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 60d3d808c0887cebe4b303a2bfc67232e216fa60..7e2613b08147aab7dac05f1e7189e002b49e12f8 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
@@ -24,62 +24,65 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public PathwayCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public PathwayCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
- /**
- * Background color of drawn compartments.
- */
- private Color backgroundColor = Color.LIGHT_GRAY;
+ /**
+ * Background color of drawn compartments.
+ */
+ private Color backgroundColor = Color.LIGHT_GRAY;
- @Override
- public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of colors and line
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
+ @Override
+ public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params)
+ throws DrawingException {
+ // keep the old values of colors and line
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
- Shape shape = new Rectangle2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
+ Shape shape = new Rectangle2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(),
+ compartment.getHeight());
- Color color = compartment.getColor();
+ Color color = compartment.getColor();
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(backgroundColor);
- } else {
- Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(shape);
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(backgroundColor);
+ } else {
+ Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(shape);
- // draw the border
- graphics.setColor(color);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(shape);
+ // draw the border
+ graphics.setColor(color);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(shape);
- // restore old color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
+ // draw description of the compartment
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ } else {
+ if (!compartment.containsIdenticalSpecies()) {
+ drawText(compartment, graphics, params);
+ }
+ }
- // draw description of the compartment
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- } else {
- if (!compartment.containsIdenticalSpecies()) {
- drawText(compartment, graphics, params);
- }
- }
- }
+ // restore old color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ }
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 57800a7e4ff81eea83fa2c8ee4fe230288939e33..176be3522ad1dd56eca522b8390f04a74bad7fae 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -31,355 +31,356 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
public class CreateHierarchyCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
- /**
- * Natural logarithm of four.
- */
- private static final double LOG_4 = Math.log(4);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
+ /**
+ * Natural logarithm of four.
+ */
+ private static final double LOG_4 = Math.log(4);
- /**
- * Top left corner x coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
- /**
- * Top left corner y coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ /**
+ * Top left corner x coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ /**
+ * Top left corner y coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
- /**
- * How many levels are possible.
- */
- private int zoomLevels;
- /**
- * What is the maximum zoom factor in the view.
- */
- private double maxZoomFactor;
+ /**
+ * How many levels are possible.
+ */
+ private int zoomLevels;
+ /**
+ * What is the maximum zoom factor in the view.
+ */
+ private double maxZoomFactor;
- /**
- * Default constructor that intializes data.
- *
- * @param model
- * model on which command will be executed
- * @param maxZoomFactor
- * what is the maximum zoom out factor
- * @param zoomLevels
- * how many levels are possible
- */
- public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
- super(model);
- this.zoomLevels = zoomLevels;
- this.maxZoomFactor = maxZoomFactor;
- }
+ /**
+ * Default constructor that intializes data.
+ *
+ * @param model
+ * model on which command will be executed
+ * @param maxZoomFactor
+ * what is the maximum zoom out factor
+ * @param zoomLevels
+ * how many levels are possible
+ */
+ public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
+ super(model);
+ this.zoomLevels = zoomLevels;
+ this.maxZoomFactor = maxZoomFactor;
+ }
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
- @Override
- protected void executeImplementation() {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- }
- Model model = getModel();
- List<Species> compacts = new ArrayList<>();
- for (Element alias : model.getElements()) {
- if (alias instanceof Complex) {
- if (((Complex) alias).getState().contains("brief")) {
- compacts.add((Species) alias);
- compacts.addAll(((Complex) alias).getElements());
- }
- }
- }
- model.getElements().removeAll(compacts);
- clean();
- createArtificials();
- assignAliases();
+ @Override
+ protected void executeImplementation() {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException(
+ "To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ }
+ Model model = getModel();
+ List<Species> compacts = new ArrayList<>();
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Complex) {
+ if (((Complex) alias).getState().contains("brief")) {
+ compacts.add((Species) alias);
+ compacts.addAll(((Complex) alias).getElements());
+ }
+ }
+ }
+ model.getElements().removeAll(compacts);
+ clean();
+ createArtificials();
+ assignAliases();
- List<Element> sortedAliases = model.getElementsSortedBySize();
- setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
- model.getElements().addAll(compacts);
- sortedAliases = model.getElementsSortedBySize();
- preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
- settingOfTransparencyLevel(sortedAliases);
+ List<Element> sortedAliases = model.getElementsSortedBySize();
+ setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
+ model.getElements().addAll(compacts);
+ sortedAliases = model.getElementsSortedBySize();
+ preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
+ settingOfTransparencyLevel(sortedAliases);
- setStatus(ModelCommandStatus.EXECUTED);
- }
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
- /**
- * Cleans hierarchical information from the model.
