method names unified

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

@@ -42,7 +42,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
   @Override
   protected void drawImpl(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
     Color oldColor = graphics.getColor();
-    GeneralPath path = getAntisenseRnaPath(antisenseRna);
+    GeneralPath path = getShape(antisenseRna);
     graphics.setColor(antisenseRna.getFillColor());
     graphics.fill(path);
     Stroke stroke = graphics.getStroke();
@@ -66,7 +66,8 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
    *          {@link AntisenseRna} for which we want to get border
    * @return border of the {@link AntisenseRna}
    */
-  private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
+  @Override
+  protected GeneralPath getShape(final AntisenseRna antisenseRna) {
     // CHECKSTYLE:OFF
     GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
     path.moveTo(antisenseRna.getX(), antisenseRna.getY());
@@ -80,7 +81,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
 
   @Override
   public PathIterator getBoundPathIterator(final AntisenseRna alias) {
-    return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
+    return getShape(alias).getPathIterator(new AffineTransform());
   }
 
 }

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

@@ -68,7 +68,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
       complex.setX(complex.getX() - SpeciesConverter.HOMODIMER_OFFSET);
       complex.setY(complex.getY() - SpeciesConverter.HOMODIMER_OFFSET);
 
-      GeneralPath path = getAliasPath(complex);
+      GeneralPath path = getShape(complex);
 
       Stroke stroke = graphics.getStroke();
       graphics.setColor(complex.getFillColor());
@@ -79,14 +79,14 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
 
       if (complex.getState().equals("brief")) {
         complex.increaseBorder(-INTERNAL_BORDER_DIST);
-        path = getAliasPath(complex);
+        path = getShape(complex);
         complex.increaseBorder(INTERNAL_BORDER_DIST);
         graphics.setStroke(LineType.DOTTED.getStroke());
         graphics.draw(path);
       }
       if (complex.getActivity() && !params.isSbgnFormat()) {
         complex.increaseBorder(INTERNAL_BORDER_DIST);
-        path = getAliasPath(complex);
+        path = getShape(complex);
         complex.increaseBorder(-INTERNAL_BORDER_DIST);
         graphics.setStroke(LineType.DOTTED.getStroke());
         graphics.draw(path);
@@ -128,7 +128,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
 
   @Override
   public PathIterator getBoundPathIterator(final Complex complex) {
-    return getAliasPath(complex).getPathIterator(new AffineTransform());
+    return getShape(complex).getPathIterator(new AffineTransform());
   }
 
   /**
@@ -138,7 +138,8 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
    *          exact object for which we want to get a border
    * @return border of the {@link Complex}
    */
-  private GeneralPath getAliasPath(final Complex complex) {
+  @Override
+  protected GeneralPath getShape(final Complex complex) {
     GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
     path.moveTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY());
     path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY());

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

@@ -45,6 +45,21 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
 
   @Override
   protected void drawImpl(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
+    Area a1 = getShape(degraded);
+    Color oldColor = graphics.getColor();
+    graphics.setColor(degraded.getFillColor());
+    graphics.fill(a1);
+    graphics.setColor(degraded.getBorderColor());
+    Stroke stroke = graphics.getStroke();
+    graphics.setStroke(getBorderLine(degraded));
+    graphics.draw(a1);
+    graphics.setStroke(stroke);
+    drawText(degraded, graphics, params);
+    graphics.setColor(oldColor);
+  }
+
+  @Override
+  protected Area getShape(final Degraded degraded) {
     double diameter = getDiameter(degraded);
     double x = getXCoord(degraded, diameter);
     double y = getYCoord(degraded);
@@ -64,16 +79,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
     path.closePath();
 
     a1.exclusiveOr(new Area(path));
-    Color oldColor = graphics.getColor();
-    graphics.setColor(degraded.getFillColor());
-    graphics.fill(a1);
-    graphics.setColor(degraded.getBorderColor());
-    Stroke stroke = graphics.getStroke();
-    graphics.setStroke(getBorderLine(degraded));
-    graphics.draw(a1);
-    graphics.setStroke(stroke);
-    drawText(degraded, graphics, params);
-    graphics.setColor(oldColor);
+    return a1;
   }
 
   /**

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

@@ -56,14 +56,15 @@ public class DrugConverter extends SpeciesConverter<Drug> {
    *          {@link Drug} for which we are looking for a border
    * @return Shape object defining given alias
    */
-  private Shape getDrugShape(final Drug drug) {
+  @Override
+  protected Shape getShape(final Drug drug) {
     return new RoundRectangle2D.Double(drug.getX(), drug.getY(), drug.getWidth(), drug.getHeight(),
         RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
   }
 
