issue #10 - sbgn format moved from model to project

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

@@ -108,7 +108,6 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
 		CellDesignerElementCollection elements = new CellDesignerElementCollection();
 
 		Model model = new ModelFullIndexed(null);
-		model.setSbgnFormat(params.isSbgnFormat());
 
 		if (params.getFilename() != null) {
 			model.setName(FilenameUtils.getBaseName(params.getFilename()));
@@ -198,7 +197,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
 			}
 
 			if (reactionsNode != null) {
-				ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements);
+				ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, params.isSbgnFormat());
 				List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
 				model.addReactions(reactions);
 			}
@@ -561,7 +560,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
 		CellDesignerElementCollection elements = new CellDesignerElementCollection();
 
 		SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
-		ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements);
+		ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
 		aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
 
 		StringBuilder result = new StringBuilder();

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java

@@ -23,7 +23,7 @@ import lcsb.mapviewer.model.map.species.Element;
  * @param <T>
  */
 public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
-	
+
 	/**
 	 * Default class logger.
 	 */
@@ -33,17 +33,17 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
 	 * CellDesigner graphical helper with polygon transformation functions.
 	 */
 	private CellDesignerPolygonTransformation		polygonTransformation		= new CellDesignerPolygonTransformation();
-	
+
 	/**
 	 * CellDesigner graphical helper with lin transformation functions.
 	 */
 	private LineTransformation									lineTransformation			= new LineTransformation();
-	
+
 	/**
 	 * CellDesigner graphical helper with ellipse transformation functions.
 	 */
 	private CellDesignerEllipseTransformation		ellipseTransformation		= new CellDesignerEllipseTransformation();
-	
+
 	/**
 	 * CellDesigner graphical helper with rectangle transformation functions.
 	 */
@@ -54,10 +54,19 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
 	 */
 	public static final int											HOMODIMER_OFFSET				= 6;
 
+	/**
+	 * Should the converter use sbgn standard.
+	 */
+	private boolean															sbgn;
+
 	/**
 	 * Default constructor that prevents from instatiation of the class.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
 	 */
-	protected AbstractCellDesignerAliasConverter() {
+	protected AbstractCellDesignerAliasConverter(boolean sbgn) {
+		this.sbgn = sbgn;
 	};
 
 	@Override
@@ -215,4 +224,21 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
 		this.rectangleTransformation = rectangleTransformation;
 	}
 
+	/**
+	 * @return the sbgn
+	 * @see #sbgn
+	 */
+	protected boolean isSbgn() {
+		return sbgn;
+	}
+
+	/**
+	 * @param sbgn
+	 *          the sbgn to set
+	 * @see #sbgn
+	 */
+	protected void setSbgn(boolean sbgn) {
+		this.sbgn = sbgn;
+	}
+
 }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java

@@ -20,18 +20,28 @@ import lcsb.mapviewer.model.map.species.Species;
 public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
 
 	/**
-	 * How big should be the arc in rectangle for nucleic acid feature representation.
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected AntisenseRnaCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
+	/**
+	 * How big should be the arc in rectangle for nucleic acid feature
+	 * representation.
 	 */
-	private static final int	RECTANGLE_CORNER_ARC_SIZE	= 5;
+	private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
 
 	@Override
 	public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
 		if (invalidAnchorPosition(alias, anchor)) {
 			return alias.getCenter();
 		}
-		if (alias.getModel().isSbgnFormat()) {
-			return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
-																																			alias.getWidth(), alias.getHeight(), anchor);
+		if (isSbgn()) {
+			return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
 		}
 		ArrayList<Point2D> points = getPoints(alias);
 		return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
@@ -79,7 +89,7 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
 	private GeneralPath getAntisebseRnaPath(Element alias) {
 		// CHECKSTYLE:OFF
 		GeneralPath path;
-		if (!alias.getModel().isSbgnFormat()) {
+		if (!isSbgn()) {
 			path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
 			path.moveTo(alias.getX(), alias.getY());
 			path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
@@ -89,16 +99,12 @@ public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesigner
 		} else {
 			path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
 			double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-			
+
 			path.moveTo(x, y);
 			path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
-			path.curveTo(x, y + height,
-																			x + RECTANGLE_CORNER_ARC_SIZE, y + height,
-																			x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+			path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
 			path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
-			path.curveTo(x + width, y + height,
-																			x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
-																			x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+			path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
 			path.lineTo(x + width, y);
 			path.closePath();
 		}

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java

 package lcsb.mapviewer.converter.model.celldesigner.geometry;
 
 import java.awt.geom.Point2D;
-import java.util.HashMap;
-import java.util.Map;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.AntisenseRna;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Degraded;
 import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
 import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.Rna;
 import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
 import lcsb.mapviewer.model.map.species.Unknown;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
- * This class is designed to obtain CellDesigner specific data from alias. It
- * contains static instances of converter for every type and use one that is
- * needed for currently processed alias.
+ * This class is designed to obtain CellDesigner specific data from
+ * {@link Element}.
  * 
  * @author Piotr Gawron
  * 
@@ -35,83 +30,54 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Element> {
 
