render information for modification residues

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java

@@ -54,6 +54,7 @@ public class SbmlExporter {
       return stream.toString("UTF-8")
           // COPASI does not accept double coordinates
           .replace(".0\"", "\"")
+          .replace(".0+", "+")
           .replace(".0%\"", "%\"");
     } catch (UnsupportedEncodingException | XMLStreamException e) {
       throw new InvalidStateException(e);

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

 package lcsb.mapviewer.converter.model.sbml.species;
 
 import java.awt.Color;
+import java.util.Objects;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.render.*;
 
 import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
+import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.map.species.field.*;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class ModificationResidueExporter {
 
+  /**
+   * Default diameter of the modification residues.
+   */
+  public static final int DEFAULT_MODIFICATION_DIAMETER = 15;
+
+  private static Logger logger = LogManager.getLogger();
+
   private SbmlModelUtils sbmlModelUtils;
 
   public ModificationResidueExporter(Model sbmlModel) {
@@ -18,20 +32,143 @@ public class ModificationResidueExporter {
   }
 
   public LocalStyle createStyle(ModificationResidue element) {
-    return createStyle();
+    if (element instanceof Residue) {
+      return createEllipseStyle();
+    } else if (element instanceof ModificationSite) {
+      return createModificationSiteStyle((ModificationSite) element);
+    } else if (element instanceof TranscriptionSite) {
+      return createTranscriptionSiteStyle((TranscriptionSite) element);
+    } else if (element instanceof RegulatoryRegion) {
+      return createRectangleStyle();
+    } else if (element instanceof BindingRegion) {
+      return createRectangleStyle();
+    } else if (element instanceof CodingRegion) {
+      return createRectangleStyle();
+    } else if (element instanceof ProteinBindingDomain) {
+      return createRectangleStyle();
+    } else {
+      logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, element.getSpecies()),
+          "Don't know how to render modification residue: " + new ElementUtils().getElementTag(element));
+      return createEllipseStyle();
+    }
   }
-  public LocalStyle createStyle(StructuralState structuralState) {
-    return createStyle();
+
+  private LocalStyle createRectangleStyle() {
+    LocalStyle style = createGenericStyle();
+
+    Rectangle rectangle = new Rectangle();
+    rectangle.setRx(new RelAbsVector(0, 0));
+    rectangle.setRy(new RelAbsVector(0, 0));
+    rectangle.setX(new RelAbsVector(0, 0));
+    rectangle.setY(new RelAbsVector(0, 0));
+    rectangle.setWidth(new RelAbsVector(0, 100));
+    rectangle.setHeight(new RelAbsVector(0, 100));
+
+    style.getGroup().addElement(rectangle);
+
+    return style;
   }
 
