drawing parameters doesn't have fill and tetCentered options

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

@@ -739,20 +739,9 @@ public abstract class AbstractImageGenerator {
 	 *           thrown when there was a problem with drawing {@link Compartment}
 	 */
 	protected void drawCompartment(final Compartment compartment, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
-		/**
-		 * This part is responsible for transparency of compartments. Compartment
-		 * should be transparent if the field of it is big enough, its visibility
-		 * level is sufficient.
-		 */
-
-		boolean fill = true;
-		if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
-			fill = false;
-		}
-
 		// get a converter for this compartment
 		BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
-		ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).nested(params.nested);
+		ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
 
 		if (params.nested) {
 			compartmentParams.scale(Math.max(scale, 1));
@@ -767,30 +756,29 @@ public abstract class AbstractImageGenerator {
 		// If compartment should be filled, then we could skip drawing the inside
 		// compartments.
 
-		if (fill) {
-			return;
-		}
-		List<Element> result = new ArrayList<>();
-		result.addAll(compartment.getElements());
-		Collections.sort(result, Element.SIZE_COMPARATOR);
+		if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
+			List<Element> result = new ArrayList<>();
+			result.addAll(compartment.getElements());
+			Collections.sort(result, Element.SIZE_COMPARATOR);
+
+			// draw all children of this compartment
+			for (Element element : 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);
+				} else {
+					// if a child is not a compartment or a species then we have a
+					// problem
+					throw new DrawingException(eu.getElementTag(compartment) + "Unknown Element type");
+				}
 
-		// draw all children of this compartment
-		for (Element element : 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);
-			} else {
-				// if a child is not a compartment or a species then we have a
-				// problem
-				throw new DrawingException(eu.getElementTag(compartment) + "Unknown Element type");
 			}
-
-		}
-		if (!compartment.containsIdenticalSpecies()) {
-			if (!(compartment instanceof PathwayCompartment)) {
-				converter.drawText(compartment, graphics, compartmentParams);
+			if (!compartment.containsIdenticalSpecies()) {
+				if (!(compartment instanceof PathwayCompartment)) {
+					converter.drawText(compartment, graphics, compartmentParams);
+				}
 			}
 		}
 	}
@@ -839,9 +827,7 @@ public abstract class AbstractImageGenerator {
 		if (rescale) {
 			customScale = scale;
 		}
-		converter.draw(
-				species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
-				visibleLayouts);
+		converter.draw(species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested), visibleLayouts);
 
 		// if the species is a complex then we may want to draw children
 		// objects

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

@@ -19,11 +19,6 @@ public class ConverterParams {
 	 */
 	private double	scale				 = 1;
 
-	/**
-	 * Should the text describing element be centered or not.
-	 */
-	private boolean	textCentered = false;
-
 	/**
 	 * Should the map be displayed in SBGN format.
 	 */
@@ -53,17 +48,6 @@ public class ConverterParams {
 		return this;
 	}
 
-	/**
-	 * @param textCentered
-	 *          the textCentered to set
-	 * @return object with all parameters
-	 * @see #textCentered
-	 */
-	public ConverterParams textCentered(final boolean textCentered) {
-		this.textCentered = textCentered;
-		return this;
-	}
-
 	/**
 	 * @return the level
 	 * @see #level
@@ -102,14 +86,6 @@ public class ConverterParams {
 		return scale;
 	}
 
-	/**
-	 * @return the textCentered
-	 * @see #textCentered
-	 */
-	public boolean isTextCentered() {
-		return textCentered;
-	}
-
 	/**
 	 * @return the sbgnFormat
 	 * @see #sbgnFormat
@@ -131,7 +107,6 @@ public class ConverterParams {
 		String result = "[" + this.getClass().getSimpleName() + "] " + //
 				"level:" + level + "," + //
 				"scale:" + scale + "," + //
-				"textCentered:" + textCentered + "," + //
 				"nested:" + nested + "," + //
 				"sbgnFormat:" + sbgnFormat;
 		return result;

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

@@ -206,7 +206,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
 	 *         otherwise
 	 */
 	protected boolean isTransparent(Element bioEntity, ConverterParams params) {
-		return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel());
+		return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel()) || !params.isNested();
 	}
 
 	/**

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

@@ -102,19 +102,15 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
 		if (compartment.getWidth() < Configuration.EPSILON || compartment.getHeight() < Configuration.EPSILON) {
 			throw new DrawingException(new ElementUtils().getElementTag(compartment) + "Dimension of the alias must be bigger than 0.");
 		}
+		boolean textCentered = !isTransparent(compartment, params);
 		Rectangle2D border = compartment.getBorder();
-		if (isVisible(compartment, params) && !isTransparent(compartment, params)) {
+		if (textCentered) {
 			synchronized (placeFinderSynchronization) {
 				if (placeFinder == null || placeFinder.getModel() != compartment.getModelData()) {
 					placeFinder = new PlaceFinder(compartment.getModelData().getModel());
 				}
 				border = placeFinder.getRetangle(compartment, params.getLevel());
 			}
-		} else if (!params.isTextCentered()) {
-			border = new Rectangle2D.Double(
-					compartment.getNamePoint().getX(), compartment.getNamePoint().getY(),
-					compartment.getWidth() - (compartment.getNamePoint().getX() - compartment.getX()),
-					compartment.getHeight() - (compartment.getNamePoint().getY() - compartment.getY()));
 		}
 		double fontSize = DEFAULT_FONT_SIZE * params.getScale();
 		if (compartment.getFontSize() != null) {
@@ -123,7 +119,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
 		String fontName = Font.SANS_SERIF;
 		try {
 			fontSize = FontFinder.findMaxFontSize((int) Math.round(fontSize), fontName, graphics, border, compartment.getName());
-			FontFinder.drawText((int) fontSize, fontName, graphics, border, compartment.getName(), params.isTextCentered());
+			FontFinder.drawText((int) fontSize, fontName, graphics, border, compartment.getName(), textCentered);
 		} catch (RectangleTooSmallException e) {
 			// if it's too small then don't draw
 			return;

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java

@@ -35,17 +35,12 @@ public class NormalImageGeneratorTest {
 	}
 
 	Double					scale;
-	Boolean					centered;
 	private Boolean	artifitialCalled;
 
 	public void setScale(Double sc) {
 		scale = sc;
 	}
 
-	public void setCentered(Boolean ce) {
-		centered = ce;
-	}
-
 	class TmpComplexConverter extends ComplexConverter {
 		public TmpComplexConverter(ColorExtractor colorExtractor) {
 			super(colorExtractor);
@@ -54,7 +49,6 @@ public class NormalImageGeneratorTest {
 		@Override
 		public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
 			setScale(params.getScale());
-			setCentered(params.isTextCentered());
 			super.drawText(compAlias, graphics, params);
 		}