- */
- protected void clean() {
- for (Element alias : getModel().getElements()) {
- alias.setCompartment(null);
- alias.setTransparencyLevel("");
- }
- for (BioEntity bioEntity : getModel().getBioEntities()) {
- bioEntity.setVisibilityLevel("0");
- }
- Set<Compartment> toRemove = new HashSet<>();
- for (Compartment alias : getModel().getCompartments()) {
- if (alias instanceof PathwayCompartment) {
- toRemove.add(alias);
- }
- }
- for (Compartment alias : toRemove) {
- getModel().removeElement(alias);
- }
- }
+ /**
+ * Cleans hierarchical information from the model.
+ */
+ protected void clean() {
+ for (Element alias : getModel().getElements()) {
+ alias.setCompartment(null);
+ alias.setTransparencyLevel("");
+ }
+ for (BioEntity bioEntity : getModel().getBioEntities()) {
+ bioEntity.setVisibilityLevel("0");
+ }
+ Set<Compartment> toRemove = new HashSet<>();
+ for (Compartment alias : getModel().getCompartments()) {
+ if (alias instanceof PathwayCompartment) {
+ toRemove.add(alias);
+ }
+ }
+ for (Compartment alias : toRemove) {
+ getModel().removeElement(alias);
+ }
+ }
- /**
- * Creates artifitial compartment alias for rectangles and texts object on
- * additional graphic layers.
- */
- private void createArtificials() {
- Model model = getModel();
- int id = 0;
- for (Layer layer : model.getLayers()) {
- for (LayerRect rect : layer.getRectangles()) {
- PathwayCompartment alias = new PathwayCompartment("art" + (id++));
- alias.setX(rect.getX());
- alias.setY(rect.getY());
- alias.setWidth(rect.getWidth());
- alias.setHeight(rect.getHeight());
- alias.setColor(rect.getColor());
- alias.setNamePoint(
- new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+ /**
+ * Creates artificial compartment alias for rectangles and texts object on
+ * additional graphic layers.
+ */
+ private void createArtificials() {
+ Model model = getModel();
+ int id = 0;
+ for (Layer layer : model.getLayers()) {
+ for (LayerRect rect : layer.getRectangles()) {
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
+ alias.setX(rect.getX());
+ alias.setY(rect.getY());
+ alias.setWidth(rect.getWidth());
+ alias.setHeight(rect.getHeight());
+ alias.setColor(rect.getColor());
+ alias.setNamePoint(new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT,
+ rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
- model.addElement(alias);
- }
- for (LayerText text : layer.getTexts()) {
- PathwayCompartment alias = new PathwayCompartment("art" + (id++));
- alias.setX(text.getX());
- alias.setY(text.getY());
- alias.setWidth(text.getWidth());
- alias.setHeight(text.getHeight());
- alias.setColor(text.getColor());
- alias.setName(text.getNotes().trim());
- alias.setNamePoint(
- new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+ model.addElement(alias);
+ }
+ for (LayerText text : layer.getTexts()) {
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
+ alias.setX(text.getX());
+ alias.setY(text.getY());
+ alias.setWidth(text.getWidth());
+ alias.setHeight(text.getHeight());
+ alias.setColor(text.getColor());
+ alias.setName(text.getNotes().trim());
+ alias.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT,
+ text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
- model.addElement(alias);
+ model.addElement(alias);
- }
- }
- }
+ }
+ }
+ }
- /**
- * Assign aliases in hierarchical structure.
- */
- private void assignAliases() {
- assignToCompartments();
- }
+ /**
+ * Assign aliases in hierarchical structure.
+ */
+ private void assignAliases() {
+ assignToCompartments();
+ }
- /**
- * Computes visibility levels for aliases based on the size.
