diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index db00f59da024510942394ca4db3cf790efa3d0f4..f9ec3e0770b7e80ca0f178a8dded4d8d3aa8dcf8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -5,6 +5,8 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Describes structural information that appears in the cell designer notes.
@@ -116,7 +118,12 @@ public enum NoteField {
/**
* {@link Species#charge}.
*/
- CHARGE("Charge", CellDesignerSpecies.class, null); //
+ CHARGE("Charge", CellDesignerSpecies.class, null), //
+
+ /**
+ * {@link Element#getSemanticZoomLevelVisibility()}.
+ */
+ SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", AnnotatedObject.class, null); //
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index b46d75a00ff20d1f8623ba227e437b44f9d5ce6c..24021c6d339acc1db72e219a2ef94d811c14c5a2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -562,6 +562,20 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ private void setSemanticZoomLevelVisibility(AnnotatedObject element, String annotationString) {
+ String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
+ if (zoomLevelVisibility == null) {
+ return;
+ }
+ if (element.getSemanticZoomLevelVisibility() == null) {
+ element.setSemanticZoomLevelVisibility(zoomLevelVisibility);
+ } else if (!element.getSemanticZoomLevelVisibility().equals(zoomLevelVisibility)) {
+ logger.warn(
+ elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
+ + zoomLevelVisibility + "][" + element.getSemanticZoomLevelVisibility() + "]. Ignoring.");
+ }
+ }
+
/**
* Assigns notes to the element from notes string. This might look strange.
* The idea is that sometimes we have notes from more then one source. And the
@@ -620,6 +634,7 @@ public class RestAnnotationParser extends XmlParser {
setNotes(object, ann);
setSymbol(object, ann);
setSynonyms(object, ann);
+ setSemanticZoomLevelVisibility(object, ann);
setAbbreviation(object, ann);
setFormula(object, ann);
if (object instanceof Reaction) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index e452e977f39d17e4ce86d0f06631430afd253bc9..b68a48171a95b851ea030085623717a0388ef1ca 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -17,7 +17,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
@@ -173,6 +172,7 @@ public abstract class AbstractImageGenerator {
* Should the visualization include hierarchical view or not.
*/
private boolean nested = false;
+ private boolean semanticZoom = false;
/**
* Should sbgn standard be used.
@@ -208,6 +208,11 @@ public abstract class AbstractImageGenerator {
this.scale = scale;
return this;
}
+
+ public Params semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
/**
* @param scale
@@ -661,13 +666,13 @@ public abstract class AbstractImageGenerator {
// compartment/complexes)
if (element instanceof Species) {
if (((Species) element).getComplex() == null) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
}
}
}
// draw all reactions
for (Reaction reaction : params.getModel().getSortedReactions()) {
- drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
+ drawReaction(reaction, params.getVisibleLayoutsForElement(reaction), params);
}
// draw all compartments
for (Compartment compartment : params.getModel().getSortedCompartments()) {
@@ -741,7 +746,7 @@ public abstract class AbstractImageGenerator {
// get a converter for this compartment
BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
- ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level);
+ ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).semanticZoomingOn(params.semanticZoom);
if (nested) {
compartmentParams.fill(fill).scale(Math.max(scale, 1));
@@ -771,7 +776,7 @@ public abstract class AbstractImageGenerator {
for (Element element : result) {
// if a child is a standard species
if (element instanceof Species) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
} else if (element instanceof Compartment) {
drawCompartment((Compartment) element, nested, params.getVisibleLayoutsForElement(element), params);
} else {
@@ -795,10 +800,11 @@ public abstract class AbstractImageGenerator {
* object to be drawn
* @param visibleLayouts
* list of {@link ColorSchema} used for coloring species in layouts
+ * @param params
* @throws DrawingException
* thrown when there was a problem with drawing a {@link Species}
*/
- protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts) throws DrawingException {
+ protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
// The displaying of species is indicated by values of VisibilityLevel. If
// VisibilityLevel is big enough, then it is
@@ -833,7 +839,10 @@ public abstract class AbstractImageGenerator {
customScale = scale;
}
try {
- converter.draw(species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
+ converter.draw(
+ species, graphics,
+ new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom),
+ visibleLayouts);
} catch (Exception e) {
throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
}
@@ -848,7 +857,7 @@ public abstract class AbstractImageGenerator {
// depending on current zoom level, children are drawn or not
if (complex.getTransparencyLevel() <= level) {
for (Species a : complex.getElements()) {
- drawSpecies(a, visibleLayouts);
+ drawSpecies(a, visibleLayouts, params);
}
}
}
@@ -862,13 +871,14 @@ public abstract class AbstractImageGenerator {
* object to be drawn
* @param visibleLayouts
* list of {@link ColorSchema} used for coloring reaction in layouts
+ * @param params
*/
- protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts) {
+ protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) {
if (!cross(reaction.getLines())) {
return;
}
BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
- converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat), visibleLayouts);
+ converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom).level(level), visibleLayouts);
}
/**
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index d9e35b48dfd43e10d49d4a9e2c4a9a7a61bb8f05..56c6e0722c2e4db01ae81a39bd1ce76b475959c8 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -58,6 +58,7 @@ public class MapGenerator {
*
*/
private boolean nested = false;
+ private boolean semanticZoom = false;
/**
* Should we remove empty elements in nested view.
*
@@ -134,6 +135,11 @@ public class MapGenerator {
this.nested = nested;
return this;
}
+
+ public MapGeneratorParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
/**
* @return the removeEmpty
@@ -326,6 +332,8 @@ public class MapGenerator {
imgParams.height(TILE_SIZE * TILES_CACHE_NUM);
imgParams.model(params.model);
imgParams.sbgn(params.sbgn);
+ imgParams.level(i);
+ imgParams.semanticZoom(params.semanticZoom);
if (params.nested) {
imgParams.level(i).nested(params.nested);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index b08d9376456080ddffacf74664e64b7a29815dd8..b8a32ba7767c231bda64d3693e75733a51df6187 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -4,11 +4,22 @@ import java.awt.Graphics2D;
import java.util.ArrayList;
import java.util.List;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This interface defines what operations should be possible to convert
@@ -20,11 +31,17 @@ import lcsb.mapviewer.model.map.species.Element;
* class of alias to convert
*/
public abstract class BioEntityConverter<T extends AnnotatedObject> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+
/**
* Alpha value (0..255) used for visualizing overlay data that are normally
* visualized in javascript.
*/
- public static final int LAYOUT_ALPHA = 200;
+ public static final int LAYOUT_ALPHA = 200;
/**
* This function draw representation of the alias on the graphics object.
@@ -77,4 +94,69 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
*/
public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+ protected boolean isVisible(AbstractNode node, ConverterParams params) {
+ if (node instanceof NodeOperator) {
+ return isVisible((NodeOperator) node, params);
+ } else if (node instanceof ReactionNode) {
+ return isVisible(((ReactionNode) node).getElement(), params);
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + node.getClass());
+ }
+ }
+
+ protected boolean isVisible(NodeOperator operator, ConverterParams params) {
+ boolean result = false;
+ if (operator.isModifierOperator() || operator.isReactantOperator()) {
+ for (AbstractNode input : operator.getInputs()) {
+ result |= isVisible(input, params);
+ }
+ } else if (operator.isProductOperator()) {
+ for (AbstractNode output : operator.getOutputs()) {
+ result |= isVisible(output, params);
+ }
+ } else {
+ throw new InvalidStateException("Unknown class state: " + operator);
+ }
+ return result;
+ }
+
+ protected boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
