diff --git a/CHANGELOG b/CHANGELOG
index fa49ad394f4fc9d7af2c1da7c48949278edd6c2a..6f38b6fe064e297a192544e7aac676decfeee533 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,78 +1,47 @@
-minerva (12.1.0~beta.4) experimental; urgency=medium
- * Bug fix: partial zooming is disabled due to issues with hierarchical overlay
- * Bug fix: search results were not visible after initial search on top map
- * Bug fix: going to export page and back was breaking a map
- * Bug fix: export of special characters in pdf is working
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 17 Oct 2018 14:00:00 +0200
-
-minerva (12.1.0~beta.3) experimental; urgency=medium
- * Bug fix: double login with new LDAP credentials doesn't raise error
- * Bug fix: empty LDAP filter doesn't raise error
- * Bug fix: migration scripts work with database without superadmin privileges
- * Bug fix: export didn't work
- * Bug fix: coordinates of selected area wasn't processed properly when they
- exceeded canvas
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Oct 2018 14:00:00 +0200
-
-minerva (12.1.0~beta.2) experimental; urgency=medium
- * Bug fix: postgres migration script fixed to work with new docker compose
- * Bug fix: double click on user add button disabled
- * Bug fix: privileges are mirrored correctly across different popups
- * Bug fix: plugin tab css fixed
- * Small improvement: all ldap parameters are configurable
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Oct 2018 11:00:00 +0200
-
-minerva (12.1.0~beta.1) experimental; urgency=medium
- * Bug fix: uploading sbml file with no ids in glyphs returned error that
- could not be easily understand
- * Bug fix: sometimes single variant in genomic view was hidden from initial
- view
- * Bug fix: ds_store files in subfolders crashed zip upload
- * Bug fix: when creating new user default privileges were not filled
+minerva (12.1.0) stable; urgency=medium
* Small improvement: default privilege value for 'Custom overlays' added
* Small improvement: explicit logging of successful and unsuccessful logins
* Small improvement: clicking on search result icon (on the map) change tab to
the corresponding search results
- * Bug fix: passwords in the configuration tab are hidden with '*'
- * Bug fix: user has access to transparency level when creating custom semantic
- view (without this parametere functionality was very difficult to use)
- * Bug fix: loading invalid plugin doesn't render empty div anymore
- * Bug fix: sorting of custom overlays was broken when description of overlay
- was present
- * Bug fix: when there is a problem with adjusting font in complexes (because
- the font should be smaller than 1pt) description is not drawn anymore
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 18 Sep 2018 20:00:00 +0200
-
-minerva (12.1.0~beta.0) experimental; urgency=medium
* Small improvement: option to remove additional overlays generated by custom
semantic zoom
* Small improvement: 'Reduced modulation' edge was displayed differently in
CellDesigner and Minerva
* Small improvement: user-friendly documentation for plugin URL field
* Small improvement: plugins have to access information about active submap
- * Small improvement: miriam support for VMH reaction and VMH metabolite
-
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 05 Sep 2018 17:00:00 +0200
-
-minerva (12.1.0~alpha.0) experimental; urgency=medium
* Feature: genome browser with gene variants
* Feature: support of all CellDesigner element modifications
* Feature: ldap authentication
* Feature: multicolored anchors for data overlays
* Feature: minerva is distributed using rpm packages
- * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
- weren't provided properly
* Small improvement: annotations from RHEA are handled
* Small improvement: changing of Terms of Service url allows admin to reset
the status of ToS acceptance for all users
* Small improvement: description of a grouped results in improved
* Small improvement: selection of required annotation on map upload improved
+ * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
+ weren't provided properly
+ * Bug fix: passwords in the configuration tab are hidden with '*'
+ * Bug fix: user has access to transparency level when creating custom semantic
+ view (without this parametere functionality was very difficult to use)
+ * Bug fix: loading invalid plugin doesn't render empty div anymore
