Merge branch '130-semantic-zoom' into 'master'

Basic semantic zooming functionality

See merge request !25

annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java

@@ -4,7 +4,6 @@ import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.net.ConnectException;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -85,8 +84,8 @@ public class WebPageDownloader {
 					urlConn.setRequestMethod("GET");
 					urlConn.addRequestProperty("User-Agent", "minerva-framework");
 					try {
-					urlConn.connect();
-					code = urlConn.getResponseCode();
+						urlConn.connect();
+						code = urlConn.getResponseCode();
 					} catch (FileNotFoundException e) {
 						code = HttpURLConnection.HTTP_NOT_FOUND;
 					} catch (IOException e) {

commons/src/main/java/lcsb/mapviewer/common/Configuration.java

@@ -67,6 +67,10 @@ public final class Configuration {
 	 * Where the main webpgae is located.
 	 */
 	public static final String	MAIN_PAGE																= "/index.xhtml";
+
+	/**
+	 * Name of the cookie for authentication token.
+	 */
 	public static final String	AUTH_TOKEN															= "MINERVA_AUTH_TOKEN";
 
 	/**

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java

@@ -5,6 +5,8 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies
 import lcsb.mapviewer.model.map.AnnotatedObject;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
 
 /**
  * Describes structural information that appears in the cell designer notes.
@@ -116,7 +118,12 @@ public enum NoteField {
 	/**
 	 * {@link Species#charge}.
 	 */
-	CHARGE("Charge", CellDesignerSpecies.class, null); //
+	CHARGE("Charge", CellDesignerSpecies.class, null), //
+
+	/**
+	 * {@link Element#getSemanticZoomLevelVisibility()}.
+	 */
+	SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", AnnotatedObject.class, null); //
 
 	/**
 	 * Name used in the notes to distinguish fields.

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -562,6 +562,28 @@ public class RestAnnotationParser extends XmlParser {
 		}
 	}
 
+	/**
+	 * Assigns semanticZoomingLevel to the element from notes string.
+	 * 
+	 * @param element
+	 *          element to which data should be put to
+	 * @param annotationString
+	 *          notes string
+	 */
+	private void setSemanticZoomLevelVisibility(AnnotatedObject element, String annotationString) {
+		String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
+		if (zoomLevelVisibility == null) {
+			return;
+		}
+		if (element.getSemanticZoomLevelVisibility() == null) {
+			element.setSemanticZoomLevelVisibility(zoomLevelVisibility);
+		} else if (!element.getSemanticZoomLevelVisibility().equals(zoomLevelVisibility)) {
+			logger.warn(
+					elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
+							+ zoomLevelVisibility + "][" + element.getSemanticZoomLevelVisibility() + "]. Ignoring.");
+		}
+	}
+
 	/**
 	 * Assigns notes to the element from notes string. This might look strange.
 	 * The idea is that sometimes we have notes from more then one source. And the
@@ -620,6 +642,7 @@ public class RestAnnotationParser extends XmlParser {
 		setNotes(object, ann);
 		setSymbol(object, ann);
 		setSynonyms(object, ann);
+		setSemanticZoomLevelVisibility(object, ann);
 		setAbbreviation(object, ann);
 		setFormula(object, ann);
 		if (object instanceof Reaction) {

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java

@@ -417,6 +417,18 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
 					// TODO Auto-generated method stub
 					return null;
 				}
+
+				@Override
+				public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+					// TODO Auto-generated method stub
+
+				}
+
+				@Override
+				public String getSemanticZoomLevelVisibility() {
+					// TODO Auto-generated method stub
+					return null;
+				}
 			});
 			fail("Exception expected");
 		} catch (NotImplementedException e) {

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -27,7 +27,7 @@ import org.sbgn.bindings.Sbgn;
 
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -28,7 +28,7 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.graphics.species.SpeciesConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
 import lcsb.mapviewer.converter.model.sbgnml.structures.Process;

