From 9cde97803b7739d0789f03a57ebc40e08d7b6297 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 31 Oct 2018 15:25:34 +0100
Subject: [PATCH] custom semantic zooming is always processed
---
.../src/main/js/gui/admin/AddProjectDialog.js | 15 -
.../src/main/js/map/data/UserPreferences.js | 3 -
.../js/gui/admin/AddProjectDialog-test.js | 2 -
.../commands/CreateHierarchyCommand.java | 667 ++++-----
.../commands/CreateHierarchyCommandTest.java | 70 +
.../testFiles/custom_semantic_zooming.xml | 1195 +++++++++++++++++
.../api/projects/ProjectRestImpl.java | 1 -
.../services/impl/ProjectService.java | 26 +-
.../services/utils/CreateProjectParams.java | 14 -
.../services/utils/data/BuildInLayout.java | 1 -
.../services/impl/ProjectServiceTest.java | 1 -
11 files changed, 1614 insertions(+), 381 deletions(-)
create mode 100644 model-command/testFiles/custom_semantic_zooming.xml
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 4655bf308c..b33a5ef53a 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -286,11 +286,6 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
help: 'If this checkbox is checked, the uploaded model will be displayed in SBGN format, instead of default ' +
'CellDesigner format.'
}));
- table.appendChild(self.createCheckboxRow({
- labelName: "Custom semantic zooming:",
- defaultValue: false,
- inputName: "project-semantic-zooming"
- }));
table.appendChild(self.createCheckboxRow({
labelName: "Custom semantic zooming contains multiple overlays:",
defaultValue: false,
@@ -709,7 +704,6 @@ AddProjectDialog.prototype.init = function () {
self.bindProjectUploadPreferences(user, "autoResize", "project-auto-margin");
self.bindProjectUploadPreferences(user, "validateMiriam", "project-verify-annotations");
self.bindProjectUploadPreferences(user, "cacheData", "project-cache-data");
- self.bindProjectUploadPreferences(user, "semanticZooming", "project-semantic-zooming");
self.bindProjectUploadPreferences(user, "semanticZoomingContainsMultipleOverlays", "project-semantic-zooming-contains-multiple-overlays");
self.bindProjectUploadPreferences(user, "sbgn", "project-sbgn-visualization");
});
@@ -1072,14 +1066,6 @@ AddProjectDialog.prototype.isSbgn = function () {
return $("[name='project-sbgn-visualization']", this.getElement()).is(':checked');
};
-/**
- *
- * @returns {boolean}
- */
-AddProjectDialog.prototype.isSemanticZooming = function () {
- return $("[name='project-semantic-zooming']", this.getElement()).is(':checked');
-};
-
/**
*
* @returns {boolean}
@@ -1158,7 +1144,6 @@ AddProjectDialog.prototype.onSaveClicked = function () {
"organism": self.getOrganism(),
"mapCanvasType": self.getMapCanvasTypeId(),
"sbgn": self.isSbgn(),
- "semantic-zoom": self.isSemanticZooming(),
"semantic-zoom-contains-multiple-layouts": self.isSemanticZoomingContainsMultipleOverlays(),
"annotate": self.isAnnotateAutomatically(),
"verify-annotations": self.isVerifyAnnotations(),
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index fba86c1bec..427e7a06c8 100644
--- a/frontend-js/src/main/js/map/data/UserPreferences.js
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -56,7 +56,6 @@ UserPreferences.prototype.update = function (userPreferences) {
* @param {boolean} projectUpload.validate-miriam
* @param {boolean} projectUpload.validate-miriam
* @param {boolean} projectUpload.cache-data
- * @param {boolean} projectUpload.semantic-zooming
* @param {boolean} projectUpload.sbgn
*/
UserPreferences.prototype.setProjectUpload = function (projectUpload) {
@@ -65,7 +64,6 @@ UserPreferences.prototype.setProjectUpload = function (projectUpload) {
validateMiriam: projectUpload["validate-miriam"],
annotateModel: projectUpload["annotate-model"],
cacheData: projectUpload["cache-data"],
- semanticZooming: projectUpload["semantic-zooming"],
semanticZoomingContainsMultipleOverlays: projectUpload["semantic-zooming-contains-multiple-overlays"],
sbgn: projectUpload["sbgn"]
};
@@ -183,7 +181,6 @@ UserPreferences.prototype.toExport = function () {
"annotate-model": this._projectUpload.annotateModel,
