colinear points are removed when exporting to sbml

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

@@ -21,6 +21,7 @@ import org.sbml.jsbml.SpeciesReference;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.BoundingBox;
 import org.sbml.jsbml.ext.layout.Curve;
+import org.sbml.jsbml.ext.layout.CurveSegment;
 import org.sbml.jsbml.ext.layout.LineSegment;
 import org.sbml.jsbml.ext.layout.Point;
 import org.sbml.jsbml.ext.layout.ReactionGlyph;
@@ -35,8 +36,10 @@ import org.w3c.dom.Node;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
 import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
@@ -295,14 +298,38 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
       assignStyleToGlyph(reactionGlyph, createStyle(reaction));
     }
-    if (reactionGlyph.getBoundingBox()==null) {
+    if (reactionGlyph.getBoundingBox() == null) {
       reactionGlyph.setBoundingBox(new BoundingBox());
     }
-    if (reactionGlyph.getBoundingBox().getPosition()==null) {
+    if (reactionGlyph.getBoundingBox().getPosition() == null) {
       reactionGlyph.getBoundingBox().setPosition(new Point());
     }
     reactionGlyph.getBoundingBox().getPosition().setZ(reaction.getZ());
 
+    removeColinearPoints(reactionGlyph);
+  }
+
+  private void removeColinearPoints(ReactionGlyph glyph) {
+    PolylineData line = createLine(glyph.getCurve());
+    logger.debug(line);
+    line = PolylineDataFactory.removeCollinearPoints(line);
+    logger.debug(line);
+    Curve curve = createCurve(line, false);
+    glyph.setCurve(curve);
+  }
+
+  private PolylineData createLine(Curve curve) {
+    PolylineData result = new PolylineData();
+    if (curve.getCurveSegmentCount() > 0) {
+      CurveSegment segment = curve.getCurveSegment(0);
+      result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
+    }
+    for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
+      CurveSegment segment = curve.getCurveSegment(i);
+      result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
+
+    }
+    return result;
   }
 
   private LocalStyle createStyle(ReactionNode node) {
@@ -358,16 +385,20 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
     SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
     reactantGlyph.setSpeciesGlyph(speciesExporter.getSbmlGlyphByElementId(node.getElement().getElementId()).getId());
-    reactantGlyph.setCurve(createCurve(node, node instanceof Reactant));
+    Curve curve = createCurve(node.getLine(), node instanceof Reactant);
+    if (curve.getCurveSegmentCount() == 0) {
+      logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
+    }
+    reactantGlyph.setCurve(curve);
     reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
     return reactantGlyph;
   }
 
-  private Curve createCurve(ReactionNode node, boolean reverse) {
+  private Curve createCurve(PolylineData polyline, boolean reverse) {
     Curve curve = new Curve();
-    List<Line2D> lines = node.getLine().getLines();
+    List<Line2D> lines = polyline.getLines();
     if (reverse) {
-      lines = node.getLine().reverse().getLines();
+      lines = polyline.reverse().getLines();
     }
     for (Line2D line : lines) {
       if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
@@ -377,9 +408,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
         curve.addCurveSegment(segment);
       }
     }
-    if (curve.getCurveSegmentCount() == 0) {
-      logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
-    }
     return curve;
   }