old reaction.getCenterLine method removed

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

 package lcsb.mapviewer.converter.model.sbgnml;
 
-import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -11,7 +10,8 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.sbgn.ArcClazz;
 import org.sbgn.GlyphClazz;
 import org.sbgn.Language;
@@ -30,6 +30,7 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
 import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -580,9 +581,9 @@ public class SbgnmlXmlExporter {
     processGlyph.setClazz(getGlyphClazzFromReaction(reaction).getClazz());
     Bbox bbox = new Bbox();
 
-    Line2D line = reaction.getCenterLine();
-    Point2D startPoint = line.getP1();
-    Point2D endPoint = line.getP2();
+    PolylineData line = reaction.getLine();
+    Point2D startPoint = line.getBeginPoint();
+    Point2D endPoint = line.getEndPoint();
 
     double pointX = (startPoint.getX() + endPoint.getX()) / 2;
     double pointY = (startPoint.getY() + endPoint.getY()) / 2;

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -562,7 +562,7 @@ public class SbgnmlXmlParser {
         productPointList.add(2, newPoint);
       }
     }
-    int reactantPointEnds = (productPointList.size()-1) / 2;
+    int reactantPointEnds = (productPointList.size() - 1) / 2;
     int productPointStarts = reactantPointEnds + 1;
 
     Reactant reactant = new Reactant(model.getElementByElementId(source.getId()));
@@ -949,7 +949,7 @@ public class SbgnmlXmlParser {
     ModifierTypeUtils utils = new ModifierTypeUtils();
     Point2D result;
 
-    Line2D centerLine = reaction.getCenterLine();
+    Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
     double dx = centerLine.getX2() - centerLine.getX1();
     double dy = centerLine.getY2() - centerLine.getY1();
     double centerLineAngle = Math.atan2(dy, dx);
@@ -1315,7 +1315,7 @@ public class SbgnmlXmlParser {
     } else {
       reaction.getProducts().get(0).getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
     }
-    
+
     PolylineData centerLine = new PolylineData(pt.copyPoint(centerPointStart), pt.copyPoint(centerPointEnd));
     reaction.setLine(centerLine);
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java

@@ -6,11 +6,11 @@ import java.awt.Graphics2D;
 import java.awt.geom.Rectangle2D;
 import java.util.List;
 
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.DrawingException;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -12,11 +12,11 @@ import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
 import java.util.List;
 
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.DrawingException;

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java

@@ -53,6 +53,7 @@ public abstract class GraphicsTestFunctions {
     reaction.addModifier(modifier);
     reaction.addProduct(product);
     reaction.addReactant(reactant);
+    reaction.setLine(new PolylineData(center, center));
     reaction.setZ(elementCounter);
     return reaction;
   }

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java

@@ -41,6 +41,7 @@ import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
 import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 
@@ -208,6 +209,7 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     result.addModifier(modifier);
     result.addProduct(product);
     result.addReactant(reactant);
+    result.setLine(new PolylineData(new Point2D.Double(105, 90), new Point2D.Double(95, 90)));
     return result;
   }
 
@@ -249,6 +251,8 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     productOperator.addOutput(product2);
     productOperator.setLine(new PolylineData(new Point2D.Double(130, 90), new Point2D.Double(110, 90)));
 
+    result.setLine(new PolylineData(new Point2D.Double(105, 90), new Point2D.Double(95, 90)));
+
     result.addModifier(modifier1);
     result.addModifier(modifier2);
     result.addNode(modifierOperator);
@@ -409,6 +413,8 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     Point2D reactantEnd = new Point2D.Double(90, 90);
     Point2D productEnd = new Point2D.Double(110, 90);
 
+    result.setLine(new PolylineData(new Point2D.Double(105, 90), new Point2D.Double(95, 90)));
+
     Reactant reactant = new Reactant(new GenericProtein("s2"));
 
     reactant.setLine(
@@ -446,4 +452,67 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     }
   }
 
