comaprtments are more scattered

CHANGELOG

 minerva (15.0.0~alpha.0) stable; urgency=medium
   * Improvement: logs provided for validation data model are structurized (#325)
+  * Small improvement: compartments in not layouted SBML file are more
+    scattered (#326) 
   * Small improvement: when downloading a map results in too big file (>1MB)
     the content is compressed and returned as a zip file (#348)
   * Small improvement: confirmation dialog when removing "general view"

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

@@ -31,6 +31,8 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
   private static final int SPECIES_WIDTH = 90;
   private static final int SPECIES_HEIGHT = 30;
   private static final double COMPLEX_PADDING = 5;
+
+  private double borderOffset = COMPARTMENT_BORDER;
   /**
    * Default class logger.
    */
@@ -113,7 +115,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
       Compartment compartment = compartments.iterator().next();
       Rectangle2D border = computeCompartmentBorder(compartment, elements, minPoint, dimension);
       compartment.setBorder(border);
-      compartment.setNamePoint(border.getX() + COMPARTMENT_BORDER, border.getY() + COMPARTMENT_BORDER);
+      compartment.setNamePoint(border.getX() + COMPARTMENT_BORDER * 2, border.getY() + COMPARTMENT_BORDER * 2);
       Point2D point = new Point2D.Double(border.getX(), border.getY());
       Dimension2D recursiveDimension = new DoubleDimension(border.getWidth(), border.getHeight());
       Set<Element> elementsToModify = new HashSet<>(compartment.getElements());
@@ -170,9 +172,9 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
 
   private Rectangle2D computeCompartmentBorder(Compartment compartment, Collection<Element> elements, Point2D minPoint,
       Dimension2D dimension) {
-    Rectangle2D border = new Rectangle2D.Double(minPoint.getX() + COMPARTMENT_BORDER,
-        minPoint.getY() + COMPARTMENT_BORDER, dimension.getWidth() - COMPARTMENT_BORDER * 2,
-        dimension.getHeight() - COMPARTMENT_BORDER * 2);
+    Rectangle2D border = new Rectangle2D.Double(minPoint.getX() + borderOffset,
+        minPoint.getY() + borderOffset, dimension.getWidth() - borderOffset * 2,
+        dimension.getHeight() - borderOffset * 2);
     for (Element element : compartment.getElements()) {
       if (!elements.contains(element) && element.getBorder() != null && element.getX() != 0 && element.getY() != 0) {
         border.add(element.getBorder());
@@ -405,6 +407,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     height = Math.max(height, minPoint.getY() + dimension.getHeight());
     model.setWidth(width);
     model.setHeight(height);
+    borderOffset = Math.max(borderOffset, Math.max(width, height) * 0.01);
   }
 
   protected Point2D estimateLayoutMinPoint(Model model) {