-	// *****************************************************************
-	//
-	// STATIC PART
-	//
-	// *****************************************************************
-
-	/**
-	 * Static map of alias converters used for conversion of aliases. Key in this
-	 * map is a class of element to which alias reference to. Value is instance of
-	 * a converter that can process the alias with the specific element type
-	 * reference.
-	 */
-	private static Map<Class<? extends Element>, ICellDesignerAliasConverter<?>> elementConverters;
-
 	/**
 	 * Class helping with transforming objectcs into meaningfull identifiers.
 	 */
-	private static ElementUtils																									 eu	= new ElementUtils();
-
-	static {
-		elementConverters = new HashMap<>();
-
-		addElementConverter(GenericProtein.class, new ProteinCellDesignerAliasConverter());
-		addElementConverter(TruncatedProtein.class, new ProteinCellDesignerAliasConverter());
-		addElementConverter(ReceptorProtein.class, new ProteinCellDesignerAliasConverter());
-		addElementConverter(IonChannelProtein.class, new ProteinCellDesignerAliasConverter());
-		addElementConverter(Degraded.class, new DegradedCellDesignerAliasConverter());
-		addElementConverter(Complex.class, new ComplexCellDesignerAliasConverter());
-		addElementConverter(SimpleMolecule.class, new SimpleMoleculeCellDesignerAliasConverter());
-		addElementConverter(Drug.class, new DrugCellDesignerAliasConverter());
-		addElementConverter(Ion.class, new IonCellDesignerAliasConverter());
-		addElementConverter(Phenotype.class, new PhenotypeCellDesignerAliasConverter());
-		addElementConverter(Rna.class, new RnaCellDesignerAliasConverter());
-		addElementConverter(AntisenseRna.class, new AntisenseRnaCellDesignerAliasConverter());
-		addElementConverter(Gene.class, new GeneCellDesignerAliasConverter());
-		addElementConverter(Unknown.class, new UnknownCellDesignerAliasConverter());
-
-	}
+	private static ElementUtils eu = new ElementUtils();
 
 	/**
-	 * Method that set a converter for element referenced by alias to process.
+	 * Returns a converter for given {@link Element}. If converter doesn't exist
+	 * exception is thrown.
 	 * 
-	 * @param clazz
-	 *          class type of element referenced by alias
-	 * @param converter
-	 *          converter that should be used for conversion of this alias
+	 * @param element
+	 *          element for which we are loooking for a converter
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 * @return converter that can be applied for the given element
 	 */
-	protected static void addElementConverter(Class<? extends Element> clazz, ICellDesignerAliasConverter<?> converter) {
-		elementConverters.put(clazz, converter);
-	}
-
-	/**
-	 * Returns a converter for given alias. If converter doesn't exist then null
-	 * is returned.
-	 * 
-	 * @param alias
-	 *          alias for which we are loooking for a converter
-	 * @return converter that can be applied for the given alias; null if such
-	 *         converter doesn't exist
-	 */
-	private static ICellDesignerAliasConverter<? extends Element> getConverterForAlias(Element alias) {
-		if (alias == null) {
-			throw new InvalidArgumentException("alias cannot be null");
+	private ICellDesignerAliasConverter<? extends Element> getConverterForAlias(Element element, boolean sbgn) {
+		if (element == null) {
+			throw new InvalidArgumentException("element cannot be null");
+		}
+		if (element instanceof Protein) {
+			return new ProteinCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Degraded) {
+			return new DegradedCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Complex) {
+			return new ComplexCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof SimpleMolecule) {
+			return new SimpleMoleculeCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Drug) {
+			return new DrugCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Ion) {
+			return new IonCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Phenotype) {
+			return new PhenotypeCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Rna) {
+			return new RnaCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof AntisenseRna) {
+			return new AntisenseRnaCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Gene) {
+			return new GeneCellDesignerAliasConverter(sbgn);
+		} else if (element instanceof Unknown) {
+			return new UnknownCellDesignerAliasConverter(sbgn);
+		} else {
+			throw new NotImplementedException(eu.getElementTag(element) + "Unknown converter for class");
 		}
-		ICellDesignerAliasConverter<?> result = elementConverters.get(alias.getClass());
-
-		return result;
 	}
 