"cache-data": this._projectUpload.cacheData,
"sbgn": this._projectUpload.sbgn,
- "semantic-zooming": this._projectUpload.semanticZooming,
"semantic-zooming-contains-multiple-overlays":this._projectUpload.semanticZoomingContainsMultipleOverlays
},
"element-annotators": this._elementAnnotators,
diff --git a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
index 65a5fcdffd..255f09191d 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -153,8 +153,6 @@ describe('AddProjectDialog', function () {
assert.ok(options["sbgn"] !== undefined);
assert.ok(options["version"] !== undefined);
- assert.ok(options["semantic-zoom"] !== undefined);
-
assert.ok(projectAdded);
}).finally(function () {
return dialog.destroy();
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 57800a7e4f..7c8d040e7d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -6,12 +6,12 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.apache.commons.lang3.math.NumberUtils;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
@@ -31,355 +31,368 @@ 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 initializes 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();
+ settingOfTransparencyLevel(sortedAliases);
- setStatus(ModelCommandStatus.EXECUTED);
- }
+ setDefaultVisibilityLevel(sortedAliases);
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
- /**
- * 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);
- }
- }
+ private void setDefaultVisibilityLevel(List<Element> sortedAliases) {
+ for (Element element: sortedAliases) {
+ if (element.getVisibilityLevel()==null||element.getVisibilityLevel().isEmpty()) {
+ element.setVisibilityLevel(0);
+ }
+ }
+ }
- /**
- * 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));
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
- 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));
+ /**
+ * Cleans hierarchical information from the model.
+ */
+ protected void clean() {
+ for (Element alias : getModel().getElements()) {
+ alias.setCompartment(null);
+ if (alias.getTransparencyLevel() == null || alias.getTransparencyLevel().isEmpty()) {
+ alias.setTransparencyLevel("");
+ }
+ }
+ Set<Compartment> toRemove = new HashSet<>();
+ for (Compartment alias : getModel().getCompartments()) {
+ if (alias instanceof PathwayCompartment) {
+ toRemove.add(alias);
+ }
+ }
+ for (Compartment alias : toRemove) {
+ getModel().removeElement(alias);
+ }
+ }
- model.addElement(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));
- }
- }
- }
+ 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));
- /**
- * Assign aliases in hierarchical structure.
- */
- private void assignAliases() {
- assignToCompartments();
- }
+ model.addElement(alias);
- /**
- * 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());
- }
- }
+ /**
+ * Assign aliases in hierarchical structure.
+ */
+ private void assignAliases() {
+ assignToCompartments();
+ }
- /**
- * 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());
- }
- }
+ private int computeVisibility(Element alias) {
+ if (!NumberUtils.isNumber(alias.getVisibilityLevel())) {
+ 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;
+ }
+ }
+ return logValue;
+ } else {
+ return Integer.valueOf(alias.getVisibilityLevel());
+ }
+ }
- /**
- * 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 compartment alias.
+ *
+ * @param compartment
+ * compartment alias
+ */
+ private void settingTransparencyLevelForCompartment(Compartment compartment) {
+ if (compartment.getTransparencyLevel() == null || compartment.getTransparencyLevel().isEmpty()) {
+ 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(computeVisibility(child)));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ compartment.setTransparencyLevel(maxVisibilityLevel + "");
+ }
+ for (Element child : compartment.getElements()) {
+ if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ child.setVisibilityLevel(compartment.getTransparencyLevel());
+ }
+ }
+ }
- /**
- * 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 transparency level in hierarchical view for complex alias.
