layer elements contain z index

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

@@ -55,6 +55,11 @@ public class LayerRect implements Serializable {
    */
   private Double y = 0.0;
 
+  /**
+   * Z index.
+   */
+  private Integer z;
+
   /**
    * Width of the rectangle.
    */
@@ -239,4 +244,12 @@ public class LayerRect implements Serializable {
   public void setHeight(Double height) {
     this.height = height;
   }
+
+  public Integer getZ() {
+    return z;
+  }
+
+  public void setZ(Integer z) {
+    this.z = z;
+  }
 }

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

@@ -66,6 +66,11 @@ public class LayerText implements Serializable {
    */
   private Double y = 0.0;
 
+  /**
+   * Z-index.
+   */
+  private Integer z;
+
   /**
    * Width of the rectangle where text is drawn.
    */
@@ -350,4 +355,12 @@ public class LayerText implements Serializable {
     return "[" + this.getClass().getSimpleName() + ": " + this.getNotes() + "]";
   }
 
+  public Integer getZ() {
+    return z;
+  }
+
+  public void setZ(Integer z) {
+    this.z = z;
+  }
+
 }

persist/src/main/resources/db/migration/13.1.0~alpha.0/V13.1.0.20190508__z_index_to_layers.sql

+-- add z-index to all layer elements
+alter table layer_rect_table add column z integer;
+alter table layer_oval_table add column z integer;
+alter table layer_text_table add column z integer;
+
+
+with v_layer_text_table as
+(
+ select id, row_number() over (order by width*height desc, id) as rn from layer_text_table
+) 
+update layer_text_table set z =  v_layer_text_table.rn
+from v_layer_text_table
+where layer_text_table.id = v_layer_text_table.id;
+
+with v_layer_oval_table as
+(
+ select id, row_number() over (order by width*height desc, id) as rn from layer_oval_table
+) 
+update layer_oval_table set z =  v_layer_oval_table.rn
+from v_layer_oval_table
+where layer_oval_table.id = v_layer_oval_table.id;
+
+with v_layer_rect_table as
+(
+ select id, row_number() over (order by width*height desc, id) as rn from layer_rect_table
+) 
+update layer_rect_table set z =  v_layer_rect_table.rn
+from v_layer_rect_table
+where layer_rect_table.id = v_layer_rect_table.id;
+
+
+ALTER TABLE layer_rect_table ALTER COLUMN z SET NOT NULL;
+ALTER TABLE layer_oval_table ALTER COLUMN z SET NOT NULL;
+ALTER TABLE layer_text_table ALTER COLUMN z SET NOT NULL;

persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java

 package lcsb.mapviewer.persist;
 
+import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -41,6 +42,7 @@ import org.xml.sax.SAXException;
 
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
 import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
 import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.AntisenseRna;
@@ -384,4 +386,12 @@ public abstract class PersistTestFunctions {
     return result;
   }
 
+  protected LayerRect createRect() {
+    LayerRect lr = new LayerRect();
+    lr.setColor(Color.YELLOW);
+    lr.setZ(0);
+    return lr;
+  }
+
+
 }

persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java

@@ -130,8 +130,7 @@ public class CommentDaoTest extends PersistTestFunctions {
     Layer layer = new Layer();
     model.addLayer(layer);
 
-    LayerRect lr = new LayerRect();
-    lr.setColor(Color.YELLOW);
+    LayerRect lr = createRect();
     layer.addLayerRect(lr);
 
     Reaction reaction = createReaction();

persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java

@@ -175,9 +175,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
     Layer layer = new Layer();
     model.addLayer(layer);
 
-    LayerRect lr = new LayerRect();
-    lr.setColor(Color.YELLOW);
-    layer.addLayerRect(lr);
+    layer.addLayerRect(createRect());
 
     Reaction reaction = createReaction();
     reaction.addProduct(new Product(alias));

persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java

@@ -431,9 +431,7 @@ public class ModelDaoTest extends PersistTestFunctions {
     Layer layer = new Layer();
     model.addLayer(layer);
 
-    LayerRect lr = new LayerRect();
-    lr.setColor(Color.YELLOW);
-    layer.addLayerRect(lr);
+    layer.addLayerRect(createRect());
 
     Reaction reaction = createReaction();
     reaction.addProduct(new Product(alias));