Merge branch '1350-catalist-point-invalid' into 'devel_15.0.x'

closest point to line was inproperly computed

See merge request !1233

CHANGELOG

@@ -14,6 +14,8 @@ minerva (15.0.3) stable; urgency=medium
     another tab there was an error thrown (#1343) 
   * Bug fix: chebi and entrez annotations were incorrectly exported to GPML
     (#1349)
+  * Bug fix: exporting to GPML sometimes resulted in invalid modification point
+    end for catalysis (#1350)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 8 Jul 2020 16:00:00 +0200
 

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java

@@ -123,24 +123,35 @@ public final class Geo {
    * @return point on line that is as close as possible to point
    */
   public static Point2D closestPointOnPolyline(PolylineData mainLine, Point2D point) {
-    Point2D res = null;
-    double distance = distanceOnPolyline(mainLine, point);
-    double lenght = 0.0;
+    Point2D res = mainLine.getBeginPoint();
     for (Line2D line : mainLine.getLines()) {
-      lenght += lineLen(line);
-    }
-    lenght *= distance;
-    for (Line2D line : mainLine.getLines()) {
-      if (lenght - lineLen(line) > 0) {
-        lenght -= lineLen(line);
-      } else {
-        double tmp = lenght / lineLen(line);
-        double x = line.getX1() + tmp * (line.getX2() - line.getX1());
-        double y = line.getY1() + tmp * (line.getY2() - line.getY1());
-        res = new Point2D.Double(x, y);
+      Point2D newPoint = getClosestPointOnSegment(line, point);
+      if (res.distanceSq(point) > newPoint.distanceSq(point)) {
+        res = newPoint;
       }
     }
     return res;
   }
 
+  static Point2D getClosestPointOnSegment(Line2D line, Point2D point) {
+    double xDelta = line.getX2() - line.getX1();
+    double yDelta = line.getY2() - line.getY1();
+
+    if ((xDelta == 0) && (yDelta == 0)) {
+      return new Point2D.Double(line.getX1(), line.getY1());
+    }
+
+    double u = ((point.getX() - line.getX1()) * xDelta + (point.getY() - line.getY1()) * yDelta)
+        / (xDelta * xDelta + yDelta * yDelta);
+
+    if (u < 0) {
+      return new Point2D.Double(line.getX1(), line.getY1());
+    } else if (u > 1) {
+      return new Point2D.Double(line.getX2(), line.getY2());
+    } else {
+      return new Point2D.Double((int) Math.round(line.getX1() + u * xDelta),
+          (int) Math.round(line.getY1() + u * yDelta));
+    }
+  }
+
 }

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java

@@ -6,11 +6,13 @@ import org.junit.runners.Suite.SuiteClasses;
 
 import lcsb.mapviewer.wikipathway.XML.AllXmlTests;
 import lcsb.mapviewer.wikipathway.model.AllModelTests;
+import lcsb.mapviewer.wikipathway.utils.GeoTest;
 
 @RunWith(Suite.class)
 @SuiteClasses({ AllModelTests.class,
     AllXmlTests.class,
     ComplexReactionToModelTest.class,
+    GeoTest.class,
     GPMLToModelTest.class,
     ReactionElbowsTest.class,
     ReactionGpmlInputToModelTest.class,

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java

@@ -23,7 +23,6 @@ import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.ModificationState;
 import lcsb.mapviewer.model.map.species.field.Residue;
@@ -307,7 +306,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
     species.setX(1);
     species.setY(1);
     species.setZ(15);
-    
+
     species.setNamePoint(species.getCenter());
     species.setNameHorizontalAlign(HorizontalAlign.CENTER);
     species.setNameVerticalAlign(VerticalAlign.MIDDLE);
@@ -419,16 +418,15 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
     model.setHeight(1000);
     model.setNotes("a < b");
 
-    
     Species p1 = createProtein();
     p1.setNotes("<a href='https://google.lu/'>link</a>");
 
     model.addElement(p1);
-    
+
     Species p2 = createProtein();
     model.addElement(p2);
-    
-    Reaction r= createReaction(p1, p2);
+
+    Reaction r = createReaction(p1, p2);
     r.setNotes("<xml>tag</xml>");
     model.addReaction(r);
 
@@ -439,5 +437,4 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
 
     assertEquals(0, new ModelComparator().compare(model, model2));
   }
-
 }

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/utils/GeoTest.java

+package lcsb.mapviewer.wikipathway.utils;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+
+import org.junit.Test;
+
+public class GeoTest {
+
+  @Test
+  public void testClosestPointOnSegment() {
+    Point2D result = Geo.getClosestPointOnSegment(new Line2D.Double(10, 10, 20, 20), new Point2D.Double(20, 10));
+    assertEquals(result, new Point2D.Double(15, 15));
+  }
+
+  @Test
+  public void testClosestPointOnSegmentEdge() {
+    Point2D result = Geo.getClosestPointOnSegment(new Line2D.Double(10, 10, 20, 20), new Point2D.Double(20, 0));
+    assertEquals(result, new Point2D.Double(10, 10));
+  }
+
+  @Test
+  public void testClosestPointOnSegmentEdge2() {
+    Point2D result = Geo.getClosestPointOnSegment(new Line2D.Double(10, 10, 20, 20), new Point2D.Double(20, 30));
+    assertEquals(result, new Point2D.Double(20, 20));
+  }
+
+}