export to sbml puts z index on every line and exports process coordinates if necessary

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

@@ -195,7 +195,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
         assignStyleToGlyph(reactantGlyph, style);
       }
     }
-    Curve curve = createCurve(reaction.getLine(), false);
+    Curve curve = createCurve(reaction.getLine(), false, reaction.getZ());
     for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
       reactionGlyph.getCurve().addCurveSegment(new LineSegment(curve.getCurveSegment(i)));
     }
@@ -227,9 +227,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
 
     for (Modifier modifier : reaction.getModifiers()) {
       SpeciesReferenceGlyph modifierGlyph = createNodeGlyph(reactionGlyph, modifier);
-      for (NodeOperator operator: reaction.getOperators()) {
+      for (NodeOperator operator : reaction.getOperators()) {
         if (operator.getInputs().contains(modifier)) {
-          modifierGlyph.setCurve(joinCurves(modifierGlyph.getCurve(), createCurve(operator.getLine(), false)));
+          modifierGlyph
+              .setCurve(joinCurves(modifierGlyph.getCurve(), createCurve(operator.getLine(), false, reaction.getZ())));
         }
       }
       if (modifier instanceof Inhibition) {
@@ -250,47 +251,22 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
       assignStyleToGlyph(reactionGlyph, createStyle(reaction));
     }
+    if (reaction.getProcessCoordinates() != null) {
       if (reactionGlyph.getBoundingBox() == null) {
         reactionGlyph.setBoundingBox(new BoundingBox());
       }
       if (reactionGlyph.getBoundingBox().getPosition() == null) {
-      reactionGlyph.getBoundingBox().setPosition(curveToPoint(reactionGlyph.getCurve()));
-      reactionGlyph.getBoundingBox().setDimensions(curveToDimension(reactionGlyph.getCurve()));
+        int rectSize = 10;
+        double x = reaction.getProcessCoordinates().getX() - rectSize / 2;
+        double y = reaction.getProcessCoordinates().getY() - rectSize / 2;
+        reactionGlyph.getBoundingBox().setPosition(new Point(x, y, reaction.getZ()));
+        reactionGlyph.getBoundingBox().setDimensions(
+            new Dimensions(rectSize, rectSize, 0, getSbmlModel().getLevel(), getSbmlModel().getVersion()));
       }
       reactionGlyph.getBoundingBox().getPosition().setZ(reaction.getZ());
-
-    removeColinearPoints(reactionGlyph);
-  }
-
-  private Dimensions curveToDimension(Curve curve) {
-    Point p = curveToPoint(curve);
-    double x = Double.MIN_VALUE;
-    double y = Double.MIN_VALUE;
-    for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
-      LineSegment segment = (LineSegment) curve.getCurveSegment(i);
-      x = Math.max(x, segment.getStart().getX());
-      x = Math.max(x, segment.getEnd().getX());
-
-      y = Math.max(y, segment.getStart().getY());
-      y = Math.max(y, segment.getEnd().getY());
-
     }
-    return new Dimensions(x - p.getX(), y - p.getY(), 0, getSbmlModel().getLevel(), getSbmlModel().getVersion());
-  }
-
-  private Point curveToPoint(Curve curve) {
-    double x = Double.MAX_VALUE;
-    double y = Double.MAX_VALUE;
-    for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
-      LineSegment segment = (LineSegment) curve.getCurveSegment(i);
-      x = Math.min(x, segment.getStart().getX());
-      x = Math.min(x, segment.getEnd().getX());
-
-      y = Math.min(y, segment.getStart().getY());
-      y = Math.min(y, segment.getEnd().getY());
 
-    }
-    return new Point(x, y);
+    removeColinearPoints(reactionGlyph);
   }
 
   @Override
@@ -320,7 +296,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   private void removeColinearPoints(ReactionGlyph glyph) {
     PolylineData line = createLine(glyph.getCurve());
     line = PolylineDataFactory.removeCollinearPoints(line);
-    Curve curve = createCurve(line, false);
+    Curve curve = createCurve(line, false, (int) glyph.getCurve().getCurveSegment(0).getStart().getZ());
     glyph.setCurve(curve);
   }
 
@@ -387,7 +363,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
     reactantGlyph.setSpeciesGlyph(
         speciesExporter.getSbmlGlyphByElementId(speciesExporter.getElementId(node.getElement())).getId());
-    Curve curve = createCurve(node.getLine(), node instanceof Reactant);
+    Curve curve = createCurve(node.getLine(), node instanceof Reactant, node.getReaction().getZ());
     if (curve.getCurveSegmentCount() == 0) {
       logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
     }
@@ -396,7 +372,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     return reactantGlyph;
   }
 
-  private Curve createCurve(PolylineData polyline, boolean reverse) {
+  private Curve createCurve(PolylineData polyline, boolean reverse, int z) {
     Curve curve = new Curve();
     List<Line2D> lines = polyline.getLines();
     if (reverse) {
@@ -405,8 +381,8 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     for (Line2D line : lines) {
       if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
         LineSegment segment = new LineSegment();
-        segment.setStart(new Point(line.getX1(), line.getY1()));
-        segment.setEnd(new Point(line.getX2(), line.getY2()));
+        segment.setStart(new Point(line.getX1(), line.getY1(), z));
+        segment.setEnd(new Point(line.getX2(), line.getY2(), z));
         curve.addCurveSegment(segment);
       }
     }
@@ -416,14 +392,14 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   private Curve joinCurves(Curve curve1, Curve curve2) {
     Curve curve = new Curve();
     for (int i = 0; i < curve1.getCurveSegmentCount(); i++) {
-      LineSegment source = ((LineSegment)curve1.getCurveSegment(i));
+      LineSegment source = ((LineSegment) curve1.getCurveSegment(i));
       LineSegment segment = new LineSegment();
       segment.setStart(new Point(source.getStart().getX(), source.getStart().getY()));
       segment.setEnd(new Point(source.getEnd().getX(), source.getEnd().getY()));
       curve.addCurveSegment(segment);
     }
     for (int i = 0; i < curve2.getCurveSegmentCount(); i++) {
-      LineSegment source = ((LineSegment)curve2.getCurveSegment(i));
+      LineSegment source = ((LineSegment) curve2.getCurveSegment(i));
       LineSegment segment = new LineSegment();
       segment.setStart(new Point(source.getStart().getX(), source.getStart().getY()));
       segment.setEnd(new Point(source.getEnd().getX(), source.getEnd().getY()));

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

@@ -91,10 +91,19 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
         reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
 
         // z index
+        if (glyph.getCurve() != null
+            && glyph.getCurve().getCurveSegmentCount() > 0
+            && glyph.getCurve().getCurveSegment(0).getStart() != null
+            && glyph.getCurve().getCurveSegment(0).getStart().isSetZ()) {
+
+          reactionWithLayout.setZ((int) glyph.getCurve().getCurveSegment(0).getStart().getZ());
+        }
+        if (reactionWithLayout.getZ() == null) {
           if (glyph.getBoundingBox() != null && glyph.getBoundingBox().getPosition() != null
               && glyph.getBoundingBox().getPosition().isSetZ()) {
             reactionWithLayout.setZ((int) glyph.getBoundingBox().getPosition().getZ());
           }
+        }
         Set<Pair<Element, ReactionNode>> usedReactionNodes = new HashSet<>();
         for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
           SpeciesGlyph speciesGlyph = getLayout().getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());