+ *
+ * @param complex
+ * complex alias
+ */
+ private void settingTransparencyLevelForComplex(Complex complex) {
+ if (complex.getTransparencyLevel() == null || complex.getTransparencyLevel().isEmpty()) {
+ 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(computeVisibility(child)));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ complex.setTransparencyLevel(maxVisibilityLevel + "");
+ }
+ for (Element child : complex.getElements()) {
+ if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ child.setVisibilityLevel(complex.getTransparencyLevel());
+ }
+ }
+ }
- /**
- * 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 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 {
+ if (alias.getTransparencyLevel() == null || alias.getTransparencyLevel().isEmpty()) {
+ alias.setTransparencyLevel("0");
+ }
+ }
+ }
+ }
- }
- 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);
- }
- }
- }
- }
- }
- }
- }
+ /**
+ * 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);
+ }
+ }
+ }
- /**
- * Set parents for the elements in hierarchical view.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
- setParentingOfNonComplexChildrens(sortedAliases);
- setChildrening(sortedAliases);
- }
+ /**
+ * 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);
+ }
+ }
+ }
- /**
- * 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);
- }
- }
- }
+ }
+ 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);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
- /**
- * 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);
- }
+ /**
+ * 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);
+ }
+ }
+ }
+
+ /**
+ * 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 visible 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);
+ }
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index 7047e09410..87f960d795 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -9,7 +9,9 @@ import static org.junit.Assert.fail;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
@@ -25,6 +27,7 @@ import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CreateHierarchyCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
@@ -304,4 +307,71 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
}
}
+ @Test
+ public void testHierarchyWithCustomSemanticZooming() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/custom_semantic_zooming.xml", false);
+
+ Map<Element, String> visibilityLevels = new HashMap<>();
+ for (Element element : model.getElements()) {
+ if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
+ visibilityLevels.put(element, element.getVisibilityLevel());
+ }
+ }
+
+ new CreateHierarchyCommand(model, 4, 80).execute();
+
+ for (Element element : model.getElements()) {
+ if (visibilityLevels.get(element) != null) {
+ assertEquals("Visibility level changed, but shouldn't", visibilityLevels.get(element),
+ element.getVisibilityLevel());
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHierarchyWithCustomSemanticZoomingPathwayLevels() throws Exception {
+ try {
+ ElementUtils eu = new ElementUtils();
+ Model model = getModelForFile("testFiles/custom_semantic_zooming.xml", false);
+
+ Map<Element, String> visibilityLevels = new HashMap<>();
+ for (Element element : model.getElements()) {
+ if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
+ visibilityLevels.put(element, element.getVisibilityLevel());
+ }
+ }
+
+ new CreateHierarchyCommand(model, 4, 80).execute();
+
+ for (Element element : model.getElements()) {
+ if (visibilityLevels.get(element) == null) {
+ int visibilityLevel = Integer.parseInt(element.getVisibilityLevel());
+ if (element.getCompartment() != null) {
+ int parentTransparency = Integer.parseInt(element.getCompartment().getTransparencyLevel());
+ assertEquals(
+ eu.getElementTag(element) + eu.getElementTag(element.getCompartment())
+ + "Element should be directly visible when parent is transparent",
+ parentTransparency, visibilityLevel);
+ } else if (element instanceof Species) {
+ int parentTransparency = Integer.parseInt(((Species) element).getComplex().getTransparencyLevel());
+ assertEquals(
+ eu.getElementTag(element) + eu.getElementTag(((Species) element).getComplex())
+ + "Element should be directly visible when parent is transparent",
+ parentTransparency, visibilityLevel);
+ }
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/model-command/testFiles/custom_semantic_zooming.xml b/model-command/testFiles/custom_semantic_zooming.xml
new file mode 100644
index 0000000000..736899cb21
--- /dev/null
+++ b/model-command/testFiles/custom_semantic_zooming.xml
@@ -0,0 +1,1195 @@
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+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="E" type="GENE">
+<celldesigner:listOfRegions>
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+<celldesigner:region id="tr2" name="Ef" size="0.16" pos="0.26999999999999996" type="CodingRegion" active="false"/>
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+<celldesigner:listOfAntisenseRNAs/>
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+<celldesigner:layerNotes>
+zoom1
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+<celldesigner:bounds x="1345.0" y="72.5" w="890.0" h="515.0"/>
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+<celldesigner:layerNotes>
+Sem
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+<celldesigner:bounds x="1210.0" y="935.0" w="480.0" h="90.0"/>
+<celldesigner:paint color="ff000000"/>
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+<celldesigner:layerNotes>
+Tran
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+<celldesigner:bounds x="45.0" y="15.0" w="2415.0" h="1980.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+</celldesigner:layer>
+</celldesigner:listOfLayers>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="mole"/>