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

@@ -16,8 +16,8 @@ import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
 import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
-import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -172,11 +172,16 @@ public abstract class AbstractImageGenerator {
 		 * Should the visualization include hierarchical view or not.
 		 */
 		private boolean												 nested					= false;
-		
+
+		/**
+		 * Should the visualization include semantic zoom view or not.
+		 */
+		private boolean												 semanticZoom		= false;
+
 		/**
 		 * Should sbgn standard be used.
 		 */
-		private boolean												 sbgn = false;
+		private boolean												 sbgn						= false;
 
 		/**
 		 * List of objects containging information about layouts visualized in the
@@ -208,6 +213,17 @@ public abstract class AbstractImageGenerator {
 			return this;
 		}
 
+		/**
+		 * @param semanticZoom
+		 *          semanticZoom to set
+		 * @return object with all parameters
+		 * @see #semanticZoom
+		 */
+		public Params semanticZoom(boolean semanticZoom) {
+			this.semanticZoom = semanticZoom;
+			return this;
+		}
+
 		/**
 		 * @param scale
 		 *          scale to set
@@ -561,7 +577,8 @@ public abstract class AbstractImageGenerator {
 		}
 
 		/**
-		 * @param sbgn the sbgn to set
+		 * @param sbgn
+		 *          the sbgn to set
 		 * @see #sbgn
 		 * @return object with all parameters
 		 */
@@ -659,13 +676,13 @@ public abstract class AbstractImageGenerator {
 			// compartment/complexes)
 			if (element instanceof Species) {
 				if (((Species) element).getComplex() == null) {
-					drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+					drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
 				}
 			}
 		}
 		// draw all reactions
 		for (Reaction reaction : params.getModel().getSortedReactions()) {
-			drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
+			drawReaction(reaction, params.getVisibleLayoutsForElement(reaction), params);
 		}
 		// draw all compartments
 		for (Compartment compartment : params.getModel().getSortedCompartments()) {
@@ -738,8 +755,8 @@ public abstract class AbstractImageGenerator {
 		}
 
 		// get a converter for this compartment
-		ElementConverterImpl converter = new ElementConverterImpl(compartment, colorExtractor);
-		ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level);
+		BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
+		ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).semanticZoomingOn(params.semanticZoom);
 
 		if (nested) {
 			compartmentParams.fill(fill).scale(Math.max(scale, 1));
@@ -749,7 +766,7 @@ public abstract class AbstractImageGenerator {
 		// standard compartment (not the pathway)
 		if (nested || !(compartment instanceof PathwayCompartment)) {
 			try {
-				converter.drawElement(compartment, graphics, compartmentParams, visibleLayouts);
+				converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
 			} catch (Exception e) {
 				throw new DrawingException(eu.getElementTag(compartment) + "Problem with drawing element.", e);
 			}
@@ -769,7 +786,7 @@ public abstract class AbstractImageGenerator {
 		for (Element element : result) {
 			// if a child is a standard species
 			if (element instanceof Species) {
-				drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+				drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
 			} else if (element instanceof Compartment) {
 				drawCompartment((Compartment) element, nested, params.getVisibleLayoutsForElement(element), params);
 			} else {
@@ -793,10 +810,12 @@ public abstract class AbstractImageGenerator {
 	 *          object to be drawn
 	 * @param visibleLayouts
 	 *          list of {@link ColorSchema} used for coloring species in layouts
+	 * @param params
+	 *          list of all params to create apropriate image
 	 * @throws DrawingException
 	 *           thrown when there was a problem with drawing a {@link Species}
 	 */
-	protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts) throws DrawingException {
+	protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
 
 		// The displaying of species is indicated by values of VisibilityLevel. If
 		// VisibilityLevel is big enough, then it is
@@ -825,14 +844,16 @@ public abstract class AbstractImageGenerator {
 		}
 