- *
- * @param sortedAliases
- * list of aliases
- * @param maxZoomFactor
- * max scale used on the map
- */
- private void preSettingOfVisibilityLevel(List<Element> sortedAliases, double maxZoomFactor) {
- for (Element alias : sortedAliases) {
- double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
- int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- boolean hasCompartment = alias.getCompartment() != null;
- boolean hasComplex = false;
- if (alias instanceof Species) {
- hasComplex = ((Species) alias).getComplex() != null;
- }
- if (!hasCompartment && !hasComplex) {
- logValue = 0;
- }
- if (logValue >= zoomLevels) {
- if (hasComplex) {
- logValue = zoomLevels - 1;
- } else {
- logValue = zoomLevels;
- }
- }
- alias.setVisibilityLevel(logValue + "");
- }
- }
+ /**
+ * Computes visibility levels for aliases based on the size.
+ *
+ * @param sortedAliases
+ * list of aliases
+ * @param maxZoomFactor
+ * max scale used on the map
+ */
+ private void preSettingOfVisibilityLevel(List<Element> sortedAliases, double maxZoomFactor) {
+ for (Element alias : sortedAliases) {
+ double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
+ int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ boolean hasCompartment = alias.getCompartment() != null;
+ boolean hasComplex = false;
+ if (alias instanceof Species) {
+ hasComplex = ((Species) alias).getComplex() != null;
+ }
+ if (!hasCompartment && !hasComplex) {
+ logValue = 0;
+ }
+ if (logValue >= zoomLevels) {
+ if (hasComplex) {
+ logValue = zoomLevels - 1;
+ } else {
+ logValue = zoomLevels;
+ }
+ }
+ alias.setVisibilityLevel(logValue + "");
+ }
+ }
- /**
- * Sets transparency level in hierarchical view for compartment alias.
- *
- * @param compartment
- * comaprtment alias
- */
- private void settingTransparencyLevelForCompartment(Compartment compartment) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Element child : compartment.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- compartment.setTransparencyLevel(maxVisibilityLevel + "");
- for (Element child : compartment.getElements()) {
- child.setVisibilityLevel(compartment.getTransparencyLevel());
- }
- }
+ /**
+ * Sets transparency level in hierarchical view for compartment alias.
+ *
+ * @param compartment
+ * comaprtment alias
+ */
+ private void settingTransparencyLevelForCompartment(Compartment compartment) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Element child : compartment.getElements()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ compartment.setTransparencyLevel(maxVisibilityLevel + "");
+ for (Element child : compartment.getElements()) {
+ child.setVisibilityLevel(compartment.getTransparencyLevel());
+ }
+ }
- /**
- * Sets transparency level in hierarchical view for complex alias.
- *
- * @param complex
- * complex alias
- */
- private void settingTransparencyLevelForComplex(Complex complex) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Element child : complex.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- complex.setTransparencyLevel(maxVisibilityLevel + "");
- for (Element child : complex.getElements()) {
- child.setVisibilityLevel(complex.getTransparencyLevel());
- }
- }
+ /**
+ * Sets transparency level in hierarchical view for complex alias.
+ *
+ * @param complex
+ * complex alias
+ */
+ private void settingTransparencyLevelForComplex(Complex complex) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Element child : complex.getElements()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ complex.setTransparencyLevel(maxVisibilityLevel + "");
+ for (Element child : complex.getElements()) {
+ child.setVisibilityLevel(complex.getTransparencyLevel());
+ }
+ }
- /**
- * Sets transparency level in hierarchical view for all elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void settingOfTransparencyLevel(List<Element> sortedAliases) {
- for (Element alias : sortedAliases) {
- if (alias instanceof Compartment) {
- settingTransparencyLevelForCompartment((Compartment) alias);
- } else if (alias instanceof Complex) {
- settingTransparencyLevelForComplex((Complex) alias);
- } else {
- alias.setTransparencyLevel("0");
- }
- }
- }
+ /**
+ * Sets transparency level in hierarchical view for all elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void settingOfTransparencyLevel(List<Element> sortedAliases) {
+ for (Element alias : sortedAliases) {
+ if (alias instanceof Compartment) {
+ settingTransparencyLevelForCompartment((Compartment) alias);
+ } else if (alias instanceof Complex) {
+ settingTransparencyLevelForComplex((Complex) alias);
+ } else {
+ alias.setTransparencyLevel("0");
+ }
+ }
+ }
- /**
- * Removes invalid compartment children.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setChildrening(List<Element> sortedAliases) {
- for (Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
- Set<Element> removable = new HashSet<>();
