jsbml upgraded to 1.5

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

@@ -300,14 +300,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
     result.setBoundingBox(boundingBox);
     Ellipse ellipse = new Ellipse();
-    ellipse.setAbsoluteCx(false);
-    ellipse.setAbsoluteCy(false);
-    ellipse.setAbsoluteRx(true);
-    ellipse.setAbsoluteRy(true);
-    ellipse.setCx(0.0);
-    ellipse.setCy(0.0);
-    ellipse.setRx(4.0);
-    ellipse.setRy(4.0);
+    ellipse.setCx(new RelAbsVector(0, 0));
+    ellipse.setCy(new RelAbsVector(0, 0));
+    ellipse.setRx(new RelAbsVector(4, 0));
+    ellipse.setRy(new RelAbsVector(4, 0));
     result.getGroup().addElement(ellipse);
   }
 
@@ -385,10 +381,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
 
   protected RenderPoint createRenderPoint(double percentX, int percentY) {
     RenderPoint result = new RenderPoint();
-    result.setAbsoluteX(false);
-    result.setX(percentX);
-    result.setAbsoluteY(false);
-    result.setY(percentY);
+    result.setX(new RelAbsVector(0, percentX));
+    result.setY(new RelAbsVector(0, percentY));
     return result;
   }
 

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

@@ -51,12 +51,7 @@ public class SbmlExporter {
 
       ByteArrayOutputStream stream = new ByteArrayOutputStream();
       SBMLWriter.write(doc, stream, "minerva", Configuration.getSystemVersion(null));
-      return stream.toString("UTF-8")
-          // TODO bug: https://github.com/sbmlteam/jsbml/issues/158
-          .replace("<listOfSpeciesFeatures>", "<multi:listOfSpeciesFeatures>")
-          .replace("</listOfSpeciesFeatures>", "</multi:listOfSpeciesFeatures>")
-          //TODO bug: https://github.com/sbmlteam/jsbml/pull/222
-          .replace("render:basepoint", "render:basePoint");
+      return stream.toString("UTF-8");
     } catch (UnsupportedEncodingException | XMLStreamException e) {
       throw new InvalidStateException(e);
     }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java

@@ -99,29 +99,19 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
     style.getGroup().setStroke(getColorDefinition(element.getBorderColor()).getId());
     if (element instanceof OvalCompartment) {
       Ellipse ellipse = new Ellipse();
-      ellipse.setAbsoluteRx(false);
-      ellipse.setAbsoluteRy(false);
-      ellipse.setAbsoluteCx(false);
-      ellipse.setAbsoluteCy(false);
-      ellipse.setCx(50);
-      ellipse.setCy(50.0);
-      ellipse.setRx(50.0);
-      ellipse.setRy(50.0);
+      ellipse.setCx(new RelAbsVector(0, 50));
+      ellipse.setCy(new RelAbsVector(0, 50));
+      ellipse.setRx(new RelAbsVector(0, 50));
+      ellipse.setRy(new RelAbsVector(0, 50));
       style.getGroup().addElement(ellipse);
     } else {
       Rectangle rectangle = new Rectangle();
-      rectangle.setAbsoluteRx(false);
-      rectangle.setAbsoluteRy(false);
-      rectangle.setAbsoluteX(false);
-      rectangle.setAbsoluteY(false);
-      rectangle.setAbsoluteHeight(false);
-      rectangle.setAbsoluteWidth(false);
-      rectangle.setRx(0);
-      rectangle.setRy(0);
-      rectangle.setX(0);
-      rectangle.setY(0);
-      rectangle.setWidth(100);
-      rectangle.setHeight(100);
+      rectangle.setRx(new RelAbsVector(0, 0));
+      rectangle.setRy(new RelAbsVector(0, 0));
+      rectangle.setX(new RelAbsVector(0, 0));
+      rectangle.setY(new RelAbsVector(0, 0));
+      rectangle.setWidth(new RelAbsVector(0, 100));
+      rectangle.setHeight(new RelAbsVector(0, 100));
       style.getGroup().addElement(rectangle);
     }
 

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

 package lcsb.mapviewer.converter.model.sbml.species;
 
-import java.lang.reflect.Method;
 import java.util.*;
 
 import org.apache.commons.lang3.StringUtils;
@@ -11,7 +10,6 @@ import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.multi.*;
 import org.sbml.jsbml.ext.render.*;
 
-import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
 import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
@@ -507,14 +505,10 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     }
 