+ if (params.isSemanticZoomingOn()) {
+ boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
+ if (bioEntity instanceof Element) {
+ Compartment compartment = ((Element) bioEntity).getCompartment();
+ if (compartment != null) {
+ result &= isVisible(compartment, params);
+ }
+ if (bioEntity instanceof Species) {
+ Complex complex = ((Species) bioEntity).getComplex();
+ if (complex != null) {
+ result &= isVisible(complex, params);
+ }
+ }
+ }
+ return result;
+ }
+ return true;
+ }
+
+ protected boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+ if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
+ return true;
+ }
+ if (semanticZoomLevelVisibility.contains("{")) {
+ String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
+ String[] ranges = strLevels.split(",");
+ for (String string : ranges) {
+ if (Integer.valueOf(string).equals(level)) {
+ return true;
+ }
+ }
+ }
+ if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
+ return true;
+ }
+ return false;
+ }
+
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index 595065c8fcd8e49a8eddf86a892502040150ea6c..bb68987a1ce1d12af1161f848bfea2622930a5ce 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -182,12 +182,17 @@ public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject>
@SuppressWarnings("unchecked")
@Override
public void drawText(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- elementConverter.drawText(element, graphics, params);
+ if (isVisible(element, params)) {
+ elementConverter.drawText(element, graphics, params);
+ }
}
@SuppressWarnings("unchecked")
@Override
public void draw(AnnotatedObject element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ if (isVisible(element, params)) {
+ elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ }
}
+
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index f325a9d8d04b78136267ae166876b1858a8303c3..b50c7ef53d1d4e382dc07264e9351a2c26ff2e9a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -15,8 +15,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
@@ -26,8 +24,6 @@ import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
@@ -36,11 +32,7 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
/**
* Thics class allows to draw reaction on the graphics2D.
@@ -230,71 +222,6 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
graphics.setColor(color);
}
- private boolean isVisible(AbstractNode node, ConverterParams params) {
- if (node instanceof NodeOperator) {
- return isVisible((NodeOperator) node, params);
- } else if (node instanceof ReactionNode) {
- return isVisible(((ReactionNode) node).getElement(), params);
- } else {
- throw new InvalidArgumentException("Unknown class type: " + node.getClass());
- }
- }
-
- private boolean isVisible(NodeOperator operator, ConverterParams params) {
- boolean result = false;
- if (operator.isModifierOperator() || operator.isReactantOperator()) {
- for (AbstractNode input : operator.getInputs()) {
- result |= isVisible(input, params);
- }
- } else if (operator.isProductOperator()) {
- for (AbstractNode output : operator.getOutputs()) {
- result |= isVisible(output, params);
- }
- } else {
- throw new InvalidStateException("Unknown class state: " + operator);
- }
- return result;
- }
-
- private boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
- if (params.isSemanticZoomingOn()) {
- boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
- if (bioEntity instanceof Element) {
- Compartment compartment = ((Element) bioEntity).getCompartment();
- if (compartment != null) {
- result &= isVisible(compartment, params);
- }
- if (bioEntity instanceof Species) {
- Complex complex = ((Species) bioEntity).getComplex();
- if (complex != null) {
- result &= isVisible(complex, params);
- }
- }
- }
- return result;
- }
- return true;
- }
-
- private boolean matchLevel(int level, String semanticZoomLevelVisibility) {
- if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
- return true;
- }
- if (semanticZoomLevelVisibility.contains("{")) {
- String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
- String[] ranges = strLevels.split(",");
- for (String string : ranges) {
- if (Integer.valueOf(string).equals(level)) {
- return true;
- }
- }
- }
- if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
- return true;
- }
- return false;
- }
-
/**
* Draw reaction on the graphics2D.
