From a00c1ad102dcc86e14c6f5db6dd3bd3c2b5f2c71 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 23 Nov 2017 17:54:18 +0100
Subject: [PATCH] parsing of relation between compartment and species added
---
.../model/sbml/SbmlCompartmentParser.java | 10 ++--
.../model/sbml/SbmlElementParser.java | 16 +++---
.../converter/model/sbml/SbmlParser.java | 42 ++++++++++++++--
.../model/sbml/SbmlSpeciesParser.java | 50 +++++++++++++++++--
.../model/sbml/GenericSbmlParserTest.java | 3 +-
.../converter/model/sbml/SbmlParserTest.java | 48 +++++++++++++++---
6 files changed, 143 insertions(+), 26 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
index 9e119bfbaf..2e19442c08 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
@@ -20,15 +20,19 @@ import lcsb.mapviewer.model.map.compartment.SquareCompartment;
public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Compartment> {
Logger logger = Logger.getLogger(SbmlCompartmentParser.class);
- public SbmlCompartmentParser(Layout layout) {
- super(layout);
+ public SbmlCompartmentParser(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ super(layout, minervaModel);
}
@Override
- protected Compartment parse(org.sbml.jsbml.Compartment compartment) throws InvalidInputDataExecption {
+ protected Compartment parse(org.sbml.jsbml.Compartment compartment, Model sbmlModel)
+ throws InvalidInputDataExecption {
Compartment result = new SquareCompartment(compartment.getId());
result.setMiriamData(parseAnnotation(compartment.getAnnotation()));
result.setName(compartment.getName());
+ if (result.getName() == null || result.getName().isEmpty()) {
+ result.setName(result.getElementId());
+ }
try {
result.setNotes(compartment.getNotesString());
} catch (XMLStreamException e) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 5b7c7edcb9..8530ae1a6b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -25,17 +25,20 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
Layout layout;
- public SbmlElementParser(Layout layout) {
- this.layout = layout;
+ lcsb.mapviewer.model.map.model.Model minervaModel;
+
+ public SbmlElementParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.layout = sbmlLayout;
+ this.minervaModel = minervaModel;
}
public List<Element> parseList(Model sbmlModel) throws InvalidInputDataExecption {
List<Element> result = new ArrayList<>();
for (T sbmlElement : getSbmlElementList(sbmlModel)) {
- result.add(parse(sbmlElement));
+ result.add(parse(sbmlElement, sbmlModel));
}
if (layout != null) {
- return mergeLayout(result, layout);
+ return mergeLayout(result, layout, sbmlModel);
} else {
return result;
}
@@ -43,7 +46,8 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
protected abstract ListOf<T> getSbmlElementList(Model sbmlModel);
- private List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout) throws InvalidInputDataExecption {
+ protected List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout, Model sbmlModel)
+ throws InvalidInputDataExecption {
Set<Element> used = new HashSet<>();
Map<String, Element> elementById = new HashMap<>();
for (Element species : elements) {
@@ -81,7 +85,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
protected abstract List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout);
- protected abstract Element parse(T species) throws InvalidInputDataExecption;
+ protected abstract Element parse(T species, Model sbmlModel) throws InvalidInputDataExecption;
protected Set<MiriamData> parseAnnotation(Annotation annotation) {
if (annotation.getCVTermCount() > 0) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 7e32722234..a14a15c80c 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.awt.Point;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
@@ -48,8 +49,8 @@ public class SbmlParser implements IConverter {
Layout layout = getSbmlLayout(sbmlModel);
- SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout);
- SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout);
+ SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
+ SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
