Merge branch '664-unknown-inhibition-is-displayed-incorrectly-in-minerva' into 'master'

Resolve "Unknown inhibition is displayed incorrectly in Minerva"

Closes #664

See merge request !707

CHANGELOG

@@ -28,6 +28,10 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed 
     (#616)
+  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and 
+    "Unknown Inhibition" reactions (#664) 
+  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is 
+    slightly separated from target phenotype (#664)
 
 minerva (12.2.0~beta.2) unstable; urgency=medium
   * Bug fix: order of the overlays is defined explicitly also for general

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java

@@ -67,7 +67,7 @@ public enum ReactionLineData {
   /**
    * Information about arrows/lines for {@link InhibitionReaction} class.
    */
-  INHIBITION(InhibitionReaction.class, "INHIBITION", LineType.SOLID, ArrowType.CROSSBAR),
+  INHIBITION(InhibitionReaction.class, "INHIBITION", LineType.SOLID, ArrowType.CROSSBAR, 3),
 
   /**
    * Information about arrows/lines for {@link KnownTransitionOmittedReaction}
@@ -150,7 +150,7 @@ public enum ReactionLineData {
   /**
    * Information about arrows/lines for {@link UnknownInhibitionReaction} class.
    */
-  UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, "UNKNOWN_INHIBITION", LineType.DASHED, ArrowType.CROSSBAR),
+  UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, "UNKNOWN_INHIBITION", LineType.DASHED, ArrowType.CROSSBAR, 3),
 
   /**
    * Information about arrows/lines for {@link UnknownNegativeInfluenceReaction}

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java

@@ -135,19 +135,26 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
 	 *          where the rectangle should be drawn
 	 */
 	protected void drawRectangleData(final Line2D line, final ReactionRect insideType, final Graphics2D graphics) {
+      Point2D startPoint = line.getP1();
+      Point2D endPoint = line.getP2();
+      double pointX = (startPoint.getX() + endPoint.getX()) / 2;
+      double pointY = (startPoint.getY() + endPoint.getY()) / 2;
+	  Point2D centerPoint = new Point2D.Double(pointX, pointY);
+      double dx = endPoint.getX() - startPoint.getX();
+      double dy = endPoint.getY() - startPoint.getY();
+      double angle = Math.atan2(dy, dx);
+
 		if (insideType == null) {
-			graphics.draw(line);
+            Point2D topPoint = new Point2D.Double(pointX + RECT_SIZE / 2, pointY);
+            topPoint = new PointTransformation().rotatePoint(topPoint , angle, centerPoint);
+            
+            Point2D bottomPoint = new Point2D.Double(pointX - RECT_SIZE / 2, pointY);
+            bottomPoint = new PointTransformation().rotatePoint(bottomPoint , angle, centerPoint);
+            graphics.draw(new Line2D.Double(topPoint, bottomPoint));
 		} else {
-			Point2D startPoint = line.getP1();
-			Point2D endPoint = line.getP2();
-			double dx = endPoint.getX() - startPoint.getX();
-			double dy = endPoint.getY() - startPoint.getY();
-			double angle = Math.atan2(dy, dx);
 
 			// find rectangle
 			Rectangle2D rect = new Rectangle2D.Double();
-			double pointX = (startPoint.getX() + endPoint.getX()) / 2;
-			double pointY = (startPoint.getY() + endPoint.getY()) / 2;
 			rect.setRect(pointX - RECT_SIZE / 2, pointY - RECT_SIZE / 2, RECT_SIZE, RECT_SIZE);
 
 			// rotate graphics by the angle defined by line (instead of rotating