drawing of glyphs implemented

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java

@@ -72,6 +72,22 @@ public abstract class BioEntityConverter<T extends BioEntity> {
     draw(bioEntity, graphics, params, new ArrayList<>());
   }
 
+  /**
+   * This function draw {@link BioEntity} on the {@link Graphics2D} object.
+   * 
+   * @param bioEntity
+   *          {@link BioEntity} that should be drawn
+   * @param graphics
+   *          where we want to draw bioEntity
+   * @param params
+   *          visualization params (like, should the object be filled with solid
+   *          color, etc.), for more information see {@link ConverterParams}
+   * @throws DrawingException
+   *           thrown when there is a problem with drawing {@link BioEntity}
+   * 
+   */
+  protected abstract void drawImpl(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+
   /**
    * This function draw representation of the alias on the graphics object.
    * 
@@ -90,7 +106,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
    *           thrown when there is a problem with drawing {@link BioEntity}
    * 
    */
-  public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params,
+  protected abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params,
       List<ColorSchema> visualizedOverlaysColorSchemas)
       throws DrawingException;
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java

@@ -199,4 +199,10 @@ public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
 		}
 	}
 
+  @SuppressWarnings("unchecked")
+  @Override
+  protected void drawImpl(BioEntity bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+    elementConverter.draw(bioEntity, graphics, params);
+  }
+
 }

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

 package lcsb.mapviewer.converter.graphics.bioEntity.element;
 
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
 import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.species.Element;
 
 /**
@@ -14,4 +24,37 @@ import lcsb.mapviewer.model.map.species.Element;
  */
 public abstract class ElementConverter<T extends Element> extends BioEntityConverter<T> {
 
+  @Override
+  public final void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+    if (bioEntity.getGlyph() != null) {
+      drawGlyph(bioEntity, graphics);
+    } else {
+      super.draw(bioEntity, graphics, params);
+    }
+  }
+
+  /**
+   * Draws a {@link Glyph} for given bioEntity.
+   * 
+   * @param bioEntity
+   *          element that should be visualized as a {@link Glyph}
+   * @param graphics
+   *          {@link Graphics2D} where we are drawing
+   * @throws DrawingException
+   *           thrown when there is a problem with drawing
+   */
+  private void drawGlyph(T bioEntity, Graphics2D graphics) throws DrawingException {
+    try {
+      Image img = ImageIO.read(new ByteArrayInputStream(bioEntity.getGlyph().getFile().getFileContent()));
+      graphics.drawImage(img,
+          bioEntity.getX().intValue(), bioEntity.getY().intValue(),
+          (int) (bioEntity.getX() + bioEntity.getWidth()), (int) (bioEntity.getY() + bioEntity.getHeight()),
+          0, 0, img.getWidth(null), img.getHeight(null),
+          null);
+    } catch (IOException e) {
+      throw new DrawingException(
+          "Problem with processing glyph file: " + bioEntity.getGlyph().getFile().getOriginalFileName(), e);
+    }
+  }
+
 }

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

@@ -45,7 +45,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
 	}
 
 	@Override
-	public void draw(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		// keep the old values of colors and line
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

@@ -179,7 +179,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
 
 	@Override
 	public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
-		draw(alias, graphics, params);
+		drawImpl(alias, graphics, params);
 
 		Color oldColor = graphics.getColor();
 		int count = 0;

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

@@ -45,7 +45,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
 	}
 
 	@Override
-	public void draw(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

@@ -48,7 +48,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
 	}
 
 	@Override
-	public void draw(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

@@ -36,7 +36,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
   }
 
   @Override
-  public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params)
+  protected void drawImpl(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params)
       throws DrawingException {
     // keep the old values of colors and line
     Color oldColor = graphics.getColor();

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

@@ -45,7 +45,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
 	}
 
 	@Override
-	public void draw(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

@@ -61,7 +61,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
 	}
 
 	@Override
-	public void draw(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

@@ -45,7 +45,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
 	}
 
 	@Override
-	public void draw(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+	protected void drawImpl(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();
 

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

@@ -44,7 +44,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
   }
 
   @Override
-  public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
     GeneralPath path = getAntisenseRnaPath(antisenseRna);
     Color c = graphics.getColor();
     graphics.setColor(antisenseRna.getColor());

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

@@ -57,7 +57,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
   }
 
   @Override
-  public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
     if (alias.getState().equalsIgnoreCase("complexnoborder")) {
       return;
     }

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

@@ -49,7 +49,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
 	}
 
 	@Override
-	public void draw(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
+	protected void drawImpl(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
 		double diameter = getDiameter(degraded);
 		double x = getXCoord(degraded, diameter);
 		double y = getYCoord(degraded);

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

@@ -67,7 +67,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
 	}
 
 	@Override
-	public void draw(Drug drug, final Graphics2D graphics, final ConverterParams params) {
+	protected void drawImpl(Drug drug, final Graphics2D graphics, final ConverterParams params) {
 		Shape a1 = getDrugShape(drug);
 		double offset = OFFSET_BETWEEN_BORDERS;
 		Shape a2 = new RoundRectangle2D.Double(

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

@@ -43,7 +43,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
   }
 
   @Override
-  public void draw(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
     Shape shape = getGeneShape(gene);
     Color c = graphics.getColor();
     graphics.setColor(gene.getColor());

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

@@ -42,7 +42,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
   }
 
   @Override
-  public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(Ion ion, final Graphics2D graphics, final ConverterParams params) {
     double diameter = getDiameter(ion);
     double x = getXCoord(ion, diameter);
     double y = getYCoord(ion);

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

@@ -42,7 +42,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
 	}
 
 	@Override
-	public void draw(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
+	protected void drawImpl(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
 		GeneralPath path = getPhenotypePath(phenotype);
 
 		Color c = graphics.getColor();

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

@@ -87,7 +87,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
   }
 
   @Override
-  public void draw(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
     // Local variable setting the SBGN visualization
     boolean sbgnFormat = params.isSbgnFormat();
 

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

@@ -50,7 +50,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
   }
 
   @Override
-  public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
+  protected void drawImpl(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
     GeneralPath path = getRnaPath(rna);
     Color c = graphics.getColor();
     graphics.setColor(rna.getColor());