@@ -108,6 +109,17 @@ public class SbmlParser implements IConverter {
}
private void createLayout(Model model, Layout layout) {
+
+ for (Element element : model.getElements()) {
+ if (element.getWidth() == 0 || element.getHeight() == 0) {
+ element.setWidth(100);
+ element.setHeight(20);
+ Point coord = nextCoordinates();
+ element.setX(coord.x * 120);
+ element.setX(coord.y * 30);
+ }
+ }
+
double width;
double height;
if (layout != null) {
@@ -119,9 +131,6 @@ public class SbmlParser implements IConverter {
double minX = Double.MAX_VALUE;
double minY = Double.MAX_VALUE;
for (Element element : model.getElements()) {
- if (element.getWidth() == 0.0) {
- throw new NotImplementedException("Element without layout not implemented");
- }
width = Math.max(width, element.getX() + element.getWidth());
height = Math.max(height, element.getY() + element.getHeight());
minX = Math.min(minX, element.getX());
@@ -139,6 +148,29 @@ public class SbmlParser implements IConverter {
model.setHeight(height);
}
+ Point coordinates = null;
+ int radius = 0;
+
+ protected Point nextCoordinates() {
+ if (coordinates == null) {
+ coordinates = new Point(0, 0);
+ } else {
+ if (coordinates.x == coordinates.y) {
+ radius++;
+ coordinates = new Point(radius, 0);
+ } else if (coordinates.x == radius) {
+ if (coordinates.y == radius - 1) {
+ coordinates = new Point(0, radius);
+ } else {
+ coordinates = new Point(coordinates.x, coordinates.y + 1);
+ }
+ } else {
+ coordinates = new Point(coordinates.x + 1, coordinates.y);
+ }
+ }
+ return coordinates;
+ }
+
private Layout getSbmlLayout(org.sbml.jsbml.Model sbmlModel) {
Layout layout = null;
if (sbmlModel.getExtensionCount() > 0) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
index e5d5547c4d..b2cf5c6150 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
@@ -10,23 +10,27 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
Logger logger = Logger.getLogger(SbmlSpeciesParser.class);
- public SbmlSpeciesParser(Layout layout) {
- super(layout);
+ public SbmlSpeciesParser(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ super(layout, minervaModel);
}
- protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
+ @Override
+ protected Species parse(org.sbml.jsbml.Species species, Model sbmlModel) throws InvalidInputDataExecption {
String type = species.getSpeciesType();
Class<? extends Species> clazz = null;
if (type == null || type.isEmpty()) {
@@ -40,6 +44,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
result = clazz.getConstructor(String.class).newInstance(species.getId());
result.setMiriamData(parseAnnotation(species.getAnnotation()));
result.setName(species.getName());
+ if (result.getName() == null || result.getName().isEmpty()) {
+ result.setName(result.getElementId());
+ }
try {
result.setNotes(species.getNotesString());
} catch (XMLStreamException e) {
@@ -52,6 +59,43 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
}
+ @Override
+ protected List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout, Model sbmlModel) throws InvalidInputDataExecption {
+ List<Element> result = super.mergeLayout(elements, sbmlLayout, sbmlModel);
+
+ for (Element element : result) {
+ String compartmentId = null;
+ if (sbmlLayout.getSpeciesGlyph(element.getElementId())!=null) {
+ compartmentId = ((org.sbml.jsbml.Species)sbmlLayout.getSpeciesGlyph(element.getElementId()).getSpeciesInstance()).getCompartment();
+ } else {
+ compartmentId = sbmlModel.getSpecies(element.getElementId()).getCompartment();
+ }
+ assignCompartment(element, compartmentId);
+ }
+ return result;
+ }
+
+ private void assignCompartment(Element element, String compartmentId) {
+ Compartment compartment = minervaModel.getElementByElementId(compartmentId);
+ if (compartment == null) {
+ List<Compartment> compartments = new ArrayList<>();
+ for (CompartmentGlyph glyph : layout.getListOfCompartmentGlyphs()) {
+ if (glyph.getCompartment().equals(compartmentId)) {
+ compartments.add(minervaModel.getElementByElementId(glyph.getId()));
+ }
+ }
+ for (Compartment compartment2 : compartments) {