+  @Test
+  public void testDrawRectangleDataSimple() throws Exception {
+    try {
+      Graphics2D graphics = createGraphicsMock();
+      ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+      PolylineData line = new PolylineData(new Point2D.Double(10, 20),
+          new Point2D.Double(10 + ReactionConverter.RECT_SIZE, 20));
+
+      rc.drawRectangleData(line, ReactionRect.RECT_EMPTY, graphics);
+
+      Mockito.verify(graphics, times(1)).fill(any(Shape.class));
+      Mockito.verify(graphics, times(1)).draw(any(Shape.class));
+
+    } catch (Exception e) {
+      throw e;
+    }
+  }
+
+  @Test
+  public void testDrawRectangleDataWithLineAround() throws Exception {
+    try {
+      Graphics2D graphics = createGraphicsMock();
+      ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+      PolylineData line = new PolylineData(new Point2D.Double(10, 20),
+          new Point2D.Double(10 + ReactionConverter.RECT_SIZE + 100, 20));
+
+      rc.drawRectangleData(line, ReactionRect.RECT_EMPTY, graphics);
+
+      Mockito.verify(graphics, times(1)).fill(any(Shape.class));
+      Mockito.verify(graphics, times(3)).draw(any(Shape.class));
+
+    } catch (Exception e) {
+      throw e;
+    }
+  }
+
+  @Test
+  public void testDrawRectangleDataWithPolyLineAround() throws Exception {
+    try {
+      Graphics2D graphics = createGraphicsMock();
+      ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+      PolylineData line = new PolylineData();
+      line.addPoint(new Point2D.Double(10, 20));
+      line.addPoint(new Point2D.Double(100, 20));
+      line.addPoint(new Point2D.Double(100, 200));
+      line.addPoint(new Point2D.Double(200, 200));
+      line.addPoint(new Point2D.Double(200, 300));
+      line.addPoint(new Point2D.Double(300, 300));
+      line.addPoint(new Point2D.Double(300, 400));
+
+      rc.drawRectangleData(line, ReactionRect.RECT_EMPTY, graphics);
+
+      Mockito.verify(graphics, times(1)).fill(any(Shape.class));
+      Mockito.verify(graphics, times(5)).draw(any(Shape.class));
+
+    } catch (Exception e) {
+      throw e;
+    }
+  }
+
 }

model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java

@@ -220,9 +220,9 @@ public class PolylineData implements Serializable, Drawable {
    * Return a line that correspond to the part of line.
    * 
    * @param from
-   *          index of the point where line should start
+   *          index of the point where line should start (included)
    * @param to
-   *          index of the point where line should end
+   *          index of the point where line should end (excluded)
    * @return line that correspond to the part of line
    */
   public PolylineData getSubline(int from, int to) {

model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java

@@ -477,16 +477,6 @@ public class Reaction implements BioEntity {
     return result;
   }
 
-  /**
-   * Returns central line of the reaction. Central line is the line that separates
-   * inputs from outputs.
-   * 
-   * @return central line of the reaction
-   */
-  public Line2D getCenterLine() {
-    return this.line.getLines().get(0);
-  }
-
   /**
    * Removes modifier.
    * 
@@ -518,18 +508,6 @@ public class Reaction implements BioEntity {
     return null;
   }
 
-  /**
-   * Returns central point of the reaction - point on central line (see:
-   * {@link #getCenterLine()}). This point determines one of the points where
-   * modifiers are attached.
-   * 
-   * @return central point of the reaction
-   */
-  public Point2D getCenterPoint() {
-    Line2D line2D = getCenterLine();
-    return new Point2D.Double((line2D.getX1() + line2D.getX2()) / 2, (line2D.getY1() + line2D.getY2()) / 2);
-  }
-
   /**
    * Check if one of the nodes reference to the element.
    * 

model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java

@@ -7,14 +7,14 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
-import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
 import org.apache.commons.lang3.SerializationUtils;
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -33,8 +33,6 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
@@ -245,119 +243,6 @@ public class ReactionTest extends ModelTestFunctions {
     }
   }
 