-	// *******************************************************
-	//
-	// NON-STATIC CLASS DEFINITION
-	//
-	// *******************************************************
-
 	/**
-	 * Converter used for operations on the alias given in constructor.
+	 * Converter used for operations on the {@link Element} given in constructor.
 	 */
 	@SuppressWarnings("rawtypes")
 	private ICellDesignerAliasConverter converter = null;
@@ -119,32 +85,30 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<E
 	/**
 	 * Default constructor.
 	 * 
-	 * @param alias
-	 *          alias for which this converter will be used
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 * @param element
+	 *          element for which this converter will be used
 	 */
-	public CellDesignerAliasConverter(Element alias) {
-		converter = getConverterForAlias(alias);
-		// if we don't know which converter to use then throw an exception
-		if (converter == null) {
-			throw new InvalidArgumentException(eu.getElementTag(alias) + "Unknown converter for class");
-		}
+	public CellDesignerAliasConverter(Element element, boolean sbgn) {
+		converter = getConverterForAlias(element, sbgn);
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public CellDesignerAnchor getAnchorForCoordinates(Element alias, Point2D point) {
-		return converter.getAnchorForCoordinates(alias, point);
+	public CellDesignerAnchor getAnchorForCoordinates(Element element, Point2D point) {
+		return converter.getAnchorForCoordinates(element, point);
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public Point2D getPointCoordinates(Element alias, CellDesignerAnchor anchor) {
-		return converter.getPointCoordinates(alias, anchor);
+	public Point2D getPointCoordinates(Element element, CellDesignerAnchor anchor) {
+		return converter.getPointCoordinates(element, anchor);
 	}
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public Point2D getAnchorPointCoordinates(Element alias, CellDesignerAnchor anchor, PolylineData line) {
-		return converter.getAnchorPointCoordinates(alias, anchor, line);
+	public Point2D getAnchorPointCoordinates(Element element, CellDesignerAnchor anchor, PolylineData line) {
+		return converter.getAnchorPointCoordinates(element, anchor, line);
 	}
 }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java

@@ -18,6 +18,16 @@ import lcsb.mapviewer.model.map.species.Complex;
  */
 public class ComplexCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Complex> {
 
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected ComplexCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * How big is the triangle trimmed part of the complex.
 	 */

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java

@@ -17,6 +17,16 @@ import lcsb.mapviewer.model.map.species.Species;
  */
 public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
 
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected DegradedCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * Part of height of the line used to cross degraded circle that goes behind
 	 * this circle.

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java

@@ -19,10 +19,21 @@ import lcsb.mapviewer.model.map.species.Species;
  * 
  */
 public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected DrugCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * 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;
 
 	@Override
 	public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java

@@ -20,6 +20,16 @@ import lcsb.mapviewer.model.map.species.Species;
  */
 public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
 
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected GeneCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * How big should be the arc in rectangle for nucleic acid feature representation.
 	 */
@@ -41,7 +51,7 @@ public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasCon
 	 * @return Shape object that represents alias
 	 */
 	private Shape getGeneShape(Element alias) {
-		if (!alias.getModel().isSbgnFormat()) {
+		if (!isSbgn()) {
 			Shape shape;
 			shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
 			return shape;

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java

@@ -17,6 +17,16 @@ import lcsb.mapviewer.model.map.species.Species;
  */
 public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
 
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected IonCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	@Override
 	public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
 		double diameter = getDiameter(alias);

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java

@@ -11,13 +11,24 @@ import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
 
 /**
- * Class that provides CellDesigner specific graphical information for Phenotype.
- * It's used for conversion from xml to normal x,y coordinates.
+ * Class that provides CellDesigner specific graphical information for
+ * Phenotype. It's used for conversion from xml to normal x,y coordinates.
  * 
  * @author Piotr Gawron
  * 
  */
 public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected PhenotypeCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	@Override
 	public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
 		if (invalidAnchorPosition(alias, anchor)) {

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java

@@ -28,6 +28,17 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
  * 
  */
 public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Protein> {
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected ProteinCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * Default class logger.
 	 */

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java

@@ -19,6 +19,16 @@ import lcsb.mapviewer.model.map.species.Species;
  */
 public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
 
+	/**
+	 * Default constructor.
+	 * 
+	 * @param sbgn
+	 *          Should the converter use sbgn standard
+	 */
+	protected RnaCellDesignerAliasConverter(boolean sbgn) {
+		super(sbgn);
+	}
+
 	/**
 	 * How big should be the arc in rectangle for nucleic acid feature representation.
 	 */	
@@ -29,7 +39,7 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
 		if (invalidAnchorPosition(alias, anchor)) {
 			return alias.getCenter();
 		}
-		if (alias.getModel().isSbgnFormat()) {
+		if (isSbgn()) {
 			return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
 																																			alias.getWidth(), alias.getHeight(), anchor);
 		}
@@ -78,7 +88,7 @@ public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
 	private GeneralPath getRnaPath(Element alias) {
 		// CHECKSTYLE:OFF