StructuralStateConverter implemented

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java

@@ -18,6 +18,8 @@ import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
 import lcsb.mapviewer.common.MimeType;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.graphics.bioentity.BioEntityConverterImpl;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.StructuralStateConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.StructuralStateSbgnConverter;
 import lcsb.mapviewer.converter.graphics.layer.LayerLineConverter;
 import lcsb.mapviewer.converter.graphics.layer.LayerOvalConverter;
 import lcsb.mapviewer.converter.graphics.layer.LayerRectConverter;
@@ -27,7 +29,6 @@ import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
 import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
 import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
 import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -36,6 +37,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
 import lcsb.mapviewer.model.overlay.DataOverlayEntry;
 
 /**
@@ -210,17 +212,11 @@ public abstract class AbstractImageGenerator {
     // Get the SBGN display format option from the model
     this.sbgnFormat = params.isSbgn();
 
-    List<Drawable> bioEntities = new ArrayList<>();
-    bioEntities.addAll(params.getModel().getBioEntities());
-    for (final Layer layer : params.getModel().getLayers()) {
-      if (layer.isVisible()) {
-        bioEntities.addAll(layer.getDrawables());
-      }
-    }
-    bioEntities.sort(BioEntity.Z_INDEX_COMPARATOR);
+    List<Drawable> drawables = new ArrayList<>(params.getModel().getDrawables());
+    drawables.sort(BioEntity.Z_INDEX_COMPARATOR);
 
     // draw all elements
-    for (final Drawable element : bioEntities) {
+    for (final Drawable element : drawables) {
       if (element instanceof Species) {
         drawSpecies((Species) element);
       } else if (element instanceof Reaction) {
@@ -235,6 +231,8 @@ public abstract class AbstractImageGenerator {
         drawRect((LayerRect) element);
       } else if (element instanceof PolylineData) {
         drawLine((PolylineData) element);
+      } else if (element instanceof StructuralState) {
+        drawStructuralState((StructuralState) element);
       } else {
         throw new DrawingException("Unknown class type: " + element);
       }
@@ -259,6 +257,14 @@ public abstract class AbstractImageGenerator {
     new LayerLineConverter().draw(element, graphics);
   }
 
+  private void drawStructuralState(final StructuralState structuralState) {
+    if (this.sbgnFormat) {
+      new StructuralStateSbgnConverter().draw(structuralState, graphics);
+    } else {
+      new StructuralStateConverter().draw(structuralState, graphics);
+    }
+  }
+
   /**
    * Method called after drawing. It should close drawing canvas properly.
    */

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexConverter.java

@@ -103,8 +103,6 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
     complex.setWidth(complex.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
     complex.setHeight(complex.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
 
-    drawStructuralState(complex.getStructuralState(), graphics);
-
     drawText(complex, graphics, params);
     graphics.setColor(oldColor);
   }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexSbgnConverter.java

@@ -2,8 +2,6 @@ package lcsb.mapviewer.converter.graphics.bioentity.element.species;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.geom.RoundRectangle2D;
 import java.util.ArrayList;
 
 import org.apache.logging.log4j.LogManager;
@@ -13,7 +11,6 @@ import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.StructuralState;
 import lcsb.mapviewer.model.overlay.DataOverlayEntry;
 
 /**
@@ -71,11 +68,4 @@ public class ComplexSbgnConverter extends ComplexConverter {
     graphics.setColor(oldColor);
   }
 
-  @Override
-  Shape getStructuralStateShape(final StructuralState state) {
-    double arcSize = Math.min(state.getWidth(), state.getHeight());
-    return new RoundRectangle2D.Double(state.getPosition().getX(), state.getPosition().getY(), state.getWidth(),
-        state.getHeight(), arcSize, arcSize);
-  }
-
 }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ProteinConverter.java

@@ -118,7 +118,6 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
       drawModification(mr, graphics, params.isSbgnFormat());
     }
 
