simplification of abstract methods syntax (unnecessary params removed)

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

@@ -679,20 +679,20 @@ public abstract class AbstractImageGenerator {
 			// compartment/complexes)
 			if (element instanceof Species) {
 				if (((Species) element).getComplex() == null && element.getCompartment() == null) {
-					drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
+					drawSpecies((Species) element);
 				}
 			}
 		}
 		// draw all reactions
 		for (Reaction reaction : params.getModel().getSortedReactions()) {
-			drawReaction(reaction, params.getVisibleLayoutsForElement(reaction), params);
+			drawReaction(reaction);
 		}
 		// draw all compartments
 		for (Compartment compartment : params.getModel().getSortedCompartments()) {
 			// draw only compartment that don't have parents (aren't included in any
 			// compartment/complexes)
 			if (compartment.getCompartment() == null) {
-				drawCompartment(compartment, params.getVisibleLayoutsForElement(compartment), params);
+				drawCompartment(compartment);
 			}
 		}
 
@@ -731,14 +731,10 @@ public abstract class AbstractImageGenerator {
 	 * 
 	 * @param compartment
 	 *          object that we want to draw
-	 * @param visibleLayouts
-	 *          list of {@link ColorSchema} used for coloring element in layouts
-	 * @param params
-	 *          list of all params to create apropriate image
 	 * @throws DrawingException
 	 *           thrown when there was a problem with drawing {@link Compartment}
 	 */
-	protected void drawCompartment(final Compartment compartment, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+	protected void drawCompartment(final Compartment compartment) throws DrawingException {
 		// get a converter for this compartment
 		BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
 		ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
@@ -750,7 +746,7 @@ public abstract class AbstractImageGenerator {
 		// we draw compartment only when we have hierarchical view or it's
 		// standard compartment (not the pathway)
 		if (params.nested || !(compartment instanceof PathwayCompartment)) {
-			converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
+			converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
 		}
 
 		// If compartment should be filled, then we could skip drawing the inside
@@ -762,12 +758,12 @@ public abstract class AbstractImageGenerator {
 			Collections.sort(result, Element.SIZE_COMPARATOR);
 
 			// draw all children of this compartment
-			for (Element element : result) {
+			for (Element child : result) {
 				// if a child is a standard species
-				if (element instanceof Species) {
-					drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
-				} else if (element instanceof Compartment) {
-					drawCompartment((Compartment) element, params.getVisibleLayoutsForElement(element), params);
+				if (child instanceof Species) {
+					drawSpecies((Species) child);
+				} else if (child instanceof Compartment) {
+					drawCompartment((Compartment) child);
 				} else {
 					// if a child is not a compartment or a species then we have a
 					// problem
@@ -788,14 +784,10 @@ public abstract class AbstractImageGenerator {
 	 * 
 	 * @param species
 	 *          object to be drawn
-	 * @param visibleLayouts
-	 *          list of {@link ColorSchema} used for coloring species in layouts
-	 * @param params
-	 *          list of all params to create apropriate image
 	 * @throws DrawingException
 	 *           thrown when there was a problem with drawing a {@link Species}
 	 */
-	protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+	protected void drawSpecies(final Species species) throws DrawingException {
 
 		/**
 		 * Last conditions in this 'ifs' provides the certainty of visibility of
@@ -827,7 +819,9 @@ public abstract class AbstractImageGenerator {
 		if (rescale) {
 			customScale = scale;
 		}
-		converter.draw(species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested), visibleLayouts);
+		converter.draw(
+				species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
+				params.getVisibleLayoutsForElement(species));
 
 		// if the species is a complex then we may want to draw children
 		// objects
@@ -838,8 +832,8 @@ public abstract class AbstractImageGenerator {
 			if (!complex.getState().equalsIgnoreCase("brief")) {
 				// depending on current zoom level, children are drawn or not
 				if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
-					for (Species a : complex.getElements()) {
-						drawSpecies(a, visibleLayouts, params);
+					for (Species child : complex.getElements()) {
+						drawSpecies(child);
 					}
 				}
 			}
@@ -851,18 +845,15 @@ public abstract class AbstractImageGenerator {
 	 * 
 	 * @param reaction
 	 *          object to be drawn
-	 * @param visibleLayouts
-	 *          list of {@link ColorSchema} used for coloring reaction in layouts
-	 * @param params
-	 *          list of all params to create apropriate image
 	 * @throws DrawingException
 	 */
-	protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+	protected void drawReaction(final Reaction reaction) throws DrawingException {
 		if (!cross(reaction.getLines())) {
 			return;
 		}
 		BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
-		converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), visibleLayouts);
+		converter.draw(
+				reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), params.getVisibleLayoutsForElement(reaction));
 	}
 
 	/**