diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index e61ab7b63071f338d189a46a389a724e0b78d37e..16b964e447a801c55e68f95a9b1695d102b4722c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/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
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
index 91932eae2e22f58cef9c22b16d29cde913c69f1c..18c165403acb5c3cca33d02833de307aa617d4e0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
+++ b/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;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index 7f85a9f5e76f309a1d654980f0a0bfe83e6c0a80..373ee420b1edf78f27fd734ae765b7c164e2a64f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/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();
}
/**
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index d9194ae326a28a7476ce04eb7dcc219003aefd79..f04d9ef0f035ac91c1a51e30e728d0b4da824784 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
+++ b/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;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index 864c939598c6397310c505a20948283409e75dc3..fbb7a6f4c728ddaab9646ba18553ca9565ff7b06 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/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);
}