   @Override
   protected void drawImpl(Drug drug, final Graphics2D graphics, final ConverterParams params) {
-    Shape a1 = getDrugShape(drug);
+    Shape a1 = getShape(drug);
     double offset = OFFSET_BETWEEN_BORDERS;
     Shape a2 = new RoundRectangle2D.Double(
         drug.getX() + offset, drug.getY() + offset, drug.getWidth() - 2 * offset, drug.getHeight() - 2 * offset,
@@ -113,7 +114,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
 
   @Override
   public PathIterator getBoundPathIterator(Drug drug) {
-    return getDrugShape(drug).getPathIterator(new AffineTransform());
+    return getShape(drug).getPathIterator(new AffineTransform());
   }
 
 }

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

@@ -41,7 +41,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
 
   @Override
   protected void drawImpl(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
-    Shape shape = getGeneShape(gene);
+    Shape shape = getShape(gene);
     Color c = graphics.getColor();
     graphics.setColor(gene.getFillColor());
     graphics.fill(shape);
@@ -66,7 +66,8 @@ public class GeneConverter extends SpeciesConverter<Gene> {
    *          {@link Gene} for which we are looking for a {@link Shape}
    * @return {@link Shape} that represents {@link Gene}
    */
-  private Shape getGeneShape(final Gene gene) {
+  @Override
+  protected Shape getShape(final Gene gene) {
     Shape shape;
     shape = new Rectangle(gene.getX().intValue(), gene.getY().intValue(), gene.getWidth().intValue(),
         gene.getHeight().intValue());
@@ -75,7 +76,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
 
   @Override
   public PathIterator getBoundPathIterator(final Gene gene) {
-    return getGeneShape(gene).getPathIterator(new AffineTransform());
+    return getShape(gene).getPathIterator(new AffineTransform());
   }
 
 }

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

@@ -40,10 +40,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
 
   @Override
   protected void drawImpl(Ion ion, final Graphics2D graphics, final ConverterParams params) {
-    double diameter = getDiameter(ion);
-    double x = getXCoord(ion, diameter);
-    double y = getYCoord(ion);
-    Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
+    Shape shape = getShape(ion);
     Color oldColor = graphics.getColor();
     graphics.setColor(ion.getFillColor());
     graphics.fill(shape);
@@ -56,6 +53,15 @@ public class IonConverter extends SpeciesConverter<Ion> {
     graphics.setColor(oldColor);
   }
 
+  @Override
+  protected Shape getShape(Ion ion) {
+    double diameter = getDiameter(ion);
+    double x = getXCoord(ion, diameter);
+    double y = getYCoord(ion);
+    Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
+    return shape;
+  }
+
   /**
    * Returns transformed y coordinate for the {@link Ion}.
    * 

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

@@ -38,7 +38,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
 
   @Override
   protected void drawImpl(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
-    GeneralPath path = getPhenotypePath(phenotype);
+    GeneralPath path = getShape(phenotype);
 
     Color oldColor = graphics.getColor();
     graphics.setColor(phenotype.getFillColor());
@@ -60,7 +60,8 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
    * @return {@link GeneralPath} object defining border of the given
    *         {@link Phenotype}
    */
-  private GeneralPath getPhenotypePath(final Phenotype phenotype) {
+  @Override
+  protected GeneralPath getShape(final Phenotype phenotype) {
     // CHECKSTYLE:OFF
     GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 6);
     path.moveTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY());
@@ -76,7 +77,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
 
   @Override
   public PathIterator getBoundPathIterator(Phenotype phenotype) {
-    return getPhenotypePath(phenotype).getPathIterator(new AffineTransform());
+    return getShape(phenotype).getPathIterator(new AffineTransform());
   }
 
 }

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

@@ -50,8 +50,8 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
    * Default constructor.
    * 
    * @param colorExtractor
-   *          Object that helps to convert {@link DataOverlayEntry} values into colors
-   *          when drawing {@link Species}
+   *          Object that helps to convert {@link DataOverlayEntry} values into
+   *          colors when drawing {@link Species}
    */
   public ProteinConverter(ColorExtractor colorExtractor) {
     super(colorExtractor);
@@ -93,7 +93,8 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
       protein.setX(protein.getX() - SpeciesConverter.HOMODIMER_OFFSET);
       protein.setY(protein.getY() - SpeciesConverter.HOMODIMER_OFFSET);
 
-      Shape shape = getShape(protein, graphics);
+      drawActivityShape(protein, graphics);
+      Shape shape = getShape(protein);
       Color oldColor = graphics.getColor();
       graphics.setColor(protein.getFillColor());
       graphics.fill(shape);
@@ -119,25 +120,27 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
     protein.setHeight(protein.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
   }
 
