diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
index bbe7a85463d49da3a0641ebe1086900535722026..def4fbc887b886ef0abcce359c77e7b2ea308ba3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
@@ -89,9 +89,11 @@ public class ImageGenerators {
* @return {@link MimeType} of the generated object
* @throws IOException
* thrown when there is a problem with output file
- * @throws DrawingException
+ * @throws DrawingException
+ * thrown when there is a problem drawing map
*/
- public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename) throws IOException, DrawingException {
+ public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename)
+ throws IOException, DrawingException {
try {
AbstractImageGenerator generator = generatorClass.getConstructor(AbstractImageGenerator.Params.class).newInstance(params);
generator.saveToFile(filename);
@@ -125,7 +127,8 @@ public class ImageGenerators {
* @return {@link MimeType} of the generated object
* @throws IOException
* thrown when there is a problem with output file
- * @throws DrawingException
+ * @throws DrawingException
+ * thrown when there is a problem drawing map
*/
public MimeType generate(String generatorClass, Params params, String filename) throws IOException, DrawingException {
for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
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 3c0969d891be604f9df1bd07431ce44885f34655..7f85a9f5e76f309a1d654980f0a0bfe83e6c0a80 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
@@ -39,18 +39,23 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+ private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* Alpha value (0..255) used for visualizing overlay data that are normally
* visualized in javascript.
*/
- public static final int LAYOUT_ALPHA = 200;
+ public static final int LAYOUT_ALPHA = 200;
/**
- * This function draw representation of the alias on the graphics object.
+ * This function draw {@link BioEntity} on the {@link Graphics2D} object.
*
* @param bioEntity
* {@link BioEntity} that should be drawn
@@ -60,7 +65,8 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* visuzalization params (like, should the object be filled with
* solid color, etc.), for more information see
* {@link ConverterParams}
- * @throws DrawingException
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
*
*/
public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
@@ -82,23 +88,25 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* list of {@link ColorSchema} that were used for visualizing this
* bioentity in different data overlays that should be overlayed on
* the alias
- * @throws DrawingException
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
*
*/
- public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas) throws DrawingException;
+ public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas)
+ throws DrawingException;
/**
* This function will find proper font size to display text within it. Then it
* will print this text.
*
* @param bioEntity
- * bioEntity with description to be drawn
+ * {@link BioEntity} with description to be drawn
* @param graphics
* where the description should be drawn
* @param params
* parameters of visualization (centering, scale)
* @throws DrawingException
- * thrown when there is a problem with drawing bioEntity
+ * thrown when there is a problem with drawing {@link BioEntity}
*/
public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
@@ -186,6 +194,17 @@ public abstract class BioEntityConverter<T extends BioEntity> {
return true;
}
+ /**
+ * Checks if {@link Element} given in the argument is transparent accordind to
+ * the level given in the {@link ConverterParams}.
+ *
+ * @param bioEntity
+ * {@link BioEntity} to be checked
+ * @param params
+ * params against which check is run
+ * @return <code>true</code> if object is transparent, <code>false</code>
+ * otherwise
+ */
protected boolean isTransparent(Element bioEntity, ConverterParams params) {
return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
index b2af327cf2453121bd80963f61a6a657b3bb54ec..862cdb82efa56b106a3f560cb038e447d77adf4a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
@@ -9,16 +9,15 @@ import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.log4j.Logger;
-
/**
* Class responsible for drawing BottomSquareCompartment on the Graphics2D.
*
@@ -31,7 +30,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
/**
* Default constructor.
@@ -45,24 +44,24 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
}
@Override
- public void draw(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
// create shape of the compartment
- Shape s1 = new Line2D.Double(0, alias.getY(), alias.getWidth(), alias.getY());
- Shape s3 = new Line2D.Double(0, alias.getY() + alias.getThickness(), alias.getWidth(), alias.getY() + alias.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, alias.getY(), alias.getWidth(), alias.getHeight()));
+ Shape s1 = new Line2D.Double(0, compartment.getY(), compartment.getWidth(), compartment.getY());
+ Shape s3 = new Line2D.Double(0, compartment.getY() + compartment.getThickness(), compartment.getWidth(), compartment.getY() + compartment.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, compartment.getY(), compartment.getWidth(), compartment.getHeight()));
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
}
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -87,10 +86,10 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
}
}
}
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 4db51f040bdcc18e9b7636c5d3abf9c386def466..2221b5a5d7acac56a3492111056ef1bf19917165 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
@@ -9,7 +9,6 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
@@ -99,32 +98,33 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
};
@Override
- public void drawText(final T alias, final Graphics2D graphics, final ConverterParams params) {
- if (alias.getWidth() < Configuration.EPSILON || alias.getHeight() < Configuration.EPSILON) {
+ public void drawText(final T compartment, final Graphics2D graphics, final ConverterParams params) {
+ if (compartment.getWidth() < Configuration.EPSILON || compartment.getHeight() < Configuration.EPSILON) {
throw new InvalidArgumentException(
- "Dimension of the alias must be bigger than 0. Alias id: " + alias.getElementId() + " (name: \"" + alias.getName() + "\")");
+ "Dimension of the alias must be bigger than 0. Alias id: " + compartment.getElementId() + " (name: \"" + compartment.getName() + "\")");
}
- Rectangle2D border = alias.getBorder();
- if (isVisible(alias, params) && !isTransparent(alias, params)) {
+ Rectangle2D border = compartment.getBorder();
+ if (isVisible(compartment, params) && !isTransparent(compartment, params)) {
synchronized (placeFinderSynchronization) {
- if (placeFinder == null || placeFinder.getModel() != alias.getModelData()) {
- placeFinder = new PlaceFinder(alias.getModelData().getModel());
+ if (placeFinder == null || placeFinder.getModel() != compartment.getModelData()) {
+ placeFinder = new PlaceFinder(compartment.getModelData().getModel());
}
- border = placeFinder.getRetangle(alias, params.getLevel());
+ border = placeFinder.getRetangle(compartment, params.getLevel());
}
} else if (!params.isTextCentered()) {
border = new Rectangle2D.Double(
- alias.getNamePoint().getX(), alias.getNamePoint().getY(), alias.getWidth() - (alias.getNamePoint().getX() - alias.getX()),
- alias.getHeight() - (alias.getNamePoint().getY() - alias.getY()));
+ 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 (alias.getFontSize() != null) {
- fontSize = alias.getFontSize() * params.getScale();
+ if (compartment.getFontSize() != null) {
+ fontSize = compartment.getFontSize() * params.getScale();
}
String fontName = Font.SANS_SERIF;
try {
- fontSize = FontFinder.findMaxFontSize((int) Math.round(fontSize), fontName, graphics, border, alias.getName());
- FontFinder.drawText((int) fontSize, fontName, graphics, border, alias.getName(), params.isTextCentered());
+ fontSize = FontFinder.findMaxFontSize((int) Math.round(fontSize), fontName, graphics, border, compartment.getName());
+ FontFinder.drawText((int) fontSize, fontName, graphics, border, compartment.getName(), params.isTextCentered());
} catch (RectangleTooSmallException e) {
// if it's too small then don't draw
return;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
index e6767a608f602797e282f952b321c19f302e23d9..cacd7fa860b2fac75d447b62ccac7d998e12cb46 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
@@ -44,24 +44,25 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
}
@Override
- public void draw(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
// create shape of the compartment
- Shape s1 = new Line2D.Double(alias.getWidth(), alias.getHeight(), alias.getWidth(), 0);
- Shape s3 = new Line2D.Double(alias.getWidth() - alias.getThickness(), 0, alias.getWidth() - alias.getThickness(), alias.getHeight());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
+ Shape s1 = new Line2D.Double(compartment.getWidth(), compartment.getHeight(), compartment.getWidth(), 0);
+ Shape s3 = new Line2D.Double(
+ compartment.getWidth() - compartment.getThickness(), 0, compartment.getWidth() - compartment.getThickness(), compartment.getHeight());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
}
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -87,10 +88,10 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
}
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
index ea5a579a5aad3c38e683933a718782a2bf05d708..94bf3c470241e0fe1c5c09feeaef1c03c3be91a2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
@@ -11,9 +11,9 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -38,27 +38,27 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
/**
* Returns shape representing alias.
*
- * @param alias
+ * @param compartment
* alias for which we are looking for a Shape
* @return Shape object that represents alias
*/
- private Shape getShape(final Element alias) {
- return new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ private Shape getShape(final Compartment compartment) {
+ return new Ellipse2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
}
@Override
- public void draw(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
// create shape of the compartment
- Shape s1 = getShape(alias);
- alias.increaseBorder(-alias.getThickness());
- Shape s3 = getShape(alias);
- alias.increaseBorder(alias.getThickness());
+ Shape s1 = getShape(compartment);
+ compartment.increaseBorder(-compartment.getThickness());
+ Shape s3 = getShape(compartment);
+ compartment.increaseBorder(compartment.getThickness());
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
@@ -68,7 +68,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
a1.subtract(new Area(s3));
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -92,13 +92,13 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
} else {
- if (!alias.containsIdenticalSpecies()) {
- drawText(alias, graphics, params);
+ if (!compartment.containsIdenticalSpecies()) {
+ drawText(compartment, graphics, params);
}
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
index b9ff85306fdb47ea1c2eee4576774e348a14cd24..fb3518522110b69d730092da16c54e940b3063e1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
@@ -40,17 +40,17 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
private Color backgroundColor = Color.LIGHT_GRAY;
@Override
- public void draw(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
- Shape shape = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ Shape shape = new Rectangle2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
- Color color = alias.getColor();
+ Color color = compartment.getColor();
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(backgroundColor);
} else {
@@ -70,13 +70,13 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
// draw description of the compartment
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
} else {
- if (!alias.containsIdenticalSpecies()) {
- drawText(alias, graphics, params);
+ if (!compartment.containsIdenticalSpecies()) {
+ drawText(compartment, graphics, params);
}
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
index 92303a36f88bcc4bcc0008c1bdb270693a1f9f90..a9461ebb57a23f986f6502d192abbe30f10ad1ea 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
@@ -44,24 +44,24 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
}
@Override
- public void draw(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
// create shape of the compartment
- Shape s1 = new Line2D.Double(alias.getX(), alias.getHeight(), alias.getX(), 0);
- Shape s3 = new Line2D.Double(alias.getX() + alias.getThickness(), alias.getHeight(), alias.getX(), 0);
- Area a1 = new Area(new Rectangle2D.Double(alias.getX(), 0.0, alias.getWidth(), alias.getHeight()));
+ Shape s1 = new Line2D.Double(compartment.getX(), compartment.getHeight(), compartment.getX(), 0);
+ Shape s3 = new Line2D.Double(compartment.getX() + compartment.getThickness(), compartment.getHeight(), compartment.getX(), 0);
+ Area a1 = new Area(new Rectangle2D.Double(compartment.getX(), 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
}
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -85,18 +85,18 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
graphics.setStroke(oldStroke);
// three lines below are only temporary fix...