-  private LocalStyle createStyle() {
-    LocalStyle style = sbmlModelUtils.createStyle();
-    ColorDefinition color = sbmlModelUtils.getColorDefinition(Color.BLACK);
-    ColorDefinition background = sbmlModelUtils.getColorDefinition(Color.WHITE);
+  private LocalStyle createTranscriptionSiteStyle(TranscriptionSite transcriptionSite) {
+    LocalStyle style = createGenericStyle();
+
+    ColorDefinition color;
+    if (transcriptionSite.getActive()) {
+      color = sbmlModelUtils.getColorDefinition(Color.RED);
+    } else {
+      color = sbmlModelUtils.getColorDefinition(Color.BLACK);
+    }
+    if (transcriptionSite.getSpecies() != null && transcriptionSite.getSpecies().getFillColor().equals(Color.WHITE)) {
+      color = sbmlModelUtils.getColorDefinition(Color.BLACK);
+    }
+
     style.getGroup().setStroke(color.getId());
-    style.getGroup().setStrokeWidth(1.0);
-    style.getGroup().setFill(background.getId());
-    style.getGroup().setFontSize((short) 10);
+    style.getGroup().setEndHead(ArrowType.FULL.name());
+    style.getGroup().setFill(color.getId());
+
+    double y = transcriptionSite.getPosition().getY();
+    double x = transcriptionSite.getPosition().getX();
+    if (Objects.equals(transcriptionSite.getDirection(), "RIGHT")) {
+      x += transcriptionSite.getWidth();
+    }
+    Polygon line = new Polygon();
+
+    RenderPoint p1 = line.createRenderPoint();
+    p1.setX(new RelAbsVector(Math.round(x - transcriptionSite.getPosition().getX()), 50));
+    p1.setY(new RelAbsVector(Math.round(y - transcriptionSite.getPosition().getY()), 50));
+
+    y -= DEFAULT_MODIFICATION_DIAMETER;
+    RenderPoint p2 = line.createRenderPoint();
+    p2.setX(new RelAbsVector(Math.round(x - transcriptionSite.getPosition().getX()), 50));
+    p2.setY(new RelAbsVector(Math.round(y - transcriptionSite.getPosition().getY()), 50));
+
+    double delta = 0;
+    if (Objects.equals(transcriptionSite.getDirection(), "RIGHT")) {
+      x -= transcriptionSite.getWidth();
+      delta = 6;
+    } else {
+      x += transcriptionSite.getWidth();
+      delta = -6;
+    }
+    RenderPoint p3 = line.createRenderPoint();
+    p3.setX(new RelAbsVector(Math.round(x - transcriptionSite.getPosition().getX()), 50));
+    p3.setY(new RelAbsVector(Math.round(y - transcriptionSite.getPosition().getY()), 50));
+
+    RenderPoint p4 = line.createRenderPoint();
+    p4.setX(new RelAbsVector(Math.round(x + delta - transcriptionSite.getPosition().getX()), 50));
+    p4.setY(new RelAbsVector(Math.round(y - 3 - transcriptionSite.getPosition().getY()), 50));
+
+    RenderPoint p5 = line.createRenderPoint();
+    p5.setX(new RelAbsVector(Math.round(x + delta - transcriptionSite.getPosition().getX()), 50));
+    p5.setY(new RelAbsVector(Math.round(y + 3 - transcriptionSite.getPosition().getY()), 50));
+
+    RenderPoint p6 = line.createRenderPoint();
+    p6.setX(new RelAbsVector(Math.round(x - transcriptionSite.getPosition().getX()), 50));
+    p6.setY(new RelAbsVector(Math.round(y - transcriptionSite.getPosition().getY()), 50));
+
+    RenderPoint p7 = line.createRenderPoint();
+    p7.setX(new RelAbsVector(p2.getX()));
+    p7.setY(new RelAbsVector(p2.getY()));
+
+    style.getGroup().addElement(line);
+
+    return style;
+  }
+
+  private LocalStyle createModificationSiteStyle(ModificationSite modificationSite) {
+    LocalStyle style = createGenericStyle();
+
+    double diameter = DEFAULT_MODIFICATION_DIAMETER;
+
+    Ellipse ellipse = new Ellipse();
+    ellipse.setCx(new RelAbsVector(0, 50));
+    ellipse.setCy(new RelAbsVector(Math.round(-diameter), 50));
+    ellipse.setRx(new RelAbsVector(Math.round(diameter / 2)));
+    ellipse.setRy(new RelAbsVector(Math.round(diameter / 2)));
+
+    style.getGroup().addElement(ellipse);
+
+    Polygon line = new Polygon();
+
+    RenderPoint p1 = line.createRenderPoint();
+    p1.setX(new RelAbsVector(0, 50));
+    p1.setY(new RelAbsVector(Math.round(-diameter / 2), 50));
+
+    RenderPoint p2 = line.createRenderPoint();
+    p2.setX(new RelAbsVector(0, 50));
+    p2.setY(new RelAbsVector(0, 50));
+
+    style.getGroup().addElement(line);
+
+    return style;
+  }
+
+  public LocalStyle createStyle(StructuralState structuralState) {
+    return createEllipseStyle();
+  }
+
+  private LocalStyle createEllipseStyle() {
+    LocalStyle style = createGenericStyle();
 
     Ellipse ellipse = new Ellipse();
     ellipse.setCx(new RelAbsVector(0, 50));
@@ -49,6 +186,14 @@ public class ModificationResidueExporter {
   }
 
   private LocalStyle createTextStyle() {
+    LocalStyle style = createGenericStyle();
+
+    style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
+    style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
+    return style;
+  }
+
+  private LocalStyle createGenericStyle() {
     LocalStyle style = sbmlModelUtils.createStyle();
     ColorDefinition color = sbmlModelUtils.getColorDefinition(Color.BLACK);
     ColorDefinition background = sbmlModelUtils.getColorDefinition(Color.WHITE);
@@ -56,9 +201,6 @@ public class ModificationResidueExporter {
     style.getGroup().setStrokeWidth(1.0);
     style.getGroup().setFill(background.getId());
     style.getGroup().setFontSize((short) 10);
-
-    style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
-    style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
     return style;
   }
 