+ * Bug fix: sorting of custom overlays was broken when description of overlay
+ was present
+ * Bug fix: when there is a problem with adjusting font in complexes (because
+ the font should be smaller than 1pt) description is not drawn anymore
+ * Bug fix: going to export page and back was breaking a map
+ * Bug fix: coordinates of selected area wasn't processed properly when they
+ exceeded canvas
+ * Bug fix: postgres migration script fixed to work with new docker compose
+ * Bug fix: double click on user add button disabled
+ * Bug fix: privileges are mirrored correctly across different popups
+ * Bug fix: plugin tab css fixed
+ * Bug fix: uploading sbml file with no ids in glyphs returned error that
+ could not be easily understand
+ * Bug fix: ds_store files in subfolders crashed zip upload
+ * Bug fix: when creating new user default privileges were not filled
- -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 03 Aug 2018 10:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Mon, 29 Oct 2018 13:00:00 +0200
minerva (12.0.4) stable; urgency=medium
* Bug fix: CellDesigner modifications that are drawn as reaction are handled
diff --git a/frontend-js/src/main/js/gui/CommentDialog.js b/frontend-js/src/main/js/gui/CommentDialog.js
index 41bf2073baeb6215502df1f3467ba27d18303fa3..de7ad0e8ec1e81b47ee84bef28bc65e6b62dbb85 100644
--- a/frontend-js/src/main/js/gui/CommentDialog.js
+++ b/frontend-js/src/main/js/gui/CommentDialog.js
@@ -29,6 +29,7 @@ function CommentDialog(params) {
var self = this;
self._createGui();
$(self.getElement()).dialog({
+ title: "Add comment",
autoOpen: false,
resizable: false,
width: window.innerWidth / 2,
diff --git a/frontend-js/src/main/js/gui/Legend.js b/frontend-js/src/main/js/gui/Legend.js
index 6be26eeed210a85883737b46b9949064d4a40b75..a976ab7a3e54e87c0575a4c5b8a62c900330b4ad 100644
--- a/frontend-js/src/main/js/gui/Legend.js
+++ b/frontend-js/src/main/js/gui/Legend.js
@@ -39,8 +39,10 @@ Legend.prototype._initializeGui = function () {
var legendDiv = Functions.createElement({
type: "div",
id: "legend-div",
- className: "carousel slide"
+ className: "carousel"
});
+ legendDiv.setAttribute("data-ride", "carousel");
+
self.getElement().appendChild(legendDiv);
var indicators = Functions.createElement({
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 4655bf308c31a6a27afc54d8a6b2f1681be001b5..b33a5ef53a40f20a5a9a695de013677e0a06ae90 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/canvas/OpenLayers/OpenLayerPolyline.js b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
index e87a516537fcec87d8c331c54d834e7413f6ac08..6ee77ee55986f8721bb867c97b5d81b45482e6e7 100644
--- a/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
+++ b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js
@@ -83,7 +83,7 @@ OpenLayerPolyline.prototype.isShown = function () {
OpenLayerPolyline.prototype.getBounds = function () {
var self = this;
- var extent = self.getOpenLayersRectangle().getGeometry().getExtent();
+ var extent = self.getOpenLayersPolyline().getGeometry().getExtent();
var projection1 = [extent[0], extent[1]];
var p1 = self.getMap().fromProjectionToPoint(projection1);
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index fba86c1bec960a5e282514b8dd16415fa4a4b0f4..427e7a06c859829efed95baac859da7480b799d9 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/main/js/map/surface/ReactionSurface.js b/frontend-js/src/main/js/map/surface/ReactionSurface.js
index b750368fcbf609325c0c9f31d3c5835b3cf59167..2ceeb217ea0c1e6937105dccb991150ceca44dfa 100644
--- a/frontend-js/src/main/js/map/surface/ReactionSurface.js
+++ b/frontend-js/src/main/js/map/surface/ReactionSurface.js
@@ -87,7 +87,7 @@ ReactionSurface.prototype.setColor = function (color) {
strokeColor: color
});
}
- this.customized = true;
+ this.setCustomized(true);
};
/**
@@ -163,7 +163,7 @@ ReactionSurface.prototype.changedToDefault = function () {
strokeWeight: 5
});
}
- this.customized = false;
+ this.setCustomized(false);
};
/**
@@ -177,7 +177,7 @@ ReactionSurface.prototype.changedToCustomized = function () {
strokeWeight: this.getWidth()
});
}
- this.customized = true;
+ this.setCustomized(true);
};
/**
diff --git a/frontend-js/src/test/js/map/canvas/OpenLayers/OpenLayersPolyline-test.js b/frontend-js/src/test/js/map/canvas/OpenLayers/OpenLayersPolyline-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..f6107f6b544f5c27ed3e063da5ffa39433a5fdc4
--- /dev/null
