From 12de5196bbb8b4a0ef06b4c5b41cdff536c6a914 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Thu, 30 Jan 2025 10:29:13 +0100
Subject: [PATCH] when creating hierarchy consider also pathways
---
.../commands/CreateHierarchyCommand.java | 75 +++++++++++++++----
1 file changed, 62 insertions(+), 13 deletions(-)
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 9db57b4061..cb4da52866 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.
*/
@@ -168,10 +168,10 @@ 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 +196,10 @@ 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);
@@ -292,12 +292,49 @@ public class CreateHierarchyCommand extends ModelCommand {
compartment.setTransparencyLevel(maxVisibilityLevel + "");
}
for (final Element child : compartment.getElements()) {
- if (child.getVisibilityLevel() == null || child.getVisibilityLevel().isEmpty()) {
+ if (!isExcludedChildVisibility(child)) {
child.setVisibilityLevel(compartment.getTransparencyLevel());
}
}
}
+ private boolean isExcludedChildVisibility(final Element child) {
+ return excluded.contains(child);
+ }
+
+ 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) {
+ children.add(element);
+ }
+ }
+ return children;
+ }
+
/**
* Sets transparency level in hierarchical view for complex alias.
*
@@ -320,20 +357,32 @@ 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);
--
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