-  Shape getShape(final Protein protein, final Graphics2D graphics) {
+  void drawActivityShape(final Protein protein, final Graphics2D graphics) {
+    if (protein instanceof GenericProtein && protein.getActivity()) {
+      drawActivityGenericProtein(protein, graphics);
+    } else if (protein instanceof TruncatedProtein && protein.getActivity()) {
+      drawActivityTruncatedShape(protein, graphics);
+    } else if (protein instanceof ReceptorProtein && protein.getActivity()) {
+      drawActivityReceptorProtein(protein, graphics);
+    }
+  }
+
+  @Override
+  protected Shape getShape(final Protein protein) {
     Shape shape = null;
     if (protein instanceof GenericProtein) {
       shape = getGenericShape(protein);
-      if (protein.getActivity()) {
-        drawActivityGenericProtein(protein, graphics);
-      }
     } else if (protein instanceof IonChannelProtein) {
       shape = getIonChannelShape(protein);
     } else if (protein instanceof TruncatedProtein) {
       shape = getTruncatedShape(protein);
-      if (protein.getActivity()) {
-        drawActivityTruncatedShape(protein, graphics);
-      }
     } else if (protein instanceof ReceptorProtein) {
       shape = getReceptorShape(protein);
-      if (protein.getActivity()) {
-        drawActivityReceptorProtein(protein, graphics);
-      }
     } else {
       logger.warn(new LogMarker(ProjectLogEntryType.DRAWING_ISSUE, protein) + "Unknown shape for protein");
       shape = getDefaultAliasShape(protein);

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

@@ -78,9 +78,13 @@ public class ProteinSbgnConverter extends ProteinConverter {
   }
 
   @Override
-  Shape getShape(final Protein protein, final Graphics2D graphics) {
+  protected Shape getShape(final Protein protein) {
     return getGenericShape(protein);
   }
+  
+  @Override
+  void drawActivityShape(final Protein protein, final Graphics2D graphics) {
+  }
 
   @Override
   Shape getStructuralStateShape(StructuralState state) {

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

@@ -46,7 +46,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
 
   @Override
   protected void drawImpl(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
-    GeneralPath path = getRnaPath(rna);
+    GeneralPath path = getShape(rna);
     Color oldColor = graphics.getColor();
     graphics.setColor(rna.getFillColor());
     graphics.fill(path);
@@ -71,7 +71,8 @@ public class RnaConverter extends SpeciesConverter<Rna> {
    *          {@link Rna} for which we are looking for a border
    * @return {@link GeneralPath} object defining border of the given {@link Rna}
    */
-  private GeneralPath getRnaPath(final Rna rna) {
+  @Override
+  protected GeneralPath getShape(final Rna rna) {
     // CHECKSTYLE:OFF
     GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
     path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
@@ -85,7 +86,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
 
   @Override
   public PathIterator getBoundPathIterator(final Rna rna) {
-    return getRnaPath(rna).getPathIterator(new AffineTransform());
+    return getShape(rna).getPathIterator(new AffineTransform());
   }
 
 }

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

@@ -42,7 +42,8 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
    *          {@link Species} for which the shape should be returned
    * @return shape of the SBGN Nucleic acid feature for given alias
    */
-  private Shape getShape(final Species species) {
+  @Override
+  protected Shape getShape(final Species species) {
     GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
     double x = species.getX(), y = species.getY(), width = species.getWidth(), height = species.getHeight();
 

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

@@ -66,7 +66,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
     drawText(simpleMolecule, graphics, params);
   }
 
-  Shape getShape(final SimpleMolecule simpleMolecule) {
+  @Override
+  protected Shape getShape(final SimpleMolecule simpleMolecule) {
     return new Ellipse2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(),
         simpleMolecule.getHeight());
   }

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

@@ -65,7 +65,8 @@ public class SimpleMoleculeSbgnConverter extends SimpleMoleculeConverter {
     graphics.setColor(oldColor);
   }
 
-  Shape getShape(final SimpleMolecule simpleMolecule) {
+  @Override
+  protected Shape getShape(final SimpleMolecule simpleMolecule) {
     int arc = (int) Math.min(simpleMolecule.getWidth(), simpleMolecule.getHeight());
     return new RoundRectangle2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(),
         simpleMolecule.getHeight(), arc, arc);

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

@@ -626,4 +626,6 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
     this.arrowTransformation = arrowTransformation;
   }
 
+  protected abstract Shape getShape(T species);
+
 }

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

@@ -45,7 +45,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
     if (unknown.getActivity()) {
       int border = ACTIVITY_BORDER_DISTANCE;
       unknown.increaseBorder(border);
-      Shape shape2 = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());