+++ b/frontend-js/src/test/js/map/canvas/OpenLayers/OpenLayersPolyline-test.js
@@ -0,0 +1,44 @@
+"use strict";
+require("../../../mocha-config");
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../../logger');
+
+var OpenLayerCanvas = require('../../../../../main/js/map/canvas/OpenLayers/OpenLayerCanvas');
+var OpenLayerPolyline = require('../../../../../main/js/map/canvas/OpenLayers/OpenLayerPolyline');
+var Bounds = require('../../../../../main/js/map/canvas/Bounds');
+var Point = require('../../../../../main/js/map/canvas/Point');
+
+var SelectionContextMenu = require('../../../../../main/js/gui/SelectionContextMenu');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+describe('OpenLayerPolyline', function () {
+ var testOptions = {
+ center: new Point(0, 0),
+ tileSize: 256,
+ width: 300,
+ height: 600,
+ zoom: 3,
+ minZoom: 2,
+ maxZoom: 10,
+ backgroundOverlays: [{
+ id: 1,
+ name: "overlay",
+ directory: "overlay_dir"
+ }]
+ };
+ it("getBounds", function () {
+ var canvas = new OpenLayerCanvas(testDiv, testOptions);
+ var path = [new Point(0, 0), new Point(10, 5)];
+
+ var polyline = canvas.createPolyline({
+ strokeWeight: 1,
+ strokeColor: "#00ff00",
+ path: path
+ });
+ polyline.show();
+ assert.ok(polyline.getBounds());
+ });
+});
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 7a6362cdbd28df18b2911f7d312c84013381d017..ab20f54a5e8146c7c246a97d22cffbf2b03cdde5 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;
@@ -60,8 +60,8 @@ public class CreateHierarchyCommand extends ModelCommand {
private double maxZoomFactor;
/**
- * Default constructor that intializes data.
- *
+ * Default constructor that initializes data.
+ *
* @param model
* model on which command will be executed
* @param maxZoomFactor
@@ -105,12 +105,21 @@ public class CreateHierarchyCommand extends ModelCommand {
setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
model.getElements().addAll(compacts);
sortedAliases = model.getElementsSortedBySize();
- preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
settingOfTransparencyLevel(sortedAliases);
+ setDefaultVisibilityLevel(sortedAliases);
+
setStatus(ModelCommandStatus.EXECUTED);
}
+ private void setDefaultVisibilityLevel(List<Element> sortedAliases) {
+ for (Element element: sortedAliases) {
+ if (element.getVisibilityLevel()==null||element.getVisibilityLevel().isEmpty()) {
+ element.setVisibilityLevel(0);
+ }
+ }
+ }
+
@Override
protected void redoImplementation() {
throw new NotImplementedException();
@@ -122,10 +131,9 @@ public class CreateHierarchyCommand extends ModelCommand {
protected void clean() {
for (Element alias : getModel().getElements()) {
alias.setCompartment(null);
- alias.setTransparencyLevel("");
- }
- for (BioEntity bioEntity : getModel().getBioEntities()) {
- bioEntity.setVisibilityLevel("0");
+ if (alias.getTransparencyLevel() == null || alias.getTransparencyLevel().isEmpty()) {
+ alias.setTransparencyLevel("");
+ }
}
Set<Compartment> toRemove = new HashSet<>();
for (Compartment alias : getModel().getCompartments()) {
@@ -183,16 +191,8 @@ public class CreateHierarchyCommand extends ModelCommand {
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) {
+ 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;
@@ -210,63 +210,73 @@ public class CreateHierarchyCommand extends ModelCommand {
logValue = zoomLevels;
}
}
- alias.setVisibilityLevel(logValue + "");
+ return logValue;
+ } else {
+ return Integer.valueOf(alias.getVisibilityLevel());
}
}
/**
* Sets transparency level in hierarchical view for compartment alias.
- *
+ *
* @param compartment
- * comaprtment alias
+ * compartment 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;
+ 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 + "");
}
- compartment.setTransparencyLevel(maxVisibilityLevel + "");
for (Element child : compartment.getElements()) {
- child.setVisibilityLevel(compartment.getTransparencyLevel());
+ if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ 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;
+ 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 + "");
}
- complex.setTransparencyLevel(maxVisibilityLevel + "");
for (Element child : complex.getElements()) {
- child.setVisibilityLevel(complex.getTransparencyLevel());
+ if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ child.setVisibilityLevel(complex.getTransparencyLevel());
+ }
}
}
/**
* Sets transparency level in hierarchical view for all elements.