- double x = alias.getNamePoint().getX() - alias.getX();
- double y = alias.getNamePoint().getY();
- alias.getNamePoint().setLocation(x, y);
+ double x = compartment.getNamePoint().getX() - compartment.getX();
+ double y = compartment.getNamePoint().getY();
+ compartment.getNamePoint().setLocation(x, y);
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
}
- x += alias.getX();
- alias.getNamePoint().setLocation(x, y);
+ x += compartment.getX();
+ compartment.getNamePoint().setLocation(x, y);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
index c19e0deb0c9fd9a2abf9735ff134fa4eee39c168..2cd4017c5eaefa760d42456e522be50c03cdf9e2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
@@ -13,13 +13,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * Class responsible for drawing SquareCompartment on the Graphics2D.
+ * Class responsible for drawing SquareCompartment on the {@link Graphics2D}.
*
* @author Piotr Gawron
*
@@ -48,29 +48,30 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
}
/**
- * Returns shape representing alias.
+ * Returns shape representing compartment.
*
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
+ * @param compartment
+ * compartment for which we are looking for a {@link Shape}
+ * @return {@link Shape} object that represents compartment
*/
- private Shape getShape(final Element alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ private Shape getShape(final Compartment compartment) {
+ return new RoundRectangle2D.Double(
+ compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
}
@Override
- public void draw(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
// create shape of the compartment
- Shape s1 = getShape(alias);
- alias.increaseBorder(-alias.getThickness());
- Shape s3 = getShape(alias);
- alias.increaseBorder(alias.getThickness());
+ Shape s1 = getShape(compartment);
+ compartment.increaseBorder(-compartment.getThickness());
+ Shape s3 = getShape(compartment);
+ compartment.increaseBorder(compartment.getThickness());
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
@@ -80,7 +81,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
a1.subtract(new Area(s3));
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -104,10 +105,10 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
}
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
index 33a325562f0c7fc4322b2083f7ea13b4166f9ffa..7832bd282364731c4245f950f3e5959ff1ea4a01 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
/**
- * Class responsible for drawing TopSquareCompartment on the Graphics2D.
+ * Class responsible for drawing TopSquareCompartment on the {@link Graphics2D}.
*
* @author Piotr Gawron
*
@@ -44,22 +44,23 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
}
@Override
- public void draw(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) {
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
- Shape s1 = new Line2D.Double(0, alias.getHeight(), alias.getWidth(), alias.getHeight());
- Shape s3 = new Line2D.Double(0, alias.getHeight() - alias.getThickness(), alias.getWidth(), alias.getHeight() - alias.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
+ Shape s1 = new Line2D.Double(0, compartment.getHeight(), compartment.getWidth(), compartment.getHeight());
+ Shape s3 = new Line2D.Double(
+ 0, compartment.getHeight() - compartment.getThickness(), compartment.getWidth(), compartment.getHeight() - compartment.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = alias.getColor();
+ Color c1 = compartment.getColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
}
// fill the background
- boolean fill = !isTransparent(alias, params);
+ boolean fill = !isTransparent(compartment, params);
if (fill) {
graphics.setColor(c1);
} else {
@@ -83,10 +84,10 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
graphics.setStroke(oldStroke);
// draw description
if (fill) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
}
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index 84d00dc02a8c969fcc03de52697d7d17a7f988cb..f8b7777cdc7a41ecf1397b49f59c5ff9c86d61e8 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -15,16 +15,15 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
- * This class defines methods used for drawing Antisense Rna SpeciesAlias on the
- * graphics2d object.
+ * This class defines methods used for drawing {@link AntisenseRna} on the
+ * {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -48,40 +47,39 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
super(colorExtractor);
}
-
@Override
- public void draw(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getAntisenseRnaPath(alias);
+ public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getAntisenseRnaPath(antisenseRna);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(antisenseRna.getColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(antisenseRna));
graphics.draw(path);
graphics.setStroke(stroke);
- for (AntisenseRnaRegion mr : alias.getRegions()) {
- drawRegion(alias, mr, graphics, false, false);
+ for (AntisenseRnaRegion mr : antisenseRna.getRegions()) {
+ drawRegion(antisenseRna, mr, graphics, false, false);
}
- drawText(alias, graphics, params);
+ drawText(antisenseRna, graphics, params);
}
/**
- * Returns alias border as a GeneralPath object.
+ * Returns {@link AntisenseRna} border as a {@link GeneralPath} object.
*
- * @param alias
- * alias for which we want to get border
- * @return border of the alias
+ * @param antisenseRna
+ * {@link AntisenseRna} for which we want to get border
+ * @return border of the {@link AntisenseRna}
*/
- private GeneralPath getAntisenseRnaPath(final Element alias) {
+ private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
+ path.moveTo(antisenseRna.getX(), antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() * 3 / 4, antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth(), antisenseRna.getY() + antisenseRna.getHeight());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() / 4, antisenseRna.getY() + antisenseRna.getHeight());
// CHECKSTYLE:ON
path.closePath();
return path;
@@ -95,33 +93,33 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
/**
* This method draws antisense rna region for given alias.
*
- * @param alias
- * alias on which region should be drawn
- * @param mr
- * region to be drawn
+ * @param antisenseRna
+ * {@link AntisenseRna} on which region should be drawn
+ * @param region
+ * {@link AntisenseRnaRegion} to be drawn
* @param graphics
- * graphics where we draw region
+ * {@link Graphics2D} where we draw region
* @param drawEmptyRegion
* flag determining if we shoudl draw empty regions
* @param drawDescription
* flag determining if we want to draw description as well
*/
- private void drawRegion(final AntisenseRna alias, final AntisenseRnaRegion mr, final Graphics2D graphics, final boolean drawEmptyRegion,
+ private void drawRegion(final AntisenseRna antisenseRna, final AntisenseRnaRegion region, final Graphics2D graphics, final boolean drawEmptyRegion,
final boolean drawDescription) {
- if ((!drawEmptyRegion) && (mr.getState() == null)) {
+ if ((!drawEmptyRegion) && (region.getState() == null)) {
return;
}
double diameter = DEFAULT_MODIFICATION_DIAMETER;
- double x = alias.getX();
- double y = alias.getY();
+ double x = antisenseRna.getX();
+ double y = antisenseRna.getY();
- double width = alias.getWidth();
+ double width = antisenseRna.getWidth();
// CHECKSTYLE:OFF
// we draw modifier on the upper border of antisense rna (which is only in
// 3/4 of the width of alias)
- Point2D p = new Point2D.Double(x + width * 3.0 / 4.0 * mr.getPos(), y - diameter);
+ Point2D p = new Point2D.Double(x + width * 3.0 / 4.0 * region.getPos(), y - diameter);
// CHECKSTYLE:ON
Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
@@ -132,13 +130,13 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
graphics.draw(ellipse);
graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
- String text = mr.getName();
+ String text = region.getName();
if (!text.equals("") && drawDescription) {
double textWidth = graphics.getFontMetrics().stringWidth(text);
Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
}
- ModificationState state = mr.getState();
+ ModificationState state = region.getState();
if (state != null) {
String str = state.getAbbreviation();
Font tmpFont = graphics.getFont();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
index 760c24e23e7f3975de8e0221491e489576ad5b20..2fa74bcc721df4921075d13d89df47699f43c564 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
@@ -12,15 +12,13 @@ import java.awt.geom.PathIterator;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines methods used for drawing ComplexAlias on the graphics2d
@@ -143,50 +141,50 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
}
@Override
- public void drawText(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
- if (((Complex) alias).getElements().size() > 0) {
- if (isTransparent(alias, params)) {
- super.drawText(alias, graphics, params);
+ public void drawText(final Complex complex, final Graphics2D graphics, final ConverterParams params) {
+ if (complex.getElements().size() > 0) {
+ if (isTransparent(complex, params)) {
+ super.drawText(complex, graphics, params);
return;
}
}
- String text = getText(alias);
+ String text = getText(complex);
try {
double fontSize = DEFAULT_SPECIES_FONT_SIZE;
- if (alias.getFontSize() != null) {
- fontSize = alias.getFontSize();
+ if (complex.getFontSize() != null) {
+ fontSize = complex.getFontSize();
}
- int size = (int) FontFinder.findMaxFontSize(params.getScale() * fontSize, Font.SANS_SERIF, graphics, alias.getBorder(), text);
- FontFinder.drawText(size, Font.SANS_SERIF, graphics, alias.getBorder(), text);
+ int size = (int) FontFinder.findMaxFontSize(params.getScale() * fontSize, Font.SANS_SERIF, graphics, complex.getBorder(), text);
+ FontFinder.drawText(size, Font.SANS_SERIF, graphics, complex.getBorder(), text);
} catch (RectangleTooSmallException e) {
logger.warn("Problem with finding font size", e);
- super.drawText(alias, graphics, params);
+ super.drawText(complex, graphics, params);
}
}
/**
- * Returns the border of complex alias.
