issues that were discovered during biohackathon 2019 in Paris

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

@@ -10,8 +10,8 @@ import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.common.geometry.DoubleDimension;
-import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.common.geometry.*;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -36,7 +36,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
   /**
    * Default class logger.
    */
-  private Logger logger = LogManager.getLogger(ApplySimpleLayoutModelCommand.class);
+  private Logger logger = LogManager.getLogger();
   private PointTransformation pt = new PointTransformation();
 
   public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, Double minX, Double minY,
@@ -79,7 +79,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
 
     modifyElementLocation(elements, null, minPoint, dimension);
     modifyReactionLocation(reactions);
-
   }
 
   protected void modifyElementLocation(Collection<Element> elements, Compartment parent, Point2D minPoint,
@@ -241,9 +240,14 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
       middle = operatorPoint;
     }
     for (Reactant reactant : reaction.getReactants()) {
+      Element element = reactant.getElement();
       PolylineData line = new PolylineData();
-      line.addPoint(reactant.getElement().getCenter());
+      line.addPoint(element.getCenter());
       line.addPoint(middle);
+      Point2D startPoint = findCrossPoint(element, line);
+      if (startPoint != null) {
+        line.getBeginPoint().setLocation(startPoint);
+      }
       if (reaction.isReversible()) {
         line.getBeginAtd().setArrowType(ArrowType.FULL);
       }
@@ -254,9 +258,22 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     }
   }
 
+  private Point2D findCrossPoint(Element element, PolylineData line) {
+    LineTransformation lt = new LineTransformation();
+    Point2D startPoint = lt.getIntersectionWithPathIterator(
+        new Line2D.Double(line.getBeginPoint(), line.getEndPoint()),
+        element.getBorder().getPathIterator(new AffineTransform()));
+    return startPoint;
+  }
+
   private void modifyModifiers(Reaction reaction, Point2D middle) {
     for (Modifier modifier : reaction.getModifiers()) {
-      PolylineData line = new PolylineData(middle, modifier.getElement().getCenter());
+      Element element = modifier.getElement();
+      PolylineData line = new PolylineData(element.getCenter(), middle);
+      Point2D startPoint = findCrossPoint(element, line);
+      if (startPoint != null) {
+        line.getBeginPoint().setLocation(startPoint);
+      }
       modifier.setLine(line);
       new ModifierTypeUtils().updateLineEndPoint(modifier);
     }
@@ -279,7 +296,12 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
       middle = operatorPoint;
     }
     for (Product product : reaction.getProducts()) {
-      PolylineData line = new PolylineData(middle, product.getElement().getCenter());
+      Element element = product.getElement();
+      PolylineData line = new PolylineData(middle, element.getCenter());
+      Point2D endPoint = findCrossPoint(element, line);
+      if (endPoint != null) {
+        line.getEndPoint().setLocation(endPoint);
+      }
       line.getEndAtd().setArrowType(ArrowType.FULL);
       product.setLine(line);
       if (operator != null) {
@@ -427,8 +449,14 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
   }
 
   protected Dimension2D estimateDimension(Collection<BioEntity> bioEntites) {
-    double suggestedSize = Math.max(100 * bioEntites.size() / 4,
-        Math.sqrt((SPECIES_WIDTH + 10) * (SPECIES_HEIGHT + 10) * bioEntites.size()));
+    int elementsCount = 0;
+    for (BioEntity bioEntity : bioEntites) {
+      if (bioEntity instanceof Element) {
+        elementsCount++;
+      }
+    }
+    double suggestedSize = Math.max(100 * elementsCount,
+        Math.sqrt((SPECIES_WIDTH + 10) * (SPECIES_HEIGHT + 10) * elementsCount));
     if (bioEntites.size() > 0) {
       suggestedSize = Math.max(suggestedSize, 2 * (SPECIES_WIDTH + 10));
     }
@@ -467,6 +495,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         }
         createLayout(model, bioEntites, null, minPoint, dimension);
       }
+      new ZIndexPopulator().populateZIndex(bioEntites);
     }
   }