 		// at the beginning try to find an appropriate converter
-		ElementConverterImpl converter = new ElementConverterImpl(species, sbgnFormat, colorExtractor);
+		BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
 		double customScale = 1;
 		if (rescale) {
 			customScale = scale;
 		}
 		try {
-			converter
-					.drawElement(species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
+			converter.draw(
+					species, graphics,
+					new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom),
+					visibleLayouts);
 		} catch (Exception e) {
 			throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
 		}
@@ -847,7 +868,7 @@ public abstract class AbstractImageGenerator {
 				// depending on current zoom level, children are drawn or not
 				if (complex.getTransparencyLevel() <= level) {
 					for (Species a : complex.getElements()) {
-						drawSpecies(a, visibleLayouts);
+						drawSpecies(a, visibleLayouts, params);
 					}
 				}
 			}
@@ -861,13 +882,15 @@ public abstract class AbstractImageGenerator {
 	 *          object to be drawn
 	 * @param visibleLayouts
 	 *          list of {@link ColorSchema} used for coloring reaction in layouts
+	 * @param params
+	 *          list of all params to create apropriate image
 	 */
-	protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts) {
+	protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) {
 		if (!cross(reaction.getLines())) {
 			return;
 		}
-		ReactionConverter converter = new ReactionConverter(colorExtractor);
-		converter.drawReaction(reaction, graphics, sbgnFormat, visibleLayouts);
+		BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
+		converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom).level(level), visibleLayouts);
 	}
 
 	/**

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

@@ -11,28 +11,33 @@ public class ConverterParams {
 	 * Should the object be filled with the solid color. In other words it tells
 	 * us if the object is not transparent.
 	 */
-	private boolean fill				 = false;
+	private boolean	fill							= false;
 
 	/**
 	 * At which level the object is visualized. It helps to deterimine font size.
 	 * However it's possible that this value is not required.
 	 */
-	private int		 level				= 0;
+	private int			level							= 0;
 
 	/**
 	 * What is the scale. It allows to adjust font size to be readable.
 	 */
-	private double	scale				= 1;
+	private double	scale							= 1;
 
 	/**
 	 * Should the text describing element be centered or not.
 	 */
-	private boolean textCentered = false;
+	private boolean	textCentered			= false;
 
 	/**
 	 * Should the map be displayed in SBGN format.
 	 */
-	private boolean sbgnFormat	 = false;
+	private boolean	sbgnFormat				= false;
+
+	/**
+	 * Is the semantic zooming filtered.
+	 */
+	private boolean	semanticZoomingOn	= false;
 
 	/**
 	 * @param fill
@@ -56,6 +61,17 @@ public class ConverterParams {
 		return this;
 	}
 
+	/**
+	 * @param semanticZoomingOn
+	 *          the semanticZoomingOn to set
+	 * @return object with all parameters
+	 * @see #semanticZoomingOn
+	 */
+	public ConverterParams semanticZoomingOn(final boolean semanticZoomingOn) {
+		this.semanticZoomingOn = semanticZoomingOn;
+		return this;
+	}
+
 	/**
 	 * @param textCentered
 	 *          the textCentered to set
@@ -129,6 +145,14 @@ public class ConverterParams {
 		return sbgnFormat;
 	}
 
+	/**
+	 * @return the semanticZoomingOn
+	 * @see #semanticZoomingOn
+	 */
+	public boolean isSemanticZoomingOn() {
+		return semanticZoomingOn;
+	}
+
 	@Override
 	public String toString() {
 		String result = "[" + this.getClass().getSimpleName() + "] " + //
@@ -136,6 +160,7 @@ public class ConverterParams {
 				"level:" + level + "," + //
 				"scale:" + scale + "," + //
 				"textCentered:" + textCentered + "," + //
+				"semanticZoomingOn:" + semanticZoomingOn + "," + //
 				"sbgnFormat:" + sbgnFormat;
 		return result;
 	}