+ * Returns the border of {@link Complex}.
*
- * @param alias
+ * @param complex
* exact object for which we want to get a border
- * @return border of the alias
+ * @return border of the {@link Complex}
*/
- private GeneralPath getAliasPath(final Element alias) {
+ private GeneralPath getAliasPath(final Complex complex) {
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
- path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX(), alias.getY() + TRIMMED_CORNER_SIZE);
+ path.moveTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY());
+ path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY());
+ path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
+ path.lineTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
+ path.lineTo(complex.getX(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX(), complex.getY() + TRIMMED_CORNER_SIZE);
path.closePath();
return path;
}
@Override
- public PathIterator getBoundPathIterator(final Complex alias) {
- return getAliasPath(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(final Complex complex) {
+ return getAliasPath(complex).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
index 42152ef9f1c518e85485ab9c268049202831b667..2b8c6d163a165b366e4a93d36dd316f69263d822 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
@@ -16,12 +16,11 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines methods used for drawing Degraded SpeciesAlias on the
- * graphics2d object.
+ * This class defines methods used for drawing {@link Degraded} on the
+ * {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -50,17 +49,17 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
}
@Override
- public void draw(final Degraded alias, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
+ public void draw(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
+ double diameter = getDiameter(degraded);
+ double x = getXCoord(degraded, diameter);
+ double y = getYCoord(degraded);
Area a1 = new Area(new Ellipse2D.Double(x, y, diameter, diameter));
- double lineX1 = alias.getX() + alias.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
- double lineY1 = alias.getY();
+ double lineX1 = degraded.getX() + degraded.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
+ double lineY1 = degraded.getY();
- double lineX2 = alias.getX() + alias.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
- double lineY2 = alias.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
+ double lineX2 = degraded.getX() + degraded.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
+ double lineY2 = degraded.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 2);
path.moveTo(lineX1, lineY1);
@@ -71,51 +70,51 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
a1.exclusiveOr(new Area(path));
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(degraded.getColor());
graphics.fill(a1);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(degraded));
graphics.draw(a1);
graphics.setStroke(stroke);
- drawText(alias, graphics, params);
+ drawText(degraded, graphics, params);
}
/**
- * Returns transformed y coordinate for the degraded alias.
+ * Returns transformed y coordinate for the {@link Degraded} bioentity.
*
- * @param alias
- * object alias to to which we are looking for y coordinate
+ * @param degraded
+ * {@link Degraded} to to which we are looking for y coordinate
* @return y coordinate of the alias
*/
- private double getYCoord(final Element alias) {
- double y = alias.getY() + CROSS_LINE_EXTENDED_LENGTH;
+ private double getYCoord(final Degraded degraded) {
+ double y = degraded.getY() + CROSS_LINE_EXTENDED_LENGTH;
return y;
}
/**
* Returns transformed x coordinate for the degraded alias.
*
- * @param alias
+ * @param degraded
* object alias to to which we are looking for x coordinate
* @param diameter
* diameter of cross line used in this alias
- * @return x coordinate of the alias
+ * @return x coordinate of the {@link Degraded} bioentity.
*/
- private double getXCoord(final Element alias, final double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ private double getXCoord(final Degraded degraded, final double diameter) {
+ double x = degraded.getX() + (degraded.getWidth() - diameter) / 2;
return x;
}
/**
* Computes diameter of cross line for the degraded alias.
*
- * @param alias
+ * @param degraded
* object alias to to which we are looking for diameter.
* @return diameter of the cross line
*/
- private double getDiameter(final Element alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
+ private double getDiameter(final Degraded degraded) {
+ double diameter = Math.min(degraded.getWidth(), degraded.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
if (diameter < 0) {
logger.warn("Diameter cannot be negative...");
diameter = 0;
@@ -124,12 +123,12 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
}
@Override
- public String getText(Degraded alias) {
+ public String getText(Degraded degraded) {
return "";
}
@Override
- public PathIterator getBoundPathIterator(Degraded alias) {
+ public PathIterator getBoundPathIterator(Degraded degraded) {
throw new InvalidStateException("This class doesn't have bound");
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
index 4c412634f46f78414c63f1a7426463cd1aaeb92d..8765dd6e30dc0e71b8bac1382537e92fa97d0a77 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
@@ -10,15 +10,14 @@ import java.awt.geom.Point2D;
import java.awt.geom.RoundRectangle2D;
import java.util.ArrayList;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.log4j.Logger;
-
/**
* This class defines methods used for drawing Drug SpeciesAlias on the
* graphics2d object.
@@ -27,23 +26,23 @@ import org.apache.log4j.Logger;
*
*/
public class DrugConverter extends SpeciesConverter<Drug> {
-
+
/**
* Distance between internal and external border of drug graphical
* representation.
*/
- private static final int OFFSET_BETWEEN_BORDERS = 4;
-
+ private static final int OFFSET_BETWEEN_BORDERS = 4;
+
/**
* How big should be the arc in rectangle for drug representation.
*/
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
-
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
+ private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
/**
* Default constructor.
@@ -59,47 +58,47 @@ public class DrugConverter extends SpeciesConverter<Drug> {
/**
* Returns shape of the Drug .
*
- * @param alias
- * alias for which we are looking for a border
+ * @param drug
+ * {@link Drug} for which we are looking for a border
* @return Shape object defining given alias
*/
- private Shape getDrugShape(final Element alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ private Shape getDrugShape(final Drug drug) {
+ return new RoundRectangle2D.Double(drug.getX(), drug.getY(), drug.getWidth(), drug.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
}
@Override
- public void draw(Drug alias, final Graphics2D graphics, final ConverterParams params) {
- Shape a1 = getDrugShape(alias);
+ public void draw(Drug drug, final Graphics2D graphics, final ConverterParams params) {
+ Shape a1 = getDrugShape(drug);
double offset = OFFSET_BETWEEN_BORDERS;
Shape a2 = new RoundRectangle2D.Double(
- alias.getX() + offset, alias.getY() + offset, alias.getWidth() - 2 * offset, alias.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
+ drug.getX() + offset, drug.getY() + offset, drug.getWidth() - 2 * offset, drug.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
RECTANGLE_CORNER_ARC_SIZE);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(drug.getColor());
graphics.fill(a1);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(drug));
graphics.draw(a1);
graphics.draw(a2);
graphics.setStroke(stroke);
- drawText(alias, graphics, params);
+ drawText(drug, graphics, params);
}
/**
- * Returns shape of the Drug as a list of points.
+ * Returns shape of the {@link Drug} as a list of points.
*
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
+ * @param drug
+ * {@link Drug} for which we are looking for a border
+ * @return list of points defining border of the given {@link Drug}
*/
- protected ArrayList<Point2D> getDrugPoints(final Species alias) {
+ protected ArrayList<Point2D> getDrugPoints(final Drug drug) {
ArrayList<Point2D> list = new ArrayList<Point2D>();
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
+ double x = drug.getX();
+ double y = drug.getY();
+ double width = drug.getWidth();
+ double height = drug.getHeight();
// CHECKSTYLE:OFF
list.add(new Point2D.Double(x, y + height / 2));
@@ -116,8 +115,8 @@ public class DrugConverter extends SpeciesConverter<Drug> {
}
@Override
- public PathIterator getBoundPathIterator(Drug alias) {
- return getDrugShape(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(Drug drug) {
+ return getDrugShape(drug).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
index 514475cf86205411fc334f3dc88b411aecde5443..8528b749fca21bab36324abe8e66c7d5f29cb16e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
@@ -16,7 +16,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -48,22 +47,22 @@ public class GeneConverter extends SpeciesConverter<Gene> {
}
@Override
- public void draw(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
- Shape shape = getGeneShape(alias);
+ public void draw(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
+ Shape shape = getGeneShape(gene);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(gene.getColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(gene));
graphics.draw(shape);
graphics.setStroke(stroke);
- for (ModificationResidue mr : alias.getModificationResidues()) {
- drawModification(alias, mr, graphics, false, false);
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ drawModification(gene, mr, graphics, false, false);
}
- drawText(alias, graphics, params);
+ drawText(gene, graphics, params);
}
/**
@@ -72,7 +71,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
* set then also description (position) of the modification is drawn on the
* canvas.
*
- * @param alias
+ * @param gene
* object that is 'parent' of the residue
* @param mr
* modification to be drawn
@@ -84,17 +83,17 @@ public class GeneConverter extends SpeciesConverter<Gene> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final Gene alias, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Gene gene, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
if ((!drawEmptyModification) && (mr.getState() == null)) {
return;
}
double diameter = DEFAULT_MODIFICATION_DIAMETER;
- double x = alias.getX();
- double y = alias.getY();
+ double x = gene.getX();
+ double y = gene.getY();
- double width = alias.getWidth();
+ double width = gene.getWidth();
Point2D p = new Point2D.Double(x + width * mr.getAngle(), y - DEFAULT_MODIFICATION_DIAMETER);
@@ -126,21 +125,21 @@ public class GeneConverter extends SpeciesConverter<Gene> {
}
/**
- * Shape representation of the gene alias.
