Merge branch '736-overlapping-compartments' into 'devel_12.2.x'

Resolve "Overlapping compartments in non-layout SBML upload"

See merge request minerva/core!689

CHANGELOG

@@ -6,8 +6,10 @@ minerva (12.2.0~beta.3) unstable; urgency=medium
     invalid (#735)
   * Bug fix: closing Add Project window was taking infinity (#734)
   * Bug fix: align of checkboxes in top right corner fixed (#733)
+  * Bug fix: uploading SBML file without layout resulted in overlapping 
+    compartments (#736)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 6 Mar 2019 17:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 6 Mar 2019 14:00:00 +0200
 
 minerva (12.2.0~beta.2) unstable; urgency=medium
   * Bug fix: order of the overlays is defined explicitly also for general 

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -219,7 +219,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         minPoint.getY() + COMPARTMENT_BORDER, dimension.getWidth() - COMPARTMENT_BORDER * 2,
         dimension.getHeight() - COMPARTMENT_BORDER * 2);
     for (Element element : compartment.getElements()) {
-      if (!elements.contains(element) && element.getBorder()!=null) {
+      if (!elements.contains(element) && element.getBorder() != null && element.getX() != 0 && element.getY() != 0) {
         border.add(element.getBorder());
       }
     }

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

@@ -151,7 +151,7 @@ public interface Model {
    * @param elements
    *          list of elements
    */
-  void addElements(List<? extends Element> elements);
+  void addElements(Collection<? extends Element> elements);
 
   /**
    * Sets new short description of the model.

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

@@ -198,7 +198,7 @@ public class ModelFullIndexed implements Model {
   }
 
   @Override
-  public void addElements(List<? extends Element> elements) {
+  public void addElements(Collection<? extends Element> elements) {
     for (Element element : elements) {
       addElement(element);
     }

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

@@ -322,7 +322,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    * @see x
    */
   public void setX(String string) {
-    this.x = Double.parseDouble(string);
+    setX(Double.parseDouble(string));
   }
 
   /**
@@ -483,7 +483,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    * @return rectangle border
    */
   public Rectangle2D getBorder() {
-    if (x == null || y == null || width == null || height == null) {
+    if (x == null || y == null || width == null || height == null || width == 0.0 || height == 0.0) {
       return null;
     }
     return new Rectangle2D.Double(x, y, width, height);