Resolve "Inability to export network to CellDesigner + probably invalid SBGN"

Closes #1131 (closed)

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java

@@ -7,6 +7,7 @@ import java.util.List;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.common.geometry.PointTransformation;
@@ -67,6 +68,15 @@ public class CellDesignerLineTransformation extends LineTransformation {
     double dx2 = -dy1;
     double dy2 = dx1;
 
+    double distDx = dx1 * dx1 + dy1 * dy1;
+
+    // this is special case if end and start point are equal then CellDesigner uses
+    // relative coordinates
+    if (distDx <= Configuration.EPSILON) {
+      dx1 = 1;
+      dy2 = 1;
+    }
+
     result.add(new Point2D.Double(startPoint.getX(), startPoint.getY()));
 
     if (midPoints != null) {
@@ -74,6 +84,7 @@ public class CellDesignerLineTransformation extends LineTransformation {
         if (!pt.isValidPoint(p)) {
           throw new InvalidArgumentException("Invalid point: " + p);
         }
+
         double x = startPoint.getX() + dx1 * p.getX() + dx2 * p.getY();
         double y = startPoint.getY() + dy1 * p.getX() + dy2 * p.getY();
         result.add(new Point2D.Double(x, y));
@@ -86,8 +97,8 @@ public class CellDesignerLineTransformation extends LineTransformation {
   }
 
   /**
-   * Transform line of typical xy coordinates into coordinates used by
-   * celldesigner.
+   * Transform line of typical x,y coordinates into coordinates used by
+   * CellDesigner.
    * 
    * CellDesigner format stores coordinates of a line in a different base. In this
    * base we have two points that define a base: vector between these points is 1
@@ -120,19 +131,24 @@ public class CellDesignerLineTransformation extends LineTransformation {
     List<Point2D> result = new ArrayList<Point2D>();
 
     if (dy * dy + dx * dx == 0) {
-      throw new InvalidArgumentException("First and last point in the line must differ but found: "
-          + line.getBeginPoint() + ", " + line.getEndPoint());
-    }
+      // this is special case - if start and end point are equals then cell designer
+      // requires relative coordinates
+      for (int i = 1; i < line.getPoints().size() - 1; i++) {
+        double ox = line.getPoints().get(i).getX();
+        double oy = line.getPoints().get(i).getY();
 
-    for (int i = 1; i < line.getPoints().size() - 1; i++) {
-      double ox = line.getPoints().get(i).getX();
-      double oy = line.getPoints().get(i).getY();
-
-      double py = (dy * (ax - ox) + dx * (oy - ay)) / (dy * dy + dx * dx);
-      double px = (dx * (ox - ax) + dy * (oy - ay)) / (dx * dx + dy * dy);
-      result.add(new Point2D.Double(px, py));
+        result.add(new Point2D.Double(ox - ax, oy - ay));
+      }
+    } else {
+      for (int i = 1; i < line.getPoints().size() - 1; i++) {
+        double ox = line.getPoints().get(i).getX();
+        double oy = line.getPoints().get(i).getY();
+
+        double py = (dy * (ax - ox) + dx * (oy - ay)) / (dy * dy + dx * dx);
+        double px = (dx * (ox - ax) + dy * (oy - ay)) / (dx * dx + dy * dy);
+        result.add(new Point2D.Double(px, py));
+      }
     }
-
     return result;
   }
 }