+ * Shape representation of the {@link Gene}.
*
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
+ * @param gene
+ * {@link Gene} for which we are looking for a {@link Shape}
+ * @return {@link Shape} that represents {@link Gene}
*/
- private Shape getGeneShape(final Element alias) {
+ private Shape getGeneShape(final Gene gene) {
Shape shape;
- shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
+ shape = new Rectangle(gene.getX().intValue(), gene.getY().intValue(), gene.getWidth().intValue(), gene.getHeight().intValue());
return shape;
}
@Override
- public PathIterator getBoundPathIterator(final Gene alias) {
- return getGeneShape(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(final Gene gene) {
+ return getGeneShape(gene).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
index 733f3b7ddb0dcf1f165360352c9e603854b8db3f..6b0237b7498984c0ee2b5f301a2b725a9fcb8c18 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
@@ -14,14 +14,12 @@ import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Ion
- * Ion} on the {@link Graphics2D} object.
+ * This class defines methods used for drawing SpeciesAlias of {@link Ion} on
+ * the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -45,57 +43,57 @@ public class IonConverter extends SpeciesConverter<Ion> {
}
@Override
- public void draw(Ion alias, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
+ public void draw(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);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(ion.getColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(ion));
graphics.draw(shape);
graphics.setStroke(stroke);
- drawText(alias, graphics, params);
+ drawText(ion, graphics, params);
}
/**
- * Returns transformed y coordinate for the ion alias.
+ * Returns transformed y coordinate for the {@link Ion}.
*
- * @param alias
- * object alias to to which we are looking for y coordinate
- * @return y coordinate of the alias
+ * @param ion
+ * {@link Ion} to to which we are looking for y coordinate
+ * @return y coordinate of the {@link Ion}
*/
- private double getYCoord(final Element alias) {
- double y = alias.getY();
+ private double getYCoord(final Ion ion) {
+ double y = ion.getY();
return y;
}
/**
- * Returns transformed x coordinate for the ion alias.
+ * Returns transformed x coordinate for the {@link Ion}.
*
- * @param alias
- * object alias to to which we are looking for x coordinate
+ * @param ion
+ * {@link Ion} to which we are looking for x coordinate
* @param diameter
* diameter of circle representation of ion
- * @return x coordinate of the alias
+ * @return x coordinate of the {@link Ion}
*/
- private double getXCoord(final Element alias, final double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ private double getXCoord(final Ion ion, final double diameter) {
+ double x = ion.getX() + (ion.getWidth() - diameter) / 2;
return x;
}
/**
- * Returns diameter of circle representation of ion.
+ * Returns diameter of circle representation of an {@link Ion}.
*
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of ion circle representation
+ * @param ion
+ * {@link Ion} to to which we are looking for diameter.
+ * @return diameter of {@link Ion} circle representation
*/
- private double getDiameter(final Element alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight());
+ private double getDiameter(final Ion ion) {
+ double diameter = Math.min(ion.getWidth(), ion.getHeight());
if (diameter < 0) {
logger.warn("Something is wrong. Size cannot be negative");
diameter = 0;
@@ -105,19 +103,19 @@ public class IonConverter extends SpeciesConverter<Ion> {
}
@Override
- public PathIterator getBoundPathIterator(Ion alias) {
+ public PathIterator getBoundPathIterator(Ion ion) {
throw new InvalidStateException("This class doesn't have bound");
}
@Override
- public Point2D getPointCoordinatesOnBorder(Ion alias, final double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ public Point2D getPointCoordinatesOnBorder(Ion ion, final double angle) {
+ if (ion.getWidth() == 0 && ion.getHeight() == 0) {
logger.warn("Looking for coordinates for the alias with 0 size");
- return alias.getCenter();
+ return ion.getCenter();
}
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
+ double diameter = getDiameter(ion);
+ double x = getXCoord(ion, diameter);
+ double y = getYCoord(ion);
Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
return result;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
index 0a6a2a059b9bd3d4cf9024797bd17d88c112b949..b9674dc86420941f54ea81233b83f62ddafda7d5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
@@ -13,13 +13,11 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Phenotype;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Phenotype
- * Phenotype} on the {@link Graphics2D} object.
+ * This class defines methods used for drawing SpeciesAlias of {@link Phenotype}
+ * on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -44,44 +42,45 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
}
@Override
- public void draw(Phenotype alias, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getPhenotypePath(alias);
+ public void draw(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getPhenotypePath(phenotype);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(phenotype.getColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(phenotype));
graphics.draw(path);
graphics.setStroke(stroke);
- drawText(alias, graphics, params);
+ drawText(phenotype, graphics, params);
}
/**
- * Returns shape of the Phenotype as a GeneralPath object.
+ * Returns shape of the {@link Phenotype} as a {@link GeneralPath} object.
*
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
+ * @param phenotype
+ * {@link Phenotype} for which we are looking for a border
+ * @return {@link GeneralPath} object defining border of the given
+ * {@link Phenotype}
*/
- private GeneralPath getPhenotypePath(final Element alias) {
+ private GeneralPath getPhenotypePath(final Phenotype phenotype) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 6);
- path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() / 2);
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() / 2);
+ path.moveTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY());
+ path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY());
+ path.lineTo(phenotype.getX() + phenotype.getWidth(), phenotype.getY() + phenotype.getHeight() / 2);
+ path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY() + phenotype.getHeight());
+ path.lineTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY() + phenotype.getHeight());
+ path.lineTo(phenotype.getX(), phenotype.getY() + phenotype.getHeight() / 2);
// CHECKSTYLE:ON
path.closePath();
return path;
}
@Override
- public PathIterator getBoundPathIterator(Phenotype alias) {
- return getPhenotypePath(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(Phenotype phenotype) {
+ return getPhenotypePath(phenotype).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index 0e794ffa6e425ca2af04a2a9d87c185b3728ebb3..0f97b3998052c234e8602675ece715111de38352 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -23,7 +23,6 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.IonChannelProtein;
import lcsb.mapviewer.model.map.species.Protein;
@@ -47,6 +46,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
* Width of the ion part in the open channel representation.
*/
private static final int ION_CHANNEL_WIDTH = 20;
+
/**
* Width of the gap in the open channel representation.
*/
@@ -56,6 +56,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
* How big should be the arc in rectangle for protein representation.
*/
private static final int RECTANGLE_CORNER_ARC_SIZE = 10;
+
/**
* Default class logger.
*/
@@ -78,29 +79,30 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
}
/**
- * Returns shape of generic protein.
+ * Returns shape of {@link Protein}.
*
- * @param alias
- * alias for which we are looking for a border
+ * @param protein
+ * {@link Protein} for which we are looking for a border
* @return Shape object defining given alias
*/
- private Shape getGenericShape(final Element alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ private Shape getGenericShape(final Protein protein) {
+ return new RoundRectangle2D.Double(
+ protein.getX(), protein.getY(), protein.getWidth(), protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
}
@Override
- public void draw(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
// Local variable setting the SBGN visualization
boolean sbgnFormat = params.isSbgnFormat();
// Unit of information text (multimer cardinality and/or ion channel's
// state)
String unitOfInformationText = "";
- if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
- if (alias.getStatePrefix().equals("free input")) {
- unitOfInformationText = alias.getStateLabel();
+ if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
+ if (protein.getStatePrefix().equals("free input")) {
+ unitOfInformationText = protein.getStateLabel();
} else {
- unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
+ unitOfInformationText = protein.getStatePrefix() + ":" + protein.getStateLabel();
}
}
@@ -108,88 +110,88 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
if (sbgnFormat) {
// If the SBGN display mode is set, multimer is shown as two stacked
// glyphs
- if (alias.getHomodimer() > 1) {
+ if (protein.getHomodimer() > 1) {
homodir = 2;
} else {
homodir = 1;
}
} else {
- homodir = alias.getHomodimer();
+ homodir = protein.getHomodimer();
}
- alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ protein.setWidth(protein.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+ protein.setHeight(protein.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
- alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ protein.setX(protein.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ protein.setY(protein.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
for (int homodimerId = 0; homodimerId < homodir; homodimerId++) {
- alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+ protein.setX(protein.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ protein.setY(protein.getY() - SpeciesConverter.HOMODIMER_OFFSET);
Shape shape = null;
- if (alias instanceof GenericProtein || sbgnFormat) {
- shape = getGenericShape(alias);
- if (alias.getActivity() && !sbgnFormat) {