-    drawStructuralState(protein.getStructuralState(), graphics);
     if (!params.isSbgnFormat()) {
       drawUnitOfInformation(unitOfInformationText, protein, graphics);
     }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ProteinSbgnConverter.java

@@ -2,7 +2,6 @@ package lcsb.mapviewer.converter.graphics.bioentity.element.species;
 
 import java.awt.Graphics2D;
 import java.awt.Shape;
-import java.awt.geom.RoundRectangle2D;
 import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
@@ -13,7 +12,6 @@ import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.model.map.species.IonChannelProtein;
 import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.StructuralState;
 
 /**
  * This class defines methods used for drawing {@link Protein} on the
@@ -31,8 +29,8 @@ public class ProteinSbgnConverter extends ProteinConverter {
    * Default constructor.
    * 
    * @param colorExtractor
-   *          Object that helps to convert {@link ColorSchema} values into colors
-   *          when drawing {@link Species}
+   *          Object that helps to convert {@link ColorSchema} values into
+   *          colors when drawing {@link Species}
    */
   public ProteinSbgnConverter(final ColorExtractor colorExtractor) {
     super(colorExtractor);
@@ -53,7 +51,7 @@ public class ProteinSbgnConverter extends ProteinConverter {
     protein.setHomodimer(homodir);
     super.drawImpl(protein, graphics, params);
     protein.setHomodimer(originalHomodimer);
-    
+
     drawUnitOfInformation(unitOfInformationText, protein, graphics);
   }
 
@@ -85,12 +83,4 @@ public class ProteinSbgnConverter extends ProteinConverter {
   @Override
   void drawActivityShape(final Protein protein, final Graphics2D graphics) {
   }
-
-  @Override
-  Shape getStructuralStateShape(final StructuralState state) {
-    double arcSize = Math.min(state.getWidth(), state.getHeight());
-    return new RoundRectangle2D.Double(state.getPosition().getX(), state.getPosition().getY(), state.getWidth(),
-        state.getHeight(), arcSize, arcSize);
-  }
-
 }

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

@@ -39,7 +39,6 @@ import lcsb.mapviewer.model.map.species.field.ModificationState;
 import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
 import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
 import lcsb.mapviewer.model.map.species.field.Residue;
-import lcsb.mapviewer.model.map.species.field.StructuralState;
 import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
 import lcsb.mapviewer.model.overlay.DataOverlayEntry;
 
@@ -355,53 +354,6 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
     this.unitOfInformationFont = unitOfInformationFont;
   }
 
-  /**
-   * Draws structural state description of the alias (ellipse in the top part of
-   * the alias).
-   *
-   * @param state
-   *          state description text
-   * @param species
-   *          state description should be drawn on this {@link Species}
-   * @param graphics
-   *          where the drawing should be performed
-   */
-  protected void drawStructuralState(final StructuralState state, final Graphics2D graphics) {
-    if (state == null) {
-      return;
-    }
-
-    double width = state.getWidth();
-    double height = state.getHeight();
-
-    Shape ellipse = getStructuralStateShape(state);
-    Color c = graphics.getColor();
-    graphics.setColor(Color.WHITE);
-    graphics.fill(ellipse);
-    graphics.setColor(c);
-    graphics.draw(ellipse);
-    if (!state.getValue().equals("")) {
-      Font tmpFont = graphics.getFont();
-      Font font = new Font(Font.SANS_SERIF, 0, state.getFontSize().intValue());
-      graphics.setFont(font);
-
-      width = graphics.getFontMetrics().stringWidth(state.getValue());
-      height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
-
-      double x = state.getPosition().getX() + (state.getWidth() - width) / 2;
-      double y = state.getPosition().getY() + (state.getHeight() + height) / 2;
-
-      graphics.drawString(state.getValue(), (int) x, (int) y);
-      graphics.setFont(tmpFont);
-    }
-
-  }
-
-  Shape getStructuralStateShape(final StructuralState state) {
-    return new Ellipse2D.Double(state.getPosition().getX(), state.getPosition().getY(), state.getWidth(),
-        state.getHeight());
-  }
-
   /**
    * Draws unit of information for the {@link Species} (rectangle in the top
    * part of the alias).