@@ -67,14 +209,8 @@ public class ModificationResidueExporter {
   }
 
   public BoundingBox createBoundingBoxForModification(ModificationResidue mr) {
-    double width, height;
-    if (mr instanceof AbstractRegionModification) {
-      width = ((AbstractRegionModification) mr).getWidth();
-      height = ((AbstractRegionModification) mr).getHeight();
-    } else {
-      width = 12;
-      height = 12;
-    }
+    double width = getModificationWidth(mr);
+    double height = getModificationHeight(mr);
     double x = mr.getPosition().getX() - width / 2;
     double y = mr.getPosition().getY() - height / 2;
     BoundingBox boundingBox = new BoundingBox();
@@ -86,13 +222,28 @@ public class ModificationResidueExporter {
     return boundingBox;
   }
 
+  private double getModificationHeight(ModificationResidue mr) {
+    if (mr instanceof AbstractRegionModification) {
+      return ((AbstractRegionModification) mr).getHeight();
+    } else {
+      return 12;
+    }
+  }
+
+  private double getModificationWidth(ModificationResidue mr) {
+    if (mr instanceof AbstractRegionModification) {
+      return ((AbstractRegionModification) mr).getWidth();
+    } else {
+      return 12;
+    }
+  }
+
   public BoundingBox createBoundingBoxForModificationText(ModificationResidue mr) {
     BoundingBox result = createBoundingBoxForModification(mr);
     result.getPosition().setZ(result.getPosition().getZ() + 1);
     return result;
   }
 
-
   public BoundingBox createBoundingBoxForStructuralState(StructuralState structuralState) {
     double width = structuralState.getWidth();
     double height = structuralState.getHeight();
@@ -113,6 +264,4 @@ public class ModificationResidueExporter {
     return result;
   }
 
-
-
 }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/AllSbmlSpeciesTests.java

@@ -6,9 +6,9 @@ import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
 @SuiteClasses({
+  ModificationResidueExporterTest.class,
   SbmlSpeciesExporterRenderShapeTest.class,
   SbmlSpeciesExporterTest.class,
-  
   SbmlSpeciesParserTest.class })
 public class AllSbmlSpeciesTests {
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/ModificationResidueExporterTest.java

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.Point2D;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.reflections.Reflections;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+@RunWith(Parameterized.class)
+public class ModificationResidueExporterTest extends SbmlTestFunctions {
+
+  Logger logger = LogManager.getLogger();
+  private Model sbmlModel;
+
+  ModificationResidue mr;
+
+  public ModificationResidueExporterTest(String name, ModificationResidue mr) {
+    this.mr = mr;
+  }
+
+  @Before
+  public void setUp() {
+    SBMLDocument doc = new SBMLDocument(3, 1);
+    sbmlModel = doc.createModel();
+    LayoutModelPlugin plugin = new LayoutModelPlugin(sbmlModel);
+    sbmlModel.addExtension("layout", plugin);
+    Layout layout = new Layout();
+    plugin.addLayout(layout);
+
+    RenderLayoutPlugin renderPlugin = new RenderLayoutPlugin(layout);
+    layout.addExtension("render", renderPlugin);
+  }
+
+  @Parameters(name = "{index} : {0}")
+  public static Collection<Object[]> data() throws Exception {
+    Protein protein = createProtein();
+
+    Collection<Object[]> data = new ArrayList<Object[]>();
+    Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
+    for (Class<? extends ModificationResidue> class1 : reflections.getSubTypesOf(ModificationResidue.class)) {
+      if (Modifier.isAbstract(class1.getModifiers())) {
+        continue;
+      }
+      ModificationResidue mr = class1.getConstructor().newInstance();
+      mr.setPosition(new Point2D.Double(10, 20));
+      mr.setSpecies(protein);
+      data.add(new Object[] { mr.getClass().getName(), mr });
+    }
+    return data;
+  }
+
+  @Test
+  public void testCreateStyle() throws Exception {
+    ModificationResidueExporter mre = new ModificationResidueExporter(sbmlModel);
+
+    LocalStyle style = mre.createStyle(mr);
+    assertNotNull(style);
+    assertEquals("Problem with creating style for: " + mr.getClass(), 0, super.getWarnings().size());
+  }
+
+}