+ if (compartment2.contains(element)) {
+ compartment = compartment2;
+ }
+ }
+ }
+ if (compartment != null) {
+ compartment.addElement(element);
+ }
+
+ }
+
@Override
protected ListOf<org.sbml.jsbml.Species> getSbmlElementList(Model sbmlModel) {
return sbmlModel.getListOfSpecies();
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index d28517873a..252a952df8 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -27,8 +27,6 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -63,6 +61,7 @@ public class GenericSbmlParserTest {
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
+ logger.debug(model.getElements().size());
// Create and display image of parsed map
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 72a079086f..adef0ecf5b 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -5,6 +5,7 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+import java.awt.Point;
import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
@@ -29,8 +30,8 @@ public class SbmlParserTest {
Compartment compartment = model.getElementByElementId("CompartmentGlyph_1");
assertNotNull(compartment.getX());
assertNotNull(compartment.getY());
- assertTrue(compartment.getWidth()>0);
- assertTrue(compartment.getHeight()>0);
+ assertTrue(compartment.getWidth() > 0);
+ assertTrue(compartment.getHeight() > 0);
assertNotNull(model.getHeight());
assertNotNull(model.getWidth());
assertTrue(model.getWidth() >= compartment.getX() + compartment.getWidth());
@@ -40,15 +41,15 @@ public class SbmlParserTest {
@Test
public void testParseSpecies() throws FileNotFoundException, InvalidInputDataExecption {
- Model model = parser.createModel(
- new ConverterParams().filename("testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml"));
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml"));
assertNotNull(model);
assertEquals(1, model.getElements().size());
Species glucoseSpecies = model.getElementByElementId("SpeciesGlyph_Glucose");
assertNotNull(glucoseSpecies.getX());
assertNotNull(glucoseSpecies.getY());
- assertTrue(glucoseSpecies.getWidth()>0);
- assertTrue(glucoseSpecies.getHeight()>0);
+ assertTrue(glucoseSpecies.getWidth() > 0);
+ assertTrue(glucoseSpecies.getHeight() > 0);
assertNotNull(model.getHeight());
assertNotNull(model.getWidth());
assertTrue(model.getWidth() >= glucoseSpecies.getX() + glucoseSpecies.getWidth());
@@ -56,5 +57,38 @@ public class SbmlParserTest {
assertFalse(glucoseSpecies.getClass().equals(Species.class));
}
-
+ @Test
+ public void testParseSpeciesInCompartments() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/layoutExample/SpeciesGlyph_Example.xml"));
+ assertNotNull(model);
+ assertEquals(2, model.getElements().size());
+ Compartment compartment = model.getElementByElementId("Yeast");
+ assertNotNull(compartment.getX());
+ assertNotNull(compartment.getY());
+ assertTrue(compartment.getWidth() > 0);
+ assertTrue(compartment.getHeight() > 0);
+ assertNotNull(model.getHeight());
+ assertNotNull(model.getWidth());
+ assertTrue(model.getWidth() >= compartment.getX() + compartment.getWidth());
+ assertTrue(model.getHeight() >= compartment.getY() + compartment.getHeight());
+ assertFalse(compartment.getClass().equals(Compartment.class));
+ assertTrue(compartment.getElements().size() > 0);
+ }
+
+ @Test
+ public void testNextCoordinates() throws FileNotFoundException, InvalidInputDataExecption {
+ parser = new SbmlParser();
+ assertEquals(new Point(0, 0), parser.nextCoordinates());
+ assertEquals(new Point(1, 0), parser.nextCoordinates());
+ assertEquals(new Point(0, 1), parser.nextCoordinates());
+ assertEquals(new Point(1, 1), parser.nextCoordinates());
+ assertEquals(new Point(2, 0), parser.nextCoordinates());
+ assertEquals(new Point(2, 1), parser.nextCoordinates());
+ assertEquals(new Point(0, 2), parser.nextCoordinates());
+ assertEquals(new Point(1, 2), parser.nextCoordinates());
+ assertEquals(new Point(2, 2), parser.nextCoordinates());
+ assertEquals(new Point(3, 0), parser.nextCoordinates());
+
+ }
}
--
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