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/StructuralStateConverter.java

+package lcsb.mapviewer.converter.graphics.bioentity.element.species;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+
+import lcsb.mapviewer.model.map.species.field.StructuralState;
+
+public class StructuralStateConverter {
+
+  public void draw(final StructuralState state, final Graphics2D graphics) {
+    if (state == null) {
+      return;
+    }
+
+    double width = state.getWidth();
+    double height = state.getHeight();
+
+    Shape ellipse = getStructuralStateShape(state);
+    Color c = graphics.getColor();
+    graphics.setColor(Color.WHITE);
+    graphics.fill(ellipse);
+    graphics.setColor(c);
+    graphics.draw(ellipse);
+    if (!state.getValue().equals("")) {
+      Font tmpFont = graphics.getFont();
+      Font font = new Font(Font.SANS_SERIF, 0, state.getFontSize().intValue());
+      graphics.setFont(font);
+
+      width = graphics.getFontMetrics().stringWidth(state.getValue());
+      height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
+
+      double x = state.getPosition().getX() + (state.getWidth() - width) / 2;
+      double y = state.getPosition().getY() + (state.getHeight() + height) / 2;
+
+      graphics.drawString(state.getValue(), (int) x, (int) y);
+      graphics.setFont(tmpFont);
+    }
+
+  }
+
+  Shape getStructuralStateShape(final StructuralState state) {
+    return new Ellipse2D.Double(
+        state.getPosition().getX(),
+        state.getPosition().getY(),
+        state.getWidth(),
+        state.getHeight());
+  }
+
+}

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/StructuralStateSbgnConverter.java

+package lcsb.mapviewer.converter.graphics.bioentity.element.species;
+
+import java.awt.Shape;
+import java.awt.geom.RoundRectangle2D;
+
+import lcsb.mapviewer.model.map.species.field.StructuralState;
+
+public class StructuralStateSbgnConverter extends StructuralStateConverter {
+
+  @Override
+  Shape getStructuralStateShape(final StructuralState state) {
+    double arcSize = Math.min(state.getWidth(), state.getHeight());
+    
+    return new RoundRectangle2D.Double(
+        state.getPosition().getX(),
+        state.getPosition().getY(),
+        state.getWidth(),
+        state.getHeight(),
+        arcSize,
+        arcSize);
+  }
+
+}

model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java

@@ -702,6 +702,11 @@ public class ModelFullIndexed implements Model {
   public Set<Drawable> getDrawables() {
     Set<Drawable> result = new HashSet<>();
     result.addAll(getBioEntities());
+    for (Species species : getSpeciesList()) {
+      if (species.getStructuralState() != null) {
+        result.add(species.getStructuralState());
+      }
+    }
     for (final Layer layer : getLayers()) {
       result.addAll(layer.getDrawables());
     }

model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java

@@ -34,6 +34,7 @@ import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
 
 public class ModelFullIndexedTest extends ModelTestFunctions {
 
@@ -525,4 +526,20 @@ public class ModelFullIndexedTest extends ModelTestFunctions {
     assertEquals(2, obj.size());
   }
 
+  @Test
+  public void testGetDrawables() {
+    ModelFullIndexed model = new ModelFullIndexed(null);
+    Reaction reaction = new Reaction("re");
+    reaction.setIdReaction("id_r");
+    model.addReaction(reaction);
+    Species protein = new GenericProtein("2");
+    StructuralState state = new StructuralState();
+    protein.setStructuralState(state);
+    model.addElement(protein);
+
+    assertTrue(model.getDrawables().contains(reaction));
+    assertTrue(model.getDrawables().contains(protein));
+    assertTrue(model.getDrawables().contains(state));
+  }
+
 }