- drawActivityGenericProtein(alias, graphics);
+ if (protein instanceof GenericProtein || sbgnFormat) {
+ shape = getGenericShape(protein);
+ if (protein.getActivity() && !sbgnFormat) {
+ drawActivityGenericProtein(protein, graphics);
}
- } else if (alias instanceof IonChannelProtein) {
+ } else if (protein instanceof IonChannelProtein) {
Area a1;
- if (!alias.getActivity()) {
+ if (!protein.getActivity()) {
a1 = new Area(
new RoundRectangle2D.Double(
- alias.getX(), alias.getY(), alias.getWidth() - ION_CHANNEL_WIDTH - 1, alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
+ protein.getX(), protein.getY(), protein.getWidth() - ION_CHANNEL_WIDTH - 1, protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
RECTANGLE_CORNER_ARC_SIZE));
} else {
a1 = new Area(
new RoundRectangle2D.Double(
- alias.getX(), alias.getY(), alias.getWidth() - ION_CHANNEL_WIDTH - OPEN_ION_CHANNEL_WIDTH - 1, alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
- RECTANGLE_CORNER_ARC_SIZE));
+ protein.getX(), protein.getY(), protein.getWidth() - ION_CHANNEL_WIDTH - OPEN_ION_CHANNEL_WIDTH - 1, protein.getHeight(),
+ RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE));
}
Area a2 = new Area(
new RoundRectangle2D.Double(
- alias.getX() + alias.getWidth() - ION_CHANNEL_WIDTH, alias.getY(), ION_CHANNEL_WIDTH, alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
+ protein.getX() + protein.getWidth() - ION_CHANNEL_WIDTH, protein.getY(), ION_CHANNEL_WIDTH, protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
RECTANGLE_CORNER_ARC_SIZE));
a1.add(a2);
shape = a1;
- } else if (alias instanceof TruncatedProtein) {
- shape = getTruncatedShape(alias);
- if (alias.getActivity()) {
- drawActivityTruncatedShape(alias, graphics);
+ } else if (protein instanceof TruncatedProtein) {
+ shape = getTruncatedShape(protein);
+ if (protein.getActivity()) {
+ drawActivityTruncatedShape(protein, graphics);
}
- } else if (alias instanceof ReceptorProtein) {
- shape = getReceptorShape(alias);
- if (alias.getActivity()) {
- drawActivityReceptorProtein(alias, graphics);
+ } else if (protein instanceof ReceptorProtein) {
+ shape = getReceptorShape(protein);
+ if (protein.getActivity()) {
+ drawActivityReceptorProtein(protein, graphics);
}
} else {
- logger.warn(eu.getElementTag(alias) + "Unknown shape for protein");
- shape = getDefaultAliasShape(alias);
+ logger.warn(eu.getElementTag(protein) + "Unknown shape for protein");
+ shape = getDefaultAliasShape(protein);
}
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(protein.getColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(protein));
graphics.draw(shape);
graphics.setStroke(stroke);
// SBGN display mode - units of information and state variables are
// printed on the top element only
if (!sbgnFormat || (homodimerId == homodir - 1)) {
- for (ModificationResidue mr : alias.getModificationResidues()) {
+ for (ModificationResidue mr : protein.getModificationResidues()) {
// SBGN display mode - print empty state variables
- drawModification(alias, mr, graphics, sbgnFormat, false);
+ drawModification(protein, mr, graphics, sbgnFormat, false);
}
if (sbgnFormat) {
// SBGN display mode - ion channel's state is marked as a unit of
// information
- if (alias instanceof IonChannelProtein) {
+ if (protein instanceof IonChannelProtein) {
if (!unitOfInformationText.equals("")) {
unitOfInformationText = unitOfInformationText.concat("; ");
}
- if (alias.getActivity()) {
+ if (protein.getActivity()) {
unitOfInformationText = unitOfInformationText.concat("open");
} else {
unitOfInformationText = unitOfInformationText.concat("closed");
@@ -202,7 +204,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
if (!unitOfInformationText.equals("")) {
unitOfInformationText = unitOfInformationText.concat("; ");
}
- unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(alias.getHomodimer()));
+ unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(protein.getHomodimer()));
}
}
}
@@ -212,81 +214,81 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
unitOfInformationText = null;
}
- String text = alias.getStructuralState();
- drawStructuralState(text, alias, graphics);
- drawUnitOfInformation(unitOfInformationText, alias, graphics);
- drawText(alias, graphics, params);
- alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ String text = protein.getStructuralState();
+ drawStructuralState(text, protein, graphics);
+ drawUnitOfInformation(unitOfInformationText, protein, graphics);
+ drawText(protein, graphics, params);
+ protein.setWidth(protein.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+ protein.setHeight(protein.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
}
/**
* Draws activity border of {@link GenericProtein}.
*
- * @param alias
- * {@link Species} that will be drawn
+ * @param protein
+ * {@link Protein} that will be drawn
* @param graphics
* where we are drawing
*/
- private void drawActivityGenericProtein(final Protein alias, final Graphics2D graphics) {
+ private void drawActivityGenericProtein(final Protein protein, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
- alias.increaseBorder(border);
- Shape shape2 = getGenericShape(alias);
+ protein.increaseBorder(border);
+ Shape shape2 = getGenericShape(protein);
Stroke stroke = graphics.getStroke();
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(shape2);
graphics.setStroke(stroke);
- alias.increaseBorder(-border);
+ protein.increaseBorder(-border);
}
/**
* Draws activity border of {@link ReceptorProtein}.
*
- * @param alias
- * {@link Species} that will be drawn
+ * @param protein
+ * {@link Protein} that will be drawn
* @param graphics
* where we are drawing
*/
- public void drawActivityReceptorProtein(final Protein alias, final Graphics2D graphics) {
+ public void drawActivityReceptorProtein(final Protein protein, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
- alias.setX(alias.getX() - border);
- alias.setY(alias.getY() - border);
- alias.setWidth(alias.getWidth() + border * 2);
- alias.setHeight(alias.getHeight() + border * 2);
- Shape shape2 = getReceptorShape(alias);
+ protein.setX(protein.getX() - border);
+ protein.setY(protein.getY() - border);
+ protein.setWidth(protein.getWidth() + border * 2);
+ protein.setHeight(protein.getHeight() + border * 2);
+ Shape shape2 = getReceptorShape(protein);
Stroke stroke = graphics.getStroke();
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(shape2);
graphics.setStroke(stroke);
- alias.setX(alias.getX() + border);
- alias.setY(alias.getY() + border);
- alias.setWidth(alias.getWidth() - border * 2);
- alias.setHeight(alias.getHeight() - border * 2);
+ protein.setX(protein.getX() + border);
+ protein.setY(protein.getY() + border);
+ protein.setWidth(protein.getWidth() - border * 2);
+ protein.setHeight(protein.getHeight() - border * 2);
}
/**
* Draws activity border of {@link TruncatedProtein}.
*
- * @param alias
- * {@link Species} that will be drawn
+ * @param protein
+ * {@link Protein} that will be drawn
* @param graphics
* where we are drawing
*/
- public void drawActivityTruncatedShape(final Protein alias, final Graphics2D graphics) {
+ public void drawActivityTruncatedShape(final Protein protein, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
- alias.setX(alias.getX() - border);
- alias.setY(alias.getY() - border);
- alias.setWidth(alias.getWidth() + border * 2);
- alias.setHeight(alias.getHeight() + border * 2);
- Shape shape2 = getTruncatedShape(alias);
+ protein.setX(protein.getX() - border);
+ protein.setY(protein.getY() - border);
+ protein.setWidth(protein.getWidth() + border * 2);
+ protein.setHeight(protein.getHeight() + border * 2);
+ Shape shape2 = getTruncatedShape(protein);
Stroke stroke = graphics.getStroke();
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(shape2);
graphics.setStroke(stroke);
- alias.setX(alias.getX() + border);
- alias.setY(alias.getY() + border);
- alias.setWidth(alias.getWidth() - border * 2);
- alias.setHeight(alias.getHeight() - border * 2);
+ protein.setX(protein.getX() + border);
+ protein.setY(protein.getY() + border);
+ protein.setWidth(protein.getWidth() - border * 2);
+ protein.setHeight(protein.getHeight() - border * 2);
}
/**
@@ -295,7 +297,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
* set then also description (position) of the modification is drawn on the
* canvas.
*
- * @param alias
+ * @param protein
* object that is 'parent' of the residue
* @param mr
* modification to be drawn
@@ -307,7 +309,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final Protein alias, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Protein protein, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
if ((!drawEmptyModification) && (mr.getState() == null)) {
return;
@@ -321,7 +323,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
angle -= Math.PI * 2;
}
- Point2D p = getResidueCoordinates(alias, mr.getAngle());
+ Point2D p = getResidueCoordinates(protein, mr.getAngle());
Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
Color c = graphics.getColor();
graphics.setColor(Color.WHITE);
@@ -332,9 +334,9 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
String text = mr.getName();
if (!text.equals("") && drawDescription) {
- alias.increaseBorder(-diameter / 2);
- Point2D p2 = getResidueCoordinates(alias, mr.getAngle());
- alias.increaseBorder(diameter / 2);
+ protein.increaseBorder(-diameter / 2);
+ Point2D p2 = getResidueCoordinates(protein, mr.getAngle());
+ protein.increaseBorder(diameter / 2);
double width = graphics.getFontMetrics().stringWidth(text);
double height = graphics.getFontMetrics().getHeight();
@@ -368,14 +370,14 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
/**
* Returns shape of receptor protein.
*
- * @param alias
+ * @param protein
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getReceptorShape(final Element alias) {
+ protected Shape getReceptorShape(final Protein protein) {
Shape shape;
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
- ArrayList<Point2D> points = getReceptorPoints(alias);
+ ArrayList<Point2D> points = getReceptorPoints(protein);
path.moveTo(points.get(0).getX(), points.get(0).getY());
for (int i = 1; i < points.size(); i++) {
path.lineTo(points.get(i).getX(), points.get(i).getY());
@@ -388,25 +390,25 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
/**
* Returns shape of truncated protein.
