setCharge((Species) object, ann);
+        }
+      } else {
+        throw new NotImplementedException("Don't know how to process class: " + object.getClass());
       }
-    } else {
-      throw new NotImplementedException("Don't know how to process class: " + object.getClass());
-    }
 
-    try {
-      processRdfDescription(object);
-    } catch (InvalidXmlSchemaException e) {
-      String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
-      logger.warn(warning);
+      try {
+        processRdfDescription(bioEntity);
+      } catch (InvalidXmlSchemaException e) {
+        String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
+        logger.warn(warning);
+      }
     }
   }
 

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

@@ -391,6 +391,19 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testGetLayerTextWithZIndex() throws Exception {
+    try {
+      String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml");
+      Node node = getNodeFromXmlString(xmlString);
+      LayerText layer = parser.getLayerText(node);
+      assertEquals((Integer) 19, layer.getZ());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseInvalidLayerText() throws Exception {
     try {

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

@@ -295,17 +295,19 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
 
       for (NoteField field : NoteField.values()) {
         boolean deprecated = false;
+        boolean importOnly = false;
         try {
           Field f = NoteField.class.getField(field.name());
           if (f.isAnnotationPresent(Deprecated.class))
             deprecated = true;
+          if (f.isAnnotationPresent(ImportOnly.class))
+            importOnly = true;
 
         } catch (NoSuchFieldException | SecurityException e) {
         }
 
-        if (!deprecated) {
+        if (!deprecated && !importOnly) {
           if (field.getClazz().isAssignableFrom(element.getClass())
-
               || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
             assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
                 str.indexOf(field.getCommonName()) >= 0);

converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml

+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+Z-Index: 19
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>

model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java

@@ -551,4 +551,8 @@ public class PolylineData implements Serializable, Drawable {
     return 0;
   }
 
+  @Override
+  public String getElementId() {
+    return toString();
+  }
 }

model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java

@@ -196,8 +196,6 @@ public interface BioEntity extends Serializable, Drawable {
    */
   Model getModel();
 
-  String getElementId();
-
   BioEntity copy();
 
 }

model/src/main/java/lcsb/mapviewer/model/map/Drawable.java

@@ -37,5 +37,7 @@ public interface Drawable {
    */
   void setZ(Integer z);
 
+  String getElementId();
+
   double getSize();
 }

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java

@@ -276,7 +276,12 @@ public class LayerOval implements Serializable, Drawable {
 
   @Override
   public double getSize() {
-    return width*height;
+    return width * height;
+  }
+
+  @Override
+  public String getElementId() {
+    return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
   }
 
 }

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java

@@ -261,4 +261,10 @@ public class LayerRect implements Serializable, Drawable {
   public double getSize() {
     return width * height;
   }
+  
+  @Override
+  public String getElementId() {
+    return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+  }
+  
 }

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java

@@ -372,4 +372,9 @@ public class LayerText implements Serializable, Drawable {
     return width * height;
   }
 
+  @Override
+  public String getElementId() {
+    return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+  }
+
 }

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -640,10 +640,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
     this.fontSize = fontSize;
   }
 
-  /**
-   * @return the elementId
-   * @see #elementId
-   */
+  @Override
   public String getElementId() {
     return elementId;
   }

model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java

@@ -11,8 +11,8 @@ import java.util.Set;
 import org.apache.log4j.Logger;
 import org.reflections.Reflections;
 
-import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.species.Element;
@@ -57,7 +57,7 @@ public final class ElementUtils {
    *          tag for this element is created
    * @return tag that identifies element
    */
-  public String getElementTag(BioEntity element) {
+  public String getElementTag(Drawable element) {
     return getElementTag(element, null);
   }
 
@@ -72,15 +72,8 @@ public final class ElementUtils {
    *          null (in such situation it will be skipped in the tag)
    * @return tag that identifies element
    */
-  public String getElementTag(BioEntity element, Object annotator) {
-    String id = null;
-    if (element instanceof Element) {
-      id = ((Element) element).getElementId();
-    } else if (element instanceof Reaction) {
-      id = ((Reaction) element).getIdReaction();
-    } else {
-      throw new NotImplementedException("Unknown class: " + element.getClass());
-    }
+  public String getElementTag(Drawable element, Object annotator) {
+    String id = element.getElementId();
     if (annotator != null) {
       return "[" + annotator.getClass().getSimpleName() + "]\t[" + element.getClass().getSimpleName() + " " + id
           + "]\t";