diff --git a/CHANGELOG b/CHANGELOG
index 8fddbae2aa28cd9acd012c9e659cb67dbebf66a7..27846d35f885565812fe10b3aaa33fdf41a86b97 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -15,7 +15,7 @@ minerva (18.1.0) stable; urgency=medium
* Bug fix: exporting degraded to SBGN-ML should not produce a label for it
(#2194)
- -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Dec 2024 13:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 30 Jan 2025 15:00:00 +0200
minerva (18.0.7) stable; urgency=medium
* Bug fix: plugin re-validate did not update md5 of javascript content - this
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index f4293a2a30e835de5a9a48719103bfd3fa9b8946..d63c4b03e7e06cd9d3fc647b1f7147a9f3026fe6 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -1,19 +1,19 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
public class NormalImageGeneratorTest extends GraphicsTestFunctions {
@@ -44,7 +44,8 @@ public class NormalImageGeneratorTest extends GraphicsTestFunctions {
}
@Test
- public void testArtifitialInHierarchicalView() throws Exception {
+ public void testArtificialInHierarchicalView() throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = createCompartmentModel();
Layer layer = model.getLayers().iterator().next();
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 9db57b4061672e6de5512e362c745ed4468d6409..9f43ffdc9d6ebc9ea170f5a7384caf2bf8c80ec8 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -42,11 +42,11 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Top left corner x coordinate of the text associated with compartment.
*/
- private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFICIAL_COMPARTMENT = 10;
/**
* Top left corner y coordinate of the text associated with compartment.
*/
- private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFICIAL_COMPARTMENT = 10;
/**
* Default class logger.
*/
@@ -130,6 +130,7 @@ public class CreateHierarchyCommand extends ModelCommand {
protected void clean() {
for (final Element alias : getModel().getElements()) {
alias.setCompartment(null);
+ alias.setPathway(null);
if (alias.getTransparencyLevel() == null || alias.getTransparencyLevel().isEmpty()) {
alias.setTransparencyLevel("");
}
@@ -168,10 +169,10 @@ public class CreateHierarchyCommand extends ModelCommand {
if (rect.getFillColor() != null) {
compartment.setFillColor(rect.getFillColor());
}
- compartment.setNameX(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameY(rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameWidth(rect.getWidth() - 2 * DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameHeight(rect.getHeight() - 2 * DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT);
+ compartment.setNameX(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameY(rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameWidth(rect.getWidth() - 2 * DEFAULT_TITLE_X_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameHeight(rect.getHeight() - 2 * DEFAULT_TITLE_Y_COORD_IN_ARTIFICIAL_COMPARTMENT);
compartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
compartment.setNameVerticalAlign(VerticalAlign.TOP);
compartment.setZ(rect.getZ());
@@ -196,10 +197,10 @@ public class CreateHierarchyCommand extends ModelCommand {
rap.processNotes(compartment);
text.setNotes(compartment.getName() + "\n" + compartment.getNotes());
- compartment.setNameX(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameY(text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameWidth(text.getWidth() - 2 * DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT);
- compartment.setNameHeight(text.getHeight() - 2 * DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT);
+ compartment.setNameX(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameY(text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameWidth(text.getWidth() - 2 * DEFAULT_TITLE_X_COORD_IN_ARTIFICIAL_COMPARTMENT);
+ compartment.setNameHeight(text.getHeight() - 2 * DEFAULT_TITLE_Y_COORD_IN_ARTIFICIAL_COMPARTMENT);
compartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
compartment.setNameVerticalAlign(VerticalAlign.TOP);
@@ -250,11 +251,12 @@ public class CreateHierarchyCommand extends ModelCommand {
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 hasPathway = alias.getPathway() != null;
boolean hasComplex = false;
if (alias instanceof Species) {
hasComplex = ((Species) alias).getComplex() != null;
}
- if (!hasCompartment && !hasComplex) {
+ if (!hasCompartment && !hasPathway && !hasComplex) {
logValue = 0;
}
if (logValue >= zoomLevels) {
@@ -280,7 +282,7 @@ public class CreateHierarchyCommand extends ModelCommand {
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 (final Element child : compartment.getElements()) {
+ for (final Element child : getCompartmentElements(compartment)) {
maxVisibilityLevel = Math.min(maxVisibilityLevel, computeVisibility(child));
}
if (maxVisibilityLevel >= zoomLevels) {
@@ -291,13 +293,68 @@ public class CreateHierarchyCommand extends ModelCommand {
}
compartment.setTransparencyLevel(maxVisibilityLevel + "");
}
- for (final Element child : compartment.getElements()) {
- if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ for (final Element child : getCompartmentElements(compartment)) {
+ if (!isExcludedChildVisibility(child)) {
child.setVisibilityLevel(compartment.getTransparencyLevel());
}
}
}
+ private Set<Element> getCompartmentElements(final Compartment compartment) {
+ Set<Element> children = new HashSet<>();
+ for (Element element : compartment.getModel().getElements()) {
+ if (element.getCompartment() == compartment) {
+ if (element.getPathway() == null) {
+ children.add(element);
+ } else if (element.getCompartment().getSize() < element.getPathway().getSize()) {
+ children.add(element);
+ }
+ }
+ }
+ return children;
+ }
+
+ private boolean isExcludedChildVisibility(final Element child) {
+ return child.getVisibilityLevel() != null && !child.getVisibilityLevel().isEmpty();
+ }
+
+ private void settingTransparencyLevelForPathway(final PathwayCompartment pathway) {
+ Set<Element> pathwayChildren = getPathwayChildren(pathway);
+ if (pathway.getTransparencyLevel() == null || pathway.getTransparencyLevel().isEmpty()) {
+ double rate = computeRate(pathway, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ int maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (final Element child : pathwayChildren) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, computeVisibility(child));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ pathway.setTransparencyLevel(maxVisibilityLevel + "");
+ }
+ for (final Element child : pathwayChildren) {
+ if (!isExcludedChildVisibility(child)) {
+ child.setVisibilityLevel(pathway.getTransparencyLevel());
+ }
+ }
+ }
+
+ private Set<Element> getPathwayChildren(final PathwayCompartment pathway) {
+ Set<Element> children = new HashSet<>();
+ for (Element element : pathway.getModel().getElements()) {
+ if (element.getPathway() == pathway) {
+ if (element.getCompartment() == null) {
+ children.add(element);
+ } else if (element.getPathway().getSize() < element.getCompartment().getSize()) {
+ children.add(element);
+ }
+ }
+ }
+ return children;
+ }
+
/**
* Sets transparency level in hierarchical view for complex alias.