- *
+ *
* @param sortedAliases
* list of aliases
*/
@@ -277,14 +287,16 @@ public class CreateHierarchyCommand extends ModelCommand {
} else if (alias instanceof Complex) {
settingTransparencyLevelForComplex((Complex) alias);
} else {
- alias.setTransparencyLevel("0");
+ if (alias.getTransparencyLevel() == null || alias.getTransparencyLevel().isEmpty()) {
+ alias.setTransparencyLevel("0");
+ }
}
}
}
/**
* Removes invalid compartment children.
- *
+ *
* @param sortedAliases
* list of aliases
*/
@@ -304,7 +316,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Sets parent for elements.
- *
+ *
* @param sortedAliases
* list of aliases
*/
@@ -337,7 +349,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Set parents for the elements in hierarchical view.
- *
+ *
* @param sortedAliases
* list of aliases
*/
@@ -369,11 +381,11 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* 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
+ * size of the minimal visible object
* @return ratio between the minimal object that should be visible, and alias
* visible on the top level
*/
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 7047e094100318c2aba0bf6b41fe80272a288b7f..87f960d7952a1504565b2dd9d267769e0c608439 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 0000000000000000000000000000000000000000..736899cb21c573b480920833537d6151426122a6
--- /dev/null
+++ b/model-command/testFiles/custom_semantic_zooming.xml
@@ -0,0 +1,1195 @@
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+<celldesigner:bounds x="1610.0" y="1160.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="470.0" y="1115.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa26" species="s24" compartmentAlias="ca4">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1540.0" y="1510.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="415.0" y="105.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="BID" type="GENERIC"/>
+<celldesigner:protein id="pr3" name="BAD" type="GENERIC"/>
+<celldesigner:protein id="pr5" name="DAD" type="GENERIC"/>
+<celldesigner:protein id="pr6" name="B" type="GENERIC"/>
+<celldesigner:protein id="pr7" name="AAA" type="GENERIC"/>
+<celldesigner:protein id="pr8" name="AA0" type="GENERIC"/>
+<celldesigner:protein id="pr9" name="AA1" type="GENERIC"/>
+<celldesigner:protein id="pr10" name="AA3" type="GENERIC"/>
+<celldesigner:protein id="pr11" name="empty" type="GENERIC"/>
+<celldesigner:protein id="pr12" name="ST1" type="GENERIC"/>
+<celldesigner:protein id="pr14" name="T1" type="GENERIC"/>
+<celldesigner:protein id="pr15" name="S2T2" type="GENERIC"/>
+<celldesigner:protein id="pr13" name="S0T1" type="GENERIC"/>
+<celldesigner:protein id="pr16" name="S2" type="GENERIC"/>
+<celldesigner:protein id="pr17" name="TL0" type="GENERIC"/>
+<celldesigner:protein id="pr18" name="TL1" type="GENERIC"/>
+<celldesigner:protein id="pr19" name="S0" type="GENERIC"/>
+<celldesigner:protein id="pr20" name="T2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="E" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="Ee" size="0.2" pos="0.03" type="CodingRegion" active="false"/>
+<celldesigner:region id="tr2" name="Ef" size="0.16" pos="0.26999999999999996" type="CodingRegion" active="false"/>
+<celldesigner:region id="tr3" name="Eg" size="0.1" pos="0.46" type="transcriptionStartingSiteL" active="false"/>
+<celldesigner:region id="tr4" name="Eh" size="0.1" pos="0.72" type="transcriptionStartingSiteR" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+zoom1
+</celldesigner:layerNotes>
+<celldesigner:bounds x="1345.0" y="72.5" w="890.0" h="515.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Sem
+</celldesigner:layerNotes>
+<celldesigner:bounds x="1210.0" y="935.0" w="480.0" h="90.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+Tran
+</celldesigner:layerNotes>
+<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"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00009" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00014" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00015" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c2" id="c2" name="Cell" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>Cell</celldesigner:name>
+</celldesigner:extension>
+</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>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</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="#s1">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:uniprot:Q9BXM7"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</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>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</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="#s3">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:936"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:rhea:12345"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s5" id="s5" name="DAD" compartment="c1" 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>pr5</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="E" 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>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s7" id="s7" name="DAD" 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>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>DAD</celldesigner:name>
+</celldesigner:speciesIdentity>
+</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="#s7">
+<bqmodel:isDescribedBy>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:rhea:21220"/>
+</rdf:Bag>
+</bqmodel:isDescribedBy>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s8" id="s8" name="B" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr6</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s9" id="s9" name="AAA" compartment="c2" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr7</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s10" id="s10" name="AA0" 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>pr8</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s11" id="s11" name="AA1" compartment="c2" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>SemanticZoomLevelVisibility: 1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr9</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</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>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr10</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s13" id="s13" name="empty" compartment="c2" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<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/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 5cdce9d91ecd41feac15217bd81a8f4721713a4c..0b458250840d9ca44b1d9972419c0e7d944b857a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -465,20 +465,20 @@ public enum MiriamType {
new Class<?>[] {}, null),
/**
- * VMH reaction
+ * VMH metabolite: https://vmh.uni.lu/.