*
- * @param alias
+ * @param protein
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getTruncatedShape(final Element alias) {
+ protected Shape getTruncatedShape(final Protein protein) {
Shape shape;
GeneralPath path = new GeneralPath();
// CHECKSTYLE:OFF
- path.moveTo(alias.getX() + 10, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() * 3 / 5);
- path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight() * 2 / 5);
- path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + 10, alias.getY() + alias.getHeight());
+ path.moveTo(protein.getX() + 10, protein.getY());
+ path.lineTo(protein.getX() + protein.getWidth(), protein.getY());
+ path.lineTo(protein.getX() + protein.getWidth(), protein.getY() + protein.getHeight() * 3 / 5);
+ path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight() * 2 / 5);
+ path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight());
+ path.lineTo(protein.getX() + 10, protein.getY() + protein.getHeight());
path.curveTo(
- alias.getX() + 5, alias.getY() + alias.getHeight() - 2, alias.getX() + 2, alias.getY() + alias.getHeight() - 5, alias.getX(),
- alias.getY() + alias.getHeight() - 10);
- path.lineTo(alias.getX(), alias.getY() + 10);
- path.curveTo(alias.getX() + 2, alias.getY() + 5, alias.getX() + 5, alias.getY() + 2, alias.getX() + 10, alias.getY());
+ protein.getX() + 5, protein.getY() + protein.getHeight() - 2, protein.getX() + 2, protein.getY() + protein.getHeight() - 5, protein.getX(),
+ protein.getY() + protein.getHeight() - 10);
+ path.lineTo(protein.getX(), protein.getY() + 10);
+ path.curveTo(protein.getX() + 2, protein.getY() + 5, protein.getX() + 5, protein.getY() + 2, protein.getX() + 10, protein.getY());
// CHECKSTYLE:ON
path.closePath();
@@ -417,15 +419,15 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
/**
* Returns shape of receptor protein as a list of points.
*
- * @param alias
+ * @param protein
* alias for which we are looking for a border
* @return list of points defining border of the given alias
*/
- private ArrayList<Point2D> getReceptorPoints(final Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
+ private ArrayList<Point2D> getReceptorPoints(final Protein protein) {
+ double x = protein.getX();
+ double y = protein.getY();
+ double width = protein.getWidth();
+ double height = protein.getHeight();
ArrayList<Point2D> points = new ArrayList<Point2D>();
// CHECKSTYLE:OFF
@@ -443,17 +445,17 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
}
@Override
- public PathIterator getBoundPathIterator(final Protein alias) {
- if (alias instanceof GenericProtein) {
- return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof ReceptorProtein) {
- return getReceptorShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof IonChannelProtein) {
- return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof TruncatedProtein) {
- return getTruncatedShape(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(final Protein protein) {
+ if (protein instanceof GenericProtein) {
+ return getGenericShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof ReceptorProtein) {
+ return getReceptorShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof IonChannelProtein) {
+ return getGenericShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof TruncatedProtein) {
+ return getTruncatedShape(protein).getPathIterator(new AffineTransform());
} else {
- throw new InvalidArgumentException("Not implemented protein converter for type: " + alias.getClass());
+ throw new InvalidArgumentException("Not implemented protein converter for type: " + protein.getClass());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index 277a8afc651d80665eaf652fd9d4dae4622926b4..bf0b0533f521cf4572b7b00fdcca619f978c9263 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -1,10 +1,10 @@
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
+/**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
@@ -23,7 +23,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -55,46 +54,46 @@ public class RnaConverter extends SpeciesConverter<Rna> {
}
@Override
- public void draw(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getRnaPath(alias);
+ public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getRnaPath(rna);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(rna.getColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(rna));
graphics.draw(path);
graphics.setStroke(stroke);
- for (RnaRegion mr : alias.getRegions()) {
- drawModification(alias, mr, graphics, false, false);
+ for (RnaRegion mr : rna.getRegions()) {
+ drawModification(rna, mr, graphics, false, false);
}
- drawText(alias, graphics, params);
+ drawText(rna, graphics, params);
}
/**
- * Returns shape of the Rna as a GeneralPath object.
+ * Returns shape of the {@link Rna} as a {@link GeneralPath} object.
*
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
+ * @param 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 Element alias) {
+ private GeneralPath getRnaPath(final Rna rna) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
+ path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth(), rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth() * 3 / 4, rna.getY() + rna.getHeight());
+ path.lineTo(rna.getX(), rna.getY() + rna.getHeight());
// CHECKSTYLE:ON
path.closePath();
return path;
}
@Override
- public PathIterator getBoundPathIterator(final Rna alias) {
- return getRnaPath(alias).getPathIterator(new AffineTransform());
+ public PathIterator getBoundPathIterator(final Rna rna) {
+ return getRnaPath(rna).getPathIterator(new AffineTransform());
}
/**
@@ -103,10 +102,10 @@ public class RnaConverter extends SpeciesConverter<Rna> {
* set then also description (position) of the modification is drawn on the
* canvas.
*
- * @param alias
+ * @param rna
* object that is 'parent' of the residue
- * @param mr
- * modification to be drawn
+ * @param region
+ * {@link RnaRegion modification} to be drawn
* @param graphics
* - where the modification should be drawn
* @param drawEmptyModification
@@ -115,22 +114,22 @@ public class RnaConverter extends SpeciesConverter<Rna> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final Rna alias, final RnaRegion mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Rna rna, final RnaRegion region, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
- if ((!drawEmptyModification) && (mr.getState() == null)) {
+ if ((!drawEmptyModification) && (region.getState() == null)) {
return;
}
double diameter = DEFAULT_MODIFICATION_DIAMETER;
- double x = alias.getX();
- double y = alias.getY();
+ double x = rna.getX();
+ double y = rna.getY();
- double width = alias.getWidth();
+ double width = rna.getWidth();
// CHECKSTYLE:OFF
// we draw modifier on the upper border of rna (which is only in
// 3/4 of the width of alias, but starts in 1/4 of the width)
- Point2D p = new Point2D.Double(x + width / 4.0 + width * 3.0 / 4.0 * mr.getPos(), y - DEFAULT_MODIFICATION_DIAMETER);
+ Point2D p = new Point2D.Double(x + width / 4.0 + width * 3.0 / 4.0 * region.getPos(), y - DEFAULT_MODIFICATION_DIAMETER);
// CHECKSTYLE:ON
Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
@@ -141,13 +140,13 @@ public class RnaConverter extends SpeciesConverter<Rna> {
graphics.draw(ellipse);
graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
- String text = mr.getName();
+ String text = region.getName();
if (!text.equals("") && drawDescription) {
double textWidth = graphics.getFontMetrics().stringWidth(text);
Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
}
- ModificationState state = mr.getState();
+ ModificationState state = region.getState();
if (state != null) {
String str = state.getAbbreviation();
Font tmpFont = graphics.getFont();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
index 5412c1b961a4f388bf754aea9e8452528312722c..cd82b37bc9e91e2e3aba4f947c688f2de3ec4d73 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
@@ -11,11 +11,10 @@ import java.awt.geom.PathIterator;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines methods used for drawing SpeciesAlias of nucleic acid
+ * This class defines methods used for drawing {@link Species} of nucleic acid
* feature in the SBGN way on the {@link Graphics2D} object.
*
* @author Michał Kuźma
@@ -44,13 +43,13 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
/**
* Returns shape of SBGN Nucleic acid feature.
*
- * @param alias
- * alias for which the shape should be returned
+ * @param 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 Element alias) {
+ private Shape getShape(final Species species) {
GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+ double x = species.getX(), y = species.getY(), width = species.getWidth(), height = species.getHeight();
bottomRoundedRectangle.moveTo(x, y);
bottomRoundedRectangle.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
@@ -64,24 +63,24 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
}
@Override
- public void draw(Species alias, Graphics2D graphics, ConverterParams params) {
+ public void draw(Species species, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
- if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
- if (alias.getStatePrefix().equals("free input")) {
- unitOfInformationText = alias.getStateLabel();
+ if (species.getStatePrefix() != null && species.getStateLabel() != null) {
+ if (species.getStatePrefix().equals("free input")) {
+ unitOfInformationText = species.getStateLabel();
} else {
- unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
+ unitOfInformationText = species.getStatePrefix() + ":" + species.getStateLabel();
}
}
- int homodir = alias.getHomodimer();
+ int homodir = species.getHomodimer();
- alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ species.setWidth(species.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
+ species.setHeight(species.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
- alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
- alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
+ species.setX(species.getX() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
+ species.setY(species.getY() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
int glyphCount;
if (homodir > 1) {
@@ -90,18 +89,18 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
glyphCount = 1;
}
for (int i = 0; i < glyphCount; i++) {
- alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+ species.setX(species.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ species.setY(species.getY() - SpeciesConverter.HOMODIMER_OFFSET);
- Shape shape = getShape(alias);
+ Shape shape = getShape(species);
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(species.getColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(species));
graphics.draw(shape);
graphics.setStroke(stroke);
@@ -118,16 +117,16 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
}
- drawUnitOfInformation(unitOfInformationText, alias, graphics);
- drawText(alias, graphics, params);
+ drawUnitOfInformation(unitOfInformationText, species, graphics);
+ drawText(species, graphics, params);
- alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ species.setWidth(species.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ species.setHeight(species.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
}
@Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return getShape(alias).getPathIterator(new AffineTransform());
+ protected PathIterator getBoundPathIterator(Species species) {
+ return getShape(species).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
index 8abca141bd11232bed19933a0737079b56a8c016..8ce04bcc3d88e37d14e34c3f439c3cf2f9bd26c0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
@@ -18,8 +18,8 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines methods used for drawing {@link SimpleMolecule} on
- * the {@link Graphics2D} object.
