From 1678d9505ba79c040517709e9c9e284349c06aaa Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 18:21:16 +0100
Subject: [PATCH] renaming of methods
---
.../model/sbml/SbmlBioEntityExporter.java | 8 ++++----
.../model/sbml/SbmlElementExporter.java | 4 ++--
.../converter/model/sbml/SbmlExporter.java | 2 ++
.../converter/model/sbml/SbmlParser.java | 16 ++++++++++------
.../model/sbml/reaction/SbmlReactionParser.java | 1 -
.../model/sbml/GenericSbmlToXmlParserTest.java | 2 +-
6 files changed, 19 insertions(+), 14 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index 604b95c7cb..fdd811ae6c 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -84,11 +84,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
protected abstract void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph);
protected AbstractReferenceGlyph createGlyph(T element) {
- String sbmlCompartmentId = sbmlElementByElementId.get(element.getElementId()).getId();
+ String sbmlElementId = sbmlElementByElementId.get(element.getElementId()).getId();
String glyphId = element.getElementId();
- AbstractReferenceGlyph compartmentGlyph = createElementGlyph(sbmlCompartmentId, glyphId);
- assignLayoutToGlyph(element, compartmentGlyph);
- return compartmentGlyph;
+ AbstractReferenceGlyph elementGlyph = createElementGlyph(sbmlElementId, glyphId);
+ assignLayoutToGlyph(element, elementGlyph);
+ return elementGlyph;
}
protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index d0aebc087f..6b2433971b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -17,7 +17,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
super(sbmlLayout, minervaModel);
}
- protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph) {
+ protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
BoundingBox boundingBox = new BoundingBox();
boundingBox.setPosition(new Point(element.getX(), element.getY()));
@@ -26,7 +26,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
dimensions.setHeight(element.getHeight());
boundingBox.setDimensions(dimensions);
- compartmentGlyph.setBoundingBox(boundingBox);
+ speciesGlyph.setBoundingBox(boundingBox);
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 947e74f635..15a7771f0d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.converter.model.sbml;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
public class SbmlExporter {
+ Logger logger = Logger.getLogger(SbmlExporter.class);
public String toXml(lcsb.mapviewer.model.map.model.Model model)
throws SBMLException, XMLStreamException, InconsistentModelException {
SBMLDocument doc = new SBMLDocument(3, 1);
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 510455100b..9d6c69c344 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
@@ -89,6 +89,7 @@ public class SbmlParser implements IConverter {
if (layout.getDimensions() != null) {
model.setWidth(layout.getDimensions().getWidth());
model.setHeight(layout.getDimensions().getHeight());
+
}
compartmentParser.mergeLayout(model.getCompartments(), layout, sbmlModel);
speciesParser.mergeLayout(model.getSpeciesList(), layout, sbmlModel);
@@ -117,15 +118,14 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getRuleCount() > 0) {
throw new NotImplementedException("Rule not implemented for model");
}
-
- createLayout(model, layout);
+ createLayout(model, layout, params.isSizeAutoAdjust());
return model;
} catch (XMLStreamException e) {
throw new InvalidInputDataExecption(e);
}
}
- private void createLayout(Model model, Layout layout) throws InvalidInputDataExecption {
+ private void createLayout(Model model, Layout layout, boolean resize) throws InvalidInputDataExecption {
if (model.getWidth() == null) {
double maxY = 0;
double maxX = 0;
@@ -133,8 +133,10 @@ public class SbmlParser implements IConverter {
maxY = Math.max(maxY, element.getY() + element.getHeight() + 10);
maxX = Math.max(maxX, element.getX() + element.getWidth() + 10);
}
- model.setWidth(maxX);
- model.setHeight(maxY);
+ if (resize) {
+ model.setWidth(maxX);
+ model.setHeight(maxY);
+ }
}
Collection<BioEntity> bioEntitesRequiringLayout = new HashSet<>();
@@ -150,7 +152,9 @@ public class SbmlParser implements IConverter {
}
}
try {
- new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
+ if (bioEntitesRequiringLayout.size() > 0) {
+ new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
+ }
} catch (CommandExecutionException e) {
throw new InvalidInputDataExecption("Problem with generating layout", e);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index af039111eb..e9101d7518 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -153,7 +153,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
nodeClass = Modulation.class;
}
if (minervaNode == null) {
- logger.debug(nodeClass);
throw new InvalidInputDataExecption(
"Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index c3f9c5bfa6..7f589568fd 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -66,7 +66,7 @@ public class GenericSbmlToXmlParserTest {
String xmlFilePath = pathWithouExtension.concat(".xml");
converter.exportModelToFile(model, xmlFilePath);
- Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath));
+ Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
model2.setName(null);
assertNotNull(model2);
--
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