     Ellipse ellipse = new Ellipse();
-    ellipse.setAbsoluteRx(true);
-    ellipse.setAbsoluteRy(true);
-    ellipse.setAbsoluteCx(true);
-    ellipse.setAbsoluteCy(true);
-    ellipse.setCx(degraded.getWidth() / 2);
-    ellipse.setCy(diameter / 2 + DEGRADED_CROSS_LINE_EXTENDED_LENGTH);
-    ellipse.setRx(diameter / 2);
-    ellipse.setRy(diameter / 2);
+    ellipse.setCx(new RelAbsVector(degraded.getWidth() / 2));
+    ellipse.setCy(new RelAbsVector(diameter / 2 + DEGRADED_CROSS_LINE_EXTENDED_LENGTH));
+    ellipse.setRx(new RelAbsVector(diameter / 2));
+    ellipse.setRy(new RelAbsVector(diameter / 2));
 
     result.add(ellipse);
 
@@ -685,31 +679,21 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
 
   private Rectangle createDeafultShape() {
     Rectangle rectangle = new Rectangle();
-    rectangle.setAbsoluteRx(false);
-    rectangle.setAbsoluteRy(false);
-    rectangle.setAbsoluteX(false);
-    rectangle.setAbsoluteY(false);
-    rectangle.setAbsoluteHeight(false);
-    rectangle.setAbsoluteWidth(false);
-    rectangle.setRx(0);
-    rectangle.setRy(0);
-    rectangle.setX(0);
-    rectangle.setY(0);
-    rectangle.setWidth(100);
-    rectangle.setHeight(100);
+    rectangle.setRx(new RelAbsVector(0, 0));
+    rectangle.setRy(new RelAbsVector(0, 0));
+    rectangle.setX(new RelAbsVector(0, 0));
+    rectangle.setY(new RelAbsVector(0, 0));
+    rectangle.setWidth(new RelAbsVector(0, 100));
+    rectangle.setHeight(new RelAbsVector(0, 100));
     return rectangle;
   }
 
   private Ellipse createEllipseShape() {
     Ellipse ellipse = new Ellipse();
-    ellipse.setAbsoluteRx(false);
-    ellipse.setAbsoluteRy(false);
-    ellipse.setAbsoluteCx(false);
-    ellipse.setAbsoluteCy(false);
-    ellipse.setCx(50);
-    ellipse.setCy(50.0);
-    ellipse.setRx(50.0);
-    ellipse.setRy(50.0);
+    ellipse.setCx(new RelAbsVector(0, 50));
+    ellipse.setCy(new RelAbsVector(0, 50));
+    ellipse.setRx(new RelAbsVector(0, 50));
+    ellipse.setRy(new RelAbsVector(0, 50));
     return ellipse;
   }
 
@@ -754,44 +738,25 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
 
   private void createRelativePoint(Polygon polygon, double x, double y) {
     RenderPoint p1 = polygon.createRenderPoint();
-    p1.setAbsoluteX(false);
-    p1.setAbsoluteY(false);
-    p1.setX(x);
-    p1.setY(y);
+    p1.setX(new RelAbsVector(0, x));
+    p1.setY(new RelAbsVector(0, y));
   }
 
   private void createAbsolutePoint(Polygon polygon, double x, double y) {
     RenderPoint p1 = polygon.createRenderPoint();
-    p1.setAbsoluteX(true);
-    p1.setAbsoluteY(true);
-    p1.setX(Math.round(x));
-    p1.setY(Math.round(y));
+    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();
-    result.setAbsoluteX(true);
-    result.setAbsoluteY(true);
-    result.setX(Math.round(x));
-    result.setY(Math.round(y));
-    result.setAbsoluteX1(true);
-    result.setAbsoluteY1(true);
-    result.setX1(Math.round(x1));
-    result.setY1(Math.round(y1));
-    result.setAbsoluteX2(true);
-    result.setAbsoluteY2(true);
-    result.setX2(Math.round(x2));
-    result.setY2(Math.round(y2));
-
-    try {
-      Method method = RenderCurveSegment.class.getDeclaredMethod("setType", RenderCurveSegment.Type.class);
-      method.setAccessible(true);
-      method.invoke(result, RenderCurveSegment.Type.RENDER_CUBIC_BEZIER);
-    } catch (Exception e) {
-      throw new InvalidStateException("Problem with JSBML", e);
-    }
-
+    result.setX(new RelAbsVector(Math.round(x)));
+    result.setY(new RelAbsVector(Math.round(y)));
+    result.setX1(new RelAbsVector(Math.round(x1)));
+    result.setY1(new RelAbsVector(Math.round(y1)));
+    result.setX2(new RelAbsVector(Math.round(x2)));
+    result.setY2(new RelAbsVector(Math.round(y2)));
   }
 
   @Override

pom.xml

@@ -100,7 +100,7 @@
 
 		<commons-validator.version>1.6</commons-validator.version>
 
-		<jsbml.version>1.4</jsbml.version>
+		<jsbml.version>1.5</jsbml.version>
 
 		<chebi-ws.version>2.4</chebi-ws.version>