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

-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This interface defines what operations should be possible to convert
- * {@link Element} into a graphics on Graphics2D object.
- * 
- * @author Piotr Gawron
- * 
- * @param <T>
- *          class of alias to convert
- */
-public interface ElementConverter<T extends Element> {
-	/**
-	 * Alpha value (0..255) used for visualizing layout data that are normally
-	 * visualized in javascript.
-	 */
-	int LAYOUT_ALPHA = 200;
-
-	/**
-	 * This function draw representation of the alias on the graphics object.
-	 * 
-	 * @param alias
-	 *          alias that should be drawn
-	 * @param graphics
-	 *          where we want to draw alias
-	 * @param params
-	 *          visuzalization params (like, should the object be filled with
-	 *          solid color, etc.), for more information see
-	 *          {@link ConverterParams}
-	 * 
-	 */
-	void drawElement(T alias, Graphics2D graphics, ConverterParams params);
-
-	/**
-	 * This function draw representation of the alias on the graphics object.
-	 * 
-	 * @param alias
-	 *          alias that should be drawn
-	 * @param graphics
-	 *          where we want to draw alias
-	 * @param params
-	 *          visuzalization params (like, should the object be filled with
-	 *          solid color, etc.), for more information see
-	 *          {@link ConverterParams}
-	 * @param visualizedLayoutsColorSchemas
-	 *          list of {@link ColorSchema} that were used for visualizing this
-	 *          alias in different layouts that should be overlayed on the alias
-	 * 
-	 */
-	void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas);
-
-	/**
-	 * This function will find proper font size to display text within it. Then it
-	 * will print this text.
-	 * 
-	 * @param alias
-	 *          alias 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 alias
-	 */
-	void drawText(T alias, Graphics2D graphics, ConverterParams params) throws DrawingException;
-
-}

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

@@ -57,21 +57,25 @@ public class MapGenerator {
 		 * Do we want to generate images in hierarchical view or normal.
 		 * 
 		 */
-		private boolean					 nested			 = false;
+		private boolean					 nested				= false;
+		/**
+		 * Do we want to generate images with semantic zoom view or not.
+		 */
+		private boolean					 semanticZoom	= false;
 		/**
 		 * Should we remove empty elements in nested view.
 		 * 
 		 */
-		private boolean					 removeEmpty = false;
+		private boolean					 removeEmpty	= false;
 		/**
 		 * Callback function that update progress information.
 		 * 
 		 */
-		private IProgressUpdater updater		 = new IProgressUpdater() {
-																					 @Override
-																					 public void setProgress(double progress) {
-																					 }
-																				 };
+		private IProgressUpdater updater			= new IProgressUpdater() {
+																						@Override
+																						public void setProgress(double progress) {
+																						}
+																					};
 
 		/**
 		 * Zoom factor on the lowest level.
@@ -135,6 +139,17 @@ public class MapGenerator {
 			return this;
 		}
 
+		/**
+		 * @param semanticZoom
+		 *          the semanticZoom to set
+		 * @see #nested
+		 * @return full {@link MapGeneratorParams} object
+		 */
+		public MapGeneratorParams semanticZoom(boolean semanticZoom) {
+			this.semanticZoom = semanticZoom;
+			return this;
+		}
+
 		/**
 		 * @return the removeEmpty
 		 * @see #removeEmpty
@@ -326,6 +341,8 @@ public class MapGenerator {
 						imgParams.height(TILE_SIZE * TILES_CACHE_NUM);
 						imgParams.model(params.model);
 						imgParams.sbgn(params.sbgn);
+						imgParams.level(i);
+						imgParams.semanticZoom(params.semanticZoom);
 
 						if (params.nested) {
 							imgParams.level(i).nested(params.nested);