+ * This class defines methods used for drawing {@link SimpleMolecule} on the
+ * {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -42,42 +42,42 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
}
@Override
- public void draw(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
// glyphs
- if (alias.getHomodimer() > 1) {
+ if (simpleMolecule.getHomodimer() > 1) {
homodir = 2;
} else {
homodir = 1;
}
} else {
- homodir = alias.getHomodimer();
+ homodir = simpleMolecule.getHomodimer();
}
- alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ simpleMolecule.setWidth(simpleMolecule.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ simpleMolecule.setHeight(simpleMolecule.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
// SBGN view - simple molecules are represented as circles
if (params.isSbgnFormat()) {
- alias.setX(alias.getX() + (alias.getWidth() - alias.getHeight()) / 2);
- alias.setWidth(alias.getHeight());
+ simpleMolecule.setX(simpleMolecule.getX() + (simpleMolecule.getWidth() - simpleMolecule.getHeight()) / 2);
+ simpleMolecule.setWidth(simpleMolecule.getHeight());
}
- alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ simpleMolecule.setX(simpleMolecule.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ simpleMolecule.setY(simpleMolecule.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
for (int i = 0; i < homodir; i++) {
- alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
- Shape shape = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ simpleMolecule.setX(simpleMolecule.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ simpleMolecule.setY(simpleMolecule.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+ Shape shape = new Ellipse2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(), simpleMolecule.getHeight());
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(simpleMolecule.getColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(simpleMolecule));
graphics.draw(shape);
graphics.setStroke(stroke);
@@ -85,8 +85,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
// containing cardinality
if (params.isSbgnFormat() && (i == homodir - 1)) {
String unitOfInformationText = null;
- if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
- unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
+ if (simpleMolecule.getStatePrefix() != null && simpleMolecule.getStateLabel() != null) {
+ unitOfInformationText = simpleMolecule.getStatePrefix() + ":" + simpleMolecule.getStateLabel();
}
if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
if (unitOfInformationText != null) {
@@ -94,30 +94,31 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
} else {
unitOfInformationText = "";
}
- unitOfInformationText += "N:" + alias.getHomodimer();
+ unitOfInformationText += "N:" + simpleMolecule.getHomodimer();
}
- drawUnitOfInformation(unitOfInformationText, alias, graphics);
+ drawUnitOfInformation(unitOfInformationText, simpleMolecule, graphics);
}
}
- alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- drawText(alias, graphics, params);
+ simpleMolecule.setWidth(simpleMolecule.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ simpleMolecule.setHeight(simpleMolecule.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ drawText(simpleMolecule, graphics, params);
}
@Override
- public PathIterator getBoundPathIterator(final SimpleMolecule alias) {
+ public PathIterator getBoundPathIterator(final SimpleMolecule simpleMolecule) {
throw new InvalidStateException("This class doesn't provide boundPath");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final SimpleMolecule alias, final double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ public Point2D getPointCoordinatesOnBorder(final SimpleMolecule simpleMolecule, final double angle) {
+ if (simpleMolecule.getWidth() == 0 && simpleMolecule.getHeight() == 0) {
logger.warn("Looking for coordinates on border of alias of size 0");
- return alias.getCenter();
+ return simpleMolecule.getCenter();
}
Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
+ result = getEllipseTransformation()
+ .getPointOnEllipseByRadian(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(), simpleMolecule.getHeight(), angle);
return result;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index fb2460619fcd85d355aac51b301c351525d48b53..2bf368852c188ceceb829c2009a4541d6007d2df 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -16,7 +16,6 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
@@ -27,22 +26,19 @@ import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines basics used for drawing aliases of {@link Species} (node
- * in the graph representation) on the graphics2d object.
+ * This class defines basics used for drawing {@link Species} (node in the graph
+ * representation) on the {@link Graphics2D} object.
*
* @param <T>
- * alias class that can be drawn with this converter
+ * type of {@link Species} class that can be drawn with this converter
* @author Piotr Gawron
*
*/
public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
/**
* PI value.
*/
@@ -167,45 +163,47 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
};
/**
- * Returns coordinates on the alias border for given angle.
+ * Returns coordinates on the {@link Species} border for given angle.
*
- * @param alias
- * object on border which the point is looked for
+ * @param species
+ * {@link Species} on border which the point is looked for
* @param angle
- * angle between X axis center point of alias and point that we are
- * looking for
- * @return coordinates on the alias border that correspond to the angle
+ * angle between X axis center point of {@link Species} and point
+ * that we are looking for
+ * @return coordinates on the {@link Species} border that correspond to the
+ * angle
*/
- protected Point2D getPointCoordinatesOnBorder(final T alias, final double angle) {
+ protected Point2D getPointCoordinatesOnBorder(final T species, final double angle) {
Point2D result = null;
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- result = alias.getCenter();
+ if (species.getWidth() == 0 && species.getHeight() == 0) {
+ result = species.getCenter();
} else {
- double dist = Math.max(alias.getWidth(), alias.getHeight()) * 2;
- Point2D startPoint = alias.getCenter();
+ double dist = Math.max(species.getWidth(), species.getHeight()) * 2;
+ Point2D startPoint = species.getCenter();
double x = startPoint.getX() + Math.cos(angle) * dist;
double y = startPoint.getY() - Math.sin(angle) * dist;
Point2D endPoint = new Point2D.Double(x, y);
Line2D line = new Line2D.Double(startPoint, endPoint);
- result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(alias));
+ result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(species));
}
return result;
}
/**
- * Returns coordinates on the alias border for given angle for residues.
+ * Returns coordinates on the {@link Species} border for given angle for
+ * residues.
*
- * @param alias
+ * @param species
* object on border which the point is looked for
* @param angle
* CellDEsigner specific angle defining coordinates (;/)
* @return coordinates on the alias border that correspond to the angle
*/
- protected Point2D getResidueCoordinates(final T alias, double angle) {
+ protected Point2D getResidueCoordinates(final T species, double angle) {
Point2D result = null;
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- result = alias.getCenter();
+ if (species.getWidth() == 0 && species.getHeight() == 0) {
+ result = species.getCenter();
} else {
double x = 0;
double y = 0;
@@ -219,74 +217,76 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
// CHECKSTYLE:OFF 0.5 is much readable than any other suggestion
double ratio = 0.5 + angle / (PI / 2);
// CHECKSTYLE:ON
- x = alias.getX() + alias.getWidth();
- y = alias.getY() + alias.getHeight() * (1 - ratio);
+ x = species.getX() + species.getWidth();
+ y = species.getY() + species.getHeight() * (1 - ratio);
} else if (angle < TOP_RESIDUE_MAX_ANGLE) {
double ratio = (angle - RIGHT_TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = alias.getY();
- x = alias.getX() + alias.getWidth() * (1 - ratio);
+ y = species.getY();
+ x = species.getX() + species.getWidth() * (1 - ratio);
} else if (angle < LEFT_RESIDUE_MAX_ANGLE) {
double ratio = (angle - TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = alias.getY() + alias.getHeight() * (ratio);
- x = alias.getX();
+ y = species.getY() + species.getHeight() * (ratio);
+ x = species.getX();
} else if (angle < BOTTOM_RESIDUE_MAX_ANGLE) {
double ratio = (angle - LEFT_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = alias.getY() + alias.getHeight();
- x = alias.getX() + alias.getWidth() * ratio;
+ y = species.getY() + species.getHeight();
+ x = species.getX() + species.getWidth() * ratio;
} else if (angle <= 2 * PI + Configuration.EPSILON) {
double ratio = (angle - BOTTOM_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = alias.getY() + alias.getHeight() * (1 - ratio);
- x = alias.getX() + alias.getWidth();
+ y = species.getY() + species.getHeight() * (1 - ratio);
+ x = species.getX() + species.getWidth();
} else {
throw new InvalidStateException();
}
- Point2D center = alias.getCenter();
+ Point2D center = species.getCenter();
double correctedAngle = -Math.atan2((y - center.getY()), (x - center.getX()));
- result = getPointCoordinatesOnBorder(alias, correctedAngle);
+ result = getPointCoordinatesOnBorder(species, correctedAngle);
}
return result;
}
/**
- * Returns default shape of the alias.
+ * Returns default shape of the {@link Species}.
*
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
+ * @param species
+ * {@link Species} for which we are looking for a border
+ * @return {@link Shape} object defining given {@link Species}
*/
- protected Shape getDefaultAliasShape(final Element alias) {
+ protected Shape getDefaultAliasShape(final Species species) {
Shape shape;
- shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
+ shape = new Rectangle(species.getX().intValue(), species.getY().intValue(), species.getWidth().intValue(), species.getHeight().intValue());
return shape;
}
/**
- * Returns font that should be used for drawing description of the alias.
+ * Returns font that should be used for drawing description of the
+ * {@link Species}.
*
- * @param alias
- * alias for which we are looking for a font
+ * @param species
+ * {@link Species} for which we are looking for a font
* @param params
* specific drawing parameters (like scale)
- * @return Font that should be used for drawing alias description
+ * @return {@link Font} that should be used for drawing {@link Species}
+ * description
*/
- protected Font getFont(final Element alias, ConverterParams params) {
+ protected Font getFont(final Species species, ConverterParams params) {
double fontSize = DEFAULT_SPECIES_FONT_SIZE;
- if (alias.getFontSize() != null) {
- fontSize = alias.getFontSize();
+ if (species.getFontSize() != null) {
+ fontSize = species.getFontSize();
}
return new Font(Font.SANS_SERIF, 0, (int) (fontSize * params.getScale()));
}
/**
- * Returns text describing alias.
+ * Returns text describing {@link Species}.