*/
- VMH_REACTION("VMH reaction", //
- "http://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000640"),
+ VMH_METABOLITE("VMH metabolite", //
+ "https://vmh.uni.lu/", //
+ "urn:miriam:vmhmetabolite", //
+ new Class<?>[] { Chemical.class }, "MIR:00000636"),
/**
- * VMH reaction
+ * VMH reaction: https://vmh.uni.lu/.
*/
- VMH_METABOLITE("VMH metabolite", //
- "http://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000636"),
+ VMH_REACTION("VMH reaction", //
+ "https://vmh.uni.lu/", //
+ "urn:miriam:vmhreaction", //
+ new Class<?>[] { Reaction.class }, "MIR:00000640"),
/**
* Wikidata: https://www.wikidata.org/.
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
index 75aad77291d822abd604338c02b98538737a6caa..5e6f427b8cc6ba075f4de2d5bfbc651364dee584 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
@@ -88,16 +88,27 @@ public class MiriamTypeTest {
assertNull(MiriamType.getTypeByCommonName("xyz"));
}
- @Test
- public void testGetMiriamByUri1() throws Exception {
- try {
- MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384:SF5");
- assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testGetMiriamByUri1() throws Exception {
+ try {
+ MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384:SF5");
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamForVmhMetabolite() throws Exception {
+ try {
+ MiriamData md = MiriamType.getMiriamByUri("urn:miriam:vmhmetabolite:o2");
+ assertNotNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
@Test
public void testGetMiriamByUri2() throws Exception {
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 528c189b5d01beacf58f447900357a3f34efa075..2872961ab979a2a2f4bfa8c13c8963c65ca3a3eb 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
@@ -378,7 +378,6 @@ 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/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index de4428df9f88304e9b3591f8c7f2d899d4935bda..c0540b1f76da9760f3947807504d305998ca2202 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -143,7 +143,7 @@ public class OverlayRestImpl extends BaseRestImpl {
if (columns != null && !columns.trim().isEmpty()) {
columnSet = columns.split(",");
} else {
- columnSet = new String[] { "modelId", "idObject", "value", "color", "uniqueId" };
+ columnSet = new String[] { "modelId", "idObject", "value", "color", "uniqueId", "width" };
}
List<Map<String, Object>> result = new ArrayList<>();
@@ -426,6 +426,12 @@ public class OverlayRestImpl extends BaseRestImpl {
}
} else if (column.equals("description")) {
value = colorSchema.getDescription();
+ } else if (column.equals("width")) {
+ if (bioEntity instanceof Reaction) {
+ value = colorSchema.getLineWidth();
+ } else {
+ continue;
+ }
} else if (column.equals("type")) {
if (colorSchema instanceof GeneVariationColorSchema) {
value = ColorSchemaType.GENETIC_VARIANT;
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 94e6941ca0410fc960ae95a773116183261cf293..db4b994f6c1b9ca1fc0bbfcdbfccd03734112b28 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -604,17 +604,11 @@ 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);
@@ -633,7 +627,7 @@ 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() + "/";
@@ -657,7 +651,7 @@ 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 + "/";
@@ -800,13 +794,11 @@ 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 a7b7d87c1e5eab3bbc80dfdcebba84a7010a68f4..ca990427c6a0d2394d170f6ec103470e326624c2 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 3a54c156fb71a5dd2a4d16d28ae1f6039d451d74..8f30ecde5992625ca63ea397e685eeea258856b0 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 f1f91b5ad3eeae570530239881a28ca32921baea..73d4df551ad3c4985cebf845a492654479b511c4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -173,8 +173,8 @@ public class ProjectServiceTest extends ServiceTestFunctions {
addZipEntry(entry4).//
addZipEntry(entry5).//
annotations(true).//
- semanticZoom(true).//
- semanticZoomContainsMultipleLayouts(true).images(true).//
+ semanticZoomContainsMultipleLayouts(true).//
+ images(true).//
async(false).//
projectDir(tmpResultDir).//
addUser("admin", "admin").//