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

+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import java.awt.Graphics2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link AnnotatedObject} into a graphics on Graphics2D object.
+ * 
+ * @author Piotr Gawron
+ * 
+ * @param <T>
+ *          class of alias to convert
+ */
+public abstract class BioEntityConverter<T extends AnnotatedObject> {
+
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private final Logger		logger			 = Logger.getLogger(BioEntityConverter.class);
+
+	/**
+	 * Alpha value (0..255) used for visualizing overlay data that are normally
+	 * visualized in javascript.
+	 */
+	public static final int	LAYOUT_ALPHA = 200;
+
+	/**
+	 * This function draw representation of the alias on the graphics object.
+	 * 
+	 * @param bioEntity
+	 *          {@link AnnotatedObject} that should be drawn
+	 * @param graphics
+	 *          where we want to draw bioEntity
+	 * @param params
+	 *          visuzalization params (like, should the object be filled with
+	 *          solid color, etc.), for more information see
+	 *          {@link ConverterParams}
+	 * 
+	 */
+	public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) {
+		draw(bioEntity, graphics, params, new ArrayList<>());
+	}
+
+	/**
+	 * This function draw representation of the alias on the graphics object.
+	 * 
+	 * @param bioEntity
+	 *          {@link AnnotatedObject} that should be drawn
+	 * @param graphics
+	 *          where we want to draw bioEntity
+	 * @param params
+	 *          visuzalization params (like, should the object be filled with
+	 *          solid color, etc.), for more information see
+	 *          {@link ConverterParams}
+	 * @param visualizedOverlaysColorSchemas
+	 *          list of {@link ColorSchema} that were used for visualizing this
+	 *          bioentity in different data overlays that should be overlayed on
+	 *          the alias
+	 * 
+	 */
+	public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas);
+
+	/**
+	 * 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
+	 * @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
+	 */
+	public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+
+	/**
+	 * Checks if {@link AbstractNode} is visible according to visualization given
+	 * in params.
+	 * 
+	 * @param node
+	 *          visibility of this object will be checked
+	 * @param params
+	 *          visualization params
+	 * @return true if object is visible
+	 */
+	protected boolean isVisible(AbstractNode node, ConverterParams params) {
+		if (node instanceof NodeOperator) {
+			return isVisible((NodeOperator) node, params);
+		} else if (node instanceof ReactionNode) {
+			return isVisible(((ReactionNode) node).getElement(), params);
+		} else {
+			throw new InvalidArgumentException("Unknown class type: " + node.getClass());
+		}
+	}
+
+	/**
+	 * Checks if {@link NodeOperator} is visible according to visualization given
+	 * in params.
+	 * 
+	 * @param operator
+	 *          visibility of this object will be checked
+	 * @param params
+	 *          visualization params
+	 * @return true if object is visible
+	 */
+	protected boolean isVisible(NodeOperator operator, ConverterParams params) {
+		boolean result = false;
+		if (operator.isModifierOperator() || operator.isReactantOperator()) {
+			for (AbstractNode input : operator.getInputs()) {
+				result |= isVisible(input, params);
+			}
+		} else if (operator.isProductOperator()) {
+			for (AbstractNode output : operator.getOutputs()) {
+				result |= isVisible(output, params);
+			}
+		} else {
+			throw new InvalidStateException("Unknown class state: " + operator);
+		}
+		return result;
+	}
+
+	/**
+	 * Checks if {@link AnnotatedObject} is visible according to visualization
+	 * given in params.
+	 * 
+	 * @param bioEntity
+	 *          visibility of this object will be checked
+	 * @param params
+	 *          visualization params
+	 * @return true if object is visible
+	 */
+	protected boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
+		if (params.isSemanticZoomingOn()) {
+			boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
+			if (bioEntity instanceof Element) {
+				Compartment compartment = ((Element) bioEntity).getCompartment();
+				if (compartment != null) {
+					result &= isVisible(compartment, params);
+				}
+				if (bioEntity instanceof Species) {
+					Complex complex = ((Species) bioEntity).getComplex();
+					if (complex != null) {
+						result &= isVisible(complex, params);
+					}
+				}
+			} else if (bioEntity instanceof Reaction) {
+				if (!isAnyProductVisible(((Reaction) bioEntity).getProducts(), params)) {
+					result = false;
+				} else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
+					result = false;
+				}
+
+			} else {
+				throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
+			}
+
+			return result;
+		}
+		return true;
+	}
+
+	/**
+	 * Checks if at least one reactant is visible.
+	 * 
+	 * @param reactants
+	 *          list of reactants
+	 * @param params
+	 *          params against which check is run
+	 * @return true if at least one reactant is visible
+	 */
+	private boolean isAnyReactantVisible(List<Reactant> reactants, ConverterParams params) {
+		boolean result = false;
+		for (Reactant reactant : reactants) {
+			if (isVisible(reactant, params)) {
+				result = true;
+			}
+		}
+		return result;
+	}
+
+	/**
+	 * Checks if at least one product is visible.
+	 * 
+	 * @param products
+	 *          list of products
+	 * @param params
+	 *          params against which check is run
+	 * @return true if at least one product is visible
+	 */
+	private boolean isAnyProductVisible(List<Product> products, ConverterParams params) {
+		boolean result = false;
+		for (Product product : products) {
+			if (isVisible(product, params)) {
+				result = true;
+			}
+		}
+		return result;
+	}
+
+	/**
+	 * Checks if level belongs to the range defined in
+	 * semanticZoomLevelVisibility.
+	 * 
+	 * @param level
+	 *          level to ve checked
+	 * @param semanticZoomLevelVisibility
+	 *          range of levels to be checked
+	 * @return true if level is in the range
+	 */
+	protected boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+		if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
+			return true;
+		}
+		if (semanticZoomLevelVisibility.contains("{")) {
+			String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
+			String[] ranges = strLevels.split(",");
+			for (String string : ranges) {
+				if (Integer.valueOf(string).equals(level)) {
+					return true;
+				}
+			}
+		}
+		if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
+			return true;
+		}
+		return false;
+	}
+
+}