*
- * @param alias
+ * @param species
* object under investigation
- * @return description of the alias
+ * @return description of the {@link Species}
*/
- protected String getText(final T alias) {
- String name = alias.getName();
+ protected String getText(final T species) {
+ String name = species.getName();
if (name.equals("")) {
name = " ";
}
@@ -295,18 +295,18 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
@Override
- public void drawText(final T alias, final Graphics2D graphics, final ConverterParams params) {
- String text = getText(alias);
+ public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
+ String text = getText(species);
Font oldFont = graphics.getFont();
- Font font = getFont(alias, params);
+ Font font = getFont(species, params);
graphics.setColor(Color.BLACK);
graphics.setFont(font);
- Point2D point = alias.getCenter();
- if (alias instanceof Complex) {
- if (((Complex) alias).getElements().size() > 0) {
- if (zoomLevelMatcher.isTransparent(params.getLevel(), alias.getTransparencyLevel())) {
- point.setLocation(point.getX(), alias.getY() + alias.getHeight() - graphics.getFontMetrics().getAscent());
+ Point2D point = species.getCenter();
+ if (species instanceof Complex) {
+ if (((Complex) species).getElements().size() > 0) {
+ if (isTransparent(species, params)) {
+ point.setLocation(point.getX(), species.getY() + species.getHeight() - graphics.getFontMetrics().getAscent());
}
}
}
@@ -403,19 +403,19 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Returns line style used for drawing alias border.
*
- * @param alias
- * alias to be drawn
- * @return style of the line used to draw alias
+ * @param species
+ * {@link Species} to be drawn
+ * @return style of the line used to draw {@link Species}
*/
- protected Stroke getBorderLine(final Species alias) {
- if (!alias.isHypothetical()) {
- if (alias instanceof Complex) {
+ protected Stroke getBorderLine(final Species species) {
+ if (!species.isHypothetical()) {
+ if (species instanceof Complex) {
return LineType.SOLID_BOLD.getStroke();
} else {
return LineType.SOLID.getStroke();
}
} else {
- if (alias instanceof Complex) {
+ if (species instanceof Complex) {
return LineType.DASHED_BOLD.getStroke();
} else {
return LineType.DASHED.getStroke();
@@ -424,13 +424,13 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
/**
- * Returns border of the alias as PathIterator.
+ * Returns border of the {@link Species} as {@link PathIterator}.
*
- * @param alias
- * alias for which we are looking for a border
- * @return PathIterator object defining given alias
+ * @param species
+ * {@link Species} for which we are looking for a border
+ * @return {@link PathIterator} object defining given {@link Species}
*/
- protected abstract PathIterator getBoundPathIterator(T alias);
+ protected abstract PathIterator getBoundPathIterator(T species);
/**
* @return the lineTransformation
@@ -498,23 +498,23 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
*
* @param text
* state description text
- * @param alias
- * state description should be drawn on this alias
+ * @param species
+ * state description should be drawn on this {@link Species}
* @param graphics
* where the drawing should be performed
*/
- protected void drawStructuralState(String text, T alias, final Graphics2D graphics) {
+ protected void drawStructuralState(String text, T species, final Graphics2D graphics) {
if (text == null) {
return;
}
- Point2D p = getPointCoordinatesOnBorder(alias, Math.PI / 2);
+ Point2D p = getPointCoordinatesOnBorder(species, Math.PI / 2);
double width = MIN_STRUCTURAL_STATE_WIDTH;
if (!text.trim().equals("")) {
width = Math.max(MIN_STRUCTURAL_STATE_WIDTH, graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC);
}
- width = Math.min(width, alias.getWidth());
+ width = Math.min(width, species.getWidth());
double height = STRUCTURAL_STATE_HEIGHT;
Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
@@ -537,28 +537,28 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
/**
- * Draws unit of information for the alias (rectangle in the top part of the
- * alias).
+ * Draws unit of information for the {@link Species} (rectangle in the top
+ * part of the alias).
*
* @param text
* unit of information text
- * @param alias
- * unit of information should be drawn on this alias
+ * @param species
+ * unit of information should be drawn on this {@link Species}
* @param graphics
* where the drawing should be performed
*/
- protected void drawUnitOfInformation(String text, T alias, final Graphics2D graphics) {
+ protected void drawUnitOfInformation(String text, T species, final Graphics2D graphics) {
if (text == null) {
return;
}
- Point2D p = getPointCoordinatesOnBorder(alias, Math.PI / 2);
+ Point2D p = getPointCoordinatesOnBorder(species, Math.PI / 2);
double width = MIN_UNIT_OF_INFORMATION_WIDTH;
if (!text.trim().equals("")) {
width = Math.max(MIN_UNIT_OF_INFORMATION_WIDTH, graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC);
}
- width = Math.min(width, alias.getWidth());
+ width = Math.min(width, species.getWidth());
double height = UNIT_OF_INFORMATION_HEIGHT;
Rectangle2D rectangle = new Rectangle2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
@@ -580,24 +580,24 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
@Override
- public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- draw(alias, graphics, params);
+ public void draw(T species, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ draw(species, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
- double width = alias.getWidth() / visualizedLayoutsColorSchemas.size();
+ double width = species.getWidth() / visualizedLayoutsColorSchemas.size();
for (ColorSchema schema : visualizedLayoutsColorSchemas) {
if (schema != null) {
double startX = (double) count / (double) visualizedLayoutsColorSchemas.size();
graphics.setColor(Color.BLACK);
- int x = (int) (startX * alias.getWidth() + alias.getX());
- graphics.drawRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
+ int x = (int) (startX * species.getWidth() + species.getX());
+ graphics.drawRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
Color color = colorExtractor.getNormalizedColor(schema);
Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
graphics.setColor(bgAlphaColor);
- graphics.fillRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
+ graphics.fillRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
}
count++;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
index e304953c08b75d94805cb84ae052e4c912611228..8103b5141e06e83004616ac0ccd9e8941fdd2e97 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
@@ -19,9 +19,8 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Unknown
- * Unknown} on the {@link Graphics2D} object.
+ * This class defines methods used for drawing {@link Unknown} on the
+ * {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -45,41 +44,39 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
}
@Override
- public void draw(Unknown alias, final Graphics2D graphics, final ConverterParams params) {
- if (alias.getActivity()) {
+ public void draw(Unknown unknown, final Graphics2D graphics, final ConverterParams params) {
+ if (unknown.getActivity()) {
int border = ACTIVITY_BORDER_DISTANCE;
- alias.increaseBorder(border);
- Shape shape2 = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ unknown.increaseBorder(border);
+ Shape shape2 = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
Stroke stroke = graphics.getStroke();
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(shape2);
graphics.setStroke(stroke);
- alias.increaseBorder(-border);
+ unknown.increaseBorder(-border);
}
- Shape shape = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ Shape shape = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
+ graphics.setColor(unknown.getColor());
graphics.fill(shape);
graphics.setColor(c);
- drawText(alias, graphics, params);
+ drawText(unknown, graphics, params);
}
@Override
- public PathIterator getBoundPathIterator(Unknown alias) {
+ public PathIterator getBoundPathIterator(Unknown unknown) {
throw new InvalidStateException("This class doesn't provide boundPath");
}
@Override
- public Point2D getPointCoordinatesOnBorder(Unknown alias, final double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ public Point2D getPointCoordinatesOnBorder(Unknown unknown, final double angle) {
+ if (unknown.getWidth() == 0 && unknown.getHeight() == 0) {
logger.warn("Looking for coordinates for unknown of 0 size");
- return alias.getCenter();
+ return unknown.getCenter();
}
Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
+ result = getEllipseTransformation().getPointOnEllipseByRadian(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight(), angle);
return result;
-
}
-
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
index 474275f24240426e29992f8e95fb33107f37f06b..48de38bd017c4be0b12050ec89d03c1a3dfae26f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
@@ -8,13 +8,13 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import org.apache.log4j.Logger;
-
/**
* This class allows to find free space where description should appear for the
* alias in hierarchical view.
@@ -24,6 +24,11 @@ import org.apache.log4j.Logger;
*/
public class PlaceFinder {
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
@@ -339,24 +344,27 @@ public class PlaceFinder {
}
/**
- * This method looks for a place to put description of the alias on the map.
+ * This method looks for a place to put description of the {@link Compartment}
+ * on the map.
*
- * @param alias
- * alias for which we try to determine text position
+ * @param compartment
+ * {@link Compartment} for which we try to determine text position
+ * @param level
+ * level at which we will visualize element
* @return bounds where text could be put
*/
- public Rectangle2D getRetangle(Compartment alias, int level) {
- Map<Integer, List<Compartment>> lists = otherAliases.get(alias);
+ public Rectangle2D getRetangle(Compartment compartment, int level) {
+ Map<Integer, List<Compartment>> lists = otherAliases.get(compartment);
if (lists == null) {
lists = new HashMap<>();
- otherAliases.put(alias, lists);
+ otherAliases.put(compartment, lists);
}
List<Compartment> list = lists.get(level);
if (list == null) {
list = new ArrayList<Compartment>();
for (Compartment compAlias : model.getCompartments()) {
if (zoomLevelMatcher.isVisible(level, compAlias.getVisibilityLevel()) && !zoomLevelMatcher.isTransparent(level, compAlias.getTransparencyLevel())) {
- if (compAlias.cross(alias) && compAlias.getSize() <= alias.getSize()) {
+ if (compAlias.cross(compartment) && compAlias.getSize() <= compartment.getSize()) {
list.add(compAlias);
}
}
@@ -364,13 +372,13 @@ public class PlaceFinder {
lists.put(level, list);
}
- this.mainAlias = alias;
+ this.mainAlias = compartment;
this.aliases = list;
- leftBound = alias.getX();
- rightBound = (alias.getX() + alias.getWidth());
- upBound = alias.getY();
- bottomBound = (alias.getY() + alias.getHeight());
+ leftBound = compartment.getX();
+ rightBound = (compartment.getX() + compartment.getWidth());
+ upBound = compartment.getY();
+ bottomBound = (compartment.getY() + compartment.getHeight());
createMatrix();