*
@@ -320,20 +377,32 @@ public class CreateHierarchyCommand extends ModelCommand {
complex.setTransparencyLevel(maxVisibilityLevel + "");
}
for (final Element child : complex.getElements()) {
- if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ if (!isExcludedChildVisibility(child)) {
child.setVisibilityLevel(complex.getTransparencyLevel());
}
}
}
+ private final Set<Element> excluded = new HashSet<>();
+
/**
* Sets transparency level in hierarchical view for all elements.
*
* @param sortedAliases list of aliases
*/
private void settingOfTransparencyLevel(final List<Element> sortedAliases) {
+ excluded.clear();
+
+ for (final Element alias : sortedAliases) {
+ if (alias.getVisibilityLevel() != null && !alias.getVisibilityLevel().isEmpty()) {
+ excluded.add(alias);
+ }
+ }
+
for (final Element alias : sortedAliases) {
- if (alias instanceof Compartment) {
+ if (alias instanceof PathwayCompartment) {
+ settingTransparencyLevelForPathway((PathwayCompartment) alias);
+ } else if (alias instanceof Compartment) {
settingTransparencyLevelForCompartment((Compartment) alias);
} else if (alias instanceof Complex) {
settingTransparencyLevelForComplex((Complex) alias);
@@ -351,15 +420,16 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param sortedAliases list of aliases
*/
private void setChildrening(final List<Element> sortedAliases) {
- for (final Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
+ for (final Element element : sortedAliases) {
+ if (element instanceof Compartment) {
+ Compartment compartment = (Compartment) element;
Set<Element> removable = new HashSet<>();
- for (final Element alias : ((Compartment) compartment).getElements()) {
+ for (final Element alias : compartment.getElements()) {
if (alias.getCompartment() != compartment) {
removable.add(alias);
}
}
- ((Compartment) compartment).getElements().removeAll(removable);
+ compartment.getElements().removeAll(removable);
}
}
}
@@ -373,7 +443,11 @@ public class CreateHierarchyCommand extends ModelCommand {
for (final Element element : getModel().getElements()) {
if (element.getCompartment() == null) {
for (final Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
+ if (compartment instanceof PathwayCompartment) {
+ if (compartment.contains(element)) {
+ element.setPathway((PathwayCompartment) compartment);
+ }
+ } else if (compartment instanceof Compartment) {
if (((Compartment) compartment).getElements().contains(element)) {
element.setCompartment((Compartment) compartment);
}
@@ -414,7 +488,7 @@ public class CreateHierarchyCommand extends ModelCommand {
nullCompartment.setWidth(Double.MAX_VALUE);
nullCompartment.setHeight(Double.MAX_VALUE);
for (final Element element : getModel().getElements()) {
- Compartment supposedParent = nullCompartment;
+ Compartment supposedCompartment = nullCompartment;
PathwayCompartment supposedPathway = null;
for (final Compartment compartment : getModel().getCompartments()) {
if (compartment instanceof PathwayCompartment) {
@@ -423,12 +497,12 @@ public class CreateHierarchyCommand extends ModelCommand {
supposedPathway = (PathwayCompartment) compartment;
}
}
- } else if (compartment.contains(element) && compartment.getSize() < supposedParent.getSize()) {
- supposedParent = compartment;
+ } else if (compartment.contains(element) && compartment.getSize() < supposedCompartment.getSize()) {
+ supposedCompartment = compartment;
}
}
- if (supposedParent != nullCompartment) {
- supposedParent.addElement(element);
+ if (supposedCompartment != nullCompartment) {
+ supposedCompartment.addElement(element);
}
element.setPathway(supposedPathway);
}