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java

-package lcsb.mapviewer.converter.graphics;
+package lcsb.mapviewer.converter.graphics.bioEntity;
 
 import java.awt.Graphics2D;
 import java.util.List;
@@ -8,25 +8,29 @@ import org.apache.log4j.Logger;
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.graphics.compartment.BottomSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.LeftSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.OvalCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.PathwayCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.RightSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.SquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.TopSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.species.AntisenseRnaConverter;
-import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
-import lcsb.mapviewer.converter.graphics.species.DegradedConverter;
-import lcsb.mapviewer.converter.graphics.species.DrugConverter;
-import lcsb.mapviewer.converter.graphics.species.GeneConverter;
-import lcsb.mapviewer.converter.graphics.species.IonConverter;
-import lcsb.mapviewer.converter.graphics.species.PhenotypeConverter;
-import lcsb.mapviewer.converter.graphics.species.ProteinConverter;
-import lcsb.mapviewer.converter.graphics.species.RnaConverter;
-import lcsb.mapviewer.converter.graphics.species.SBGNNucleicAcidFeatureConverter;
-import lcsb.mapviewer.converter.graphics.species.SimpleMoleculeConverter;
-import lcsb.mapviewer.converter.graphics.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.BottomSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.LeftSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.OvalCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.PathwayCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.RightSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.SquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.TopSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AntisenseRnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DegradedConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DrugConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.GeneConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.IonConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.PhenotypeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.RnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAcidFeatureConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.model.map.AnnotatedObject;
 import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
 import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
 import lcsb.mapviewer.model.map.compartment.OvalCompartment;
@@ -35,6 +39,7 @@ import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.AntisenseRna;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Degraded;
@@ -59,13 +64,13 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
  * @author Piotr Gawron
  * 
  */
-public class ElementConverterImpl implements ElementConverter<Element> {
+public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject> {
 
 	/**
 	 * Default class logger.
 	 */
 	@SuppressWarnings("unused")
-	private static Logger logger = Logger.getLogger(ElementConverterImpl.class.getName());
+	private static Logger logger = Logger.getLogger(BioEntityConverterImpl.class.getName());
 
 	/**
 	 * Returns a converter for given element. If converter doesn't exist then
@@ -77,7 +82,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 	 *          object that helps to convert overlay values into colors
 	 * @return converter that can be applied for the given element
 	 */
-	private ElementConverter<? extends Element> getConverterForElement(Element element, ColorExtractor colorExtractor) {
+	private BioEntityConverter<? extends AnnotatedObject> getConverterForElement(AnnotatedObject element, ColorExtractor colorExtractor) {
 		if (element == null) {
 			throw new InvalidArgumentException("element cannot be null");
 		}
@@ -123,6 +128,8 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 			return new LeftSquareCompartmentConverter(colorExtractor);
 		} else if (element instanceof RightSquareCompartment) {
 			return new RightSquareCompartmentConverter(colorExtractor);
+		} else if (element instanceof Reaction) {
+			return new ReactionConverter(colorExtractor);
 		} else {
 			throw new NotImplementedException(new ElementUtils().getElementTag(element) + "Unknown element class");
 		}
@@ -132,7 +139,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 	 * Converter used for conversion of the {@link Element} given in constructor.
 	 */
 	@SuppressWarnings("rawtypes")
-	private ElementConverter elementConverter = null;
+	private BioEntityConverter elementConverter = null;
 
