Merge branch '966-npe-in-converter' into 'devel_14.0.x'

modification residues were not layouted inside complexes

See merge request minerva/core!1001

CHANGELOG

@@ -3,6 +3,8 @@ minerva (14.0.3) stable; urgency=medium
     due to problems with identifiers used by SBGN (#1006)
   * Bug fix: upload of data overlay with conflicting overlay types caused error
     (#998)
+  * Bug fix: upload of sbml file with protein modifications inside complex 
+    crashed visualization (#966)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 06 Nov 2019 12:00:00 +0200
 

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

@@ -318,9 +318,12 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         element.setX(elementCenterX - SPECIES_WIDTH / 2);
         element.setY(elementCenterY - SPECIES_HEIGHT / 2);
         index++;
-        if (element instanceof SpeciesWithModificationResidue) {
-          modifyElementModificationResiduesLocation((SpeciesWithModificationResidue) element);
-        }
+      }
+    }
+
+    for (Species element : speciesList) {
+      if (element instanceof SpeciesWithModificationResidue) {
+        modifyElementModificationResiduesLocation((SpeciesWithModificationResidue) element);
       }
     }
 

model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommandTest.java

@@ -19,6 +19,7 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
 import lcsb.mapviewer.model.map.species.field.Residue;
 
 public class ApplySimpleLayoutModelCommandTest extends CommandTestFunctions {
@@ -198,6 +199,27 @@ public class ApplySimpleLayoutModelCommandTest extends CommandTestFunctions {
 
   }
 
+  @Test
+  public void testModifyResiduesLocationInComplex() {
+    ApplySimpleLayoutModelCommand layoutModelCommand = new ApplySimpleLayoutModelCommand(null);
+    GenericProtein p1 = createProtein();
+    Complex c1 = createComplex();
+    c1.addSpecies(p1);
+    BindingRegion r = new BindingRegion(); 
+    p1.addBindingRegion(r);
+    Set<Species> elements = new HashSet<>();
+    elements.add(p1);
+    elements.add(c1);
+
+    layoutModelCommand.modifySpeciesListLocation(elements, new Point2D.Double(100, 100), new DoubleDimension(200, 200));
+
+    assertTrue(p1.getX() >= 100);
+    assertTrue(p1.getY() >= 100);
+    assertTrue(p1.getBorder().getMaxX() <= 300);
+    assertTrue(p1.getBorder().getMaxY() <= 300);
+    assertNotNull(r.getPosition());
+  }
+
   @Test
   public void testModifyElementLocation() {
     ApplySimpleLayoutModelCommand layoutModelCommand = new ApplySimpleLayoutModelCommand(null);