*
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 eea455176c321f0b3e8fc651fc288a3196ff29fa..212e7360c7dcd0c7e1849862b1e3126a30c488ac 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -636,6 +636,9 @@ public class ProjectService implements IProjectService {
IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
}
});
+ if (layout.getTitle().contains(BuildInLayout.SEMANTIC.getTitle())) {
+ imgParams.semanticZoom(params.isSemanticZoom());
+ }
generator.generateMapImages(imgParams);
}
counter++;
@@ -704,18 +707,21 @@ public class ProjectService implements IProjectService {
if (params.isNetworkLayoutAsDefault()) {
buildInLayouts.add(BuildInLayout.NORMAL);
for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NORMAL)) {
+ if (!buildInLayout.equals(BuildInLayout.NORMAL) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
buildInLayouts.add(buildInLayout);
}
}
} else {
buildInLayouts.add(BuildInLayout.NESTED);
for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NESTED)) {
+ if (!buildInLayout.equals(BuildInLayout.NESTED) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
buildInLayouts.add(buildInLayout);
}
}
}
+ if (params.isSemanticZoom()) {
+ buildInLayouts.add(BuildInLayout.SEMANTIC);
+ }
// reverse the order of build in layouts, so we can insert them at the
// beginning of list of layouts (the order will be the same)
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 7edaee16379296a7511c59557ccdcb652ddc5ba4..21df2ed92d971e0160604b9b9f9b859b8075fdcf 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -59,6 +59,7 @@ public class CreateProjectParams {
* Is the project a complex multi-file project.
*/
private boolean complex;
+ private boolean semanticZoom;
/**
* List of zip entries in the complex model definition.
@@ -722,4 +723,13 @@ public class CreateProjectParams {
return this;
}
+ public CreateProjectParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
+ public boolean isSemanticZoom() {
+ return this.semanticZoom;
+ }
+
}
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 13011324b3e60a4f273d4a3e8fe6cef6be72938a..3bdf5704f793378735a463ae359cb91e99cd36fe 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
@@ -32,6 +32,7 @@ public enum BuildInLayout { //
* Standard visualization with hierarchical view.
*/
NESTED("Pathways and compartments", "_nested", null, true),
+ SEMANTIC("Semantic zoom", "_semantic", null, false),
/**
* Clean visualization (with colors reset to black and white).
*/
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
index bafe1cd65ace628698072d51d347e9bc89035db9..0e08e4a105f21283040a4609fe99c885458f1cfb 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
@@ -209,6 +209,8 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
*/
private String sbgnFormat = "false";
+ private String semanticOverlay = "false";
+
/**
* List of zip entries corresponding to
* {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} files in the
@@ -664,6 +666,7 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
params.addZipEntry(submodel);
}
params.sbgnFormat("true".equalsIgnoreCase(sbgnFormat));
+ params.semanticZoom("true".equalsIgnoreCase(semanticOverlay));
params.networkLayoutAsDefault("true".equalsIgnoreCase(networkLayoutAsDefault));
projectService.createProject(params);
projectService.updateClassAnnotatorTreeForUser(
@@ -1485,4 +1488,21 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
this.newProjectOrganism = newProjectOrganism;
}
+ /**
+ * @return the semanticOverlay
+ * @see #semanticOverlay
+ */
+ public String getSemanticOverlay() {
+ return semanticOverlay;
+ }
+
+ /**
+ * @param semanticOverlay
+ * the semanticOverlay to set
+ * @see #semanticOverlay
+ */
+ public void setSemanticOverlay(String semanticOverlay) {
+ this.semanticOverlay = semanticOverlay;
+ }
+
}
diff --git a/web/src/main/webapp/admin/projects.xhtml b/web/src/main/webapp/admin/projects.xhtml
index a036465233728e14a31fb7ed97666ede4951fb0d..ba3c03ba04460b79659a3220a86625450d5ff672 100644
--- a/web/src/main/webapp/admin/projects.xhtml
+++ b/web/src/main/webapp/admin/projects.xhtml
@@ -303,6 +303,10 @@ configurations of the source file are discussed in <a href="#{request.context
<p:selectBooleanCheckbox value="#{projectMB.networkLayoutAsDefault}" />
<cc:helpButton helpText='If this checkbox is checked, the default overlay in User panel will present pure network. If the checkbox is unchecked then default overlay will present pathways and compartments view.'/>
+ <h:outputText value="Semantic zooming: " />
+ <p:selectBooleanCheckbox value="#{projectMB.semanticOverlay}" />
+ <cc:helpButton helpText=''/>
+
</h:panelGrid>
<center>
<p:commandButton value="Submit" icon="ui-icon-disk" actionListener="#{projectMB.createProject}" onclick="PF('addProjectDialog').hide();" update=":projectForm:projectDataTable"/>