shapes for all species are implemnted in sbml

CHANGELOG

@@ -15,6 +15,8 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
     (#1376)
   * Small improvement: context menu exporting map is more precise about scope
     (#1447)
+  * Small improvement: SBML render contains information about species shapes
+    (#1055)
   * Bug fix: refreshing page after removing last project on the page redirect to
     proper page (#1051)
   * Bug fix: removing plugin that does not exist anymore does not raise an error

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

@@ -26,8 +26,9 @@ import lcsb.mapviewer.model.map.species.field.*;
 
 public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
 
+  private static final double ION_CHANNEL_WIDTH = 20;
   private static final double DEGRADED_CROSS_LINE_EXTENDED_LENGTH = 7;
-  private static final double RECTANGLE_CORNER_ARC_SIZE = 10;
+  private static final double RECTANGLE_CORNER_ARC_SIZE = 5;
   private static final double COMPLEX_TRIMMED_CORNER_SIZE = 5;
 
   private static final double DRUG_OFFSET_BETWEEN_BORDERS = 4;
@@ -469,10 +470,18 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
       shapes.addAll(createDrugShapes((Drug) element));
     } else if (element instanceof GenericProtein) {
       shapes.add(createGenericProteinShape((GenericProtein) element));
+    } else if (element instanceof ReceptorProtein) {
+      shapes.add(createReceptorProteinShape());
+    } else if (element instanceof TruncatedProtein) {
+      shapes.add(createTruncatedProteinShape((TruncatedProtein) element));
+    } else if (element instanceof IonChannelProtein) {
+      shapes.addAll(createIonChannelShapes((IonChannelProtein) element));
     } else if (element instanceof Complex) {
       shapes.add(createComplexShape((Complex) element));
     } else if (element instanceof Gene) {
       shapes.add(createGeneShape());
+    } else if (element instanceof Phenotype) {
+      shapes.add(createPhenotypeShape((Phenotype) element));
     } else if (element instanceof AntisenseRna) {
       shapes.add(createAntisenseRnaShape());
     } else if (element instanceof Degraded) {
@@ -519,6 +528,19 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     return result;
   }
 
+  private List<GraphicalPrimitive1D> createIonChannelShapes(IonChannelProtein ionChannel) {
+    List<GraphicalPrimitive1D> result = new ArrayList<>();
+
+    result.add(createRoundedRect(0, 0,
+        ionChannel.getWidth() - ION_CHANNEL_WIDTH - 1, ionChannel.getHeight(),
+        RECTANGLE_CORNER_ARC_SIZE));
+    result.add(createRoundedRect(ionChannel.getWidth() - ION_CHANNEL_WIDTH, 0,
+        ION_CHANNEL_WIDTH, ionChannel.getHeight(),
+        RECTANGLE_CORNER_ARC_SIZE));
+
+    return result;
+  }
+
   private List<GraphicalPrimitive1D> createDrugShapes(Drug drug) {
     List<GraphicalPrimitive1D> result = new ArrayList<>();
 
@@ -561,25 +583,56 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
   }
 
   private GraphicalPrimitive1D createGenericProteinShape(GenericProtein protein) {
+    double x = 0;
+    double y = 0;
+    double width = protein.getWidth();
+    double height = protein.getHeight();
+
+    double arcSize = RECTANGLE_CORNER_ARC_SIZE;
+
+    return createRoundedRect(x, y, width, height, arcSize);
+  }
+
+  private Polygon createRoundedRect(double x, double y, double width, double height, double arcSize) {
     Polygon polygon = new Polygon();
 