- for (Element alias : ((Compartment) compartment).getElements()) {
- if (alias.getCompartment() != compartment) {
- removable.add(alias);
- }
- }
- ((Compartment) compartment).getElements().removeAll(removable);
- }
- }
- }
+ /**
+ * Removes invalid compartment children.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setChildrening(List<Element> sortedAliases) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ Set<Element> removable = new HashSet<>();
+ for (Element alias : ((Compartment) compartment).getElements()) {
+ if (alias.getCompartment() != compartment) {
+ removable.add(alias);
+ }
+ }
+ ((Compartment) compartment).getElements().removeAll(removable);
+ }
+ }
+ }
- /**
- * Sets parent for elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
- for (Element element : getModel().getElements()) {
- if (element.getCompartment() == null) {
- for (Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
- if (((Compartment) compartment).getElements().contains(element)) {
- element.setCompartment((Compartment) compartment);
- }
- }
- }
+ /**
+ * Sets parent for elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
+ for (Element element : getModel().getElements()) {
+ if (element.getCompartment() == null) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ if (((Compartment) compartment).getElements().contains(element)) {
+ element.setCompartment((Compartment) compartment);
+ }
+ }
+ }
- }
- if (element instanceof Species) {
- Species species = (Species) element;
- if (species.getComplex() == null) {
- for (Element complex : sortedAliases) {
- if (complex instanceof Complex) {
- if (((Complex) complex).getElements().contains(element)) {
- species.setComplex((Complex) complex);
- }
- }
- }
- }
- }
- }
- }
+ }
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ if (species.getComplex() == null) {
+ for (Element complex : sortedAliases) {
+ if (complex instanceof Complex) {
+ if (((Complex) complex).getElements().contains(element)) {
+ species.setComplex((Complex) complex);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
- /**
- * Set parents for the elements in hierarchical view.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
- setParentingOfNonComplexChildrens(sortedAliases);
- setChildrening(sortedAliases);
- }
+ /**
+ * Set parents for the elements in hierarchical view.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
+ setParentingOfNonComplexChildrens(sortedAliases);
+ setChildrening(sortedAliases);
+ }
- /**
- * Assign aliases to compartments.
- */
- private void assignToCompartments() {
- Compartment nullCompartment = new Compartment("null");
- nullCompartment.setWidth(Double.MAX_VALUE);
- nullCompartment.setHeight(Double.MAX_VALUE);
- for (Element element : getModel().getElements()) {
- Compartment supposedParent = nullCompartment;
- for (Compartment alias : getModel().getCompartments()) {
- if (alias.contains(element) && alias.getSize() < supposedParent.getSize()) {
- supposedParent = alias;
- }
- }
- if (supposedParent != nullCompartment) {
- supposedParent.addElement(element);
- }
- }
- }
+ /**
+ * Assign aliases to compartments.
+ */
+ private void assignToCompartments() {
+ Compartment nullCompartment = new Compartment("null");
+ nullCompartment.setWidth(Double.MAX_VALUE);
+ nullCompartment.setHeight(Double.MAX_VALUE);
+ for (Element element : getModel().getElements()) {
+ Compartment supposedParent = nullCompartment;
+ for (Compartment alias : getModel().getCompartments()) {
+ if (alias.contains(element) && alias.getSize() < supposedParent.getSize()) {
+ supposedParent = alias;
+ }
+ }
+ if (supposedParent != nullCompartment) {
+ supposedParent.addElement(element);
+ }
+ }
+ }
- /**
- * Computes the ratio between the minimal object that should be visible, and
- * alias visible on the top level.
- *
- * @param alias
- * alias for which computation is done
- * @param limit
- * size of the minimal visibe object
- * @return ratio between the minimal object that should be visible, and alias
- * visible on the top level
- */
- private double computeRate(Element alias, double limit) {
- double length = alias.getWidth() / maxZoomFactor;
- double height = alias.getHeight() / maxZoomFactor;
- double size = length * height;
- return (double) Math.ceil(limit / size);
- }
+ /**
+ * Computes the ratio between the minimal object that should be visible, and
+ * alias visible on the top level.
+ *
+ * @param alias
+ * alias for which computation is done
+ * @param limit
+ * size of the minimal visibe object
+ * @return ratio between the minimal object that should be visible, and alias
+ * visible on the top level
+ */
+ private double computeRate(Element alias, double limit) {
+ double length = alias.getWidth() / maxZoomFactor;
+ double height = alias.getHeight() / maxZoomFactor;
+ double size = length * height;
+ return (double) Math.ceil(limit / size);
+ }
}