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+<listOfUnits>
+<unit metaid="CDMT00008" kind="litre"/>
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+<compartment metaid="c2" id="c2" name="Cell" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>Cell</celldesigner:name>
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+</annotation>
+</compartment>
+<compartment metaid="c1" id="c1" name="nucleus" size="1" units="volume" outside="c2">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>nucleus</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c3" id="c3" name="pink" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 1
+TransparencyZoomLevelVisibility: 2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>pink</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c4" id="c4" name="black" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>black</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="BID" compartment="c1" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
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+<rdf:Description rdf:about="#s1">
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+<rdf:Bag>
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+</bqmodel:isDescribedBy>
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+</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="BAD" compartment="c1" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+<rdf:Description rdf:about="#s3">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:936"/>
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+<bqmodel:isDescribedBy>
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+<rdf:li rdf:resource="urn:miriam:rhea:12345"/>
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+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 0
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+</species>
+<species metaid="s6" id="s6" name="E" compartment="c1" initialAmount="0">
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+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
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+<celldesigner:speciesIdentity>
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+</species>
+<species metaid="s7" id="s7" name="DAD" compartment="c1" initialAmount="0">
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+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+</species>
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+<species metaid="s10" id="s10" name="AA0" compartment="c2" initialAmount="0">
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+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 0
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+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+</species>
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+<notes>
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+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
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+<celldesigner:proteinReference>pr9</celldesigner:proteinReference>
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+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s12" id="s12" name="AA3" compartment="c2" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
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+</species>
+<species metaid="s13" id="s13" name="empty" compartment="c2" initialAmount="0">
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+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr11</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s16" id="s16" name="ST1" compartment="c1" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 1
+TransparencyZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr12</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s18" id="s18" name="T1" compartment="c2" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr14</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s19" id="s19" name="S2T2" compartment="c2" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 2
+TransparencyZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr15</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s17" id="s17" name="S0T1" compartment="c1" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr13</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s20" id="s20" name="S2" compartment="c3" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s21" id="s21" name="TL0" compartment="c4" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility: 0
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr17</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s22" id="s22" name="TL1" compartment="c4" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr18</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s23" id="s23" name="S0" compartment="c2" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 0
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr19</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s24" id="s24" name="T2" compartment="c4" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility: 2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr20</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re1">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:rhea:16508"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re4" id="re4" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>REDUCED_MODULATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s5" alias="sa5">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00010" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00011" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re5" id="re5" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s6" alias="sa6">
