Merge branch '1457-generate-process-rectangles-for-sbml-render-layout' into 'master'

Resolve "generate process rectangles for SBML render layout"

Closes #1457

See merge request !1286

CHANGELOG

@@ -22,13 +22,15 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
     residues (#1456)
   * Small improvement: SBML render contains information about structural states
     (#1456)
+  * Small improvement: SBML render contains process rectangle for reactions
+    (#1457)
   * Bug fix: refreshing page after removing last project on the page redirect to
     proper page (#1051)
   * Bug fix: removing plugin that does not exist anymore does not raise an error
     (#1289)
   * Bug fix: broken overlays crashed minerva upgrade (#1453)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2020 08:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 19 Mar 2021 10:00:00 +0200
 
 minerva (16.0.0~alpha.0) stable; urgency=medium
   * Backward incompatibility: deprecated columns in data overlay table are no

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java

@@ -228,4 +228,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return sbmlModelUtils.createStyle();
   }
 
+  protected void createAbsolutePoint(Polygon polygon, double x, double y) {
+    RenderPoint p1 = polygon.createRenderPoint();
+    p1.setX(new RelAbsVector(Math.round(x)));
+    p1.setY(new RelAbsVector(Math.round(y)));
+  }
+
 }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

 package lcsb.mapviewer.converter.model.sbml.reaction;
 
-import java.awt.BasicStroke;
-import java.awt.Stroke;
+import java.awt.*;
 import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
 import java.util.*;
+import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbml.jsbml.*;
 import org.sbml.jsbml.ext.layout.*;
-import org.sbml.jsbml.ext.render.*;
+import org.sbml.jsbml.ext.layout.Point;
+import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.Polygon;
 import org.w3c.dom.Node;
 
 import lcsb.mapviewer.common.Configuration;
@@ -38,6 +42,8 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
    */
   private static Logger logger = LogManager.getLogger();
 
+  private static final double RECT_SIZE = 10;
+
   private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
 
   private SbmlBioEntityExporter<Compartment, org.sbml.jsbml.Compartment> compartmentExporter;
@@ -289,7 +295,38 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
 
   @Override
   protected LocalStyle createStyle(Reaction reaction) {
-    return createStyle(reaction.getLine());
+    LocalStyle style = createStyle(reaction.getLine());
+    ColorDefinition color = getColorDefinition(Color.WHITE);
+    style.getGroup().setFill(color.getId());
+
+    Point2D startPoint = reaction.getLine().getLines().get((reaction.getLine().getLines().size() - 1) / 2).getP1();
+    Point2D endPoint = reaction.getLine().getLines().get((reaction.getLine().getLines().size() - 1) / 2).getP2();
+
+    double pointX = (startPoint.getX() + endPoint.getX()) / 2;
+    double pointY = (startPoint.getY() + endPoint.getY()) / 2;
+    double dx = endPoint.getX() - startPoint.getX();
+    double dy = endPoint.getY() - startPoint.getY();
+    double angle = Math.atan2(dy, dx);
+
+    if (reaction.getProcessCoordinates() != null) {
+      angle = 0;
+      pointX = reaction.getProcessCoordinates().getX();
+      pointY = reaction.getProcessCoordinates().getY();
+    }
+    angle += Math.PI / 4;
+
+    Polygon polygon = new Polygon();
+
+    double dist = Math.sqrt(2) * RECT_SIZE / 2;
+
+    createAbsolutePoint(polygon, pointX - dist * Math.cos(angle), pointY - dist * Math.sin(angle));
+    createAbsolutePoint(polygon, pointX + dist * Math.sin(angle), pointY - dist * Math.cos(angle));
+    createAbsolutePoint(polygon, pointX + dist * Math.cos(angle), pointY + dist * Math.sin(angle));
+    createAbsolutePoint(polygon, pointX - dist * Math.sin(angle), pointY + dist * Math.cos(angle));
+    style.getGroup().addElement(polygon);
+
+    return style;
+
   }
 
   void removeColinearPoints(ReactionGlyph glyph) {

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

@@ -745,12 +745,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     p1.setY(new RelAbsVector(0, Math.round(y)));
   }
 
-  private void createAbsolutePoint(Polygon polygon, double x, double y) {
-    RenderPoint p1 = polygon.createRenderPoint();
-    p1.setX(new RelAbsVector(Math.round(x)));
-    p1.setY(new RelAbsVector(Math.round(y)));
-  }
-
   private void createAbsoluteBezierPoint(Polygon polygon, double x, double y, double x1, double y1, double x2,
       double y2) {
     RenderCubicBezier result = (RenderCubicBezier) polygon.createRenderCubicBezier();

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java

@@ -10,8 +10,7 @@ import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 
-import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
-import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.converter.model.sbml.*;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -38,7 +37,7 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
     model.addElement(protein1);
     model.addElement(protein2);
 
-    SbmlSpeciesExporter exporter = helper.createExporter(model);
+    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> exporter = helper.createExporter(model);
 
     exporter.exportElements();
 
@@ -58,7 +57,7 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
     model.addElement(protein2);
     model.addElement(compartment);
 
-    SbmlSpeciesExporter exporter = helper.createExporter(model);
+    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> exporter = helper.createExporter(model);
 
     exporter.exportElements();
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTestHelper.java

@@ -5,11 +5,11 @@ import java.util.Collection;
 
 import org.sbml.jsbml.SBMLDocument;
 
-import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
-import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
+import lcsb.mapviewer.converter.model.sbml.*;
 import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlSpeciesExporterTestHelper {
   org.sbml.jsbml.Model sbmlModel;