-  @Test
-  public void testGetCenterLine() {
-    try {
-      Reaction reaction1 = new Reaction();
-
-      Reactant reactant = new Reactant();
-      PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      reactant.setLine(line1);
-      reaction1.addReactant(reactant);
-
-      Product product = new Product();
-      PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
-      product.setLine(line2);
-      reaction1.addProduct(product);
-
-      Line2D line = reaction1.getCenterLine();
-      assertEquals(4.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
-  @Test
-  public void testGetCenterPoint() {
-    try {
-      Reaction reaction1 = new Reaction();
-
-      Reactant reactant = new Reactant();
-      PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      reactant.setLine(line1);
-      reaction1.addReactant(reactant);
-
-      Product product = new Product();
-      PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
-      product.setLine(line2);
-      reaction1.addProduct(product);
-
-      assertEquals(0.0, reaction1.getCenterPoint().distance(new Point2D.Double(2.0, 0.0)), Configuration.EPSILON);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
-  @Test
-  public void testGetCenterLine2() {
-    try {
-      Reaction reaction1 = new HeterodimerAssociationReaction();
-
-      Reactant reactant = new Reactant();
-      PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      reactant.setLine(line1);
-      reaction1.addReactant(reactant);
-
-      Reactant reactant2 = new Reactant();
-      PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      reactant2.setLine(line3);
-      reaction1.addReactant(reactant2);
-      AndOperator operator = new AndOperator();
-      operator.addInput(reactant);
-      operator.addInput(reactant2);
-      PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 11.0));
-      operator.setLine(line4);
-      reaction1.addNode(operator);
-
-      Product product = new Product();
-      PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
-      product.setLine(line2);
-      reaction1.addProduct(product);
-
-      Line2D line = reaction1.getCenterLine();
-      assertEquals(6.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
-  @Test
-  public void testGetCenterLine3() {
-    try {
-      Reaction reaction1 = new DissociationReaction();
-
-      Reactant reactant = new Reactant();
-      PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      reactant.setLine(line1);
-      reaction1.addReactant(reactant);
-
-      Product product = new Product();
-      PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
-      product.setLine(line2);
-      reaction1.addProduct(product);
-
-      Product product2 = new Product();
-      PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
-      product2.setLine(line3);
-      reaction1.addProduct(product2);
-      SplitOperator operator = new SplitOperator();
-      operator.addOutput(product);
-      operator.addOutput(product2);
-      PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 0.0));
-      operator.setLine(line4);
-      reaction1.addNode(operator);
-
-      Line2D line = reaction1.getCenterLine();
-      assertEquals(10.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testSerialization() {
     try {

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java

@@ -805,6 +805,8 @@ public class ModelContructor {
       output.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
       line.addPoint(pt.copyPoint(output.getLine().getBeginPoint()));
     }
+    line.setType(input.getLine().getType());
+    line.setColor(input.getLine().getColor());
     reaction.setLine(line);
   }
 

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

@@ -5,10 +5,13 @@ import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
+import java.awt.geom.Line2D;
+
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -27,6 +30,8 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
 
   private ModelComparator mc = new ModelComparator(1.0);
 
+  private PointTransformation pt = new PointTransformation();
+
   @Test
   public void DopamineTest() throws Exception {
     try {
@@ -437,7 +442,9 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
 
       Reaction reaction = model1.getReactions().iterator().next();
 
-      double distance = reaction.getCenterPoint().distance(reaction.getModifiers().get(0).getLine().getEndPoint());
+      Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
+      double distance = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5)
+          .distance(reaction.getModifiers().get(0).getLine().getEndPoint());
       assertTrue("Modifier is too far from center point: " + distance,
           distance < ReactionCellDesignerConverter.RECT_SIZE);
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java

 package lcsb.mapviewer.api.projects.comments;
 
+import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.LinkedHashSet;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.api.ObjectNotFoundException;
 import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.Comment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -43,6 +45,8 @@ public class CommentRestImpl extends BaseRestImpl {
   private ReactionDao reactionDao;
 
   private ElementDao elementDao;
+  
+  private PointTransformation pt = new PointTransformation();
 
   @Autowired
   public CommentRestImpl(ICommentService commentService, ReactionDao reactionDao, ElementDao elementDao) {
@@ -212,7 +216,8 @@ public class CommentRestImpl extends BaseRestImpl {
       if (comment.getTableName().getName().contains("Reaction")) {
         Reaction reaction = reactionDao.getById(comment.getTableId());
         if (reaction != null) {
-          coordinates = reaction.getCenterPoint();
+          Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
+          coordinates = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
         } else {
           logger.warn("Invalid reaction dbID: " + comment.getTableId());
         }

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java

@@ -19,6 +19,7 @@ import org.springframework.transaction.annotation.Transactional;
 import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
 import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
@@ -39,6 +40,8 @@ import lcsb.mapviewer.services.UserAccessException;
 @Service
 public class ReactionsRestImpl extends BaseRestImpl {
 
+  private PointTransformation pt = new PointTransformation();
+
   /**
    * Default class logger.
    */
@@ -110,7 +113,8 @@ public class ReactionsRestImpl extends BaseRestImpl {
       } else if (column.equals("name")) {
         value = reaction.getName();
       } else if (column.equals("centerpoint")) {
-        value = reaction.getCenterPoint();
+        Line2D centerLine = reaction.getLine().getLines().get(reaction.getLine().getLines().size() / 2);
+        value = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
       } else if (column.equals("products")) {
         List<Map<String, Object>> ids = new ArrayList<>();
         for (Product product : reaction.getProducts()) {