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s5" alias="sa5">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00012" species="s6">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa6</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00013" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re6" id="re6" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s5" alias="sa5">
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s7" alias="sa7">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00005" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00006" species="s7">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa7</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re7" id="re7" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s8" alias="sa8"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00003" species="s8">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa8</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00004" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index b0d4cee6b5..0acdd3af10 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -635,7 +635,6 @@ public class ProjectRestImpl extends BaseRestImpl {
params.projectName(getFirstValue(data.get("name")));
params.projectOrganism(getFirstValue(data.get("organism")));
params.sbgnFormat(getFirstValue(data.get("sbgn")));
- params.semanticZoom(getFirstValue(data.get("semantic-zoom")));
params.semanticZoomContainsMultipleLayouts(getFirstValue(data.get("semantic-zoom-contains-multiple-layouts")));
params.version(getFirstValue(data.get("version")));
params.annotations(getFirstValue(data.get("annotate")));
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 78f9c1a5ec..10adc7f4a5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -616,17 +616,11 @@ public class ProjectService implements IProjectService {
projectDao.flush();
List<BuildInLayout> buildInLayouts = new ArrayList<>();
- BuildInLayout nested = null;
- if (params.isSemanticZoom()) {
- nested = BuildInLayout.SEMANTIC;
- } else {
- nested = BuildInLayout.NESTED;
- }
if (params.isNetworkLayoutAsDefault()) {
buildInLayouts.add(BuildInLayout.NORMAL);
- buildInLayouts.add(nested);
+ buildInLayouts.add(BuildInLayout.NESTED);
} else {
- buildInLayouts.add(nested);
+ buildInLayouts.add(BuildInLayout.NESTED);
buildInLayouts.add(BuildInLayout.NORMAL);
}
buildInLayouts.add(BuildInLayout.CLEAN);
@@ -645,7 +639,7 @@ public class ProjectService implements IProjectService {
topLayout.setHierarchicalView(buildInLayout.isNested());
topModel.addLayout(0, topLayout);
List<Layout> semanticLevelOverlays = new ArrayList<>();
- if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
+ if (params.isSemanticZoomContainsMultipleLayouts()) {
for (int i = 0; i <= topModel.getZoomLevels(); i++) {
String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ topModel.getId() + "/";
@@ -669,7 +663,7 @@ public class ProjectService implements IProjectService {
connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
- if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
+ if (params.isSemanticZoomContainsMultipleLayouts()) {
for (int i = 0; i <= topModel.getZoomLevels(); i++) {
String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ submodelId + "/";
@@ -812,13 +806,11 @@ public class ProjectService implements IProjectService {
createModel(params, project);
Model originalModel = project.getModels().iterator().next().getModel();
- if (!params.isSemanticZoom()) {
- new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
- generator.computeZoomFactor(originalModel)).execute();
- for (Model model : originalModel.getSubmodels()) {
- new CreateHierarchyCommand(model, generator.computeZoomLevels(model), generator.computeZoomFactor(model))
- .execute();
- }
+ new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
+ generator.computeZoomFactor(originalModel)).execute();
+ for (Model model : originalModel.getSubmodels()) {
+ new CreateHierarchyCommand(model, generator.computeZoomLevels(model), generator.computeZoomFactor(model))
+ .execute();
}
addUsers(project, params);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
index a7b7d87c1e..ca990427c6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -63,7 +63,6 @@ public class CreateProjectParams {
* Is the project a complex multi-file project.
*/
private boolean complex;
- private boolean semanticZoom;
private boolean semanticZoomContainsMultipleLayouts = false;
/**
@@ -782,19 +781,6 @@ public class CreateProjectParams {
return this;
}
- public CreateProjectParams semanticZoom(boolean semanticZoom) {
- this.semanticZoom = semanticZoom;
- return this;
- }
-
- public CreateProjectParams semanticZoom(String value) {
- return this.semanticZoom("true".equals(value));
- }
-
- public boolean isSemanticZoom() {
- return this.semanticZoom;
- }
-
public CreateProjectParams semanticZoomContainsMultipleLayouts(boolean semanticZoomContainsMultipleLayouts) {
this.semanticZoomContainsMultipleLayouts = semanticZoomContainsMultipleLayouts;
return this;
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index 3a54c156fb..8f30ecde59 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -32,7 +32,6 @@ public enum BuildInLayout { //
* Standard visualization with hierarchical view.
*/
NESTED("Pathways and compartments", "_nested", null, true), //
- SEMANTIC("Semantic zoom", "_semantic", null, true),
/**
* Clean visualization (with colors reset to black and white).
*/
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 3c3b575db1..d743432d06 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -169,7 +169,6 @@ public class ProjectServiceTest extends ServiceTestFunctions {
addZipEntry(entry4).//
addZipEntry(entry5).//
annotations(true).//
- semanticZoom(true).//
images(true).//
async(false).//
projectDir(tmpResultDir).//
--
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