 	/**
 	 * Support constructor. Used in case of SBGN format display
@@ -144,7 +151,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 	 * @param sbgnFormat
 	 *          boolean value indicating if SBGN display format should be used
 	 */
-	public ElementConverterImpl(final Element element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
+	public BioEntityConverterImpl(final AnnotatedObject element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
 
 		// If element is a nucleic acid feature to be displayed in SBGN
 		if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
@@ -156,7 +163,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 
 		// if we don't know which converter to use then throw an exception
 		if (elementConverter == null) {
-			throw new InvalidArgumentException("Unknown converter for class: " + element.getClass() + ". Element id: " + element.getElementId());
+			throw new InvalidArgumentException(new ElementUtils().getElementTag(element) + "Unknown converter for class: " + element.getClass());
 		}
 	}
 
@@ -168,25 +175,24 @@ public class ElementConverterImpl implements ElementConverter<Element> {
 	 * @param element
 	 *          {@link Element} for which this converter will be used
 	 */
-	public ElementConverterImpl(final Element element, ColorExtractor colorExtractor) {
+	public BioEntityConverterImpl(final Element element, ColorExtractor colorExtractor) {
 		this(element, false, colorExtractor);
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public void drawElement(final Element element, final Graphics2D graphics, final ConverterParams params) {
-		elementConverter.drawElement(element, graphics, params);
+	public void drawText(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+		if (isVisible(element, params)) {
+			elementConverter.drawText(element, graphics, params);
+		}
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public void drawText(final Element element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
-		elementConverter.drawText(element, graphics, params);
+	public void draw(AnnotatedObject element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+		if (isVisible(element, params)) {
+			elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+		}
 	}
 
-	@SuppressWarnings("unchecked")
-	@Override
-	public void drawElement(Element element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
-		elementConverter.drawElement(element, graphics, params, visualizedLayoutsColorSchemas);
-	}
 }

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

+package lcsb.mapviewer.converter.graphics.bioEntity.element;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link Element} into a graphics on Graphics2D object.
+ * 
+ * @author Piotr Gawron
+ * 
+ * @param <T>
+ *          class of alias to convert
+ */
+public abstract class ElementConverter<T extends Element> extends BioEntityConverter<T> {
+
+}

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
 	}
 
 	@Override
-	public void drawElement(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+	public void draw(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
 		// keep the old values of colors and line
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.geometry.EllipseTransformation;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.ElementConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
 import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
 import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
 import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
@@ -31,7 +31,7 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
  *          class for which the comparator is created
  * 
  */
-public abstract class CompartmentConverter<T extends Compartment> implements ElementConverter<T> {
+public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
 
 	/**
 	 * Default class logger.
@@ -175,8 +175,8 @@ public abstract class CompartmentConverter<T extends Compartment> implements Ele
 	}
 
 	@Override
-	public void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
-		drawElement(alias, graphics, params);
+	public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+		draw(alias, graphics, params);
 
 		Color oldColor = graphics.getColor();
 		int count = 0;

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
 	}
 
 	@Override
-	public void drawElement(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+	public void draw(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -47,7 +47,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
 	}
 
 	@Override
-	public void drawElement(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+	public void draw(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -40,7 +40,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
 	private Color backgroundColor = Color.LIGHT_GRAY;
 
 	@Override
-	public void drawElement(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+	public void draw(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
 		// keep the old values of colors and line
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();

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

-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
 	}
 
 	@Override
-	public void drawElement(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+	public void draw(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
 		// keep the old values of color and line type
 		Color oldColor = graphics.getColor();
 		Stroke oldStroke = graphics.getStroke();