From 76d6bcf1ebab4076a091f675943777f37b681661 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 30 Jun 2017 11:33:47 +0200
Subject: [PATCH] compartments have parent compartments assigned
---
.../model/sbgnml/SbgnmlXmlParser.java | 55 ++++++++++++-------
1 file changed, 35 insertions(+), 20 deletions(-)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index bbc79aa9d9..3733c04f54 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -62,6 +62,7 @@ import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Phenotype;
@@ -622,49 +623,58 @@ public class SbgnmlXmlParser {
}
}
- parseAlias(g, newSpecies, model);
+ parseSpecies(g, newSpecies, model);
}
/**
* Method used to create a new alias from SBGN-ML glyph.
*
- * @param g
+ * @param glyph
* SBGN-ML glyph representing the alias
- * @param newSpecies
+ * @param species
* species of the alias
* @param model
* model to be updated
*/
- private void parseAlias(Glyph g, Species newSpecies, Model model) {
- newSpecies.setHeight(new Double(g.getBbox().getH()));
- newSpecies.setWidth(new Double(g.getBbox().getW()));
- newSpecies.setX(new Double(g.getBbox().getX()));
- newSpecies.setY(new Double(g.getBbox().getY()));
+ private void parseSpecies(Glyph glyph, Species species, Model model) {
+ species.setHeight(new Double(glyph.getBbox().getH()));
+ species.setWidth(new Double(glyph.getBbox().getW()));
+ species.setX(new Double(glyph.getBbox().getX()));
+ species.setY(new Double(glyph.getBbox().getY()));
Compartment parentCompartment = null;
- if (g.getCompartmentRef() != null) {
- Glyph compartmentGlyph = (Glyph) g.getCompartmentRef();
+ if (glyph.getCompartmentRef() != null) {
+ Glyph compartmentGlyph = (Glyph) glyph.getCompartmentRef();
parentCompartment = model.getElementByElementId(compartmentGlyph.getId());
- } else if (newSpecies.getComplex() == null) {
- // If the alias is in any compartment, assign it to that compartment
- parentCompartment = findParentCompartment(newSpecies, model);
+ } else if (species.getComplex() == null) {
+ parentCompartment = findParentCompartment(species, model);
}
- if (parentCompartment!=null) {
- newSpecies.setCompartment(parentCompartment);
- parentCompartment.addElement(newSpecies);
+ if (parentCompartment != null) {
+ species.setCompartment(parentCompartment);
+ parentCompartment.addElement(species);
}
// Parse units of information
- for (Glyph child : g.getGlyph()) {
+ for (Glyph child : glyph.getGlyph()) {
if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.UNIT_OF_INFORMATION)) {
- parseUnitOfInformation(child, newSpecies);
+ parseUnitOfInformation(child, species);
}
}
- model.addElement(newSpecies);
+ model.addElement(species);
}
- private Compartment findParentCompartment(Species child, Model model) {
+ /**
+ * Finds a compartment where element should be located (base on the
+ * coordinates).
+ *
+ * @param child
+ * {@link Element} for which we want to find compartment
+ * @param model
+ * {@link Model} where we look for a compartment
+ * @return parent {@link Compartment}
+ */
+ private Compartment findParentCompartment(Element child, Model model) {
Compartment nullParent = new Compartment("null");
nullParent.setWidth(Double.MAX_VALUE);
nullParent.setHeight(Double.MAX_VALUE);
@@ -1514,6 +1524,11 @@ public class SbgnmlXmlParser {
compartment.setNamePoint(
compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN, compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
}
+ Compartment parent = findParentCompartment(compartment, model);
+ if (parent != null) {
+ compartment.setCompartment(parent);
+ parent.addElement(compartment);
+ }
model.addElement(compartment);
}
--
GitLab