Merge branch '366-missing-line-segments-in-sbml-layout' into 'master'

Missing line segments in SBML layout are put into reaction 'Curve' object

Closes #366

See merge request piotr.gawron/minerva!266

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

 package lcsb.mapviewer.converter.model.sbml.reaction;
 
 import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
@@ -34,6 +35,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
 import lcsb.mapviewer.model.map.modifier.Inhibition;
 import lcsb.mapviewer.model.map.modifier.Trigger;
 import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
 import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -170,20 +172,57 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph compartmentGlyph) {
     ReactionGlyph reactionGlyph = (ReactionGlyph) compartmentGlyph;
     boolean firstReactant = true;
+    reactionGlyph.setCurve(new Curve());
+
+    Point2D reactantEndPoint = null;
+
     for (Reactant reactant : reaction.getReactants()) {
       SpeciesReferenceGlyph reactantGlyph = createNodeGlyph(reactionGlyph, reactant);
       if (firstReactant) {
         reactantGlyph.setRole(SpeciesReferenceRole.SUBSTRATE);
+        for (NodeOperator operator : reaction.getOperators()) {
+          if (operator.isReactantOperator()) {
+            addOperatorLineToGlyph(reactionGlyph, operator, true);
+            if (reactantEndPoint == null) {
+              reactantEndPoint = operator.getLine().getEndPoint();
+            }
+          }
+        }
+        if (reactantEndPoint == null) {
+          reactantEndPoint = reactant.getLine().getEndPoint();
+        }
       } else {
         reactantGlyph.setRole(SpeciesReferenceRole.SIDESUBSTRATE);
       }
       firstReactant = false;
     }
     boolean firstProduct = true;
+    Point2D productStartPoint = null;
     for (Product product : reaction.getProducts()) {
       SpeciesReferenceGlyph productGlyph = createNodeGlyph(reactionGlyph, product);
       if (firstProduct) {
         productGlyph.setRole(SpeciesReferenceRole.PRODUCT);
+        for (NodeOperator operator : reaction.getOperators()) {
+          if (operator.isProductOperator()) {
+            if (productStartPoint == null) {
+              productStartPoint = operator.getLine().getBeginPoint();
+              LineSegment segment = new LineSegment();
+              segment.setStart(new Point(reactantEndPoint.getX(), reactantEndPoint.getY()));
+              segment.setEnd(new Point(productStartPoint.getX(), productStartPoint.getY()));
+              reactionGlyph.getCurve().addCurveSegment(segment);
+            }
+            addOperatorLineToGlyph(reactionGlyph, operator, false);
+          }
+        }
+
+        if (productStartPoint == null) {
+          productStartPoint = product.getLine().getBeginPoint();
+          LineSegment segment = new LineSegment();
+          segment.setStart(new Point(reactantEndPoint.getX(), reactantEndPoint.getY()));
+          segment.setEnd(new Point(productStartPoint.getX(), productStartPoint.getY()));
+          reactionGlyph.getCurve().addCurveSegment(segment);
+        }
+
       } else {
         productGlyph.setRole(SpeciesReferenceRole.SIDEPRODUCT);
       }
@@ -201,6 +240,23 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     }
   }
 
+  private void addOperatorLineToGlyph(ReactionGlyph reactantGlyph, NodeOperator operator, boolean reverse) {
+    Curve curve = reactantGlyph.getCurve();
+    List<Line2D> lines = operator.getLine().getLines();
+    if (reverse) {
+      lines = operator.getLine().reverse().getLines();
+    }
+    for (Line2D line : lines) {
+      if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
+        LineSegment segment = new LineSegment();
+        segment.setStart(new Point(line.getX1(), line.getY1()));
+        segment.setEnd(new Point(line.getX2(), line.getY2()));
+        curve.addCurveSegment(segment);
+      }
+    }
+
+  }
+
   private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
     SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
     reactantGlyph.setSpeciesGlyph(speciesExporter.getSbmlGlyphByElementId(node.getElement().getElementId()).getId());
@@ -209,11 +265,11 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     return reactantGlyph;
   }
 
-  private Curve createCurve(ReactionNode reactant, boolean reverse) {
+  private Curve createCurve(ReactionNode node, boolean reverse) {
     Curve curve = new Curve();
-    List<Line2D> lines = reactant.getLine().getLines();
+    List<Line2D> lines = node.getLine().getLines();
     if (reverse) {
-      lines = reactant.getLine().reverse().getLines();
+      lines = node.getLine().reverse().getLines();
     }
     for (Line2D line : lines) {
       if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {

frontend-js/package-lock.json

@@ -45,30 +45,38 @@
         "litemol": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
       },
       "dependencies": {
+        "ProtVista": {
+          "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
+          "dev": true,
+          "requires": {
+            "d3": "3.5.17",
+            "file-saver": "1.3.3",
+            "jquery": "2.2.4",
+            "jszip": "3.1.4",
+            "underscore": "1.8.3"
+          },
+          "dependencies": {
+            "jquery": {
+              "version": "2.2.4",
+              "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
+              "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
+              "dev": true
+            }
+          }
+        },
         "jquery": {
           "version": "3.3.1",
           "resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
           "integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
           "dev": true
-        }
-      }
-    },
-    "ProtVista": {
-      "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
-      "dev": true,
-      "requires": {
-        "d3": "3.5.17",
-        "file-saver": "1.3.3",
-        "jquery": "2.2.4",
-        "jszip": "3.1.4",
-        "underscore": "1.8.3"
-      },
-      "dependencies": {
-        "jquery": {
-          "version": "2.2.4",
-          "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
-          "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
-          "dev": true
+        },
+        "litemol": {
+          "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
+          "dev": true,
+          "requires": {
+            "@types/react": "15.6.14",
+            "@types/react-dom": "15.5.7"
+          }
         }
       }
     },
@@ -2050,14 +2058,6 @@
         "immediate": "3.0.6"
       }
     },
-    "litemol": {
-      "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
-      "dev": true,
-      "requires": {
-        "@types/react": "15.6.14",
-        "@types/react-dom": "15.5.7"
-      }
-    },
     "lodash": {
       "version": "4.17.4",
       "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",