-    createAbsolutePoint(polygon, RECTANGLE_CORNER_ARC_SIZE, 0);
-    createAbsolutePoint(polygon, protein.getWidth() - RECTANGLE_CORNER_ARC_SIZE, 0);
-    createArc(polygon, protein.getWidth() - RECTANGLE_CORNER_ARC_SIZE, 0,
-        protein.getWidth(), RECTANGLE_CORNER_ARC_SIZE,
-        protein.getWidth() - RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
-    createAbsolutePoint(polygon, protein.getWidth(), protein.getHeight() - RECTANGLE_CORNER_ARC_SIZE);
-    createArc(polygon, protein.getWidth(), protein.getHeight() - RECTANGLE_CORNER_ARC_SIZE,
-        protein.getWidth() - RECTANGLE_CORNER_ARC_SIZE, protein.getHeight(),
-        protein.getWidth() - RECTANGLE_CORNER_ARC_SIZE, protein.getHeight() - RECTANGLE_CORNER_ARC_SIZE);
-    createAbsolutePoint(polygon, RECTANGLE_CORNER_ARC_SIZE, protein.getHeight());
-    createArc(polygon, RECTANGLE_CORNER_ARC_SIZE, protein.getHeight(),
-        0, protein.getHeight() - RECTANGLE_CORNER_ARC_SIZE,
-        RECTANGLE_CORNER_ARC_SIZE, protein.getHeight() - RECTANGLE_CORNER_ARC_SIZE);
-    createAbsolutePoint(polygon, 0, RECTANGLE_CORNER_ARC_SIZE);
-    createArc(polygon, 0, RECTANGLE_CORNER_ARC_SIZE,
-        RECTANGLE_CORNER_ARC_SIZE, 0,
-        RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+    createAbsolutePoint(polygon, x + arcSize, y);
+    createAbsolutePoint(polygon, x + width - arcSize, y);
+    createArc(polygon, x + width - arcSize, y,
+        x + width, y + arcSize,
+        x + width - arcSize, y + arcSize);
+    createAbsolutePoint(polygon, x + width, y + height - arcSize);
+    createArc(polygon, x + width, y + height - arcSize,
+        x + width - arcSize, y + height,
+        x + width - arcSize, y + height - arcSize);
+    createAbsolutePoint(polygon, x + arcSize, y + height);
+    createArc(polygon, x + arcSize, y + height,
+        x, y + height - arcSize,
+        x + arcSize, y + height - arcSize);
+    createAbsolutePoint(polygon, x, y + arcSize);
+    createArc(polygon, x, y + arcSize,
+        x + arcSize, y,
+        x + arcSize, y + arcSize);
+    return polygon;
+  }
+
+  private GraphicalPrimitive1D createTruncatedProteinShape(TruncatedProtein protein) {
+    Polygon polygon = new Polygon();
+
+    createAbsolutePoint(polygon, 10, 0);
+    createAbsolutePoint(polygon, protein.getWidth(), 0);
+    createAbsolutePoint(polygon, protein.getWidth(), protein.getHeight() * 3 / 5);
+    createAbsolutePoint(polygon, protein.getWidth() * 4 / 5, protein.getHeight() * 2 / 5);
+    createAbsolutePoint(polygon, protein.getWidth() * 4 / 5, protein.getHeight());
+    createAbsolutePoint(polygon, 10, protein.getHeight());
+    createAbsoluteBezierPoint(polygon, 0, protein.getHeight() - 10,
+        5, protein.getHeight() - 2,
+        2, protein.getHeight() - 5);
+    createAbsolutePoint(polygon, 0, 10);
+    createAbsoluteBezierPoint(polygon, 10, 0,
+        2, 5,
+        5, 2);
+
     return polygon;
   }
 
@@ -597,6 +650,18 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     return polygon;
   }
 
+  private GraphicalPrimitive1D createPhenotypeShape(Phenotype complex) {
+    Polygon polygon = new Polygon();
+
+    createAbsolutePoint(polygon, 0, complex.getHeight() / 2);
+    createAbsolutePoint(polygon, complex.getHeight() / 2, 0);
+    createAbsolutePoint(polygon, complex.getWidth() - complex.getHeight() / 2, 0);
+    createAbsolutePoint(polygon, complex.getWidth(), complex.getHeight() / 2);
+    createAbsolutePoint(polygon, complex.getWidth() - complex.getHeight() / 2, complex.getHeight());
+    createAbsolutePoint(polygon, complex.getHeight() / 2, complex.getHeight());
+    return polygon;
+  }
+
   private void createArc(Polygon polygon, double x1, double y1, double x4, double y4, double xc, double yc) {
     // math taken from https://stackoverflow.com/a/44829356/1127920
     double ax = x1 - xc;
@@ -667,6 +732,17 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     return polygon;
   }
 
+  private Polygon createReceptorProteinShape() {
+    Polygon polygon = new Polygon();
+    createRelativePoint(polygon, 0, 0);
+    createRelativePoint(polygon, 50, 20);
+    createRelativePoint(polygon, 100, 0);
+    createRelativePoint(polygon, 100, 80);
+    createRelativePoint(polygon, 50, 100);
+    createRelativePoint(polygon, 0, 80);
+    return polygon;
+  }
+
   private Polygon createAntisenseRnaShape() {
     Polygon polygon = new Polygon();
     createRelativePoint(polygon, 0, 0);